diff --git a/.dockerignore b/.dockerignore index 83edc646..f10e69d7 100644 --- a/.dockerignore +++ b/.dockerignore @@ -10,7 +10,7 @@ notebook.ipynb Dockerfile Dockerfile_base Dockerfile_dev -node_modules +webapp/node_modules webapp/build webapp/geppetto-client workspace @@ -23,4 +23,5 @@ app.log /.pytest_cache .jupyter-config **/*.pyc -**/__pycache__ \ No newline at end of file +**/__pycache__ +app.log \ No newline at end of file diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 00000000..61201c39 --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,258 @@ +# name: Tests Workflow + +# # Controls when the workflow will run +# on: +# # Triggers the workflow on push or pull request events but only for the specified branch +# push: +# branches: +# - "master" +# - "development" +# pull_request: +# branches: +# - "master" +# - "development" + +# # A workflow run is made up of one or more jobs that can run sequentially or in parallel +# jobs: +# EEG_Dipole-test: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: EEG and Dipole Plot snapshot test using Tut#1 +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run EEG and Dipole Plot test +# npm run EEG_Dipole_test +# env: +# CI: true +# Experiment_Manager-test: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Experiment Manager snapshot test using Tut#1 +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Experiment Manager test +# npm run Experiment_Manager_test +# env: +# CI: true +# Control_Panel-test: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Control Panel test using Tut#2 +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Control Panel test +# npm run Control_Panel_test +# env: +# CI: true +# Save_and_Open_File-test: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Test for Opening and Saving a file +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Control Panel test +# npm run Save_Open_File_test +# env: +# CI: true +# RxD-test: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Test for RxD plot +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run RxD Plot test +# npm run RxD_test +# env: +# CI: true +# Tutorial_1-SmokeTest: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Tutorial 1 Plot Tests +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Tutorial 1 Plot Tests +# npm run Tutorial_1_test +# env: +# CI: true +# Tutorial_2-SmokeTest: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Tutorial 2 Plot Tests +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Tutorial 2 Plot Tests +# npm run Tutorial_2_test +# env: +# CI: true +# Tutorial_3a-SmokeTest: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Tutorial 3a Plot Tests +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Tutorial 3a Plot Tests +# npm run Tutorial_3A_test +# env: +# CI: true +# Tutorial_3b-SmokeTest: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Tutorial 3b Plot Tests +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Tutorial 3b Plot Tests +# npm run Tutorial_3B_test +# env: +# CI: true +# Tutorial_3c-SmokeTest: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Tutorial 3c Plot Tests +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Tutorial 3c Plot Tests +# npm run Tutorial_3C_test +# env: +# CI: true +# Tutorial_4-SmokeTest: +# # The type of runner that the job will run on +# runs-on: ubuntu-20.04 +# container: lironavon/docker-puppeteer-container:14.16.0 +# env: +# CI: true +# steps: +# - uses: actions/checkout@v1 +# - name: Use Node.js ${{ matrix.node-version }} +# uses: actions/setup-node@v1 +# with: +# node-version: ${{ matrix.node-version }} +# cache-dependency-path: frontend/e2e/tests/package-lock.json +# - name: Tutorial 4 Plot Tests +# run: | +# cd tests/frontend/e2e +# #install dependencies +# npm ci +# # run Tutorial 4 Plot Tests +# npm run Tutorial_4_test +# env: +# CI: true \ No newline at end of file diff --git a/.gitignore b/.gitignore index 8e8498bb..6a73d2c5 100644 --- a/.gitignore +++ b/.gitignore @@ -13,6 +13,7 @@ init.py webapp/node_modules webapp/geppetto-client webapp/build +webapp/.yalc workspace netpyne_workspace tests/frontend/e2e/node_modules @@ -24,4 +25,10 @@ utilities/x86_64 .idea *.iml x86_64 -.jupyter-config \ No newline at end of file +.jupyter-config +venv +webapp/build +webapp/.yalc +node_modules +sa_nyhead.mat +workspace \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 11bf9ff5..f4062502 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,33 +1,101 @@ -FROM frodriguez4600/jupyter-neuron:v7.8.0 -ARG INSTALLATION_FOLDER=/home/jovyan/work/NetPyNE-UI -ARG NETPYNE_VERSION=development -ARG WORKSPACE_VERSION=nov2020 -ARG JUPYTER_GEPPETTO_VERSION=development -ARG PYGEPPETTO_VERSION=development +FROM node:18 as jsbuild + +ENV FOLDER=netpyne + +WORKDIR $FOLDER/webapp +COPY webapp/package.json . +COPY webapp/yarn.lock . + +RUN yarn install --network-timeout 1000000000 + +COPY webapp . +RUN yarn build-dev + +### Download on a separate stage to run in parallel with buildkit +FROM jupyter/base-notebook:hub-1.5.0 as downloads +USER root +RUN wget --no-check-certificate -O /nyhead.mat https://www.parralab.org/nyhead/sa_nyhead.mat + +### +FROM jupyter/base-notebook:hub-1.5.0 +ENV NB_UID=jovyan +ENV FOLDER=netpyne +ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat + +USER root + +RUN rm -rf /var/lib/apt/lists +RUN apt-get update -qq &&\ + apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y +RUN apt-get install openjdk-11-jre-headless -y +RUN conda install python=3.7 -y + + +WORKDIR $FOLDER +COPY --chown=1000:1000 requirements.txt requirements.txt +RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ + pip install -r requirements.txt --prefer-binary + + +# ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default +# and thus removes the frame ancestor cors settings +RUN rm -f ~/.jupyter/*.json +RUN chown $NB_UID . +RUN chown $NB_UID /opt +RUN rm -Rf workspace +# sym link workspace pvc to $FOLDER +RUN mkdir -p /opt/workspace +RUN mkdir -p /opt/user + +COPY netpyne_ui netpyne_ui +COPY utilities utilities +COPY setup.py . +COPY tests tests +COPY NetPyNE-UI . +COPY README.rst . +COPY requirements-test.txt . + + +USER $NB_UID + + + + +ENV NEURON_HOME=/opt/conda + + +USER root + +RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto +RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto +RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension +RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto + ARG BUILD_ARGS="" +ARG WORKSPACE_VERSION=master + +RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ + python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION --npm-skip + + +RUN mv workspace /opt/workspace/tutorials +RUN chown -R $NB_UID /opt/workspace +RUN ln -s /opt/workspace workspace + +RUN jupyter labextension disable @jupyterlab/hub-extension -USER $NB_USER +COPY --from=downloads --chown=1000:1000 /nyhead.mat $NP_LFPYKIT_HEAD_FILE +COPY --from=jsbuild --chown=1000:1000 $FOLDER/webapp/build webapp/build -ENV INSTALLATION_FOLDER=$INSTALLATION_FOLDER -ENV NETPYNE_VERSION=$NETPYNE_VERSION -ENV WORKSPACE_VERSION=$WORKSPACE_VERSION -ENV JUPYTER_GEPPETTO_VERSION=$JUPYTER_GEPPETTO_VERSION -ENV PYGEPPETTO_VERSION=$PYGEPPETTO_VERSION -ENV BUILD_ARGS=$BUILD_ARGS +RUN chown -R $NB_UID /home/jovyan/.jupyter +RUN touch app.log && chown $NB_UID app.log +USER $NB_UID -WORKDIR /home/jovyan/work -COPY --chown=1000:1000 requirements.txt ${INSTALLATION_FOLDER}/requirements.txt -WORKDIR ${INSTALLATION_FOLDER} -RUN pip install -r requirements.txt +EXPOSE 8888 -COPY --chown=1000:1000 . . -WORKDIR ${INSTALLATION_FOLDER}/utilities +ENTRYPOINT ["tini", "-g", "--"] -RUN python install.py ${BUILD_ARGS} -WORKDIR ${INSTALLATION_FOLDER} -RUN pip install -r requirements-test.txt -RUN pytest tests/backend -CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True" \ No newline at end of file +CMD ./NetPyNE-UI diff --git a/NetPyNE-UI b/NetPyNE-UI index abfedaeb..c7a58998 100755 --- a/NetPyNE-UI +++ b/NetPyNE-UI @@ -1,4 +1,4 @@ #!/bin/sh CONFIG=$(pwd)/.jupyter-config export JUPYTER_CONFIG_DIR=$CONFIG -exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True +exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --NotebookApp.notebook_dir=workspace --library=netpyne_ui --NotebookApp.disable_check_xsrf=True diff --git a/README.md b/README.md index 82a06054..3c2cc245 100644 --- a/README.md +++ b/README.md @@ -7,13 +7,18 @@ ![Screenshot](https://github.com/MetaCell/NetPyNE-UI/raw/documentation/docs/netpyneui.png) -This repository hosts the User Interface for [NetPyNE](http://www.neurosimlab.org/netpyne/). NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator. +This repository hosts the User Interface for [NetPyNE](https://netpyne.v2.opensourcebrain.org/). NetPyNE is a python package +to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON +simulator. ## Install NetPyNE User Interface -Select one option to install the NetPyNE User Interface. +Select one option to install the NetPyNE User Interface. -If you are familiar with NEURON and have already NEURON installed in your machine you can proceed using Pip. If you want a container which comes with everything preinstalled including NEURON you can use the Docker image. Using docker you will still be able to mount a local folder which will be your NetPyNE workspace. If you don't have docker installed in your system and you have had troubles installing it you can opt for the Virtual Machine installation. +If you are familiar with NEURON and have already NEURON installed in your machine you can proceed using Pip. If you want +a container which comes with everything preinstalled including NEURON you can use the Docker image. Using docker you +will still be able to mount a local folder which will be your NetPyNE workspace. If you don't have docker installed in +your system and you have had troubles installing it you can opt for the Virtual Machine installation.

Pip @@ -25,26 +30,59 @@ If you are familiar with NEURON and have already NEURON installed in your machin ### Python Dependencies -We recommend the use of a new python 3 virtual environment: +We recommend the use of a new python 3.7 virtual environment. +Currently, NetPyNE-UI only supports Python 3.7, but that can change in the future. + +For NetPyNE-UI, the preferred way of creating a virtual env is to pass by conda/miniconda or mamba/micromamba. +The pyenv tool can be also used, but it requires to be compiled with some special options to have NEURON running properly the simulation using `nrniv`. +The reason behind this is that NEURON is distributed as a Python wheel with a specific option which force NEURON to look for the CPython dynamic lib. +However, pyenv by default installs the static version of the CPython lib, resulting in `nrniv -python` not being able to run. + +The way of creating the virtualenv using (mini)conda is the following + +```bash +conda create -n netpyne python=3.7 +conda activate netpyne +``` + +Here is how to create the virtualenv using (micro)mamba + +```bash +mamba create -n netpyne python=3.7 -c conda-forge +mamba activate netpyne +``` + +You can also directly create a virtualenv using your `python3` executable, obviously if it's the 3.7 version. ```bash python3 -m venv npenv source npenv/bin/activate ``` -Or, with conda +If you want to use anyway pyenv, here is how to properly create the virtualenv and activate it. ```bash -conda create -n netpyne python=3.7 -conda activate netpyne +env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install --verbose 3.7.17 +pyenv virtualenv 3.7.17 netpyne +pyenv shell netpyne ``` ### Run install script +When you are in your virtualenv, here is how you can install the "basic" version of NetPyNE-UI: + ```bash python utilities/install.py ``` +If you want to have a different version of NetPyNE or geppetto meta, you can pass the version you want to the installer: + +```bash +python utilities/install.py --dev --netpyne development --geppetto development --no-test +``` + +This command will install the `development` version of netpyne and geppetto and disable the tests during the installation. + ### Start application ```bash @@ -57,6 +95,14 @@ For debugging you can use `run.py` instead python run.py ``` +To run the UI in dev mode, you need to run `python run.py` in one terminal, and use `yarn` from the `webapp` folder, using node v14 (use `nvm` if you need to have a different version of node than the one installed on your system): + +```bash +cd webapp +yarn start +``` + +You can then navigate to `http://127.0.0.1:8081/` to access the dev version of the UI. ## Run NetPyNE User Interface in Docker @@ -65,19 +111,19 @@ Ensure that you have Docker installed on your system. Build the image ```bash -docker build -t netpyne-ui +docker build -t netpyne-ui . ``` Run the image ```bash -docker run -p 8888:8888 netpyne-ui +docker run -p 8888:8888 netpyne-ui ``` ## End-to-end tests -End-to-end tests are located in `tests/deployment/frontend/e2e`. -Ensure that the application is running in a blank state, since end-to-end tests interact with the running application. +End-to-end tests are located in `tests/deployment/frontend/e2e`. Ensure that the application is running in a blank +state, since end-to-end tests interact with the running application. Install packages @@ -92,11 +138,9 @@ Start tests npm run test ``` - #### Containerized tests -You can also use `docker-compose` to run the tests. -Ensure that you have Docker installed on your system. +You can also use `docker-compose` to run the tests. Ensure that you have Docker installed on your system. Build the images @@ -111,8 +155,7 @@ Run the tests docker-compose up --abort-on-container-exit --exit-code-from netpyne-ui-e2e ``` - ## Additional Notes -NetPyNE-UI is being developed in collaboration with the [Neurosim Lab](http://neurosimlab.org/). -See the [Wiki](https://github.com/MetaCell/NetPyNE-UI/wiki) for more info! \ No newline at end of file +NetPyNE-UI is being developed in collaboration with the [Neurosim Lab](http://neurosimlab.org/). See +the [Wiki](https://github.com/MetaCell/NetPyNE-UI/wiki) for more info! diff --git a/example.db b/example.db new file mode 100644 index 00000000..173a80be Binary files /dev/null and b/example.db differ diff --git a/jupyter_hub/Dockerfile_spawner b/jupyter_hub/Dockerfile_spawner index 6c919e57..6a1b503a 100644 --- a/jupyter_hub/Dockerfile_spawner +++ b/jupyter_hub/Dockerfile_spawner @@ -16,15 +16,15 @@ RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip i # Clone NetPyNE-UI and install the development version RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q RUN unzip $netpyneuiBranch.zip -WORKDIR /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/utilities +WORKDIR /opt/workspace-$netpyneuiBranch/utilities RUN /bin/bash -c "source activate snakes && python --version" RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpyneuiBranch" WORKDIR /home/jovyan RUN git clone https://github.com/Neurosim-lab/netpyne_workspace WORKDIR /home/jovyan/workspace -RUN ln -sfn /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/netpyne_ui/tests tests +RUN ln -sfn /opt/workspace-$netpyneuiBranch/netpyne_ui/tests tests # Copy jupyterhub_config -# RUN cp /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/jupyterhub_config.py . +# RUN cp /opt/workspace-$netpyneuiBranch/jupyterhub_config.py . CMD /bin/bash -c "source activate snakes && exec jupyterhub-singleuser --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui" diff --git a/k8s/cf_values.yaml b/k8s/cf_values.yaml index 6b4cfb84..606d014a 100644 --- a/k8s/cf_values.yaml +++ b/k8s/cf_values.yaml @@ -2,35 +2,19 @@ hub: image: name: gcr.io/metacellllc/netpyne-hub pullPolicy: IfNotPresent - + allowNamedServers: true resources: requests: cpu: 100m memory: 128Mi - - allowNamedServers: true namedServerLimitPerUser: 2 shutdownOnLogout: true - extraConfig: timing: | - c.JupyterHub.allow_named_servers = True - c.Spawner.port = 8000 - c.Spawner.http_timeout = 300 - c.Spawner.start_timeout = 300 - c.Spawner.notebook_dir = '/home/jovyan/work/NetPyNE-UI' + c.Spawner.notebook_dir = '/opt/workspace' c.Spawner.default_url = '/geppetto' - c.Spawner.debug = True spawner: >- - c.Spawner.args = ["--library=netpyne_ui", "--NotebookApp.disable_check_xsrf=True"] - -scheduling: - userScheduler: - replicas: 1 - -auth: - type: tmp - + c.Spawner.args = ["--library=netpyne_ui", "--NotebookApp.default_url=/geppetto"] singleuser: storage: type: none @@ -54,4 +38,4 @@ cull: maxAge: 0 debug: - enabled: false \ No newline at end of file + enabled: false diff --git a/k8s/minikube_values.yaml b/k8s/minikube_values.yaml index 79d1b855..a70ed44d 100644 --- a/k8s/minikube_values.yaml +++ b/k8s/minikube_values.yaml @@ -20,7 +20,7 @@ hub: c.Spawner.port = 8000 c.Spawner.http_timeout = 300 c.Spawner.start_timeout = 300 - c.Spawner.notebook_dir = '/home/jovyan/work/NetPyNE-UI' + c.Spawner.notebook_dir = '/opt/workspace' c.Spawner.default_url = '/geppetto' c.Spawner.debug = True c.Spawner.disable_check_xsrf=True diff --git a/netpyne_ui/__init__.py b/netpyne_ui/__init__.py index cb0bf72e..1b003722 100644 --- a/netpyne_ui/__init__.py +++ b/netpyne_ui/__init__.py @@ -1,6 +1,34 @@ import logging -from jupyter_geppetto.webapi import RouteManager +import sys +import os +from jupyter_geppetto.webapi import RouteManager from netpyne_ui import api +from netpyne_ui.constants import HERE +import sentry_sdk + +sentry_sdk.init( + "https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6" +) + +HEAD_MODEL_FILE = os.getenv("NP_LFPYKIT_HEAD_FILE", "sa_nyhead.mat") + +def init_eeg(): + import sys + from netpyne_ui.constants import HERE + # FIXES library asking for input to download + sys.stdin = open(os.path.join(HERE, "resources/stdin.txt"),'r') + from lfpykit.eegmegcalc import NYHeadModel + try: + NYHeadModel(HEAD_MODEL_FILE) # Downloads the model if does not exist + except: + logging.error("Error initializing the EEG head model", exc_info=True) + +if not os.path.exists(HEAD_MODEL_FILE): + from multiprocessing import Process + thread = Process(target = init_eeg) + thread.start() + +RouteManager.add_controller(api.NetPyNEController) + -RouteManager.add_controller(api.NetPyNEController) \ No newline at end of file diff --git a/netpyne_ui/api.py b/netpyne_ui/api.py index 91cac361..75580c53 100644 --- a/netpyne_ui/api.py +++ b/netpyne_ui/api.py @@ -8,7 +8,8 @@ from tempfile import TemporaryDirectory from jupyter_geppetto.webapi import get, post from notebook.base.handlers import IPythonHandler -from netpyne_ui.constants import NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME, ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH +from netpyne_ui.constants import ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH + def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS): return '.' in filename and \ @@ -18,7 +19,8 @@ def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS): def send_files(handler, file_path, filename): with open(file_path, "rb") as f: handler.set_header('Content-Type', 'application/force-download') - handler.set_header('Content-Disposition', f"attachment; filename={filename}") + handler.set_header('Content-Disposition', + f"attachment; filename={filename}") try: while True: @@ -26,7 +28,7 @@ def send_files(handler, file_path, filename): if _buffer: handler.write(_buffer) else: - return + return except: handler.set_status(500, f"Error sending files") @@ -35,36 +37,57 @@ def get_file_paths(handler): file_paths = False if 'uri' in handler.request.arguments: file_paths = [] - tmp_file_paths = [path.decode('utf-8') for path in handler.request.arguments['uri']] + tmp_file_paths = [path.decode('utf-8') + for path in handler.request.arguments['uri']] for path in tmp_file_paths: if os.path.exists(path): file_paths.append(path) - + return file_paths + +def is_within_directory(directory, target): + abs_directory = os.path.abspath(directory) + abs_target = os.path.abspath(target) + + prefix = os.path.commonprefix([abs_directory, abs_target]) + + return prefix == abs_directory + + +def safe_extract_tar(tar, path=".", members=None, *, numeric_owner=False): + for member in tar.getmembers(): + member_path = os.path.join(path, member.name) + if not is_within_directory(path, member_path): + raise Exception("Attempted Path Traversal in Tar File") + tar.extractall(path, members, numeric_owner=numeric_owner) + + class NetPyNEController: # pytest: no cover @post('/uploads') def uploads(handler: IPythonHandler): files = handler.request.files files_saved = 0 - + if len(files) == 0 or 'file' not in files: - handler.set_status(400, f"Can't find 'file' or filename is empty. Files received {len(files)}") + handler.set_status( + 400, f"Can't find 'file' or filename is empty. Files received {len(files)}") else: for f in files['file']: if not allowed_file(f.filename): - logging.warn(f"Can't store file {f.filename}. Extension not allowed") + logging.warn( + f"Can't store file {f.filename}. Extension not allowed") continue - ## Save to file + # Save to file filename = f.filename file_path = os.path.join(UPLOAD_FOLDER_PATH, filename) - + with open(file_path, 'wb') as zf: zf.write(f['body']) - + files_saved += 1 if filename.endswith('.zip'): @@ -73,23 +96,20 @@ def uploads(handler: IPythonHandler): elif filename.endswith('.tar.gz'): with tarfile.open(file_path, mode='r:gz') as tar: - tar.extractall(UPLOAD_FOLDER_PATH) + safe_extract_tar(tar, UPLOAD_FOLDER_PATH) elif filename.endswith('.gz'): with gzip.open(file_path, "rb") as gz, open(file_path.replace('.gz', ''), 'wb') as ff: shutil.copyfileobj(gz, ff) - + handler.set_status(200, f"Number of files saved: {files_saved}. Number of files sent: {len(files['file'])}") handler.finish() - + @get('/downloads') def downloads(handler: IPythonHandler): - file_paths = get_file_paths(handler) - if file_paths: - if len(file_paths) == 0: handler.set_status(400, f"Files not found.") handler.finish() @@ -97,15 +117,49 @@ def downloads(handler: IPythonHandler): if len(file_paths) == 1: send_files(handler, file_paths[0], file_paths[0].split('/')[-1]) - - else : + + else: with TemporaryDirectory() as dir_path: tar_gz_file_name = f'{str(uuid.uuid4())}.tar.gz' tar_gz_file_path = os.path.join(dir_path, tar_gz_file_name) with tarfile.open(tar_gz_file_path, mode='w:gz') as tar: for file_path in file_paths: - tar.add(file_path, os.path.join('download', file_path.split('/')[-1])) + tar.add(file_path, os.path.join( + 'download', file_path.split('/')[-1])) send_files(handler, tar_gz_file_path, tar_gz_file_name) - + handler.finish() + + +def create_notebook(filename): + import nbformat as nbf + from nbformat.v4.nbbase import new_notebook + from nbformat import sign + import codecs + + directory = os.path.dirname(filename) + if not os.path.exists(directory): + os.makedirs(directory) + nb0 = new_notebook(cells=[nbf.v4.new_markdown_cell("""# Welcome to the NetPyNE-ui! + + """), + nbf.v4.new_code_cell( + 'netpyne_geppetto.netParams'), + nbf.v4.new_code_cell( + 'netpyne_geppetto.simConfig') + ], metadata={"kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }}) + + f = codecs.open(filename, encoding='utf-8', mode='w') + + nbf.write(nb0, filename) + f.close() + + +# TODO move to jupyter geppetto, using notebook dir path +if os.path.exists('workspace') and not os.path.exists('workspace/notebook.ipynb'): + create_notebook('workspace/notebook.ipynb') diff --git a/netpyne_ui/constants.py b/netpyne_ui/constants.py index 283d781c..96fe3ee6 100644 --- a/netpyne_ui/constants.py +++ b/netpyne_ui/constants.py @@ -2,12 +2,21 @@ UPLOAD_FOLDER_NAME = 'uploads' NETPYNE_WORKDIR = 'workspace' +EXPERIMENTS_FOLDER = "experiments" +MODEL_OUTPUT_FILENAME = 'model_output' -ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc"] +SIMULATION_SCRIPT_NAME = "init.py" +TEMPLATE_FILENAME_SINGLE_RUN = "run.py" +TEMPLATE_FILENAME_SINGLE_RUN_INSTANTIATED = "run_instantiated_net.py" +TEMPLATE_FILENAME_BATCH_RUN = "batch_run_single.py" +TEMPLATE_FILENAME_BATCH = "batch.py" + +ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc", "json", "xml", "nml"] HERE = os.path.dirname(os.path.abspath(__file__)) ROOT = os.path.dirname(HERE) UPLOAD_FOLDER_PATH = os.path.join(ROOT, NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME) NETPYNE_WORKDIR_PATH = os.path.join(ROOT, NETPYNE_WORKDIR) +EXPERIMENTS_FOLDER_PATH = os.path.join(ROOT, NETPYNE_WORKDIR, EXPERIMENTS_FOLDER) if not os.path.exists(NETPYNE_WORKDIR_PATH): NETPYNE_WORKDIR_PATH = os.path.join(os.getcwd(), NETPYNE_WORKDIR) diff --git a/netpyne_ui/experiments.py b/netpyne_ui/experiments.py new file mode 100644 index 00000000..2838fa56 --- /dev/null +++ b/netpyne_ui/experiments.py @@ -0,0 +1,350 @@ +import copy +import dataclasses +import datetime +import json +import logging +import shutil +import pathlib +import os + +import numpy as np +from typing import List +from dacite import from_dict +from netpyne.batch import Batch + +from netpyne_ui import utils +from netpyne_ui import constants +from netpyne_ui import model + +SIM_CONFIG_FILE = "simConfig.json" +NET_PARAMS_FILE = "netParams.json" +EXPERIMENT_FILE = "experiment.json" + +# Id for the base model trial created for an Experiment without parameters. +BASE_TRIAL_ID = "model_output" + + +class ExperimentsError(Exception): + """ Base Exception for any specific Experiment errors. """ + pass + + +def get_experiments() -> List[dict]: + """Returns the current list of experiments. + + Scans the experiments folder to read experiments from disk and includes experiment in design. + """ + # Only update Experiments stored on filesystem + stored_experiments = _scan_experiments_directory() + model.experiments = [ + e for e in model.experiments if e.state in model.ExperimentState.DESIGN + ] + model.experiments.extend(stored_experiments) + + return [dataclasses.asdict(e) for e in model.experiments] + + +def add_experiment(experiment: dict): + exp = from_dict(model.Experiment, experiment) + exp.trials = _create_trials(exp) + + if exp.state == model.ExperimentState.DESIGN: + # Only one exp in design can exist + [model.experiments.remove(e) for e in get_by_states(model.ExperimentState.DESIGN)] + + _add_experiment(exp) + + +def get_experiment(name: str) -> dict: + exp = _get_by_name(name) + return dataclasses.asdict(exp) if exp else None + + +def remove_experiment(name: str): + experiment = _get_by_name(name) + if experiment: + _delete_experiment_folder(experiment) + model.experiments.remove(experiment) + + +def edit_experiment(name: str, experiment: dict): + exp = _get_by_name(name) + if not exp: + raise ExperimentsError(f"Experiment with name {name} does not exist") + + if exp.state != model.ExperimentState.DESIGN: + raise ExperimentsError( + f"Can only edit experiment in {model.ExperimentState.DESIGN} state" + ) + + updated_exp = from_dict(model.Experiment, experiment) + updated_exp.trials = _create_trials(updated_exp) + model.experiments.remove(exp) + _add_experiment(updated_exp) + + +def replace_current_with(name: str): + """Replaces the experiment in design with a new experiment based on experiment with `name`. + + :param name: name of experiment to be cloned. + :raises ExperimentsError: thrown if Experiment with `name` doesn't exist. + """ + exp = _get_by_name(name) + if not exp: + raise ExperimentsError(f"Experiment with name {name} does not exist") + + next_name = utils.get_next_file_name(constants.EXPERIMENTS_FOLDER_PATH, name) + new_exp = model.Experiment( + name=next_name, + state=model.ExperimentState.DESIGN, + params=exp.params, + seed=exp.seed, + initConfig=exp.initConfig, + method=exp.method, + ) + + current = get_current() + if current: + remove_experiment(current.name) + + new_exp.trials = _create_trials(new_exp) + _add_experiment(new_exp) + return + + +def get_current() -> model.Experiment: + return next( + (exp for exp in model.experiments if exp.state == model.ExperimentState.DESIGN), + None, + ) + + +def get_by_states(states: List[model.ExperimentState]) -> List[model.Experiment]: + return [e for e in model.experiments if e.state in states] + + +def any_in_state(states: List[model.ExperimentState]) -> model.Experiment: + return any(get_by_states(states)) + + +def set_to_error(experiment: model.Experiment): + """Sets the state of `experiment` to ERROR. """ + path = os.path.join( + constants.NETPYNE_WORKDIR_PATH, constants.EXPERIMENTS_FOLDER, experiment.name + ) + + try: + with open(os.path.join(path, EXPERIMENT_FILE), "r") as f: + experiment_config = json.load(f) + + with open(os.path.join(path, EXPERIMENT_FILE), "w") as f: + experiment_config["state"] = model.ExperimentState.ERROR + json.dump(experiment_config, f, default=str, sort_keys=True, indent=4) + + except IOError: + raise ExperimentsError(f"Could not find {EXPERIMENT_FILE}") + + +def get_model_specification(name: str, trial: str) -> dict: + """Returns JSON representation of the netParams & simConfig of the requested trial. + + :param name: the experiment name. + :param trial: the trial identifier. + :return: dict + """ + path = get_trial_output_path(name, trial, fallback=True) + if path is None or not os.path.exists(path): + raise ExperimentsError(f"Condition file {path} not found") + + with open(path, "r") as f: + trial_output = json.load(f) + model_spec = {} + + if "simConfig" in trial_output: + model_spec["simConfig"] = trial_output["simConfig"] + + try: + params = trial_output["net"]["params"] + except KeyError: + logging.error(f"net params is not present in {path}") + else: + model_spec["net"] = {"params": params} + + return model_spec + + +def get_trial_output_path( + experiment_name: str, trial: str, fallback: bool = False +) -> pathlib.PosixPath: + path = os.path.join(constants.EXPERIMENTS_FOLDER_PATH, experiment_name) + trial_path = next(pathlib.Path(path).glob(f"*{trial}_data.json"), None) + + if trial_path is None and fallback: + trial_path = next(pathlib.Path(path).glob(f"*{trial}_cfg.json"), None) + + return trial_path + + +def _add_experiment(experiment: model.Experiment): + if _get_by_name(experiment.name): + raise ExperimentsError(f"Experiment {experiment.name} already exists") + + model.experiments.append(experiment) + + +def _get_by_name(name: str) -> model.Experiment: + experiment = next((e for e in model.experiments if e.name == name), None) + return experiment + + +def _scan_experiments_directory() -> List[model.Experiment]: + if not pathlib.Path(constants.EXPERIMENTS_FOLDER_PATH).exists(): + return [] + + dirs = list( + [ + f + for f in os.listdir(constants.EXPERIMENTS_FOLDER_PATH) + if os.path.isdir(os.path.join(constants.EXPERIMENTS_FOLDER_PATH, f)) + ] + ) + + experiments = [] + for directory in dirs: + try: + experiment = _parse_experiment(directory) + except ExperimentsError: + logging.exception(f"Failed to parse experiment {directory}") + else: + experiments.append(experiment) + + return experiments + + +def _parse_experiment(directory: str) -> model.Experiment: + """Finds and parses Experiments stored in `directory` on the disk. + + We expect the following files to be present: + * experiment.json (Experiment model and run config) + * netParams.json + * simConfig.json + * json file for each trial in case of batch + * data files for each trial (if available) + + :raises ExperimentsError + """ + path = os.path.join( + constants.NETPYNE_WORKDIR_PATH, constants.EXPERIMENTS_FOLDER, directory + ) + + try: + with open(os.path.join(path, EXPERIMENT_FILE), "r") as f: + experiment_config = json.load(f) + except IOError: + raise ExperimentsError(f"Could not find {EXPERIMENT_FILE}") + + del experiment_config["runCfg"] + + # Convert timestamp to datetime + experiment_config["timestamp"] = datetime.datetime.fromisoformat( + experiment_config["timestamp"] + ) + + experiment = from_dict(model.Experiment, experiment_config) + experiment.folder = directory + experiment.trials = _create_trials(experiment) + return experiment + + +def _delete_experiment_folder(experiment: model.Experiment): + """Recursively deletes the associated `experiment` folder.""" + + def onerror(func, path, exc_info): + # TODO: error handling + pass + + if experiment.folder: + path = os.path.join( + constants.NETPYNE_WORKDIR_PATH, + constants.EXPERIMENTS_FOLDER, + experiment.folder, + ) + shutil.rmtree(path, onerror=onerror) + + +def _create_base_model_trial() -> model.Trial: + return model.Trial(name="Condition 1", id=BASE_TRIAL_ID) + + +def _create_trials(experiment: model.Experiment) -> List[model.Trial]: + """Gerates based on `experiment.params` all possible trial combinations. + + :param experiment: given experiment. + :return: list of generated trials. + """ + params = copy.deepcopy(experiment.params) + params = process_params(params) + + if len(experiment.params) < 1: + # No params defined -> one trial representing base model + return [_create_base_model_trial()] + + params_dict = {} + grouped_params = [] + for p in params: + params_dict[p.mapsTo] = p.values + if p.inGroup: + grouped_params.append(p.mapsTo) + + # Initialize Batch so that we can call getParamCombinations() + batch = Batch(params=params_dict, groupedParams=grouped_params) + batch.method = "grid" + batch.saveFolder = "" + batch.batchLabel = "" + + # { indices, values, labels, filenames} + combinations = batch.getParamCombinations() + if not combinations["labels"]: + return [_create_base_model_trial()] + + trials = [] + for combIdx, paramValues in enumerate(combinations["values"]): + # index of paramValues := index of labels list + # value of paramValues := parameter value + params = [{combinations["labels"][idx]: v for idx, v in enumerate(paramValues)}] + + filename = combinations["filenames"][combIdx][1:] + indices = combinations["indices"][combIdx] + name = f"Condition {combIdx + 1}" + + trials.append( + model.Trial(name=name, params=params, indices=indices, id=filename) + ) + + return trials + + +def process_params(params: List[model.ExplorationParameter]) -> List[model.ExplorationParameter]: + """Cleaning, filtering and converting of experiment `params`. + + :param params: given parameters. + :raises ExperimentsError: thrown for invalid parameter configuration. + :return: processed list of params. + """ + params = [p for p in params if p.mapsTo != ''] + + for param in params: + if param.type == "range": + if param.step > 0: + # Final values must be either of type int or float depending on the range parameters. + convert_type = int if all(type(t) == int for t in [param.min, param.max, param.step]) else float + param.values = [convert_type(e) for e in list(np.arange(param.min, param.max, param.step))] + else: + raise ExperimentsError("Invalid step value, must be greater than 0") + + elif param.type == "list": + # nothing to do here + pass + + params = [p for p in params if p.values is not None and len(p.values) > 0] + return params diff --git a/netpyne_ui/helpers/neuroml.py b/netpyne_ui/helpers/neuroml.py new file mode 100644 index 00000000..84ad5a7f --- /dev/null +++ b/netpyne_ui/helpers/neuroml.py @@ -0,0 +1,129 @@ +import os +import sys +import logging +from netpyne.specs import simConfig +from packaging import version + +import pyneuroml +from pyneuroml import pynml +from pyneuroml.lems import generate_lems_file_for_neuroml +from pyneuroml.pynml import read_neuroml2_file + +from netpyne_ui.mod_utils import loadModMechFiles + + +def convertLEMSSimulation(lemsFileName, compileMod=True): + """Converts a LEMS Simulation file + + Converts a LEMS Simulation file + (https://docs.neuroml.org/Userdocs/LEMSSimulation.html) pointing to a + NeuroML 2 file into the equivalent in NetPyNE + + Returns: + simConfig, netParams for the model in NetPyNE + """ + current_path = os.getcwd() + try: + + fullLemsFileName = os.path.abspath(lemsFileName) + tmp_path = os.path.dirname(fullLemsFileName) + if tmp_path: + os.chdir(tmp_path) + logging.info( + "Importing LEMSSimulation with NeuroML 2 network from: %s" + % fullLemsFileName + ) + + # feature to return output added in 1.0.9 + if version.parse(pyneuroml.__version__) >= version.parse("1.0.9"): + result, output_msg = pynml.run_lems_with_jneuroml_netpyne( + lemsFileName, only_generate_json=True, exit_on_fail=False, + return_string=True, max_memory="1G") + + if result is False: + raise Exception(f"Error loading lems file: {output_msg}") + else: + result = pynml.run_lems_with_jneuroml_netpyne( + lemsFileName, only_generate_json=True, exit_on_fail=False, + max_memory="1G") + + if result is False: + raise Exception("Error loading lems file") + + lems = pynml.read_lems_file(lemsFileName) + + np_json_fname = fullLemsFileName.replace('.xml','_netpyne_data.json') + + return np_json_fname + finally: + os.chdir(current_path) + + +def convertNeuroML2(nml2FileName, compileMod=True): + """Loads a NeuroML 2 file into NetPyNE + Loads a NeuroML 2 file into NetPyNE by creating a new LEMS Simulation + file (https://docs.neuroml.org/Userdocs/LEMSSimulation.html) and using + jNeuroML to convert it. + + Returns: + simConfig, netParams for the model in NetPyNE + """ + current_path = os.getcwd() + try: + fullNmlFileName = os.path.abspath(nml2FileName) + work_path = os.path.dirname(fullNmlFileName) + if not os.path.exists(work_path): + os.makedirs(work_path) + os.chdir(work_path) + sys.path.append(work_path) + + logging.info( + "Importing NeuroML 2 network from: %s" + % fullNmlFileName + ) + nml_model = read_neuroml2_file(fullNmlFileName) + + target = nml_model.networks[0].id + sim_id = "Sim_%s" % target + duration = 1000 + dt = 0.025 + lems_file_name = os.path.join(os.path.dirname(fullNmlFileName), "LEMS_%s.xml" % sim_id) + lems_file_name = "LEMS_%s.xml" % sim_id + target_dir = os.path.dirname(fullNmlFileName) + target_dir = "." + + generate_lems_file_for_neuroml( + sim_id, + fullNmlFileName, + target, + duration, + dt, + lems_file_name, + target_dir, + include_extra_files=["PyNN.xml"], + gen_plots_for_all_v=True, + plot_all_segments=False, + gen_plots_for_quantities={}, # Dict with displays vs lists of quantity paths + gen_plots_for_only_populations=[], # List of populations, all pops if = [] + gen_saves_for_all_v=True, + save_all_segments=False, + gen_saves_for_only_populations=[], # List of populations, all pops if = [] + gen_saves_for_quantities={}, # Dict with file names vs lists of quantity paths + gen_spike_saves_for_all_somas=True, + report_file_name="report.txt", + copy_neuroml=True, + verbose=True, + ) + os.chdir(work_path) + res = convertLEMSSimulation(lems_file_name, compileMod=compileMod) + finally: + os.chdir(current_path) + return res + + +if __name__ == "__main__": + + if '-nml' in sys.argv: + convertNeuroML2("../../NeuroML2/Spikers.net.nml") + else: + convertLEMSSimulation("LEMS_HHSimple.xml") diff --git a/netpyne_ui/mod_utils.py b/netpyne_ui/mod_utils.py index f3f09975..3fba08a7 100644 --- a/netpyne_ui/mod_utils.py +++ b/netpyne_ui/mod_utils.py @@ -1,3 +1,4 @@ +import logging import shutil import subprocess import os @@ -26,19 +27,33 @@ def is_loaded_mechanisms(): return True -def compileModMechFiles(compileMod, modFolder): +def loadModMechFiles(compileMod, modFolder, forceRecompile=False): # Create Symbolic link - if compileMod: - modPath = os.path.join(str(modFolder), "x86_64") - - if os.path.exists(modPath): - shutil.rmtree(modPath) - - os.chdir(modFolder) - subprocess.call(["nrnivmodl"]) - os.chdir('..') try: - neuron.load_mechanisms(str(modFolder)) - except: - raise + + owd = os.getcwd() + if compileMod: + + compiledModPath = os.path.join(str(modFolder), "x86_64") + + if os.path.exists(compiledModPath) and forceRecompile: + logging.info("Forcing mod files to recompile in %s" % modFolder) + shutil.rmtree(compiledModPath) + + if not os.path.exists(compiledModPath): + logging.info("Compiling mod files in %s" % modFolder) + os.chdir(modFolder) + subprocess.call(["nrnivmodl"]) + os.chdir('..') + + try: + neuron.load_mechanisms(str(modFolder)) + except: + logging.exception("Error loading mechanisms") + if not forceRecompile: + logging.info("Trying to recompile mod files") + loadModMechFiles(True, modFolder, forceRecompile=True) + raise + finally: + os.chdir(owd) diff --git a/netpyne_ui/model.py b/netpyne_ui/model.py new file mode 100644 index 00000000..081348aa --- /dev/null +++ b/netpyne_ui/model.py @@ -0,0 +1,95 @@ +from dataclasses import dataclass +from dataclasses import field +from datetime import datetime +from typing import List, Optional + + +def register(metadata): + # Modification of metadata to enable validation of experiment parameters. + metadata['netParams']['children']['popParams']['container'] = True + metadata['netParams']['children']['cellParams']['container'] = True + metadata['netParams']['children']['cellParams']['children']['conds']['container'] = True + metadata['netParams']['children']['cellParams']['children']['secs']['container'] = True + metadata['netParams']['children']['synMechParams']['container'] = True + metadata['netParams']['children']['connParams']['container'] = True + metadata['netParams']['children']['stimSourceParams']['container'] = True + metadata['netParams']['children']['stimTargetParams']['container'] = True + + +class ExperimentState: + DESIGN = "DESIGN" + PENDING = "PENDING" + SIMULATING = "SIMULATING" + INSTANTIATING = "INSTANTIATING" + SIMULATED = "SIMULATED" + INSTANTIATED = "INSTANTIATED" + ERROR = "ERROR" + + +@dataclass +class ExplorationParameter: + """ Parameter with possible values that will be explored in netpyne.batch. """ + + # Path to target parameter in netParams dict + mapsTo: str + # Type can be either 'list' or 'range' + type: str + # List of values of different type + values: Optional[List] = None + # Range fields + min: Optional[float] = None + max: Optional[float] = None + step: Optional[float] = None + # If True, parameter is added to grouped parameters + inGroup: bool = False + # Set in cfg.py to cfg.label = + label: str = "" + + +@dataclass +class Trial: + # Display name. + name: str = '' + # Unique id to find trial on disk. + # Concatenated str of indices e.g. "0_1_1" with 3 parameters. + id: str = '' + # [{ "paramX": 0.2, "paramY": "0.4"}] + params: list = field(default_factory=list) + indices: list = field(default_factory=list) + + +@dataclass +class Experiment: + # Name is the unique identifier + name: str + # DESIGN, INSTANTIATING, INSTANTIATED, SIMULATING, SIMULATED + state: str = ExperimentState.DESIGN + # Exploration parameter config + params: List[ExplorationParameter] = field(default_factory=list) + # Generated based on params + trials: List[Trial] = field(default_factory=list) + # SIMULATED or INSTANTIATED date + timestamp: datetime = field(default_factory=datetime.today) + + # Overwrites simConfig parameters + initConfig: dict = field(default_factory=dict) + method: str = "grid" + # Part of initCfg? + seed: Optional[int] = None + + # Folder in workspace, empty in DESIGN + folder: Optional[str] = None + + +@dataclass +class RunConfig: + """ Run config for either single or batch simulation.""" + parallel: bool = True + asynchronous: bool = True + cores: int = 1 + resource: str = "local" + # or mpi_direct (doesn't support waiting for processes to finish) + type: str = 'mpi_bulletin' + + +experiments = [] diff --git a/netpyne_ui/netpyne_geppetto.py b/netpyne_ui/netpyne_geppetto.py index bd0a6a64..8922e3c6 100644 --- a/netpyne_ui/netpyne_geppetto.py +++ b/netpyne_ui/netpyne_geppetto.py @@ -1,34 +1,84 @@ """ netpyne_geppetto.py + Initialise NetPyNE Geppetto, this class contains methods to connect NetPyNE with the Geppetto based UI """ import json import os +from os.path import join, dirname +from glob import glob +import copy +import dataclasses import importlib -import sys -import subprocess +import json import logging +import os +from pathlib import Path +import pprint import re +import sys +from shutil import copyfile +from dacite import from_dict +import base64 +import jsonpickle +import neuron +import numpy as np from netpyne import specs, sim, analysis -from netpyne.specs.utils import validateFunction from netpyne.conversion.neuronPyHoc import mechVarList from netpyne.metadata import metadata +from netpyne.specs.utils import validateFunction +from netpyne.sim import utils as netpyne_utils + +from netpyne_ui import experiments +from netpyne_ui import constants +from netpyne_ui import model +from netpyne_ui import simulations +from netpyne_ui import utils as netpyne_ui_utils from netpyne_ui.netpyne_model_interpreter import NetPyNEModelInterpreter +from netpyne_ui.simulations import InvalidConfigError from pygeppetto.model.model_serializer import GeppettoModelSerializer -import matplotlib.pyplot as plt from pygeppetto import ui -import numpy as np -import neuron -from shutil import copyfile from jupyter_geppetto import jupyter_geppetto, synchronization, utils from contextlib import redirect_stdout from netpyne_ui.constants import NETPYNE_WORKDIR_PATH, NUM_CONN_LIMIT -from netpyne_ui.mod_utils import compileModMechFiles - -os.chdir(NETPYNE_WORKDIR_PATH) - -neuron.nrn_dll_loaded.append(os.path.join(NETPYNE_WORKDIR_PATH, 'mod')) # Avoids to load workspace modfiles twice +from netpyne_ui.mod_utils import loadModMechFiles + +os.chdir(constants.NETPYNE_WORKDIR_PATH) + + +class NetpyneValidationError(Exception): + ... + + +def deepcopy_wout_empty(d, memo=None): + def is_empty(x): + return x == '' or x == [] or x == () or x == set() or x == {} or x is None + + # if is_empty(d): + # return None + memo = {} if memo is None else memo + if id(d) in memo: + return memo[id(d)] + if isinstance(d, dict): + cpy = {} + for k, v in d.items(): + v_cpy = deepcopy_wout_empty(v, memo=memo) + if is_empty(v_cpy): + continue + cpy[k] = memo.setdefault(id(v), v_cpy) + return cpy + elif isinstance(d, (list, set, tuple)): + return d.__class__(memo.setdefault(id(v), deepcopy_wout_empty(v, memo=memo)) for v in d if not is_empty(v)) + elif hasattr(d, '__dict__'): + cpy = d.__new__(d.__class__) # We skip the initializer, in case it needs some arguments + for k, v in d.__dict__.items(): + v_cpy = deepcopy_wout_empty(v, memo=memo) + # if is_empty(v_cpy): # + # continue + cpy.__dict__[k] = memo.setdefault(id(v), v_cpy) + return cpy + return d class NetPyNEGeppetto: @@ -36,13 +86,33 @@ class NetPyNEGeppetto: def __init__(self): self.model_interpreter = NetPyNEModelInterpreter() + # Geppetto model of a created network + self.geppetto_model = None + self.netParams = specs.NetParams() self.simConfig = specs.SimConfig() + self.run_config = model.RunConfig() + self.simConfig.recordTraces = {'V_soma': {'sec':'soma', 'loc':0.5, 'var':'v'}} + + self.experiments = experiments + + model.register(metadata) + synchronization.startSynchronization(self.__dict__) logging.debug("Initializing the original model") jupyter_geppetto.context = {'netpyne_geppetto': self} + # Set running experiments without any subprocess to ERRROR + experiments.get_experiments() + running_exps = experiments.get_by_states([ + model.ExperimentState.PENDING, + model.ExperimentState.SIMULATING, + model.ExperimentState.INSTANTIATING + ]) + if not simulations.local.is_running(): + [experiments.set_to_error(e) for e in running_exps] + def getData(self): return { "metadata": metadata, @@ -50,73 +120,359 @@ def getData(self): "simConfig": self.simConfig.todict(), "isDocker": os.path.isfile('/.dockerenv'), "currentFolder": os.getcwd(), - "tuts": self.find_tutorials() + "tuts": self.find_tutorials(), + "cores": simulations.local.cpus } - def find_tutorials(self): - from os import listdir - from os.path import isfile, join - onlyfiles = [f for f in listdir(NETPYNE_WORKDIR_PATH) if isfile(join(NETPYNE_WORKDIR_PATH, f))] + def getModelAsJson(self): + # TODO: netpyne should offer a method asJSON (#240) + # that returns the JSON model without dumping to to disk. + obj = netpyne_utils.replaceFuncObj({"netParams": self.netParams.__dict__, "simConfig": self.simConfig.__dict__}) + obj = netpyne_utils.replaceDictODict(obj) + return obj + + def get_run_configuration(self): + return dataclasses.asdict(self.run_config) + + def edit_run_configuration(self, configDictionary: dict): + self.run_config = from_dict(model.RunConfig, configDictionary) - def _filter(_file): - return '.py' in _file and 'tut' in _file and 'gui' in _file + def cloneExperiment(self, payload: dict): + """ Loads experiment from disk and replaces experiment in design with it. - return list(filter(_filter, onlyfiles)) + 1. Replaces current experiment in design with copy of stored experiment. + 2. Replace current model specification with spec of stored experiment. + + :param payload: { name: str, replaceModelSpec: bool, replaceExperiment: bool } + """ + name = payload.get('name') + + # Creates new Experiment in design based on `name` experiment. + if payload.get('replaceExperiment', True): + experiments.replace_current_with(name) + + # Replaces model specification + if payload.get('replaceModelSpec', True): + path = os.path.join(constants.EXPERIMENTS_FOLDER_PATH, name) + if self.doIhaveInstOrSimData()['haveInstance']: + sim.clearAll() + + sim.initialize() + sim.loadNetParams(os.path.join(path, experiments.NET_PARAMS_FILE)) + sim.loadSimCfg(os.path.join(path, experiments.SIM_CONFIG_FILE)) + self.netParams = sim.net.params + self.simConfig = sim.cfg + netpyne_ui_utils.remove(self.simConfig.todict()) + netpyne_ui_utils.remove(self.netParams.todict()) + + def viewExperimentResult(self, payload: dict): + """ Loads the output file of a simulated experiment trial. + + :param payload: {name: str, trial: str, onlyModelSpecification: bool} + :return: geppetto model + """ + name = payload.get("name", None) + trial = payload.get("trial", None) + only_model_spec = payload.get("onlyModelSpecification", False) + + file = experiments.get_trial_output_path(name, trial) + if file is None or not os.path.exists(file): + return utils.getJSONError(f"Couldn't find output file of condition. Please take a look at the simulation log.", "") + + if self.doIhaveInstOrSimData()['haveInstance']: + sim.clearAll() + + sim.initialize() + + if only_model_spec: + # Load only model specification + sim.loadNetParams(file) + sim.loadSimCfg(file) + self.netParams = sim.net.params + self.simConfig = sim.cfg + netpyne_ui_utils.remove(self.simConfig.todict()) + netpyne_ui_utils.remove(self.netParams.todict()) + return + else: + # Load the complete simulation + sim.loadAll(file) + self._create3D_shapes(file) + self.geppetto_model = self.model_interpreter.getGeppettoModel(sim) + return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) + + def stopExperiment(self, experiment_name): + simulations.local.stop() + return { + "message": f"Stopped simulation of {experiment_name}" + } + + def find_tutorials(self): + return glob(join(NETPYNE_WORKDIR_PATH, "**/gui_tut*.py"), recursive=True) def instantiateNetPyNEModelInGeppetto(self, args): try: with redirect_stdout(sys.__stdout__): - if not 'usePrevInst' in args or not args['usePrevInst']: + if not args.get("usePrevInst", False): + if self.doIhaveInstOrSimData()['haveInstance']: + sim.clearAll() netpyne_model = self.instantiateNetPyNEModel() self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model) return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) - except: - return utils.getJSONError("Error while instantiating the NetPyNE model", sys.exc_info()) + except NetpyneValidationError as e: + message = ("Error while validating the NetPyNE model before instantiation.\n" + "One or more components in your model have issues, see details below:") + logging.exception(message) + return utils.getJSONError(message, '\n'.join(e.args)) + except Exception as e: + message = "Error while instantiating the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) + + def simulate_experiment_trials(self, experiment: model.Experiment): + try: + working_directory = self._prepare_batch_files(experiment) + except OSError: + experiment.state = model.ExperimentState.ERROR + return utils.getJSONError("The specified folder already exists", "") + logging.info("Running experiment %s combinations", experiment.name) + try: + simulations.run( + platform="local", + parallel=self.run_config.parallel, + cores=self.run_config.cores, + method=self.run_config.type, + batch=True, + asynchronous=self.run_config.asynchronous, + working_directory=working_directory + ) + except InvalidConfigError as e: + experiment.state = model.ExperimentState.ERROR + logging.error("Error running experiment %s: %s", experiment.name, str(e)) + return utils.getJSONError(str(e), "") + + if self.run_config.asynchronous: + message = f"Experiment {experiment.name} started. " \ + f"You can view the Experiment status in the Experiment Manager." + else: + message = f"Experiment {experiment.name} finished, you can view the results in the Experiment Manager." + + return dict(message=message) + + def simulate_single_model(self, experiment: model.Experiment = None, use_prev_inst: bool = False): + if experiment: + working_directory = self._prepare_simulation_files(experiment, use_prev_inst) + + simulations.run( + parallel=self.run_config.parallel, + cores=self.run_config.cores, + asynchronous=self.run_config.asynchronous, + method=simulations.MPI_BULLETIN, + working_directory=working_directory, + ) + + if self.run_config.asynchronous: + message = "Experiment is pending! " \ + f"Results will be stored in your workspace at ./{os.path.join(constants.EXPERIMENTS_FOLDER, experiment.name)}" + return dict(message=message) + else: + sim.load(f'{constants.MODEL_OUTPUT_FILENAME}.json') + self.geppetto_model = self.model_interpreter.getGeppettoModel(sim) + response = json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) + return response + + else: + # Run in same process + if not use_prev_inst: + logging.debug('Instantiating single thread simulation') + netpyne_model = self.instantiateNetPyNEModel() + + self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model) + + simulations.run() + + if self.geppetto_model: + response = json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) + return response + + + def validate_netParams(self): + cpy = deepcopy_wout_empty(self.netParams) + _, failed = sim.validator.validateNetParams(cpy) + if failed: + message = "" + components_error = {} + for entry in failed: + components_error.setdefault(entry.component, []).append((entry.keyPath, entry.summary)) + for component, details in components_error.items(): + message = message + f"* Error validating {component}\n" + for (keyPath, summary) in details: + path = ' -> '.join(f"{key}" for key in keyPath) + message = message + f" Error in {path}\n" + for line in summary: + message = message + f" {line}\n" + message = message + "\n" + raise NetpyneValidationError(message) + def simulateNetPyNEModelInGeppetto(self, args): + """ Starts simulation of the currently loaded NetPyNe model. + + * runConfiguration is used to determine asynch/synch & other parameters. + * complete flag in args decides if we simulate single model as Experiment or complete Experiment. + * if Experiment in design does not exist, we create a new one & start single sim. + * All Simulations run in different process. + + :param args: { allTrials: bool, usePrevInst: bool } + :return: geppetto model. + """ + allTrials = args.get('allTrials', True) + use_prev_inst = args.get('usePrevInst', False) + sim_id = args.get('simId', 0) try: - with redirect_stdout(sys.__stdout__): - # TODO mpi is not finding libmpi.dylib.. set LD_LIBRARY_PATH to openmpi bin folder, but nothing - if args['parallelSimulation']: - logging.debug('Running parallel simulation') - if not 'usePrevInst' in args or not args['usePrevInst']: - self.netParams.save("netParams.json") - self.simConfig.saveJson = True - self.simConfig.save("simParams.json") - template = os.path.join(os.path.dirname(__file__), 'template.py') + self.validate_netParams() + + experiment = experiments.get_current() + if experiment: + if self.experiments.any_in_state([model.ExperimentState.PENDING, model.ExperimentState.SIMULATING]): + return utils.getJSONError("Experiment is already simulating or pending", "") + + if simulations.local.is_running(): + simulations.local.stop() + + experiment.state = model.ExperimentState.PENDING + + try: + if allTrials: + if len(experiment.trials) == 1 and experiment.trials[0].id == experiments.BASE_TRIAL_ID: + # special case where we don't want to run a batch simulation + return self.simulate_single_model(experiment, use_prev_inst) + else: + return self.simulate_experiment_trials(experiment) else: - sim.cfg.saveJson = True - oldName = sim.cfg.filename - sim.cfg.filename = 'model_output' - sim.saveData() - sim.cfg.filename = oldName - template = os.path.join(os.path.dirname(__file__), 'template2.py') - copyfile(template, './init.py') - - cp = subprocess.run(["mpiexec", "-n", args['cores'], "nrniv", "-mpi", "-python", "init.py"], - capture_output=True) - print(cp.stdout.decode() + cp.stderr.decode()) - if cp.returncode != 0: return utils.getJSONError("Error while simulating the NetPyNE model", - cp.stderr.decode()) - sim.load('model_output.json') - self.geppetto_model = self.model_interpreter.getGeppettoModel(sim) - netpyne_model = sim + return self.simulate_single_model(experiment, use_prev_inst) + except Exception: + experiment.state = model.ExperimentState.ERROR + message = f"Unknown error during simulation of Experiment. SimulationId {sim_id}" + logging.exception(message) + # return utils.getJSONError("Unknown error during simulation of Experiment", sys.exc_info(), { "sim_id": sim_id}) + return utils.getJSONError("Unknown error during simulation of Experiment", sys.exc_info()) - else: - logging.info("Starting simulation") + else: + return self.simulate_single_model(use_prev_inst=use_prev_inst) + except NetpyneValidationError as e: + message = (f"Error while validating the NetPyNE model before simulation {sim_id}.\n" + "One or more components in your model have issues, see details below:") + logging.exception(message) + return utils.getJSONError(message, '\n'.join(e.args)) + + except Exception as e : + message = f"Error while simulating the NetPyNE model: {e}. SimulationId {sim_id}" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) + + def _prepare_simulation_files(self, experiment: model.Experiment = None, use_prev_inst: bool = False) -> str: + """Prepares template files and netpyne model files for a single simulation """ + exp = copy.deepcopy(experiment) + # Remove parameter & trials for single run + exp.params = [] + exp.trials = [] + + save_folder_path = os.path.join(constants.NETPYNE_WORKDIR_PATH, constants.EXPERIMENTS_FOLDER, exp.name) + try: + os.makedirs(save_folder_path) + except OSError: + raise - if not args.get('usePrevInst', False): - logging.debug('Instantiating single thread simulation') - netpyne_model = self.instantiateNetPyNEModel() - self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model) + if use_prev_inst: + sim.cfg.saveJson = True + oldName = sim.cfg.filename + sim.cfg.filename = constants.MODEL_OUTPUT_FILENAME - logging.debug('Running single thread simulation') - netpyne_model = self.simulateNetPyNEModel() + # workaround for issue with empty LFP dict when calling saveData() + if 'LFP' in sim.allSimData: + del sim.allSimData['LFP'] - return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) - except: - return utils.getJSONError("Error while simulating the NetPyNE model", sys.exc_info()) + # TODO: store in experiments folder! + sim.saveData() + sim.cfg.filename = oldName + template_name = constants.TEMPLATE_FILENAME_SINGLE_RUN_INSTANTIATED + else: + # Create netParams and SimConfig + self.netParams.save(os.path.join(save_folder_path, experiments.NET_PARAMS_FILE)) + + simCfg = copy.copy(self.simConfig) + # filename and simLabel must be set to define the output filename + simCfg.saveJson = True + simCfg.filename = 'model_output' + simCfg.simLabel = 'model_output' + simCfg.saveDataInclude = [ + "simData", + "simConfig", + "netParams", + "net" + ] + simCfg.save(os.path.join(save_folder_path, experiments.SIM_CONFIG_FILE)) + + template_name = constants.TEMPLATE_FILENAME_SINGLE_RUN + + # Create Experiment Config + config_dict = dataclasses.asdict(exp) + config_dict["runCfg"] = dataclasses.asdict(self.run_config) + experiment_config = os.path.join(save_folder_path, experiments.EXPERIMENT_FILE) + json.dump(config_dict, open(experiment_config, 'w'), default=str, sort_keys=True, indent=4) + + # Copy Template + template = os.path.join(os.path.dirname(__file__), "templates", template_name) + copyfile(template, os.path.join(save_folder_path, constants.SIMULATION_SCRIPT_NAME)) + + return save_folder_path + + def _prepare_batch_files(self, experiment: model.Experiment) -> str: + """Creates template files and netpyne model files in the experiment folder. + + Only for an experiment consisting of many trials. + + :param experiment: given experiment + :return: working directory path + """ + exp = copy.deepcopy(experiment) + exp.params = self.experiments.process_params(exp.params) + + netParams = copy.deepcopy(self.netParams) + netParams.mapping = {p.mapsTo.replace('netParams.', ''): p.mapsTo.split('.')[1::] for p in exp.params if 'netParams' in p.mapsTo} + + simCfg = copy.copy(self.simConfig) + simCfg.saveJson = True + simCfg.saveDataInclude = [ + "simData", + "simConfig", + "netParams", + "net" + ] + + config_dict = dataclasses.asdict(exp) + config_dict["runCfg"] = dataclasses.asdict(self.run_config) + + save_folder_path = os.path.join(constants.NETPYNE_WORKDIR_PATH, constants.EXPERIMENTS_FOLDER, exp.name) + try: + os.makedirs(save_folder_path) + except OSError: + raise + + simCfg.save(os.path.join(save_folder_path, experiments.SIM_CONFIG_FILE)) + netParams.save(os.path.join(save_folder_path, experiments.NET_PARAMS_FILE)) + + experiment_json = os.path.join(save_folder_path, experiments.EXPERIMENT_FILE) + json.dump(config_dict, open(experiment_json, 'w'), default=str, sort_keys=True, indent=4) + + template_single_run = os.path.join(os.path.dirname(__file__), "templates", constants.TEMPLATE_FILENAME_BATCH_RUN) + template_batch = os.path.join(os.path.dirname(__file__), "templates", constants.TEMPLATE_FILENAME_BATCH) + copyfile(template_single_run, os.path.join(save_folder_path, 'run.py')) + # TODO: name should be batch.py not init.py + copyfile(template_batch, os.path.join(save_folder_path, constants.SIMULATION_SCRIPT_NAME)) + + return save_folder_path def loadModel(self, args): """ Imports a model stored as file in json format. @@ -124,25 +480,16 @@ def loadModel(self, args): :param args: :return: """ - - def remove(dictionary): - # remove reserved keys such as __dict__, __Method__, etc - # they appear when we do sim.loadAll(json_file) - if isinstance(dictionary, dict): - for key, value in list(dictionary.items()): - if key.startswith('__'): - dictionary.pop(key) - else: - remove(value) - if not any([args[option] for option in ['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']]): return utils.getJSONError("Error while loading data", 'You have to select at least one option') try: owd = os.getcwd() - compileModMechFiles(args['compileMod'], args['modFolder']) - except: - return utils.getJSONError("Error while importing/compiling mods", sys.exc_info()) + loadModMechFiles(args['compileMod'], args['modFolder']) + except Exception: + message = "Error while importing/compiling mods" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) finally: os.chdir(owd) @@ -155,11 +502,12 @@ def remove(dictionary): if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll() sim.initialize() - sim.loadAll(args['jsonModelFolder']) + sim.loadAll(args['jsonModelFolder'], instantiate=False) self.netParams = sim.net.params self.simConfig = sim.cfg - remove(self.netParams.todict()) - remove(self.simConfig.todict()) + self.simConfig.saveCellSecs = True + netpyne_ui_utils.remove(self.netParams.todict()) + netpyne_ui_utils.remove(self.simConfig.todict()) else: if args['loadNet']: wake_up_geppetto = True @@ -168,7 +516,8 @@ def remove(dictionary): sim.initialize() sim.loadNet(args['jsonModelFolder']) - if args['loadSimData']: # TODO (https://github.com/Neurosim-lab/netpyne/issues/360) + # TODO (https://github.com/Neurosim-lab/netpyne/issues/360) + if args['loadSimData']: wake_up_geppetto = True if not self.doIhaveInstOrSimData()['haveInstance']: sim.create(specs.NetParams(), specs.SimConfig()) @@ -179,30 +528,69 @@ def remove(dictionary): if args['loadSimCfg']: sim.loadSimCfg(args['jsonModelFolder']) self.simConfig = sim.cfg - remove(self.simConfig.todict()) + netpyne_ui_utils.remove(self.simConfig.todict()) if args['loadNetParams']: if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll() sim.loadNetParams(args['jsonModelFolder']) self.netParams = sim.net.params - remove(self.netParams.todict()) + netpyne_ui_utils.remove(self.netParams.todict()) if wake_up_geppetto: - if len(sim.net.cells) > 0: - section = list(sim.net.cells[0].secs.keys())[0] - if 'pt3d' not in list(sim.net.cells[0].secs[section].geom.keys()): - sim.net.defineCellShapes() - sim.gatherData() - sim.loadSimData(args['jsonModelFolder']) + self._create3D_shapes(args['jsonModelFolder']) + # TODO: Fix me - gatherData will remove allSimData! sim.gatherData() + self.geppetto_model = self.model_interpreter.getGeppettoModel(sim) return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) else: return utils.getJSONReply() - except: - return utils.getJSONError("Error while loading the NetPyNE model", sys.exc_info()) + except Exception: + message = "Error while loading the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) + + def _create3D_shapes(self, json_path: str): + """ Creates cellShapes for 3D viewer. + + Performed as final step after `json_path` was loaded. + """ + if len(sim.net.cells) > 0: + section = list(sim.net.cells[0].secs.keys())[0] + if 'pt3d' not in list(sim.net.cells[0].secs[section].geom.keys()): + sim.net.defineCellShapes() + sim.gatherData() + # Load again because gatherData removed simData + sim.loadSimData(json_path) + + def loadFromIndexFile(self, json_path: str): + cfg, netParams = sim.loadModel(json_path, loadMechs=True, ignoreMechAlreadyExistsError=True) + self.simConfig = cfg + self.netParams = netParams + + if isinstance(self.netParams, dict): + self.netParams = specs.NetParams(self.netParams) + + if isinstance(self.simConfig, dict): + self.simConfig = specs.SimConfig(self.simConfig) + + for key, value in self.netParams.cellParams.items(): + if hasattr(value, 'todict'): + self.netParams.cellParams[key] = value.todict() + + # TODO: when should sim.initialize be called? + # Only on import or better before every simulation or network instantiation? + sim.initialize() + + def saveToIndexFile(self, srcPath, dstPath, exportNetParamsAsPython, exportSimConfigAsPython): + sim.saveModel(netParams=self.netParams, + simConfig=self.simConfig, + srcPath=srcPath, + dstPath=dstPath, + exportNetParamsAsPython=exportNetParamsAsPython, + exportSimConfigAsPython=exportSimConfigAsPython) def importModel(self, modelParameters): """ Imports a model stored in form of Python files. @@ -214,13 +602,16 @@ def importModel(self, modelParameters): # TODO: this must be integrated into the general lifecycle of "model change -> simulate" # Shouldn't be specific to Import sim.clearAll() - + try: + loadModMechFiles(modelParameters['compileMod'], modelParameters['modFolder'], modelParameters.get("forceRecompile", True)) + except Exception: + message = "Error while importing/compiling mods" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) try: # Get Current dir owd = os.getcwd() - compileModMechFiles(modelParameters['compileMod'], modelParameters['modFolder']) - with redirect_stdout(sys.__stdout__): # NetParams net_params_path = str(modelParameters["netParamsPath"]) @@ -231,6 +622,12 @@ def importModel(self, modelParameters): # Import Model attributes self.netParams = getattr(net_params_module_name, str(modelParameters["netParamsVariable"])) + if isinstance(self.netParams, dict): + self.netParams = specs.NetParams(self.netParams) + + if isinstance(self.simConfig, dict): + self.simConfig = specs.SimConfig(self.simConfig) + for key, value in self.netParams.cellParams.items(): if hasattr(value, 'todict'): self.netParams.cellParams[key] = value.todict() @@ -249,7 +646,69 @@ def importModel(self, modelParameters): sim.initialize() return utils.getJSONReply() except: - return utils.getJSONError("Error while importing the NetPyNE model", sys.exc_info()) + message = "Error while importing the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) + finally: + os.chdir(owd) + + def importNeuroML(self, modelParameters): + from netpyne_ui.helpers import neuroml + + + try: + # Get Current dir + owd = os.getcwd() + + with redirect_stdout(sys.__stdout__): + # NetParams + filename = str(modelParameters["fileName"]) + + json_fname = neuroml.convertNeuroML2(filename, compileMod=modelParameters["compileMod"]) + + return self.loadModel(args=dict( + compileMod=True, + modFolder=os.path.dirname(json_fname), + jsonModelFolder=json_fname, + loadNet=True, + loadSimData=True, + loadSimCfg=True, + loadNetParams=True + )) + except: + message = "Error while importing the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) + finally: + os.chdir(owd) + + def importLEMS(self, modelParameters): + from netpyne_ui.helpers import neuroml + + + try: + # Get Current dir + owd = os.getcwd() + + with redirect_stdout(sys.__stdout__): + # NetParams + filename = str(modelParameters["fileName"]) + + json_fname = neuroml.convertLEMSSimulation(filename) + + return self.loadModel(args=dict( + compileMod=True, + modFolder=os.path.dirname(json_fname), + jsonModelFolder=json_fname, + loadNet=True, + loadSimData=True, + loadSimCfg=True, + loadNetParams=True + )) + except Exception: + message = "Error while importing the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) finally: os.chdir(owd) @@ -262,7 +721,7 @@ def importCellTemplate(self, modelParameters): conds = {} if rule not in self.netParams.cellParams else self.netParams.cellParams[rule]['conds'] - compileModMechFiles(modelParameters["compileMod"], modelParameters["modFolder"]) + loadModMechFiles(modelParameters["compileMod"], modelParameters["modFolder"]) del modelParameters["modFolder"] del modelParameters["compileMod"] @@ -273,8 +732,10 @@ def importCellTemplate(self, modelParameters): self.netParams.cellParams[rule] = self.netParams.cellParams[rule].todict() return utils.getJSONReply() - except: - return utils.getJSONError("Error while importing the NetPyNE cell template", sys.exc_info()) + except Exception: + message = "Error while importing the NetPyNE cell template" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) finally: os.chdir(owd) @@ -284,29 +745,33 @@ def exportModel(self, args): if not args['netCells']: sim.initialize(netParams=self.netParams, simConfig=self.simConfig) sim.cfg.filename = args['fileName'] - include = [el for el in specs.SimConfig().saveDataInclude if el in args.keys() and args[el]] + sim_config_data_include = specs.SimConfig().saveDataInclude + include = [el for el in sim_config_data_include if args.get(el, False)] if args['netCells']: include += ['netPops'] sim.cfg.saveJson = True sim.saveData(include) sim.cfg.saveJson = False - with open(f"{sim.cfg.filename}.json") as json_file: + with open(f"{sim.cfg.filename}_data.json") as json_file: data = json.load(json_file) return data - return utils.getJSONReply() - except: - return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info()) + except Exception: + message = "Error while exporting the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) def exportNeuroML(self, modelParams): try: with redirect_stdout(sys.__stdout__): sim.exportNeuroML2(modelParams['fileName'], specs.SimConfig()) return utils.getJSONReply() - except: - return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info()) + except Exception: + message = "Error while exporting the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) - def importNeuroML(self, modelParams): + def importNeuroMLOLD(self, modelParams): try: with redirect_stdout(sys.__stdout__): sim.initialize() @@ -315,8 +780,10 @@ def importNeuroML(self, modelParams): self.geppetto_model = self.model_interpreter.getGeppettoModel(sim) return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model)) - except: - return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info()) + except Exception: + message = "Error while exporting the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) def deleteModel(self, modelParams): try: @@ -325,35 +792,33 @@ def deleteModel(self, modelParams): self.simConfig = specs.SimConfig() sim.initialize(specs.NetParams(), specs.SimConfig()) self.geppetto_model = None - except: - return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info()) + except Exception: + message = "Error while exporting the NetPyNE model" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) try: - # This function fails is some keys don't exists - # sim.clearAll() - # TODO: as part of #264 we should remove the method and use clearAll intstead - self.clearSim() + sim.clearAll() except: - pass + logging.exception("Failed to clear simulation") return utils.getJSONReply() def instantiateNetPyNEModel(self): + self.validate_netParams() with redirect_stdout(sys.__stdout__): saveData = sim.allSimData if hasattr(sim, 'allSimData') and 'spkt' in sim.allSimData.keys() and len( sim.allSimData['spkt']) > 0 else False + + #netcoded = jsonpickle.encode(self.netParams, unpicklable=False) + #simcoded = jsonpickle.encode(self.simConfig, unpicklable=False) sim.create(self.netParams, self.simConfig) sim.net.defineCellShapes() # creates 3d pt for cells with stylized geometries sim.gatherData(gatherLFP=False) - if saveData: sim.allSimData = saveData # preserve data from previous simulation - return sim + if saveData: + sim.allSimData = saveData # preserve data from previous simulation - def simulateNetPyNEModel(self): - with redirect_stdout(sys.__stdout__): - sim.setupRecording() - sim.simulate() - sim.saveData() return sim def doIhaveInstOrSimData(self): @@ -375,17 +840,21 @@ def doIhaveInstOrSimData(self): return {'haveInstance': out[0], 'haveSimData': out[1]} def rename(self, path, oldValue, newValue): - command = 'sim.rename(self.' + path + ',"' + oldValue + '","' + newValue + '")' + # command = 'sim.rename(self.' + path + ',"' + oldValue + '","' + newValue + '")' + command = f'sim.rename(self.{path}, {oldValue!r}, {newValue!r})' logging.debug('renaming ' + command) + eval(command) for model, synched_component in list(jupyter_geppetto.synched_models.items()): if model != '' and oldValue in model and path in model: # jupyter_geppetto.synched_models.pop(model) - newModel = re.sub("(['])(?:(?=(\\?))\2.)*?\1", lambda x: x.group(0).replace(oldValue, newValue, 1), - model) - logging.debug("Rename funct - Model is " + model + " newModel is " + newModel) - jupyter_geppetto.synched_models[newModel] = synched_component + new_model = re.sub("(['])(?:(?=(\\?))\2.)*?\1", + lambda x: x.group(0).replace(oldValue, newValue, 1), + model) + logging.debug("Rename funct - Model is " + model + " newModel is " + new_model) + jupyter_geppetto.synched_models[new_model] = synched_component + with redirect_stdout(sys.__stdout__): if "popParams" in path: self.propagate_field_rename("pop", newValue, oldValue) @@ -401,10 +870,21 @@ def getPlotSettings(self, plot_name): return self.simConfig.analysis[plot_name] return {} - def getDirList(self, dir=None, onlyDirs=False, filterFiles=False): + def checkFileExists(self, path): + path = Path(path or '') + return path.exists() + + def getFullPath(self, dir, subDir): + if dir is None or dir == '': + base = constants.NETPYNE_WORKDIR_PATH + if subDir: + base = os.path.join(base, subDir) + dir = os.path.join(os.getcwd(), base) + return dir + + def getDirList(self, dir=None, onlyDirs=False, filterFiles=False, subDir=None): # Get Current dir - if dir == None or dir == '': - dir = os.path.join(os.getcwd(), NETPYNE_WORKDIR_PATH) + dir = self.getFullPath(dir, subDir) dir_list = [] file_list = [] for f in sorted(os.listdir(str(dir)), key=str.lower): @@ -422,6 +902,13 @@ def checkAvailablePlots(self): def getPlot(self, plotName, LFPflavour, theme='gui'): try: with redirect_stdout(sys.__stdout__): + availablePlots = self.checkAvailablePlots() + checkCondition = availablePlots.get(plotName.replace('iplot', 'plot'), False) + + if checkCondition is False: + logging.info("Plot " + plotName + " not available") + return -1 + args = self.getPlotSettings(plotName) if LFPflavour: args['plots'] = [LFPflavour] @@ -432,9 +919,15 @@ def getPlot(self, plotName, LFPflavour, theme='gui'): # This arg brings dark theme. But some plots are broken by it args['theme'] = theme - if plotName in ("iplotConn", "iplot2Dnet") and sim.net.allCells: + if plotName in ("iplotConn", "iplot2Dnet") and hasattr(sim, 'net') and sim.net.allCells: + def conns_length(cell) -> int: + if type(cell) is dict: + return len(cell.get('conns', [])) + else: + return len(getattr(cell, 'conns', [])) + # To prevent unresponsive kernel, we don't show conns if they become too many - num_conn = sum([len(cell.conns) for cell in sim.net.allCells if cell.conns]) + num_conn = sum([conns_length(cell) for cell in sim.net.allCells]) if num_conn > NUM_CONN_LIMIT: args["showConns"] = False @@ -449,11 +942,9 @@ def getPlot(self, plotName, LFPflavour, theme='gui'): return html else: - - figData = getattr(analysis, plotName)(**args) - - if isinstance(figData, tuple): - fig = figData[0] + fig_data = getattr(analysis, plotName)(**args) + if isinstance(fig_data, tuple): + fig = fig_data[0] if fig == -1: return fig elif isinstance(fig, list): @@ -466,9 +957,13 @@ def getPlot(self, plotName, LFPflavour, theme='gui'): else: return [ui.getSVG(fig)] else: - return figData + if plotName == 'plotEEG': + return self.simConfig.filename + '_EEG.png' + elif plotName == 'plotDipole': + return self.simConfig.filename + '_dipole.png' + else: + return fig_data except Exception as e: - # TODO: Extract these two lines as a function and call it in every catch clause err = "There was an exception in %s():" % (e.plotName) logging.exception(("%s \n %s \n%s" % (err, e, sys.exc_info()))) @@ -476,19 +971,23 @@ def getAvailablePops(self): return list(self.netParams.popParams.keys()) def getAvailableCellModels(self): - cellModels = set([]) + cell_models = set([]) for p in self.netParams.popParams: if 'cellModel' in self.netParams.popParams[p]: cm = self.netParams.popParams[p]['cellModel'] - if cm not in cellModels: - cellModels.add(cm) - return list(cellModels) + if cm not in cell_models: + cell_models.add(cm) + return list(cell_models) - def getAvailableCellTypes(self): - cellTypes = set([]) - for p in self.netParams.cellParams: - cellTypes.add(p) - return list(cellTypes) + def getAvailableCellModels(self): + return ["", "VecStim", "NetStim", "IntFire1"] + + def getAvailableStimulationDistribution(self): + return ["normal", "uniform"] + + def getAvailableStimulationPattern(self): + # self.netParams.popParams[name]['spikePattern'] = {} + return ["", "rhythmic", "evoked", "poisson", "gauss"] def getAvailableSections(self): sections = {} @@ -496,9 +995,40 @@ def getAvailableSections(self): sections[cellRule] = list(self.netParams.cellParams[cellRule]['secs'].keys()) return sections + def getAvailableCellTypes(self): + cell_types = set([]) + cell_types.add('all') + for p in self.netParams.cellParams: + cell_types.add(p) + return sorted(cell_types) + + def getAvailableDensityTypes(self): + return ['uniform', '1DMap', '2DMap', 'distance'] + + def getAvailableRxDSections(self, selectedRegion = None): + sections = set([]) + sections.add('all') + if selectedRegion and selectedRegion in self.netParams.rxdParams.regions and self.netParams.rxdParams.regions[selectedRegion].get('cells'): + if 'all' in self.netParams.rxdParams.regions[selectedRegion]['cells']: + for cellRule in self.netParams.cellParams: + for cellSect in self.netParams.cellParams[cellRule]['secs']: + sections.add(cellSect) + else: + for cellRule in self.netParams.cellParams: + if cellRule in self.netParams.rxdParams.regions[selectedRegion]['cells']: + for cellSect in self.netParams.cellParams[cellRule]['secs']: + sections.add(cellSect) + return sorted(sections) + def getAvailableStimSources(self): return list(self.netParams.stimSourceParams.keys()) + def getAvailableRxdRegions(self): + return list(self.netParams.rxdParams.regions.keys()) + + def getAvailableRxdSpecies(self): + return list(self.netParams.rxdParams.species.keys()) + def getAvailableSynMech(self): return list(self.netParams.synMechParams.keys()) @@ -524,7 +1054,10 @@ def getAvailablePlots(self): "plotShape", "plot2Dnet", "iplotConn", - "granger" + "granger", + "plotDipole", + "plotEEG", + "plotRateSpectrogram" ] return [plot for plot in plots if plot not in list(self.simConfig.analysis.keys())] @@ -569,8 +1102,10 @@ def deleteParam(self, model, label): # side effect on other rules if "popParams" in model: self.propagate_field_rename("pop", None, label) - self.propagate_field_rename("cellModel", None, rule['cellModel']) - self.propagate_field_rename("cellType", None, rule['cellType']) + if 'cellModel' in rule: + self.propagate_field_rename("cellModel", None, rule['cellModel']) + if 'cellType' in rule: + self.propagate_field_rename("cellType", None, rule['cellType']) elif "stimSourceParams" in model: @@ -578,7 +1113,8 @@ def deleteParam(self, model, label): elif "synMechParams" in model: self.propagate_field_rename("synMech", None, label) return True - except: + except Exception as e : + logging.exception(f"Error while deleting parameter: {label}") return False def validateFunction(self, functionString): @@ -587,55 +1123,24 @@ def validateFunction(self, functionString): return validateFunction(functionString, self.netParams.__dict__) def exportHLS(self, args): - def convert2bool(string): - return string.replace('true', 'True').replace('false', 'False').replace('null', 'False') - - def header(title, spacer='-'): - return '\n# ' + title.upper() + ' ' + spacer * (77 - len(title)) + '\n' try: - params = ['popParams', 'cellParams', 'synMechParams'] - params += ['connParams', 'stimSourceParams', 'stimTargetParams'] - - fname = args['fileName'] if args['fileName'][-3:] == '.py' else args['fileName'] + '.py' - - with open(fname, 'w') as script: - script.write('from netpyne import specs, sim\n') - script.write(header('documentation')) - script.write("''' Script generated with NetPyNE-UI. Please visit:\n") - script.write(" - https://www.netpyne.org\n - https://github.com/MetaCell/NetPyNE-UI\n'''\n") - script.write(header('script', spacer='=')) - script.write('netParams = specs.NetParams()\n') - script.write('simConfig = specs.SimConfig()\n') - script.write(header('single value attributes')) - for attr, value in list(self.netParams.__dict__.items()): - if attr not in params: - if value != getattr(specs.NetParams(), attr): - script.write('netParams.' + attr + ' = ') - script.write(convert2bool(json.dumps(value, indent=4)) + '\n') - - script.write(header('network attributes')) - for param in params: - for key, value in list(getattr(self.netParams, param).items()): - script.write("netParams." + param + "['" + key + "'] = ") - script.write(convert2bool(json.dumps(value, indent=4)) + '\n') - - script.write(header('network configuration')) - for attr, value in list(self.simConfig.__dict__.items()): - if value != getattr(specs.SimConfig(), attr): - script.write('simConfig.' + attr + ' = ') - script.write(convert2bool(json.dumps(value, indent=4)) + '\n') - - script.write(header('create simulate analyze network')) - script.write('# sim.createSimulateAnalyze(netParams=netParams, simConfig=simConfig)\n') - - script.write(header('end script', spacer='=')) + fname = args.get('fileName', 'output.py') + if not fname[-3:] == '.py': + fname = f"{fname}.py" + + from netpyne.conversion import createPythonScript + createPythonScript(fname, self.netParams, self.simConfig) with open(fname) as f: - return f.read() + file_b64 = base64.b64encode(bytes(f.read(), 'utf-8')).decode() + export_info = {"fileContent": file_b64, "fileName": fname} + return export_info - except: - return utils.getJSONError("Error while importing the NetPyNE model", sys.exc_info()) + except Exception: + message = "Error while exporting NetPyNE model to python" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) def propagate(self, model, label, cond, new, old): with redirect_stdout(sys.__stdout__): @@ -644,7 +1149,7 @@ def propagate(self, model, label, cond, new, old): for plot in analysis.keys(): if cond in analysis[plot].keys(): for index, item in enumerate(analysis[plot][cond]): - if isinstance(item, str): + if isinstance(item, str) or isinstance(item, int): if item == old: if new == None: analysis[plot][cond].remove(item) @@ -662,11 +1167,11 @@ def propagate(self, model, label, cond, new, old): else: obj = getattr(self.netParams, model) for key in obj.keys(): - if label in list(obj[key][cond].keys()): + if cond in obj[key] and label in list(obj[key][cond].keys()): if isinstance(obj[key][cond][label], str): if old == obj[key][cond][label]: if new == '' or new == None: - obj[key].pop(label) + obj[key][cond].pop(label) else: obj[key][cond][label] = new elif isinstance(obj[key][cond][label], list): @@ -735,63 +1240,20 @@ def propagate_syn_mech_rename(self, new, old): if self.netParams.stimSourceParams[self.netParams.stimTargetParams[label]['source']][ 'type'] == 'NetStim': if old == self.netParams.stimTargetParams[label]['synMech']: - if new == None: + if new is None: self.netParams.stimTargetParams[label].pop('synMech') else: self.netParams.stimTargetParams[label]['synMech'] = new - def clearSim(self): - # clean up - sim.pc.barrier() - sim.pc.gid_clear() # clear previous gid settings - - # clean cells and simData in all nodes - sim.clearObj([cell.__dict__ if hasattr(cell, '__dict__') else cell for cell in sim.net.cells]) - if 'stims' in list(sim.simData.keys()): - sim.clearObj([stim for stim in sim.simData['stims']]) - - for key in list(sim.simData.keys()): del sim.simData[key] - - if hasattr(sim, 'net'): - for c in sim.net.cells: del c - for p in sim.net.pops: del p - if hasattr(sim.net, 'params'): - del sim.net.params - - # clean cells and simData gathered in master node - if sim.rank == 0: - if hasattr(sim.net, 'allCells'): - sim.clearObj([cell.__dict__ if hasattr(cell, '__dict__') else cell for cell in sim.net.allCells]) - if hasattr(sim, 'allSimData'): - if 'stims' in list(sim.allSimData.keys()): - sim.clearObj([stim for stim in sim.allSimData['stims']]) - for key in list(sim.allSimData.keys()): del sim.allSimData[key] - del sim.allSimData - - import matplotlib - matplotlib.pyplot.clf() - matplotlib.pyplot.close('all') - - if hasattr(sim, 'net'): - if hasattr(sim.net, 'allCells'): - for c in sim.net.allCells: del c - del sim.net.allCells - if hasattr(sim.net, 'allPops'): - for p in sim.net.allPops: del p - - del sim.net - - import gc; - gc.collect() - def create_celltype_from_template(self, label="CellType", conds={}, cell_template_name="Blank"): try: with redirect_stdout(sys.__stdout__): self.netParams.addCellParamsTemplate(label=label, template=cell_template_name) return True - except: - return utils.getJSONError(f"Error while creating cellType from template {cell_template_name}", - sys.exc_info()) + except Exception: + message = f"Error while creating cellType from template {cell_template_name}" + logging.exception(message) + return utils.getJSONError(message, sys.exc_info()) logging.info("Initialising NetPyNE UI") diff --git a/netpyne_ui/netpyne_model_interpreter.py b/netpyne_ui/netpyne_model_interpreter.py index d506a372..2175ab6e 100644 --- a/netpyne_ui/netpyne_model_interpreter.py +++ b/netpyne_ui/netpyne_model_interpreter.py @@ -20,8 +20,7 @@ def getGeppettoModel(self, netpyne_model): # We create a GeppettoModel instance and we set a name a assign a lib geppetto_model = self.factory.createGeppettoModel('NetPyNEModel') self.factory.geppetto_common_library = geppetto_model.libraries[0] - netpyne_geppetto_library = pygeppetto.GeppettoLibrary( - name='netpynelib') + netpyne_geppetto_library = pygeppetto.GeppettoLibrary(name='netpynelib') geppetto_model.libraries.append(netpyne_geppetto_library) self.extractPopulations(netpyne_model, netpyne_geppetto_library) @@ -34,9 +33,12 @@ def extractPopulations(self, netpyne_model, netpyne_geppetto_library): network = pygeppetto.CompositeType(id='network_netpyne', name='network_netpyne') netpyne_geppetto_library.types.append(network) + if not hasattr(netpyne_model.net, 'allCells'): + return + # Create intermediate population structure for easy access (by key) populations = {} - for index, cell in enumerate(netpyne_model.net.allCells): + for _, cell in enumerate(netpyne_model.net.allCells): # This will be only executed the first time for each population if cell['tags']['pop'] not in populations: # Create CellType, VisualType, ArrayType, ArrayVariable and append to netpyne library @@ -67,10 +69,9 @@ def extractPopulations(self, netpyne_model, netpyne_geppetto_library): populations[cell['tags']['pop']] = arrayType # Note: no need to check if pt3d since already done via netpyne sim.net.defineCellShapes() in instantiateNetPyNEModel - secs = cell['secs'] - # Iterate sections creating spheres and cylinders - if hasattr(secs, 'items'): + if 'secs' in cell and hasattr(cell['secs'], 'items'): + secs = cell['secs'] for sec_name, sec in list(secs.items()): if 'pt3d' in sec['geom']: points = sec['geom']['pt3d'] diff --git a/netpyne_ui/resources/stdin.txt b/netpyne_ui/resources/stdin.txt new file mode 100644 index 00000000..57dc54cc --- /dev/null +++ b/netpyne_ui/resources/stdin.txt @@ -0,0 +1,5 @@ +y +y +y +y +y diff --git a/netpyne_ui/simulations.py b/netpyne_ui/simulations.py new file mode 100644 index 00000000..df19464a --- /dev/null +++ b/netpyne_ui/simulations.py @@ -0,0 +1,144 @@ +import logging +import subprocess +import os +import multiprocessing +import platform + +from netpyne import sim +from netpyne_ui import constants + +# Available netpyne.batch.Batch methods. +MPI_DIRECT = "mpi_direct" +MPI_BULLETIN = "mpi_bulletin" + +system = platform.system() +if system == "Darwin": + import sys + + # nrniv needs NRN_PYLIB to be set to python executable path (MacOS, Python 3.7.6) + os.environ["NRN_PYLIB"] = sys.executable + + +class SimulationError(Exception): + """ Base Simulation Exception """ + + +class InvalidConfigError(Exception): + """ Thrown if invalid number of CPUs were specified. """ + + +class LocalSimulationPool: + """ Pool that manages simulation running on the same machine as Netpyne-UI. """ + + cpus = multiprocessing.cpu_count() + + def __init__(self): + # We allow to run only one asynchronous simulation at a time on the same instance. + self.subprocess = None + + def run(self, parallel, cores, method="", batch=False, asynchronous=False, working_directory=None): + if int(cores) > self.cpus: + raise InvalidConfigError( + f"Specified {cores} cores, but only {self.cpus} are available") + + logging.info(f"Scheduling simulation on {cores} cores with {method} ...") + + if batch or asynchronous or parallel: + if method == MPI_DIRECT: + self._run_in_subprocess( + _python_command(working_directory), asynchronous=asynchronous, working_directory=working_directory + ) + elif method == MPI_BULLETIN: + if parallel: + self._run_in_subprocess( + _bulletin_board_cmd(cores, working_directory), asynchronous=asynchronous, working_directory=working_directory + ) + else: + self._run_in_subprocess( + _python_command(working_directory), asynchronous=asynchronous, working_directory=working_directory + ) + else: + raise InvalidConfigError(f"Unsupported method {method}") + else: + return self._run_in_same_process() + + def is_running(self): + return self.subprocess and self.subprocess.poll() is None + + def list(self): + if not self.subprocess: + return "no_simulation" + + ret_code = self.subprocess.poll() + if ret_code is None: + return "running" + + status = "completed" if ret_code == 0 else "failed" + return [{"status": status}] + + def stop(self): + if self.is_running(): + self.subprocess.kill() + + def _run_in_same_process(self): + logging.debug('Running single core simulation') + + sim.setupRecording() + sim.simulate() + sim.saveData() + + def _run_in_subprocess(self, cmds, asynchronous=False, working_directory: str = None): + if self.is_running(): + logging.info("Another simulation is still running") + return False + logging.info("Running simulations on subprocess inside directory %s", working_directory) + logging.info("Running commands: \n%s", "\n".join(cmds)) + if working_directory: + with open(os.path.join(working_directory, 'sim.log'), 'w') as f: + self.subprocess = subprocess.Popen(cmds, stdout=f, stderr=f) + else: + self.subprocess = subprocess.Popen(cmds) + + if not asynchronous: + # blocking wait + return_code = self.subprocess.wait() + if return_code == 0: + logging.info("Simulation finished with success") + else: + logging.error("Simulation run failed") + + +def _bulletin_board_cmd(cores, working_directory=None): + """ Creates command to run batch or single simulations in parallel. + + Uses mpiexec that implements the OpenMPI protocol to schedule simulations. + Uses the master/worker pattern. + """ + return ["mpiexec", "-n", str(cores), "--use-hwthread-cpus", "nrniv", "-python", "-mpi", _script_path(working_directory)] + + +def _script_path(working_directory=None): + return os.path.join(working_directory, + constants.SIMULATION_SCRIPT_NAME) if working_directory else f"./{constants.SIMULATION_SCRIPT_NAME}" + + +def _python_command(working_directory=None): + return ["python", _script_path(working_directory)] + + +def run(platform="local", parallel=False, cores=1, method="", batch=False, asynchronous=False, working_directory=None): + if platform == "local": + local.run( + parallel=parallel, + cores=cores, + method=method, + batch=batch, + asynchronous=asynchronous, + working_directory=working_directory + ) + else: + # remote simulations in future versions + pass + + +local = LocalSimulationPool() diff --git a/netpyne_ui/template.py b/netpyne_ui/template.py deleted file mode 100644 index 2a370fd2..00000000 --- a/netpyne_ui/template.py +++ /dev/null @@ -1,8 +0,0 @@ -from netpyne import sim -netParams = sim.loadNetParams("./netParams.json", None, False) -simConfig = sim.loadSimCfg("./simParams.json", None, False) - -sim.createSimulateAnalyze(netParams, simConfig) - - - diff --git a/netpyne_ui/template2.py b/netpyne_ui/template2.py deleted file mode 100644 index 17360fc2..00000000 --- a/netpyne_ui/template2.py +++ /dev/null @@ -1,3 +0,0 @@ -from netpyne import sim -sim.load("./model_output.json") -sim.simulate() \ No newline at end of file diff --git a/netpyne_ui/templates/__init__.py b/netpyne_ui/templates/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/netpyne_ui/templates/batch.py b/netpyne_ui/templates/batch.py new file mode 100644 index 00000000..d3811e83 --- /dev/null +++ b/netpyne_ui/templates/batch.py @@ -0,0 +1,132 @@ +import json +import os +import sys +import tempfile +import pathlib +import time + +from neuron import h +from netpyne import specs +from netpyne.batch import Batch + +CURRENT_DIR = "." +try: + CURRENT_DIR = os.path.dirname(__file__) +except: + pass + +os.chdir(CURRENT_DIR) + +def is_error(): + """Validates if Experiment failed or succeeded. + + Experiment is successful if there exists a data file for every trial (cfg file) + """ + + data_files = list(pathlib.Path( + CURRENT_DIR).glob(f"*_data.json")) + cfg_files = list(pathlib.Path( + CURRENT_DIR).glob(f"*_cfg.json")) + + if len(data_files) != len(cfg_files): + print( + f"data files don't match with cfg files {len(data_files)} - {len(cfg_files)}") + return True + + return False + + +def update_state(experiment, state): + experiment["state"] = state + + with tempfile.NamedTemporaryFile('w', dir=os.path.dirname("experiment.json"), delete=False) as tf: + json.dump(experiment, tf, default=str, sort_keys=True, indent=4) + tempname = tf.name + + os.rename(tempname, "./experiment.json") + + +def run_batch(experiment): + # Map params to netpyne format + params = specs.ODict() + grouped_params = [] + for param in experiment["params"]: + params[param["mapsTo"].replace("netParams.", "")] = param["values"] + if param["inGroup"]: + grouped_params.append(param["mapsTo"].replace("netParams.", "")) + + with open("netParams.json", "r") as f: + net_params = json.load(f) + net_params = specs.NetParams(net_params["net"]["params"]) + + with open("simConfig.json", "r") as f: + sim_config = json.load(f) + sim_config = specs.SimConfig(sim_config["simConfig"]) + + batch = Batch( + cfg=sim_config, + netParams=net_params, + params=params, + groupedParams=grouped_params, + seed=experiment.get("seed", None), + ) + + # Label will be subfolder of saveFolder + batch.batchLabel = experiment.get("name", "batch_template_run") + + # Have to overwrite the saveFolder, default goes to root folder which is not always allowed by OS + batch.saveFolder = os.getcwd() + + # For now, we only support grid|list + batch.method = experiment.get("method", "grid") + + # for now, we only support mpi_direct or bulletinboard + # * mpi_direct can be started by running batch.py + # * mpi_bulletin requires to run "mpiexec -n 4 nrniv -mpi batch.py", otherwise runs in single core + run_cfg = experiment.get("runCfg", None) + + cores = run_cfg.get("cores", None) + cores = int(cores) if cores else None + + if run_cfg: + batch.runCfg = { + "type": run_cfg.get("type", "mpi_bulletin"), + "script": run_cfg.get("script", "run.py"), + "skip": run_cfg.get("skip", True), + "cores": cores, + } + + batch.run() + return batch + + +with open("experiment.json", "r") as f: + experiment = json.load(f) + if experiment['runCfg']['type'] == 'mpi_bulletin': + pc = h.ParallelContext() + if pc.id() == 0: + update_state(experiment, "SIMULATING") + else: + update_state(experiment, "SIMULATING") + + try: + batch = run_batch(experiment) + if batch.runCfg["type"] == "mpi_bulletin": + pc = h.ParallelContext() + if pc.id() != 0: + sys.exit(0) + + # wait for data file writing to complete ... + # TODO: netpyne sim needs to wait until file exists before exiting! + time.sleep(10) + if is_error(): + update_state(experiment, "ERROR") + sys.exit(1) + else: + update_state(experiment, "SIMULATED") + + except Exception as e: + print("Experiment failed ...") + print(e) + update_state(experiment, "ERROR") + sys.exit(1) diff --git a/netpyne_ui/templates/batch_run_single.py b/netpyne_ui/templates/batch_run_single.py new file mode 100644 index 00000000..52906dfe --- /dev/null +++ b/netpyne_ui/templates/batch_run_single.py @@ -0,0 +1,24 @@ +import neuron +from netpyne import sim + + +def run(): + # Folder that contains x86_64 folder + NETPYNE_WORKDIR_PATH = "../../../" + neuron.load_mechanisms(NETPYNE_WORKDIR_PATH) + + # read cfg and netParams from command line arguments if available; otherwise use default + simConfig, netParams = sim.readCmdLineArgs( + simConfigDefault="cfg.py", netParamsDefault="netParams.py" + ) + + # Create network and run simulation + sim.createSimulate(netParams=netParams, simConfig=simConfig) + sim.saveData() + + +try: + run() +except Exception as e: + print("Trial failed ...") + print(e) diff --git a/netpyne_ui/templates/run.py b/netpyne_ui/templates/run.py new file mode 100644 index 00000000..a89af07d --- /dev/null +++ b/netpyne_ui/templates/run.py @@ -0,0 +1,54 @@ +import os +import json +import neuron +import sys +import tempfile + +from neuron import h +from netpyne import sim + +os.chdir(os.path.dirname(__file__)) + + +def update_state(experiment, state): + experiment["state"] = state + + with tempfile.NamedTemporaryFile('w', dir=os.path.dirname("experiment.json"), delete=False) as tf: + json.dump(experiment, tf, default=str, sort_keys=True, indent=4) + tempname = tf.name + + os.rename(tempname, "./experiment.json") + + +def run_sim(): + # Folder that contains x86_64 folder + NETPYNE_WORKDIR_PATH = "../../../" + neuron.load_mechanisms(NETPYNE_WORKDIR_PATH) + + netParams = sim.loadNetParams("./netParams.json", None, False) + simConfig = sim.loadSimCfg("./simConfig.json", None, False) + + sim.createSimulate(netParams, simConfig) + sim.saveData() + + +with open("./experiment.json", "r") as f: + exp = json.load(f) + if exp['runCfg']['type'] == 'mpi_bulletin' and exp['runCfg']['cores'] > 1: + pc = h.ParallelContext() + if pc.id() == 0: + update_state(exp, "SIMULATING") + else: + update_state(exp, "SIMULATING") + +try: + run_sim() + update_state(exp, "SIMULATED") + sys.exit(0) + +except Exception as e: + print("Experiment failed ...") + print(e) + + update_state(exp, "ERROR") + sys.exit(1) diff --git a/netpyne_ui/templates/run_instantiated_net.py b/netpyne_ui/templates/run_instantiated_net.py new file mode 100644 index 00000000..a1bef0c1 --- /dev/null +++ b/netpyne_ui/templates/run_instantiated_net.py @@ -0,0 +1,11 @@ +import neuron + +from netpyne import sim + +# Folder that contains x86_64 folder +NETPYNE_WORKDIR_PATH = '../../../' +neuron.load_mechanisms(NETPYNE_WORKDIR_PATH) + +sim.load("./model_output.json") +sim.createSimulate() +sim.saveData() \ No newline at end of file diff --git a/netpyne_ui/utils.py b/netpyne_ui/utils.py new file mode 100644 index 00000000..646135f6 --- /dev/null +++ b/netpyne_ui/utils.py @@ -0,0 +1,23 @@ +import os + + +def remove(dictionary): + # remove reserved keys such as __dict__, __Method__, etc + # they appear when we do sim.loadAll(json_file) + if isinstance(dictionary, dict): + for key, value in list(dictionary.items()): + if key.startswith('__'): + dictionary.pop(key) + else: + remove(value) + + +def get_next_file_name(directory: str, filename: str) -> str: + if not os.path.exists(os.path.join(directory, filename)): + return filename + + i = 1 + while os.path.exists(os.path.join(directory, f"{filename}-{i}")): + i += 1 + + return f"{filename}-{i}" diff --git a/requirements.txt b/requirements.txt index 7d232b46..c2d7075e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -airspeed==0.5.4dev-20150515 +airspeed==0.5.20 alembic==1.4.2 async-generator==1.10 attrs==19.3.0 @@ -15,24 +15,26 @@ defusedxml==0.6.0 Deprecated==1.2.10 entrypoints==0.3 future==0.18.2 +h5py==3.7.0 idna==2.9 ipython-genutils==0.2.0 ipywidgets==7.5.1 jedi==0.17.0 Jinja2==2.11.2 +jsonpickle==2.1.0 jsonschema==3.2.0 -jupyter==1.0.0 -jupyter-client==6.1.3 -jupyter-console==6.1.0 -jupyter-core==4.6.3 -jupyter_geppetto==1.1.1 -jupyter-telemetry==0.0.5 -jupyterhub==1.1.0 -jupyterlab==2.1.3 +jupyter_geppetto==1.1.5 +jupyter-client==7.0.6 +jupyter-core==4.9.1 +jupyter-server==1.11.2 +jupyterhub==1.5.0 +jupyterlab==3.2.4 +neuromllite==0.5.4 jupyterthemes==0.20.0 kiwisolver==1.2.0 lesscpy==0.14.0 -libNeuroML==0.2.50 +libNeuroML==0.5.1 +lfpykit==0.5.1 lxml==4.5.1 Mako==1.1.0 MarkupSafe==1.1.1 @@ -42,11 +44,11 @@ mistune==0.8.4 multimethod==1.3 nbconvert==5.6.1 nbformat==5.0.6 -neuromllite==0.1.9 -netpyne==1.0.0.2 -NEURON==7.8.1.1 +netpyne==1.0.6 +NEURON==8.2.2 numpy==1.18.5 oauthlib==3.0.1 +optuna==2.10.1 ordered-set==4.0.2 pamela==1.0.0 pandas==0.23.4 @@ -62,10 +64,14 @@ pycosat==0.6.3 pycparser==2.20 pyecore==0.11.7 pygeppetto==0.8.1 +PyLEMS==0.5.9 +pyNeuroML==1.0.10 +sentry_sdk==1.5.2 +dacite==1.6.0 +h5py==3.7.0 +jsonpickle==2.1.0 Pygments==2.6.1 PyJWT==1.7.1 -PyLEMS==0.4.9.3 -pyNeuroML==0.3.15 pyOpenSSL==19.1.0 pyparsing==2.4.7 pyrsistent==0.16.0 @@ -85,11 +91,11 @@ scipy==1.4.1 Send2Trash==1.5.0 terminado==0.8.3 testpath==0.4.4 -tornado==6.0.4 +tornado==6.1.0 traitlets==4.3.3 typing-extensions==3.7.4.2 urllib3==1.25.9 webencodings==0.5.1 widgetsnbextension==3.5.1 wrapt==1.12.1 -zipp==3.1.0 +zipp==3.1.0 \ No newline at end of file diff --git a/run.py b/run.py index bd3d26d2..5da5f591 100644 --- a/run.py +++ b/run.py @@ -9,14 +9,15 @@ os.environ['JUPYTER_CONFIG_DIR'] = os.path.join(os.path.dirname(os.path.abspath(__file__)), '.jupyter-config') -settings.debug = True +settings.debug = False if __name__ == '__main__': sys.argv.append('--NotebookApp.default_url=/geppetto') sys.argv.append("--NotebookApp.token=''") sys.argv.append('--library=netpyne_ui') + sys.argv.append('--no-browser') sys.argv.append('--NotebookApp.disable_check_xsrf=True') - + app = NotebookApp.instance() app.initialize(sys.argv) app.file_to_run = '' diff --git a/setup.py b/setup.py index de9196c9..081b6c05 100644 --- a/setup.py +++ b/setup.py @@ -3,11 +3,14 @@ import os from glob import glob -#This block copies resources to the server so we avoid jupyter nbextension install --py --sys-prefix jupyter_geppetto +# This block copies resources to the server so we avoid jupyter nbextension install --py --sys-prefix jupyter_geppetto data_files = [] -data_files.append(('geppetto/src/main/webapp/build/', glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/*.js'))) -data_files.append(('geppetto/src/main/webapp/build/', glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/*.vm'))) -data_files.append(('geppetto/geppetto/src/main/webapp/build/', glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/fonts/*'))) +data_files.append(('geppetto/src/main/webapp/build/', + glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/*.js'))) +data_files.append(('geppetto/src/main/webapp/build/', + glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/*.vm'))) +data_files.append(('geppetto/geppetto/src/main/webapp/build/', + glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/fonts/*'))) for root, dirnames, filenames in os.walk('src/jupyter_geppetto/geppetto/src/main/webapp/js/'): for filename in fnmatch.filter(filenames, '*'): data_files.append((root[3:], [os.path.join(root, filename)])) @@ -15,7 +18,7 @@ setuptools.setup( name="netpyne_ui", - version="0.7.0", + version="1.1.0", url="https://github.com/MetaCell/NetPyNE-UI", author="MetaCell", author_email="info@metacell.us", @@ -38,7 +41,13 @@ ], install_requires=[ 'jupyter-geppetto>=1.0.0', - 'NEURON>=7.8.0' - 'netpyne>=1.0.0' + 'NEURON>=8.2.2', + 'netpyne>=1.0.6', + 'neuromllite==0.5.4', + 'pyNeuroML>=1.0.10', + 'sentry_sdk>=1.5.2', + 'dacite>=1.6.0', + 'h5py>=3.7.0', + 'jsonpickle>=2.1.0', ], ) diff --git a/tests/backend/models/gui_import_dict.py b/tests/backend/models/gui_import_dict.py new file mode 100644 index 00000000..de26e84c --- /dev/null +++ b/tests/backend/models/gui_import_dict.py @@ -0,0 +1,69 @@ +from netpyne import specs + +# Network parameters +netParams = {} # object of class NetParams to store the network parameters + +netParams['cellParams'] = {} +netParams['popParams'] = {} +netParams['stimSourceParams'] = {} +netParams['stimTargetParams'] = {} +netParams['synMechParams'] = {} +netParams['connParams'] = {} + +## Cell parameters +secs = {} # dict with section info +secs['soma'] = {'geom': {}, 'mechs': {}} +secs['soma']['geom'] = {'diam': 12, 'L': 12, 'Ra': 100.0, 'cm': 1} # soma geometry +secs['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.0003, 'el': -54.3} # soma hh mechanism + +secs['dend'] = {'geom': {}, 'mechs': {}} +secs['dend']['geom'] = {'diam': 1.0, 'L': 200.0, 'Ra': 100.0, 'cm': 1} +secs['dend']['topol'] = {'parentSec': 'soma', 'parentX': 1.0, 'childX': 0} # dend geometry +secs['dend']['mechs']['pas'] = {'g': 0.001, 'e': -70} # dend pas mechanism + +netParams['cellParams']['pyr'] = {'secs': secs} # add dict to list of cell parameters + +## Population parameters +netParams['popParams']['E'] = {'cellType': 'pyr', 'numCells': 40} + + # Stimulation parameters +netParams['stimSourceParams']['IClamp1'] = {'type': 'IClamp', 'dur': 5, 'del': 20, 'amp': 0.1} +netParams['stimTargetParams']['IClamp1->cell0'] = {'source': 'IClamp1', 'conds': {'cellList':[0]}, 'sec':'dend', 'loc':1.0} + + +# Synaptic mechanism parameters +netParams['synMechParams']['exc'] = {'mod': 'Exp2Syn', 'tau1': 0.1, 'tau2': 1.0, 'e': 0} + + +# Connectivity parameters +netParams['connParams']['E->E'] = { + 'preConds': {'pop': 'E'}, + 'postConds': {'pop': 'E'}, + 'weight': 0.005, # weight of each connection + 'probability': 0.1, + 'delay': 5, # delay min=0.2, mean=13.0, var = 1.4 + 'synMech': 'exc', + 'sec': 'dend'} + +# Simulation options +simConfig = specs.SimConfig() # object of class SimConfig to store simulation configuration + +simConfig.duration = 0.2*1e3 # Duration of the simulation, in ms +simConfig.dt = 0.1 # Internal integration timestep to use +simConfig.verbose = False # Show detailed messages +simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}, + 'V_dend': {'sec': 'dend', 'loc': 1.0, 'var':'v'}} # Dict with traces to record +simConfig.recordCells = [0] +simConfig.recordStep = 0.1 # Step size in ms to save data (eg. V traces, LFP, etc) +simConfig.filename = 'gui_tut1' # Set file output name +simConfig.saveJson = False # Save params, network and sim output to pickle file +simConfig.analysis['iplotTraces'] = {'include': [0], 'overlay': True} +simConfig.analysis['iplotRaster'] = {'markerSize': 5, 'showFig': True} + + +if __name__ == '__main__': + netpyne_geppetto.netParams=netParams + netpyne_geppetto.simConfig=simConfig + +#from netpyne import sim +#sim.createSimulateAnalyze(netParams, simConfig) diff --git a/tests/backend/models/hhcells_model.json b/tests/backend/models/hhcells_model.json new file mode 100644 index 00000000..a0e891b3 --- /dev/null +++ b/tests/backend/models/hhcells_model.json @@ -0,0 +1,27302 @@ +{ + "net": { + "cells": [ + { + "conns": [], + "gid": 0, + "secLists": null, + "secs": null, + "stims": [], + "tags": { + "cellLabel": 0, + "cellType": "hhcell", + "label": [ + "hhcell" + ], + "pop": "hhpop", + "x": 0, + "xnorm": 0.0, + "y": 20.0, + "ynorm": 0.2, + "z": 0, + "znorm": 0.0 + } + }, + { + "conns": [], + "gid": 1, + "secLists": null, + "secs": null, + "stims": [], + "tags": { + "cellLabel": 1, + "cellType": "hhcell", + "label": [ + "hhcell" + ], + "pop": "hhpop", + "x": 20.0, + "xnorm": 0.2, + "y": 10.0, + "ynorm": 0.1, + "z": 0, + "znorm": 0.0 + } + } + ], + "params": { + "cellParams": { + "hhcell": { + "secLists": { + "soma_group": [ + "soma" + ] + }, + "secs": { + "soma": { + "geom": { + "Ra": 34.56, + "cm": 1.6, + "pt3d": [ + [ + 0.0, + 0.0, + 0.0, + 17.841242 + ], + [ + 0.0, + 17.841242, + 0.0, + 17.841242 + ] + ] + }, + "ions": {}, + "mechs": { + "pas": { + "e": -57.0, + "g": 0.00031 + } + }, + "vinit": -70.0 + } + } + } + }, + "cellsVisualizationSpacingMultiplier": [ + 1, + 1, + 1 + ], + "connParams": {}, + "correctBorder": false, + "defaultDelay": 1, + "defaultThreshold": 10, + "defaultWeight": 1, + "defineCellShapes": false, + "mapping": { + "__dict__": {} + }, + "popParams": { + "hhpop": { + "cellType": "hhcell", + "cellsList": [ + { + "cellLabel": 0, + "x": 0, + "y": 20.0, + "z": 0 + }, + { + "cellLabel": 1, + "x": 20.0, + "y": 10.0, + "z": 0 + } + ], + "numCells": 2, + "originalFormat": "NeuroML2", + "pop": "hhpop" + } + }, + "popTagsCopiedToCells": [ + "cellModel", + "cellType" + ], + "propVelocity": 500.0, + "rotateCellsRandomly": false, + "rxdParams": {}, + "scale": 1, + "scaleConnWeight": 1, + "scaleConnWeightModels": false, + "scaleConnWeightNetStims": 1, + "shape": "cuboid", + "sizeX": 100, + "sizeY": 100, + "sizeZ": 100, + "stimSourceParams": {}, + "stimTargetParams": {}, + "subConnParams": {}, + "synMechParams": {} + }, + "pops": { + "hhpop": { + "cellGids": [ + 0, + 1 + ], + "tags": { + "cellType": "hhcell", + "cellsList": [ + { + "cellLabel": 0, + "x": 0, + "y": 20.0, + "z": 0 + }, + { + "cellLabel": 1, + "x": 20.0, + "y": 10.0, + "z": 0 + } + ], + "numCells": 2, + "originalFormat": "NeuroML2", + "pop": "hhpop" + } + } + } + }, + "netpyne_changeset": "", + "netpyne_version": "1.0.2", + "simConfig": { + "addSynMechs": true, + "allowConnsWithWeight0": true, + "allowSelfConns": false, + "analysis": { + "plot2Dnet": false, + "plotConn": false, + "plotRaster": false, + "plotSpikeHist": false, + "plotSpikePSD": false + }, + "backupCfgFile": [], + "cache_efficient": false, + "compactConnFormat": false, + "connRandomSecFromList": true, + "coreneuron": false, + "createNEURONObj": 1, + "createPyStruct": 1, + "cvode_active": false, + "cvode_atol": 0.001, + "distributeSynsUniformly": true, + "dt": 0.05, + "duration": 450.0, + "filename": "HHCellNetwork.txt", + "gatherOnlySimData": true, + "gpu": false, + "hParams": { + "celsius": 6.3, + "clamp_resist": 0.001, + "v_init": -65.0 + }, + "includeParamsLabel": true, + "invertedYCoord": true, + "oneSynPerNetcon": true, + "plotCells": [ + "all" + ], + "printPopAvgRates": false, + "printRunTime": false, + "printSynsAfterRule": false, + "pt3dRelativeToCellLocation": true, + "rand123GlobalIndex": null, + "random123": false, + "recordCells": [ + "all" + ], + "recordCellsSpikes": -1, + "recordDipole": false, + "recordDipolesHNN": false, + "recordLFP": [], + "recordStep": 0.05, + "recordStim": true, + "recordTime": true, + "recordTraces": { + "of0_hhpop_0_soma_v": { + "conds": { + "cellLabel": 0, + "pop": "hhpop" + }, + "loc": 0.5, + "sec": "soma", + "var": "v" + }, + "of0_hhpop_1_soma_v": { + "conds": { + "cellLabel": 1, + "pop": "hhpop" + }, + "loc": 0.5, + "sec": "soma", + "var": "v" + } + }, + "saveCSV": false, + "saveCellConns": false, + "saveCellSecs": false, + "saveDat": true, + "saveDataInclude": [ + "netParams", + "netCells", + "netPops", + "simConfig", + "simData" + ], + "saveDipoleCells": false, + "saveDipolePops": false, + "saveDpk": false, + "saveFileStep": 0.05, + "saveFolder": "", + "saveHDF5": false, + "saveJson": false, + "saveLFPCells": false, + "saveLFPPops": false, + "saveMat": false, + "savePickle": false, + "saveTiming": false, + "seeds": { + "conn": 0, + "loc": 0, + "stim": 123456789 + }, + "simLabel": "", + 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100644 index 00000000..1b3332f2 --- /dev/null +++ b/tests/backend/netpyne_model_importer_test.py @@ -0,0 +1,87 @@ +import unittest +import os +import sys +import logging +import json, urllib.request + +import netpyne + +from netpyne import specs, sim +from netpyne_ui.netpyne_model_interpreter import NetPyNEModelInterpreter +import neuron +import subprocess + +from netpyne_ui.netpyne_geppetto import NETPYNE_WORKDIR_PATH +from netpyne_ui.netpyne_geppetto import NetPyNEGeppetto + +import sentry_sdk +sentry_sdk.init() + +netpyne.__gui__ = False +sys.path.insert(0, NETPYNE_WORKDIR_PATH) + +import sentry_sdk +sentry_sdk.init() + +class TestNetPyNEModelInterpreter(unittest.TestCase): + + @classmethod + def setUpClass(cls): + HERE = os.path.dirname(os.path.realpath(__file__)) + ROOT = os.path.dirname(HERE) + cls.path = NETPYNE_WORKDIR_PATH + modelpath = os.path.join(NETPYNE_WORKDIR_PATH, 'mod') + subprocess.call(["rm", "-r", os.path.join(modelpath, "x86_64")]) + owd = os.getcwd() + os.chdir(modelpath) + p = subprocess.check_output(["nrnivmodl"]) + os.chdir(owd) + try: + neuron.load_mechanisms(modelpath) + except: + logging.error("Error loading mechanisms", exc_info=True) + + # @unittest.skip("Neuroml model import issue") + def test_netpyne_exported_model_1(self): + print("------------------------------------") + print("Netpyne exported model sim run") + print("------------------------------------") + + params = {} + + HERE = os.path.dirname(os.path.realpath(__file__)) + ROOT = os.path.dirname(HERE) + + params["areModFieldsRequired"] = False + params["compileMod"] = False + params["exploreOnlyDirs"] = False + params["explorerDialogOpen"] = False + params["explorerParameter"] = "" + params["freezeInstance"] = True + params["freezeSimulation"] = True + params["jsonModelFolder"] = ROOT + "/backend/models/hhcells_model.json" + params["jsonPath"] = "" + params["loadNet"] = True + params["loadNetParams"] = True + params["loadSimCfg"] = True + params["loadSimData"] = True + params["modFolder"] = "" + params["modPath"] = "" + params["tab"] = "simulate" + + print(params['jsonModelFolder']) + + netpyne = NetPyNEGeppetto() + + netpyne.loadModel(params) + netpyne.simulate_single_model() + + #return False + + +if __name__ == '__main__': + try: + unittest.main() + except SystemExit as inst: + if inst.args[0]: # raised by sys.exit(True) when tests failed + raise diff --git a/tests/backend/netpyne_model_interpreter_test.py b/tests/backend/netpyne_model_interpreter_test.py index af37a0fd..0bcef888 100644 --- a/tests/backend/netpyne_model_interpreter_test.py +++ b/tests/backend/netpyne_model_interpreter_test.py @@ -15,6 +15,9 @@ netpyne.__gui__ = False sys.path.insert(0, NETPYNE_WORKDIR_PATH) +import sentry_sdk +sentry_sdk.init() + class TestNetPyNEModelInterpreter(unittest.TestCase): @@ -77,7 +80,7 @@ def test_getGeppettoModelSimpleNetwork(self): self.getGeppettoModel(netParams, simConfig) - @unittest.skip("Neuron restart kernel issue") + # @unittest.skip("Neuron restart kernel issue") def test_tut1(self): print("------------------------------------") print("Tutorial 1 Instantiation:") @@ -85,7 +88,7 @@ def test_tut1(self): from gui_tut1 import netParams, simConfig self.getGeppettoModel(netParams, simConfig) - @unittest.skip("Neuron restart kernel issue") + # @unittest.skip("Neuron restart kernel issue") def test_tut2(self): print("------------------------------------") print("Tutorial 2 Instantiation:") @@ -93,7 +96,7 @@ def test_tut2(self): from gui_tut2 import netParams, simConfig self.getGeppettoModel(netParams, simConfig) - @unittest.skip("Neuron restart kernel issue") + # @unittest.skip("Neuron restart kernel issue") def test_tut3(self): print("------------------------------------") print("Tutorial 3 Instantiation:") @@ -101,7 +104,7 @@ def test_tut3(self): from gui_tut3 import netParams, simConfig self.getGeppettoModel(netParams, simConfig) - @unittest.skip("Neuron restart kernel issue") + # @unittest.skip("Neuron restart kernel issue") def test_tut4(self): print("------------------------------------") print("Tutorial 3 ip3high Instantiation:") @@ -110,7 +113,7 @@ def test_tut4(self): from gui_tut3_ip3high import netParams, simConfig self.getGeppettoModel(netParams, simConfig) - @unittest.skip("Neuron restart kernel issue") + # @unittest.skip("Neuron restart kernel issue") def test_tut5(self): print("------------------------------------") print("Tutorial 3 norxd Instantiation:") @@ -118,7 +121,7 @@ def test_tut5(self): from gui_tut3_norxd import netParams, simConfig self.getGeppettoModel(netParams, simConfig) - @unittest.skip("Neuron restart kernel issue") + # @unittest.skip("Neuron restart kernel issue") def test_tut6(self): print("------------------------------------") print("Tutorial 3 osc Instantiation:") diff --git a/tests/backend/utils_test.py b/tests/backend/utils_test.py index dde4b62b..8f49a740 100644 --- a/tests/backend/utils_test.py +++ b/tests/backend/utils_test.py @@ -4,5 +4,8 @@ from netpyne_ui import mod_utils HERE = os.path.dirname(os.path.abspath(__file__)) +import sentry_sdk +sentry_sdk.init() + def test_compile_mod(): - mod_utils.compileModMechFiles(True, NETPYNE_WORKDIR_PATH) + mod_utils.loadModMechFiles(True, NETPYNE_WORKDIR_PATH) diff --git a/tests/frontend/e2e/.eslintrc.js b/tests/frontend/e2e/.eslintrc.js index 7e6f09b8..d804684b 100644 --- a/tests/frontend/e2e/.eslintrc.js +++ b/tests/frontend/e2e/.eslintrc.js @@ -1,8 +1,5 @@ module.exports = { - extends: [ - "./node_modules/@geppettoengine/geppetto-client/.eslintrc.js", - "plugin:jest/recommended" - ], + extends: ["plugin:jest/recommended"], rules: { 'multiline-comment-style': 0, }, @@ -17,6 +14,6 @@ module.exports = { pvdr: true, net1: true, CanvasContainer: true, - patchRequire: true + patchRequire: true, } -}; \ No newline at end of file +}; diff --git a/tests/frontend/e2e/jest-puppeteer.config.js b/tests/frontend/e2e/jest-puppeteer.config.js deleted file mode 100644 index b018dba8..00000000 --- a/tests/frontend/e2e/jest-puppeteer.config.js +++ /dev/null @@ -1,11 +0,0 @@ -module.exports = { - launch: { - headless: true, - args: ['--no-sandbox', '--disable-setuid-sandbox'], - defaultViewport: { - width: 1300, - height: 1024 - }, - timeout: 120000 - }, -} \ No newline at end of file diff --git a/tests/frontend/e2e/jest.config.js b/tests/frontend/e2e/jest.config.js index 89e7ae66..3c4fc3e9 100644 --- a/tests/frontend/e2e/jest.config.js +++ b/tests/frontend/e2e/jest.config.js @@ -1,6 +1,6 @@ module.exports = { verbose: true, - preset: "jest-puppeteer", + // preset: "jest-puppeteer", testRegex : "(tests/Test.*|(\\.|/)(test|spec))\\.[jt]sx?$", setupFilesAfterEnv: ['./tests/setupTests.js'], }; \ No newline at end of file diff --git a/tests/frontend/e2e/package-lock.json b/tests/frontend/e2e/package-lock.json index 9783eaaa..1a5322d7 100644 --- a/tests/frontend/e2e/package-lock.json +++ b/tests/frontend/e2e/package-lock.json @@ -1,28 +1,60 @@ { "name": "netpyne-ui.test.e2e", 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index 78fac8eb..aa2a0a6b 100644 --- a/tests/frontend/e2e/package.json +++ b/tests/frontend/e2e/package.json @@ -4,14 +4,29 @@ "description": "NetPyNe UI tests", "license": "unlicensed", "scripts": { - "test": "jest --verbose", + "test": "sleep 60 && npm run simple_tutorials_test && npm run complex_tutorials_test && npm run features_test", + "puppeteer_test": "jest --verbose", + "simple_tutorials_test": "sleep 60 && jest --verbose Tut#1_smoke Tut#2_smoke Tut#4_smoke", + "complex_tutorials_test": "jest --verbose Tut#3a_smoke Tut#3b_smoke Tut#3c_smoke", + "features_test": "jest --verbose ControlPanel SaveOpenFile RxD EEG_and_Dipole_Tut#1 ExperimentManager_Tut#1", + "EEG_Dipole_test": "jest --verbose EEG_and_Dipole_Tut#1 ", + "Experiment_Manager_test": "jest --verbose ExperimentManager_Tut#1 ", + "Tutorial_1_test": "jest --verbose Tut#1_smoke ", + "Tutorial_2_test": "jest --verbose Tut#2_smoke ", + "Tutorial_3A_test": "jest --verbose Tut#3a_smoke ", + "Tutorial_3B_test": "jest --verbose Tut#3b_smoke ", + "Tutorial_3C_test": "jest --verbose Tut#3c_smoke ", + "Tutorial_4_test": "jest --verbose Tut#4_smoke ", + "Control_Panel_test": "jest --verbose ControlPanel ", + "Save_Open_File_test": "jest --verbose SaveOpenFile", + "RxD_test": "jest --verbose RxD", "lint": "eslint --fix --ext .js,.jsx ." }, "dependencies": { - "jest": "^24.9.0", - "jest-image-snapshot": "^4.2.0", - "jest-puppeteer": "^4.4.0", - "puppeteer": "^1.20.0" + "jest": "^27.5.1", + "jest-image-snapshot": "^4.5.1", + "jest-puppeteer": "^6.1.0", + "puppeteer": "^13.5.1" }, "devDependencies": { "@babel/core": "^7.4.5", @@ -23,13 +38,13 @@ "@babel/preset-stage-2": "^7.0.0", "@babel/runtime": "^7.4.5", "babel-eslint": "^10.0.1", - "eslint": "^6.0.1", - "eslint-plugin-jest": "^22.21.0", "babel-jest": "^24.9.0", "babel-loader": "^8.0.6", "babel-plugin-transform-decorators-legacy": "^1.3.5", "babel-plugin-transform-object-assign": "^6.8.0", - "babel-plugin-transform-runtime": "^6.15.0" + "babel-plugin-transform-runtime": "^6.15.0", + "eslint": "^6.0.1", + "eslint-plugin-jest": "^22.21.0" }, "buildOptions": { "emitEntryPoint": true, @@ -39,4 +54,4 @@ ] } } -} +} \ No newline at end of file diff --git a/tests/frontend/e2e/tests/ControlPanel.test.js b/tests/frontend/e2e/tests/ControlPanel.test.js new file mode 100644 index 00000000..9f3f0a84 --- /dev/null +++ b/tests/frontend/e2e/tests/ControlPanel.test.js @@ -0,0 +1,337 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/Tut#2_smoke.test/`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.25 +}; + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + +//TESTS: + +jest.setTimeout(3000000); +let browser_control_panel; +let control_panel_page; + + +describe('Test for the Control Panel - color picker', () => { + + beforeAll(async () => { + browser_control_panel = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + control_panel_page = await browser_control_panel.newPage(); + await control_panel_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await control_panel_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await control_panel_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(control_panel_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await control_panel_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(control_panel_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await control_panel_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await control_panel_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser_control_panel.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await control_panel_page.on("dialog", dialog => + dialog.accept()); + + await control_panel_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await control_panel_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.click(selectors.FILE_TAB_SELECTOR) + await control_panel_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.click(selectors.NEW_FILE_SELECTOR) + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await control_panel_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await control_panel_page.waitForTimeout(PAGE_WAIT * 2) + + await control_panel_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await control_panel_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + it('Load Tutorial#2', async () => { + + await control_panel_page.waitForTimeout(PAGE_WAIT * 2) + await control_panel_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await control_panel_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Loading Tutorial #2') + await control_panel_page.waitForSelector(selectors.TUTORIAL_2_SELECTOR, { timeout: TIMEOUT }) + await control_panel_page.click(selectors.TUTORIAL_2_SELECTOR, { timeout: TIMEOUT }) + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.waitForSelector(selectors.PYR_2_CELL_SELECTOR) + await control_panel_page.waitForSelector(selectors.INT_CELL_SELECTOR) + await control_panel_page.waitForTimeout(PAGE_WAIT) + + console.log('Tutorial #2 loaded successfully') + + }) + + + it('Create network', async () => { + + await control_panel_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await control_panel_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await control_panel_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await control_panel_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await control_panel_page.waitForSelector(selectors.DISABLED_RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + console.log('Network created successfully') + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + console.log('... taking snapshot ...'); + await control_panel_page.waitForTimeout(PAGE_WAIT); + expect(await control_panel_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#2 Network' + }); + }) + + it('Open Color Picker Menu', async () => { + + console.log('Opening Control Panel') + + await control_panel_page.waitForSelector(selectors.CONTROL_PANEL_TAB_SELECTOR) + await control_panel_page.click(selectors.CONTROL_PANEL_TAB_SELECTOR) + await control_panel_page.waitForSelector(selectors.NETWORKS_IN_CONTROL_PANEL_SELECTOR) + + const network_items = (await control_panel_page.$$(selectors.NETWORK_ITEMS_CONTROL_PANEL_SELECTOR)).length; + await expect(network_items).toEqual(3) + + console.log('Control Panel displayed successfully') + + }) + + it('Randomize Main Level network color', async () => { + + console.log('Randomize Main Level network color') + + await control_panel_page.waitForTimeout(PAGE_WAIT * 3) + await control_panel_page.waitForSelector(selectors.CONTROL_PANEL_TABLE_SELECTOR) + + const primary_level_colors = await control_panel_page.$$eval(selectors.COLOR_RECT_SELECTOR, primary_level_colors => { + return primary_level_colors.map(primary_level_color => primary_level_color.outerHTML); + }); + + expect(primary_level_colors[0]).toContain('fill="#FF7F99"') + expect(primary_level_colors[0]).toEqual(primary_level_colors[1]) + expect(primary_level_colors[1]).toEqual(primary_level_colors[2]) + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + const rows = await control_panel_page.$$(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR) + for (var i = 0; i < rows.length; i++) { + await rows[0].hover() + } + + const buttons = await control_panel_page.$$(selectors.COLOR_CONTROL_BUTTONS_SELECTOR) + + for (var i = 0; i < buttons.length; i++) { + await buttons[1].click() + } + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + const rndm_primary_level_colors = await control_panel_page.$$eval(selectors.COLOR_RECT_SELECTOR, rndm_primary_level_colors => { + return rndm_primary_level_colors.map(rndm_primary_level_color => rndm_primary_level_color.outerHTML); + }); + + expect(rndm_primary_level_colors[0]).toContain('fill="#989898"') + expect(rndm_primary_level_colors[2]).not.toEqual(rndm_primary_level_colors[1]) + + console.log('Main Network color randomized successfully') + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + }) + + it('Randomize Sub level E network color', async () => { + + console.log('Randomize Sub Level E network color') + await control_panel_page.waitForSelector(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR, { timeout: TIMEOUT }) + const rows = await control_panel_page.$$(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR) + for (var i = 0; i < rows.length; i++) { + await rows[1].click() + await rows[1].hover() + } + await control_panel_page.waitForTimeout(PAGE_WAIT) + + const second_level_colors = await control_panel_page.$$eval(selectors.COLOR_RECT_SELECTOR, second_level_colors => { + return second_level_colors.map(second_level_color => second_level_color.outerHTML); + }); + + + expect(second_level_colors[1]).toEqual(second_level_colors[2]) + expect(second_level_colors[2]).toEqual(second_level_colors[3]) + + + const buttons = await control_panel_page.$$(selectors.COLOR_CONTROL_BUTTONS_SELECTOR) + + for (var i = 0; i < buttons.length; i++) { + await buttons[2].click() + } + + await control_panel_page.waitForTimeout(PAGE_WAIT * 2) + + const second_level_colors_after_rndm = await control_panel_page.$$eval(selectors.COLOR_RECT_SELECTOR, second_level_colors_after_rndm => { + return second_level_colors_after_rndm.map(second_level_color_after_rndm => second_level_color_after_rndm.outerHTML); + }); + + expect(second_level_colors_after_rndm[1]).toContain('fill="#989898"') + expect(second_level_colors_after_rndm[2]).not.toEqual(second_level_colors_after_rndm[3]) + expect(second_level_colors_after_rndm[2]).not.toEqual(second_level_colors_after_rndm[1]) + + console.log('E Network color randomized successfully') + + await control_panel_page.waitForTimeout(PAGE_WAIT * 3) + + }) + + + it('Pick a color for the sublevel I netowrk', async () => { + + console.log('Selecting a color for the I network') + await control_panel_page.waitForSelector(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR, { timeout: TIMEOUT }) + const rows = await control_panel_page.$$(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR) + for (var i = 0; i < rows.length; i++) { + await rows[1].click() + } + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + const rows_ = await control_panel_page.$$(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR) + + for (var i = 0; i < rows_.length; i++) { + await rows_[2].click() + } + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + const network_colors = await control_panel_page.$$eval(selectors.COLOR_RECT_SELECTOR, network_colors => { + return network_colors.map(network_color => network_color.outerHTML); + }); + + expect(network_colors[3]).toEqual(network_colors[4]) + expect(network_colors[3]).toEqual(network_colors[2]) + + await control_panel_page.waitForTimeout(PAGE_WAIT * 3) + + const buttons = await control_panel_page.$$(selectors.COLOR_CONTROL_BUTTONS_SELECTOR) + + for (var i = 0; i < buttons.length; i++) { + await buttons[4].click() + } + + await control_panel_page.waitForTimeout(PAGE_WAIT) + + const list_bounds = await control_panel_page.$(selectors.NETWORKS_IN_CONTROL_PANEL_SELECTOR); + const rect = await control_panel_page.evaluate((list_bounds) => { + const { top, left, bottom, right } = list_bounds.getBoundingClientRect(); + return { top, left, bottom, right }; + }, list_bounds); + + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.mouse.click(Math.round(rect.right) - 40, Math.round(rect.bottom) + 40) + await control_panel_page.waitForTimeout(PAGE_WAIT * 2) + + const rows_after_colouring_I = await control_panel_page.$$(selectors.CONTROL_PANEL_NETWORK_ROWS_SELECTOR) + for (var i = 0; i < rows_after_colouring_I.length; i++) { + await rows_after_colouring_I[2].click() + } + + const network_colors_after_colouring_I = await control_panel_page.$$eval(selectors.COLOR_RECT_SELECTOR, network_colors_after_colouring_I => { + return network_colors_after_colouring_I.map(network_color_after_colouring_I => network_color_after_colouring_I.outerHTML); + }); + await control_panel_page.waitForTimeout(PAGE_WAIT) + + expect(network_colors_after_colouring_I[2]).toEqual(network_colors_after_colouring_I[3]) + expect(network_colors_after_colouring_I[2]).toEqual(network_colors_after_colouring_I[4]) + + console.log('I network color selected successfully') + + }) + + it('Filter results from the Control panel', async () => { + + await control_panel_page.waitForTimeout(PAGE_WAIT) + console.log('Filtering results') + + await control_panel_page.waitForSelector(selectors.CONTROL_PANEL_FILTER_SELECTOR, {timeout: PAGE_WAIT}) + await control_panel_page.type(selectors.CONTROL_PANEL_FILTER_SELECTOR, 'E') + + await control_panel_page.waitForTimeout(PAGE_WAIT) + await control_panel_page.waitForSelector(selectors.NETWORKS_IN_CONTROL_PANEL_SELECTOR) + + const network_items = (await control_panel_page.$$(selectors.NETWORK_ITEMS_CONTROL_PANEL_SELECTOR)).length; + await expect(network_items).toEqual(3) + + console.log('Results filtered successfully') + + }) + + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/EEG_and_Dipole_Tut#1.test.js b/tests/frontend/e2e/tests/EEG_and_Dipole_Tut#1.test.js new file mode 100644 index 00000000..4fdfa25f --- /dev/null +++ b/tests/frontend/e2e/tests/EEG_and_Dipole_Tut#1.test.js @@ -0,0 +1,246 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + customDiffConfig: { + ssim: 'fast', + }, + failureThresholdType: 'percent', + failureThreshold: 0.2 +}; + + + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(3000000); +let browser_EEG_Dipole; +let EEG_Dipole_page; + +beforeAll(async () => { + + browser_EEG_Dipole = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + EEG_Dipole_page = await browser_EEG_Dipole.newPage(); + await EEG_Dipole_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await EEG_Dipole_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await EEG_Dipole_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(EEG_Dipole_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await EEG_Dipole_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(EEG_Dipole_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await EEG_Dipole_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await EEG_Dipole_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } +}); + +afterAll(async () => { + // Close the browser instance after all tests have run + await browser_EEG_Dipole.close(); + }); + +describe('EEG and Dipole Plot Test using Tutorial#1', () => { + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await EEG_Dipole_page.on("dialog", dialog => + dialog.accept()); + + await EEG_Dipole_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await EEG_Dipole_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + await EEG_Dipole_page.click(selectors.FILE_TAB_SELECTOR) + await EEG_Dipole_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + await EEG_Dipole_page.click(selectors.NEW_FILE_SELECTOR) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + await EEG_Dipole_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await EEG_Dipole_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 2) + + await EEG_Dipole_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await EEG_Dipole_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Load Tutorial#1', async () => { + + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 3) + await EEG_Dipole_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 2 }) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 2) + await EEG_Dipole_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + await console.log('Loading Tutorial #1') + await EEG_Dipole_page.click(selectors.TUTORIAL_1_SELECTOR, { timeout: TIMEOUT }) + await EEG_Dipole_page.waitForSelector(selectors.PYR_CELL_SELECTOR, { timeout: TIMEOUT * 2 }) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + + + }) + + it('Configure recording ', async () => { + + await console.log('Setting Recording configuration') + + await EEG_Dipole_page.waitForSelector(selectors.CONFIGURATION_TAB_SELECTOR) + await EEG_Dipole_page.click(selectors.CONFIGURATION_TAB_SELECTOR) + + await EEG_Dipole_page.waitForSelector(selectors.RECORDING_CONFIGURATION_TAB_SELECTOR) + await EEG_Dipole_page.click(selectors.RECORDING_CONFIGURATION_TAB_SELECTOR) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + + await EEG_Dipole_page.waitForSelector(selectors.TRACES_TO_RECORD_SELECTOR) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + await EEG_Dipole_page.waitForSelector(selectors.DIPOLE_LFPYKIT_SELECTOR) + // await expect(page).toClick(selectors.DIPOLE_LFPYKIT_SELECTOR) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + await EEG_Dipole_page.click(selectors.DIPOLE_LFPYKIT_SELECTOR) + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + + }) + + it('Create network', async () => { + + await EEG_Dipole_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await EEG_Dipole_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await EEG_Dipole_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await EEG_Dipole_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + await console.log('Create network') + + await EEG_Dipole_page.waitForSelector(selectors.DISABLED_EEG_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + await EEG_Dipole_page.waitForSelector(selectors.DISABLED_DIPOLE_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT) + + await console.log('... taking snapshot ...'); + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT); + expect(await EEG_Dipole_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#1 Network' + }); + }) + + it('Simulate network', async () => { + + await EEG_Dipole_page.waitForSelector(selectors.SIMULATE_BUTTON_SELECTOR) + await EEG_Dipole_page.click(selectors.SIMULATE_BUTTON_SELECTOR, { timeout: TIMEOUT }); + + await console.log('Simulate network') + + await EEG_Dipole_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await EEG_Dipole_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 5 }) + await EEG_Dipole_page.waitForSelector(selectors.EEG_PLOT_SELECTOR, { timeout: TIMEOUT * 5 }) + await EEG_Dipole_page.waitForSelector(selectors.DIPOLE_PLOT_SELECTOR, { timeout: TIMEOUT * 5 }) + }); + + it('Dipole Plot', async () => { + + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 2); + await EEG_Dipole_page.waitForSelector(selectors.DIPOLE_PLOT_SELECTOR) + await EEG_Dipole_page.click(selectors.DIPOLE_PLOT_SELECTOR) + await EEG_Dipole_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await console.log('View Dipole Plot ...') + + await EEG_Dipole_page.waitForSelector('#plot > div > div > img', { timeout: TIMEOUT * 10, hidden: false}) + + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 2); + // await EEG_Dipole_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await EEG_Dipole_page.waitForTimeout(PAGE_WAIT); + // await EEG_Dipole_page.click(selectors.DIPOLE_PLOT_SELECTOR) + // await EEG_Dipole_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + // await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 3); + + await console.log('... taking snapshot ...'); + expect(await EEG_Dipole_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Dipole Plot' + }); + }); + + + it('EEG Plot', async () => { + + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 2); + await EEG_Dipole_page.waitForSelector(selectors.EEG_PLOT_SELECTOR) + await EEG_Dipole_page.click(selectors.EEG_PLOT_SELECTOR) + await EEG_Dipole_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT, hidden: false}) + + await console.log('View EEG Plot ...') + + await EEG_Dipole_page.waitForSelector('#plot > div > div > img', { timeout: TIMEOUT * 10, hidden: false}) + + await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 7); + // await EEG_Dipole_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 2); + // await EEG_Dipole_page.click(selectors.EEG_PLOT_SELECTOR) + // await EEG_Dipole_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + // await EEG_Dipole_page.waitForTimeout(PAGE_WAIT * 3); + + await console.log('... taking snapshot ...'); + expect(await EEG_Dipole_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'EEG Plot' + }); + + }); + + + + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/ExperimentManager_Tut#1.test.js b/tests/frontend/e2e/tests/ExperimentManager_Tut#1.test.js new file mode 100644 index 00000000..7cd382aa --- /dev/null +++ b/tests/frontend/e2e/tests/ExperimentManager_Tut#1.test.js @@ -0,0 +1,392 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + customDiffConfig: { + ssim: 'fast', + }, + failureThresholdType: 'percent', + failureThreshold: 0.2 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(3000000); +let browser_experiment_manager; +let experiment_manager_page; + + +describe('Experiment Manager test using Tut#1', () => { + + beforeAll(async () => { + browser_experiment_manager = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + experiment_manager_page = await browser_experiment_manager.newPage(); + await experiment_manager_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await experiment_manager_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await experiment_manager_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(experiment_manager_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await experiment_manager_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(experiment_manager_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await experiment_manager_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await experiment_manager_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser_experiment_manager.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await experiment_manager_page.on("dialog", dialog => + dialog.accept()); + + await experiment_manager_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await experiment_manager_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.click(selectors.FILE_TAB_SELECTOR) + await experiment_manager_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.click(selectors.NEW_FILE_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT * 2) + + await experiment_manager_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await experiment_manager_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + it('Load Tutorial#1', async () => { + + await experiment_manager_page.waitForTimeout(PAGE_WAIT * 2) + await experiment_manager_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await click(experiment_manager_page, selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #1') + await click(experiment_manager_page, selectors.TUTORIAL_1_SELECTOR, { timeout: TIMEOUT }) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.waitForSelector(selectors.PYR_CELL_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + + }) + + + it('Create network', async () => { + + await experiment_manager_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await click(experiment_manager_page, selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await experiment_manager_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await click(experiment_manager_page, selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await experiment_manager_page.waitForSelector(selectors.DISABLED_RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + console.log('... taking snapshot ...'); + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + expect(await experiment_manager_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#1 Network' + }); + }) + + it('Set an Experiment in the Experiment Manager ', async () => { + + console.log('Setting up experiment') + + await experiment_manager_page.waitForSelector(selectors.EXPERIMENT_MANAGER_TAB_SELECTOR) + await experiment_manager_page.click(selectors.EXPERIMENT_MANAGER_TAB_SELECTOR) + await experiment_manager_page.waitForSelector(selectors.CREATE_NEW_EXPERIMENT_SELECTOR) + await experiment_manager_page.click(selectors.CREATE_NEW_EXPERIMENT_SELECTOR) + + await experiment_manager_page.waitForSelector(selectors.CREATE_NEW_EXPERIMENT_POPUP_SELECTOR) + await experiment_manager_page.waitForSelector(selectors.CONFIRM_SELECTOR, { timeout: TIMEOUT, hidden: false }) + await experiment_manager_page.click(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.waitForSelector(selectors.EXPERIMENT_NAME_SELECTOR, { timeout: TIMEOUT , hidden: false}) + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + await expect(experiment_manager_page).toFill(selectors.EXPERIMENT_NAME_SELECTOR, 'Test Experiment', { timeout: TIMEOUT, hidden: false }) + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + await experiment_manager_page.waitForSelector(selectors.PARAMETER_SELECTION_SELECTOR) + await experiment_manager_page.click(selectors.PARAMETER_SELECTION_SELECTOR) + + + await experiment_manager_page.evaluate(() => { + let parameter = document.querySelectorAll('li[class="MuiAutocomplete-option"]'); + for (var i = 0; i < parameter.length; i++) { + parameter[i].innerHTML.includes("numCells") && parameter[i].click(); + } + }); + + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + await experiment_manager_page.waitForSelector(selectors.FROM_VALUE_SELECTOR); + const inputFromValue = await experiment_manager_page.$eval('#undefined-from', el => el.value); + await experiment_manager_page.click(selectors.FROM_VALUE_SELECTOR); + for (let i = 0; i < inputFromValue.length; i++) { + await experiment_manager_page.keyboard.press('Backspace'); + } + + await experiment_manager_page.type(selectors.FROM_VALUE_SELECTOR, '1') + await experiment_manager_page.waitForSelector(selectors.TO_VALUE_SELECTOR); + const inputToValue = await experiment_manager_page.$eval('#undefined-to', el => el.value); + await experiment_manager_page.click(selectors.TO_VALUE_SELECTOR); + for (let i = 0; i < inputToValue.length; i++) { + await experiment_manager_page.keyboard.press('Backspace'); + } + + await experiment_manager_page.type(selectors.TO_VALUE_SELECTOR, '4') + await experiment_manager_page.waitForSelector(selectors.STEP_VALUE_SELECTOR); + const inputStepValue = await experiment_manager_page.$eval('#undefined-step', el => el.value); + await experiment_manager_page.click(selectors.STEP_VALUE_SELECTOR); + for (let i = 0; i < inputStepValue.length; i++) { + await experiment_manager_page.keyboard.press('Backspace'); + } + + await experiment_manager_page.type(selectors.STEP_VALUE_SELECTOR, '1') + + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + await experiment_manager_page.waitForSelector(selectors.CREATE_EXPERIMENT_BUTTON_SELECTOR) + await experiment_manager_page.click(selectors.CREATE_EXPERIMENT_BUTTON_SELECTOR) + + await experiment_manager_page.waitForSelector(selectors.EXPERIMENT_TABLE_HEADER_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + + const experiment_name = await experiment_manager_page.evaluate(() => { + document.querySelector('h6[class="MuiTypography-root experimentHead MuiTypography-h6"]').textContent + }); + + const experimentName = await experiment_manager_page.$eval('th[class="MuiTableCell-root MuiTableCell-body"]', el => el.innerText.trim()); + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + expect(experimentName).toBe('Test_Experiment') + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + + console.log('Experiment created') + + }) + + it('Simulate All conditions', async () => { + + await experiment_manager_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await click(experiment_manager_page, selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await experiment_manager_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR) + await click(experiment_manager_page, selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Simulating all conditions') + await experiment_manager_page.waitForSelector(selectors.SIMULATE_POPUP_SELECTOR) + await experiment_manager_page.click(selectors.SIMULATE_POPUP_SELECTOR) + await experiment_manager_page.waitForSelector(selectors.CONFIRM_SIMULATE_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_SIMULATE_SELECTOR) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + + await experiment_manager_page.waitForSelector(selectors.CONFIRM_EXPERIMENT_STARTED_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_EXPERIMENT_STARTED_SELECTOR) + + await experiment_manager_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + await experiment_manager_page.waitForSelector(selectors.SIMULATION_LOADER_SELECTOR, { hidden: false, timeout: TIMEOUT * 5 }) + await experiment_manager_page.waitForSelector(selectors.SIMULATION_LOADER_SELECTOR, { hidden: true, timeout: TIMEOUT * 10 }) + console.log('Experiment Simulation finished') + + }); + + it('Check Experiment Condition #1', async () => { + + console.log('Checking experiment condition #1') + await experiment_manager_page.waitForSelector(selectors.BACK_TO_EDIT_SELECTOR) + await experiment_manager_page.click(selectors.BACK_TO_EDIT_SELECTOR) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT * 2) + + await experiment_manager_page.waitForSelector(selectors.CELL_TYPES_TAB_SELECTOR) + await experiment_manager_page.click(selectors.CELL_TYPES_TAB_SELECTOR) + + await experiment_manager_page.evaluate(() => { + let sections = document.querySelectorAll('div[class="MuiButtonBase-root MuiListItem-root makeStyles-selected-23 MuiListItem-dense MuiListItem-button"]'); + for (var i = 0; i < sections.length; i++) { + sections[i].textContent.includes("Experiment Manager") && sections[i].click(); + } + }); + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + + await experiment_manager_page.waitForSelector(selectors.EXPERIMENT_TABLE_SELECTOR) + await experiment_manager_page.click(selectors.CREATED_EXPERIMENT_SELECTOR) + + await experiment_manager_page.waitForSelector(selectors.EXPERIMENT_CONDIIONS_ROW_SELECTOR) + + await experiment_manager_page.evaluate(() => { + let results = document.querySelectorAll('button[title="Explore results"]'); + for (var i = 0; i < results.length; i++) { + results[0].innerHTML.includes("label") && results[0].click(); + } + }); + + await experiment_manager_page.waitForSelector(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + console.log('... taking snapshot ...'); + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + expect(await experiment_manager_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Experiment Condition #1' + }); + + + }) + + + + it('Check Experiment Condition #2', async () => { + + console.log('Checking experiment condition #2') + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.click(selectors.BACK_TO_EDIT_SELECTOR) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT * 3) + + await experiment_manager_page.evaluate(() => { + let results = document.querySelectorAll('button[title="Explore results"]'); + for (var i = 0; i < results.length; i++) { + results[1].innerHTML.includes("label") && results[1].click(); + } + }); + + await experiment_manager_page.waitForSelector(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + console.log('... taking snapshot ...'); + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + expect(await experiment_manager_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Experiment Condition #2' + }); + + + }) + + it('Check Experiment Condition #3', async () => { + + console.log('Checking experiment condition #3') + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.waitForSelector(selectors.BACK_TO_EDIT_SELECTOR) + await experiment_manager_page.click(selectors.BACK_TO_EDIT_SELECTOR) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT * 3) + + await experiment_manager_page.evaluate(() => { + let results = document.querySelectorAll('button[title="Explore results"]'); + for (var i = 0; i < results.length; i++) { + results[2].innerHTML.includes("label") && results[2].click(); + } + }); + + await experiment_manager_page.waitForSelector(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + console.log('... taking snapshot ...'); + await experiment_manager_page.waitForTimeout(PAGE_WAIT); + expect(await experiment_manager_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Experiment Condition #3' + }); + + + }) + + it('Delete Experiment', async () => { + + console.log('Deleting experiment') + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.waitForSelector(selectors.BACK_TO_EDIT_SELECTOR) + await experiment_manager_page.click(selectors.BACK_TO_EDIT_SELECTOR) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + await experiment_manager_page.waitForSelector(selectors.EDIT_EXPERIMENT_BACK_SELECTOR) + await experiment_manager_page.click(selectors.EDIT_EXPERIMENT_BACK_SELECTOR) + + await experiment_manager_page.waitForTimeout(PAGE_WAIT) + + await experiment_manager_page.evaluate(() => { + let results = document.querySelectorAll('button[class="MuiButtonBase-root MuiButton-root MuiButton-text experimentIcon"]'); + for (var i = 0; i < results.length; i++) { + results[1].innerHTML.includes("label") && results[1].click(); + } + }); + + await experiment_manager_page.waitForSelector(selectors.CONFIRM_SELECTOR) + await experiment_manager_page.click(selectors.CONFIRM_SELECTOR) + + await experiment_manager_page.waitForFunction(() => !document.querySelector('tr[class="MuiTableRow-root"]')); + + }) + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/RxD.test.js b/tests/frontend/e2e/tests/RxD.test.js new file mode 100644 index 00000000..d0f5d834 --- /dev/null +++ b/tests/frontend/e2e/tests/RxD.test.js @@ -0,0 +1,388 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 5000; +const TIMEOUT = 600000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + customDiffConfig: { + ssim: 'fast', + }, + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + + +//TESTS: + +jest.setTimeout(900000); +let browser_RxD; +let RxD_page; + +describe('RxD testing', () => { + + beforeAll(async () => { + browser_RxD = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + RxD_page = await browser_RxD.newPage(); + await RxD_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await RxD_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await RxD_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(RxD_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await RxD_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(RxD_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await RxD_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await RxD_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser_RxD.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page ...') + + await RxD_page.on("dialog", dialog => + dialog.accept()); + + await RxD_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await RxD_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.click(selectors.FILE_TAB_SELECTOR) + await RxD_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.click(selectors.NEW_FILE_SELECTOR) + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await RxD_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await RxD_page.waitForTimeout(PAGE_WAIT * 3) + + await RxD_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT * 3 }); + + await RxD_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + it('Load Tutorial 3b', async () => { + + await RxD_page.waitForTimeout(PAGE_WAIT * 2) + await RxD_page.waitForSelector('#selectCellButton', { timeout: TIMEOUT }) + + console.log('Loading Tutorial #3b ...') + + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.waitForSelector(selectors.TUTORIAL_3B_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.click(selectors.TUTORIAL_3B_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.waitForSelector('#E', { timeout: TIMEOUT }) + await RxD_page.waitForSelector('#I', { timeout: TIMEOUT }) + await RxD_page.waitForTimeout(PAGE_WAIT) + + console.log('Tutorial loaded') + + }) + + it.skip('Create and Simulate Network', async () => { + + + await RxD_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.click(selectors.MODEL_BUTTON_SELECTOR); + await RxD_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Creating network ...') + + await RxD_page.waitForTimeout(PAGE_WAIT * 3) + + await RxD_page.waitForSelector('div[title="3D Representation"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await RxD_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await RxD_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await RxD_page.click(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + console.log('Simulating network ...') + + await RxD_page.waitForSelector('div[title="Raster plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.waitForSelector('div[title="RxD concentration plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + + await RxD_page.waitForTimeout(PAGE_WAIT) + + console.log('Network created and simulated') + + }) + + it.skip('Check RxD Plot', async () => { + console.log('Opening the RxD plot ...') + + await RxD_page.waitForSelector('div[title="RxD concentration plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.click('div[title="RxD concentration plot"][aria-disabled="false"]') + await RxD_page.waitForFunction( + selector => document.querySelectorAll(selector).length === 2, + { timeout: TIMEOUT }, + 'div.flexlayout__tabset' + ); + + console.log('... taking snapshot ...'); + await RxD_page.waitForTimeout(PAGE_WAIT); + expect(await RxD_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'RxD Plot' + }); + await RxD_page.waitForTimeout(PAGE_WAIT); + console.log('Plot displayed') + }) + it.skip('Check LFP Time Series Plot', async () => { + console.log('Opening the LFP TS plot ...') + + await RxD_page.waitForSelector('div[title="LFP Time Series Plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.click('div[title="LFP Time Series Plot"][aria-disabled="false"]') + await RxD_page.waitForFunction( + selector => document.querySelectorAll(selector).length === 2, + { timeout: TIMEOUT }, + 'div.flexlayout__tabset' + ); + + console.log('... taking snapshot ...'); + await RxD_page.waitForTimeout(PAGE_WAIT); + expect(await RxD_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Time Series Plot Before change' + }); + await RxD_page.waitForTimeout(PAGE_WAIT); + console.log('Plot displayed') + }) + it.skip('Check LFP PSD Plot', async () => { + console.log('Opening the LFP PSD plot ...') + + await RxD_page.waitForSelector('div[title="LFP PSD Plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.click('div[title="LFP PSD Plot"][aria-disabled="false"]') + await RxD_page.waitForFunction( + selector => document.querySelectorAll(selector).length === 2, + { timeout: TIMEOUT }, + 'div.flexlayout__tabset' + ); + + console.log('... taking snapshot ...'); + await RxD_page.waitForTimeout(PAGE_WAIT); + expect(await RxD_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP PSD Plot Before change' + }); + await RxD_page.waitForTimeout(PAGE_WAIT); + console.log('Plot displayed') + + }) + + it.skip('Go back to Edit', async () => { + + console.log('Going back to Edit ...') + await RxD_page.waitForSelector('.MuiButtonBase-root.MuiButton-root.MuiButton-contained') + await RxD_page.evaluate(() => { + [...document.querySelectorAll('.MuiButtonBase-root.MuiButton-root.MuiButton-contained')].find(element => element.innerText === "BACK TO EDIT").click(); + }); + await RxD_page.waitForSelector('#E') + await RxD_page.waitForSelector('#I') + console.log('Edit mode displayed') + + }) + + it('Open RxD Tab ', async () => { + + console.log('Opening RxD tab ...') + await RxD_page.waitForSelector('div[title="Reaction-Diffusion"]') + await RxD_page.click('div[title="Reaction-Diffusion"]') + + await RxD_page.waitForSelector('#simple-tabpanel-0') + + console.log('RxD Tab Opened') + + }) + + it('Change RxD Configuration', async () => { + console.log('Opening RxD config ...') + + await RxD_page.waitForSelector('#simple-tabpanel-1') + await RxD_page.click('#simple-tab-1') + + await RxD_page.waitForSelector('button[aria-selected="true"][id = "simple-tab-1"]') + + await RxD_page.waitForSelector('#ip3') + console.log('Species tab opened') + await RxD_page.waitForTimeout(PAGE_WAIT) + + }) + + it('Increase IP3 species concentration', async () => { + + console.log('Increasing IP3 concentration ...') + + await RxD_page.waitForSelector('#ip3') + await RxD_page.click('#ip3') + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.waitForSelector('#netParamsrxdParamsspeciesip3regions') + await RxD_page.waitForSelector('#netParamsrxdParamsspeciesip3d') + await RxD_page.waitForSelector('#netParamsrxdParamsspeciesip3charge') + await RxD_page.waitForSelector('#netParamsrxdParamsspeciesip3initial') + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.click('#netParamsrxdParamsspeciesip3initial') + await RxD_page.keyboard.press('Backspace'); + await RxD_page.keyboard.press('Backspace'); + await RxD_page.keyboard.press('Backspace'); + await RxD_page.type('#netParamsrxdParamsspeciesip3initial', '2') + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.click('#netParamsrxdParamsspeciesip3charge') + await RxD_page.waitForTimeout(PAGE_WAIT) + await RxD_page.waitForSelector('#netParamsrxdParamsspeciesip3initial[value = "2"]') + + console.log('IP3 increased') + + }) + + + it('Create and Simulate Network', async () => { + + await RxD_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.click(selectors.MODEL_BUTTON_SELECTOR); + await RxD_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }) + await RxD_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Creating network ...') + + await RxD_page.waitForTimeout(PAGE_WAIT * 3) + + await RxD_page.waitForSelector('div[title="3D Representation"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await RxD_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await RxD_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await RxD_page.click(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + console.log('Simulating network ...') + + await RxD_page.waitForSelector('div[title="Raster plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.waitForSelector('div[title="RxD concentration plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + + await RxD_page.waitForTimeout(PAGE_WAIT) + }) + + it('Check RxD Plot', async () => { + + console.log('Opening the RxD plot ...') + + await RxD_page.waitForSelector('div[title="RxD concentration plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.click('div[title="RxD concentration plot"][aria-disabled="false"]') + await RxD_page.waitForFunction( + selector => document.querySelectorAll(selector).length === 2, + { timeout: TIMEOUT }, + 'div.flexlayout__tabset' + ); + + console.log('... taking snapshot ...'); + await RxD_page.waitForTimeout(PAGE_WAIT); + expect(await RxD_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'RxD Plot' + }); + await RxD_page.waitForTimeout(PAGE_WAIT); + console.log('Plot displayed') + }) + it('Check LFP Time Series Plot', async () => { + + console.log('Opening the LFP TS plot ...') + + await RxD_page.waitForSelector('div[title="LFP Time Series Plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.click('div[title="LFP Time Series Plot"][aria-disabled="false"]') + await RxD_page.waitForFunction( + selector => document.querySelectorAll(selector).length === 2, + { timeout: TIMEOUT }, + 'div.flexlayout__tabset' + ); + + console.log('... taking snapshot ...'); + await RxD_page.waitForTimeout(PAGE_WAIT); + expect(await RxD_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Time Series Plot After change' + }); + await RxD_page.waitForTimeout(PAGE_WAIT); + console.log('Plot displayed') + }) + it('Check LFP PSD Plot', async () => { + + console.log('Opening the LFP PSD plot ...') + + await RxD_page.waitForSelector('div[title="LFP PSD Plot"][aria-disabled="false"]', { timeout: TIMEOUT * 3 }) + await RxD_page.click('div[title="LFP PSD Plot"][aria-disabled="false"]') + await RxD_page.waitForFunction( + selector => document.querySelectorAll(selector).length === 2, + { timeout: TIMEOUT }, + 'div.flexlayout__tabset' + ); + + console.log('... taking snapshot ...'); + await RxD_page.waitForTimeout(PAGE_WAIT); + expect(await RxD_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP PSD Plot After change' + }); + await RxD_page.waitForTimeout(PAGE_WAIT); + console.log('Plot displayed') + + }) + + +}) \ No newline at end of file diff --git a/tests/frontend/e2e/tests/SaveOpenFile.test.js b/tests/frontend/e2e/tests/SaveOpenFile.test.js new file mode 100644 index 00000000..bc0d4633 --- /dev/null +++ b/tests/frontend/e2e/tests/SaveOpenFile.test.js @@ -0,0 +1,585 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + customDiffConfig: { + ssim: 'fast', + }, + failureThresholdType: 'percent', + failureThreshold: 0.2 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + +const EDITED_MODEL = + '{"E2": {"cellType": "E", "numCells": 5, "yRange": [100, 300]}, "E4": {"cellType": "E", "numCells": 5, "yRange": [300, 600]}, "E5": {"cellType": "E", "numCells": 5, "ynormRange": [0.6, 1]}, "I2": {"cellType": "I", "numCells": 5, "yRange": [100, 300]}, "I4": {"cellType": "I", "numCells": 5, "yRange": [300, 600]}, "I5": {"cellType": "I", "numCells": 5, "ynormRange": [0.6, 1]}}' + + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(300000); +let SaveOpen_File_browser; +let SaveOpen_File_page; + + +describe.skip('Save / Open File testing', () => { + + beforeAll(async () => { + SaveOpen_File_browser = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + SaveOpen_File_page = await SaveOpen_File_browser.newPage(); + await SaveOpen_File_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await SaveOpen_File_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await SaveOpen_File_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(SaveOpen_File_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await SaveOpen_File_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(SaveOpen_File_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await SaveOpen_File_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await SaveOpen_File_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await SaveOpen_File_browser.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await SaveOpen_File_page.on("dialog", dialog => + dialog.accept()); + + await SaveOpen_File_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await SaveOpen_File_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.click(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.click(selectors.NEW_FILE_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await SaveOpen_File_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + await SaveOpen_File_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT * 3 }); + + await SaveOpen_File_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + it('Open model from File > Open', async () => { + console.log('Opening model from File') + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + await SaveOpen_File_page.waitForSelector(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.click(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + await SaveOpen_File_page.evaluate(async () => { + document.getElementById("Open...").click(); + }) + + await SaveOpen_File_page.waitForSelector(selectors.FILE_SYSTEM_SELECTOR) + await SaveOpen_File_page.click(selectors.LEVEL_UP_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.waitForSelector(selectors.FOLDERS_SELECTOR) + + const folder_num = await SaveOpen_File_page.$$(selectors.FOLDERS_SELECTOR) + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('div[class = "rst__rowContents rst__rowContentsDragDisabled"]')].find(element => element.textContent === 'src').click(); + }); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + const folder_num_src = await SaveOpen_File_page.$$(selectors.FOLDERS_SELECTOR) + + expect(folder_num_src.length).toBeGreaterThan(folder_num.length) + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('div[class = "rst__rowContents rst__rowContentsDragDisabled"]')].find(element => element.textContent === 'netpyne').click(); + }); + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + const folder_num_netpyne = await SaveOpen_File_page.$$(selectors.FOLDERS_SELECTOR) + expect(folder_num_netpyne.length).toBeGreaterThan(folder_num_src.length) + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('div[class = "rst__rowContents rst__rowContentsDragDisabled"]')].find(element => element.textContent === 'examples').scrollIntoView(); + }); + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('div[class = "rst__rowContents rst__rowContentsDragDisabled"]')].find(element => element.textContent === 'examples').click(); + }); + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('div[class = "rst__rowContents rst__rowContentsDragDisabled"]')].find(element => element.textContent === 'HybridTut').scrollIntoView(); + }); + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('div[class = "rst__rowContents rst__rowContentsDragDisabled"]')].find(element => element.textContent === 'netClamp').click(); + }); + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + const folder_num_netClamp = await SaveOpen_File_page.$$(selectors.FOLDERS_SELECTOR) + expect(folder_num_netClamp.length).toBeGreaterThan(folder_num_netpyne.length) + + await SaveOpen_File_page.click(selectors.SELECT_BUTTON_SELECTOR) + + await SaveOpen_File_page.waitForSelector(selectors.E_RULE_SELECTOR) + + console.log('Model Loaded') + + }) + + it('Create and Simulate opened model', async () => { + console.log('Instantiating and Simulating model...') + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + await SaveOpen_File_page.waitForSelector(selectors.NETWORK_CREATION_MENU_BUTTON_SELECTOR) + await SaveOpen_File_page.click(selectors.NETWORK_CREATION_MENU_BUTTON_SELECTOR) + + await SaveOpen_File_page.waitForSelector(selectors.NETWORK_CREATION_MENU_ITEMS_SELECTOR) + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('#split-button-menu > li')].find(element => element.innerText === 'CREATE AND SIMULATE').click(); + }); + + await SaveOpen_File_page.waitForSelector(selectors.NETWORK_CREATION_BUTTON_SELECTOR) + await SaveOpen_File_page.click(selectors.NETWORK_CREATION_BUTTON_SELECTOR) + + await SaveOpen_File_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT * 2 }); + + await SaveOpen_File_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + console.log('... taking snapshot ...'); + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + expect(await SaveOpen_File_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'NetClamp Model' + }); + console.log('Model Simulated') + }) + + it('Change the instantiated model', async () => { + console.log('Editing model ...') + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('button[class = "MuiButtonBase-root MuiButton-root MuiButton-contained"]')].find(element => element.innerText === 'BACK TO EDIT').click(); + }); + await SaveOpen_File_page.waitForSelector(selectors.POPULATIONS_TAB_SELECTOR) + await SaveOpen_File_page.click(selectors.POPULATIONS_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector('#E2') + + await SaveOpen_File_page.click('#E2') + await SaveOpen_File_page.waitForSelector('#netParamspopParamsE2numCells') + expect(SaveOpen_File_page).toFill('#netParamspopParamsE2numCells', '5') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.click('#I2') + await SaveOpen_File_page.waitForSelector('#netParamspopParamsI2numCells') + expect(SaveOpen_File_page).toFill('#netParamspopParamsI2numCells', '5') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.click('#E4') + await SaveOpen_File_page.waitForSelector('#netParamspopParamsE4numCells') + expect(SaveOpen_File_page).toFill('#netParamspopParamsE4numCells', '5') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.click('#I4') + await SaveOpen_File_page.waitForSelector('#netParamspopParamsI4numCells') + expect(SaveOpen_File_page).toFill('#netParamspopParamsI4numCells', '5') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.click('#E5') + await SaveOpen_File_page.waitForSelector('#netParamspopParamsE5numCells') + expect(SaveOpen_File_page).toFill('#netParamspopParamsE5numCells', '5') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.click('#I5') + await SaveOpen_File_page.waitForSelector('#netParamspopParamsI5numCells') + expect(SaveOpen_File_page).toFill('#netParamspopParamsI5numCells', '5') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await SaveOpen_File_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await SaveOpen_File_page.waitForSelector(selectors.CREATE_AND_SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await SaveOpen_File_page.click(selectors.CREATE_AND_SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + await SaveOpen_File_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT * 2 }); + + await SaveOpen_File_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + console.log('... taking snapshot ...'); + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + expect(await SaveOpen_File_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Edited NetClamp Model' + }); + + console.log('Model updated') + }) + + it('Save model', async () => { + console.log('Saving model ...') + await SaveOpen_File_page.waitForSelector(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.click(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.evaluate(async () => { + document.getElementById("Save...").click(); + }) + await SaveOpen_File_page.waitForSelector(selectors.SAVE_MENU_SELECTOR) + + // const inputValue = await page.$eval(selectors.PATH_INPUT_SELECTOR, el => el.value); + await SaveOpen_File_page.click(selectors.PATH_INPUT_SELECTOR, { clickCount: 3 }); + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + expect(SaveOpen_File_page).toFill(selectors.PATH_INPUT_SELECTOR, 'aut_test') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + await SaveOpen_File_page.click(selectors.SAVE_BUTTON_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + console.log('Model saved as default') + }) + + it('Save model - NetParams', async () => { + console.log('Saving model with NetParams as Python ...') + + await SaveOpen_File_page.click(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.evaluate(async () => { + document.getElementById("Save...").click(); + }) + await SaveOpen_File_page.waitForSelector(selectors.SAVE_MENU_SELECTOR) + + // const inputValue = await page.$eval(selectors.PATH_INPUT_SELECTOR, el => el.value); + // for (let i = 0; i < inputValue.length; i++) { + // await page.keyboard.press('Backspace'); + // } + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + expect(SaveOpen_File_page).toFill(selectors.PATH_INPUT_SELECTOR, 'aut_test_net_params') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('.MuiAccordionSummary-content')].find(element => element.innerText === "Advanced Options").click(); + }); + + await SaveOpen_File_page.waitForSelector(selectors.EXPORT_OPTIONS_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.CHECKBOX_OPTION_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + const checkbox_buttons = await SaveOpen_File_page.$$(selectors.CHECKBOX_OPTION_SELECTOR) + + await checkbox_buttons[0].click() + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.click(selectors.SAVE_BUTTON_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + console.log('Model saved with NetParams as Python') + + }) + + it('Save model - SimConfig', async () => { + console.log('Saving model with SimConfig as Python ...') + + await SaveOpen_File_page.click(selectors.FILE_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + await SaveOpen_File_page.evaluate(async () => { + document.getElementById("Save...").click(); + }) + await SaveOpen_File_page.waitForSelector(selectors.SAVE_MENU_SELECTOR) + + const inputValue = await SaveOpen_File_page.$eval(selectors.PATH_INPUT_SELECTOR, el => el.value); + for (let i = 0; i < inputValue.length; i++) { + await SaveOpen_File_page.keyboard.press('Backspace'); + } + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + expect(SaveOpen_File_page).toFill(selectors.PATH_INPUT_SELECTOR, 'aut_test_sim_config') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + + await SaveOpen_File_page.evaluate(() => { + [...document.querySelectorAll('.MuiAccordionSummary-content')].find(element => element.innerText === "Advanced Options").click(); + }); + + await SaveOpen_File_page.waitForSelector(selectors.EXPORT_OPTIONS_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.CHECKBOX_OPTION_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + const checkbox_buttons = await SaveOpen_File_page.$$(selectors.CHECKBOX_OPTION_SELECTOR) + await checkbox_buttons[1].click() + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + await SaveOpen_File_page.click(selectors.SAVE_BUTTON_SELECTOR) + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT) + console.log('Model saved with SimConfig as Python') + + }) + + it('Check default Saved Model', async () => { + console.log('Checking default saved model ...') + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 2) + await SaveOpen_File_page.waitForSelector(selectors.PYTHON_CONSOLE_TAB_SELECTOR) + + await SaveOpen_File_page.click(selectors.PYTHON_CONSOLE_TAB_SELECTOR) + await SaveOpen_File_page.waitForSelector(selectors.PYTHON_CONSLE_SELECTOR) + + const elementHandle = await SaveOpen_File_page.waitForSelector( + selectors.PYTHON_CONSOLE_FRAME_SELECTOR + ); + + const python_frame = await elementHandle.contentFrame(); + + await python_frame.waitForSelector(selectors.MAIN_PYTHON_APP_SELECTOR) + + await python_frame.waitForSelector(selectors.PYTHON_CELL_SELECTOR) + const line = await python_frame.$(selectors.PYTHON_CELL_SELECTOR) + await line.click() + await line.type('pwd') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await python_frame.waitForSelector(selectors.PYTHON_FIRST_OUTPUT_SELECTOR) + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const first_code_output = await python_frame.$$eval(selectors.PYTHON_FIRST_OUTPUT_SELECTOR, pwd_code_outputs => { + return pwd_code_outputs.map(pwd_code_output => pwd_code_output.innerText) + }) + + expect(first_code_output[0]).toBe("'/opt/workspace/workspace'") + + const code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await code_lines[1].type('cd uploads/aut_test/src') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const second_code_output = await python_frame.$$eval(selectors.PYTHON_OUTPUT_SELECTOR, cd_code_outputs => { + return cd_code_outputs.map(cd_code_output => cd_code_output.innerText) + }) + + expect(second_code_output[0]).toBe("/opt/workspace/workspace/saved_models/aut_test/src\n") + + const ls_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await ls_code_lines[2].type('ls -l') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const third_code_output = await python_frame.$$eval(selectors.PYTHON_OUTPUT_SELECTOR, ls_code_outputs => { + return ls_code_outputs.map(ls_code_output => ls_code_output.innerText) + }) + + expect(third_code_output[1]).toContain("cfg.json") + expect(third_code_output[1]).toContain("netParams.json") + + console.log('Model saved correctly') + + }) + + it('Check netParams.py Saved Model', async () => { + console.log('Checking netParams.py saved model ...') + + await SaveOpen_File_page.waitForSelector(selectors.PYTHON_CONSLE_SELECTOR) + + const elementHandle = await SaveOpen_File_page.waitForSelector( + selectors.PYTHON_CONSOLE_FRAME_SELECTOR + ); + + const python_frame = await elementHandle.contentFrame(); + + await python_frame.waitForSelector(selectors.MAIN_PYTHON_APP_SELECTOR) + + const cd_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await cd_code_lines[2].type('cd ../../') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const net_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await net_code_lines[3].type('cd aut_test_net_params/src') + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const ls_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await ls_code_lines[4].type('ls -l') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const netParam_code_output = await python_frame.$$eval(selectors.PYTHON_OUTPUT_SELECTOR, np_code_outputs => { + return np_code_outputs.map(np_code_output => np_code_output.innerText) + }) + + expect(netParam_code_output[4]).toContain("cfg.json") + expect(netParam_code_output[4]).toContain("netParams.py") + + console.log('Model saved correctly') + }) + + it('Check cfg.py Saved Model', async () => { + console.log('Checking cfg.py saved model ...') + + await SaveOpen_File_page.waitForSelector(selectors.PYTHON_CONSLE_SELECTOR) + + const elementHandle = await SaveOpen_File_page.waitForSelector( + selectors.PYTHON_CONSOLE_FRAME_SELECTOR + ); + + const python_frame = await elementHandle.contentFrame(); + + await python_frame.waitForSelector(selectors.MAIN_PYTHON_APP_SELECTOR) + + const cd_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await cd_code_lines[5].type('cd ../../') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const net_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await net_code_lines[6].type('cd aut_test_sim_config/src') + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const ls_code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await ls_code_lines[7].type('ls -l') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const simConfig_code_output = await python_frame.$$eval(selectors.PYTHON_OUTPUT_SELECTOR, sc_code_outputs => { + return sc_code_outputs.map(sc_code_output => sc_code_output.innerText) + }) + + expect(simConfig_code_output[7]).toContain("cfg.py") + expect(simConfig_code_output[7]).toContain("netParams.json") + console.log('Model saved correctly') + + }) + + it('Check the edited Populations of the Saved Model', async () => { + + console.log('Checking the edited Populations of the saved model ...') + + await SaveOpen_File_page.waitForSelector(selectors.PYTHON_CONSLE_SELECTOR) + + const elementHandle = await SaveOpen_File_page.waitForSelector( + selectors.PYTHON_CONSOLE_FRAME_SELECTOR + ); + + const python_frame = await elementHandle.contentFrame(); + + await python_frame.waitForSelector(selectors.MAIN_PYTHON_APP_SELECTOR) + + const code_lines = await python_frame.$$(selectors.PYTHON_CELL_SELECTOR) + + await code_lines[8].type('cat netParams.json ') + + await SaveOpen_File_page.keyboard.down('Shift'); + await SaveOpen_File_page.keyboard.press('Enter'); + await SaveOpen_File_page.keyboard.up('Shift'); + + await SaveOpen_File_page.waitForTimeout(PAGE_WAIT * 3) + + const cat_code_output = await python_frame.$$eval(selectors.PYTHON_OUTPUT_SELECTOR, cat_code_outputs => { + return cat_code_outputs.map(cat_code_output => cat_code_output.innerText) + }) + + var obj = JSON.parse(cat_code_output[8]) + + expect(obj.net.params.popParams).toEqual(JSON.parse(EDITED_MODEL)) + + }) +}) \ No newline at end of file diff --git a/tests/frontend/e2e/tests/TestTutorial1.js b/tests/frontend/e2e/tests/TestTutorial1.js index eac93af8..eb809a75 100644 --- a/tests/frontend/e2e/tests/TestTutorial1.js +++ b/tests/frontend/e2e/tests/TestTutorial1.js @@ -20,7 +20,7 @@ beforeAll(async () => { await page.setUserAgent('Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/69.0.3497.100 Safari/537.36'); }); -describe('Tutorial #1', () => { +describe.skip('Tutorial #1', () => { beforeAll(async () => { await page.waitForSelector('.NetPyNE-root-1'); diff --git a/tests/frontend/e2e/tests/Tut#1_smoke.test.js b/tests/frontend/e2e/tests/Tut#1_smoke.test.js new file mode 100644 index 00000000..c0e0f8ef --- /dev/null +++ b/tests/frontend/e2e/tests/Tut#1_smoke.test.js @@ -0,0 +1,282 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +// import { expect } from 'expect-puppeteer'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) + +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + +//TESTS: + +jest.setTimeout(3000000); +let browser; +let tutorial_1_page; + +describe('Tutorial #1 for Smoke Testing', () => { + + beforeAll(async () => { + browser = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + tutorial_1_page = await browser.newPage(); + await tutorial_1_page.goto(baseURL); + + await tutorial_1_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await tutorial_1_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await tutorial_1_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(tutorial_1_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await tutorial_1_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(tutorial_1_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await tutorial_1_page.waitForSelector(selectors.LOGIN_BUTTON_SELECTOR) + await tutorial_1_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await tutorial_1_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await tutorial_1_page.on("dialog", dialog => + dialog.accept()); + + await tutorial_1_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await tutorial_1_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + await tutorial_1_page.click(selectors.FILE_TAB_SELECTOR) + await tutorial_1_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + await tutorial_1_page.click(selectors.NEW_FILE_SELECTOR) + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + await tutorial_1_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_1_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_1_page.waitForTimeout(PAGE_WAIT * 2) + + await tutorial_1_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await tutorial_1_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Create and Simulate network', async () => { + + await tutorial_1_page.waitForTimeout(PAGE_WAIT * 2) + await tutorial_1_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #1') + + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + await tutorial_1_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.TUTORIAL_1_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.TUTORIAL_1_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.PYR_CELL_SELECTOR) + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + + await tutorial_1_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await tutorial_1_page.click( selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_1_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await tutorial_1_page.click( selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + + console.log('... taking snapshot ...'); + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#1 Network' + }); + + await tutorial_1_page.waitForSelector( selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_1_page.click( selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_1_page.waitForSelector( selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await tutorial_1_page.click( selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + console.log('Simulate network') + + await tutorial_1_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await tutorial_1_page.waitForTimeout(PAGE_WAIT) + + }); + + + it('Connections Plot', async () => { + + await tutorial_1_page.waitForTimeout(PAGE_WAIT * 2); + await tutorial_1_page.waitForSelector( selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Connections Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Connections Plot' + }); + + }); + + it('2D Net Plot', async () => { + await tutorial_1_page.waitForSelector( selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View 2D Net Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT * 2); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: '2D Net Plot' + }); + }); + + it('Cell Traces Plot', async () => { + await tutorial_1_page.waitForSelector( selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Cell Traces Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Cell Traces Plot' + }); + }); + + it('Raster Plot', async () => { + await tutorial_1_page.waitForSelector( selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Raster Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Raster Plot' + }); + }); + + it('Spike Hist Plot', async () => { + await tutorial_1_page.waitForSelector( selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Spike Hist Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Spike Hist Plot' + }); + }); + + it('Granger Plot', async () => { + await tutorial_1_page.waitForSelector( selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Granger Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Granger Plot' + }); + }); + + it('Rate Spectogram Plot', async () => { + await tutorial_1_page.waitForSelector( selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.click( selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_1_page.click( selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + // await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_1_page.click( selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_1_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + console.log('View Rate Spectogram Plot ...') + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_1_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Rate Spectogram Plot' + }); + + await tutorial_1_page.waitForTimeout(PAGE_WAIT); + }); + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/Tut#2_smoke.test.js b/tests/frontend/e2e/tests/Tut#2_smoke.test.js new file mode 100644 index 00000000..97f714f2 --- /dev/null +++ b/tests/frontend/e2e/tests/Tut#2_smoke.test.js @@ -0,0 +1,279 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + +//TESTS: + +jest.setTimeout(3000000); +let browser2; +let tutorial_2_page; + +describe('Tutorial #2 for Smoke Testing', () => { + + beforeAll(async () => { + browser2 = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + tutorial_2_page = await browser2.newPage(); + await tutorial_2_page.goto(baseURL); + + await tutorial_2_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await tutorial_2_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await tutorial_2_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(tutorial_2_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await tutorial_2_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(tutorial_2_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await tutorial_2_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await tutorial_2_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser2.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await tutorial_2_page.on("dialog", dialog => + dialog.accept()); + + await tutorial_2_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await tutorial_2_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_2_page.waitForTimeout(PAGE_WAIT) + await tutorial_2_page.click(selectors.FILE_TAB_SELECTOR) + await tutorial_2_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_2_page.waitForTimeout(PAGE_WAIT) + await tutorial_2_page.click(selectors.NEW_FILE_SELECTOR) + await tutorial_2_page.waitForTimeout(PAGE_WAIT) + await tutorial_2_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_2_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_2_page.waitForTimeout(PAGE_WAIT * 2) + + await tutorial_2_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await tutorial_2_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Create and Simulate network', async () => { + + await tutorial_2_page.waitForTimeout(PAGE_WAIT * 2) + await tutorial_2_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #2') + + await tutorial_2_page.waitForTimeout(PAGE_WAIT) + await tutorial_2_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { visible: true }) + await tutorial_2_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.TUTORIAL_2_SELECTOR, { visible: true }) + await tutorial_2_page.click(selectors.TUTORIAL_2_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.PYR_2_CELL_SELECTOR) + await tutorial_2_page.waitForSelector(selectors.INT_CELL_SELECTOR) + await tutorial_2_page.waitForTimeout(PAGE_WAIT) + + await tutorial_2_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await tutorial_2_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_2_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await tutorial_2_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await tutorial_2_page.waitForTimeout(PAGE_WAIT * 3) + + await tutorial_2_page.waitForSelector(selectors.THREE_D_REP_SELECTOR, { timeout: TIMEOUT * 3 }) + + console.log('... taking snapshot ...'); + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#2 Network' + }); + await tutorial_2_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_2_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_2_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await tutorial_2_page.click(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + console.log('Simulate network') + + await tutorial_2_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await tutorial_2_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + + }); + + + it('Connections Plot', async () => { + + await tutorial_2_page.waitForTimeout(PAGE_WAIT * 2); + await tutorial_2_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Connections Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Connections Plot' + }); + + }); + + it('2D Net Plot', async () => { + await tutorial_2_page.waitForSelector(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.click(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View 2D Net Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: '2D Net Plot' + }); + }); + + it('Cell Traces Plot', async () => { + await tutorial_2_page.waitForSelector(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.click(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Cell Traces Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Cell Traces Plot' + }); + }); + + it('Raster Plot', async () => { + await tutorial_2_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.click(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Raster Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT * 3); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Raster Plot' + }); + }); + + it('Spike Hist Plot', async () => { + await tutorial_2_page.waitForSelector(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.click(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Spike Hist Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Spike Hist Plot' + }); + }); + + it('Granger Plot', async () => { + await tutorial_2_page.waitForSelector(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.click(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Granger Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Granger Plot' + }); + }); + + it('Rate Spectogram Plot', async () => { + await tutorial_2_page.waitForSelector(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { visible: true, timeout: TIMEOUT}) + await tutorial_2_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_2_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + // await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_2_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_2_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + console.log('View Rate Spectogram Plot ...') + await tutorial_2_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_2_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Rate Spectogram Plot' + }); + }); + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/Tut#3a_smoke.test.js b/tests/frontend/e2e/tests/Tut#3a_smoke.test.js new file mode 100644 index 00000000..f3d246db --- /dev/null +++ b/tests/frontend/e2e/tests/Tut#3a_smoke.test.js @@ -0,0 +1,340 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(3000000); +let browser3; +let tutorial_3a_page; + + +describe('Tutorial #3a for Smoke Testing', () => { + + beforeAll(async () => { + browser3 = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + tutorial_3a_page = await browser3.newPage(); + await tutorial_3a_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await tutorial_3a_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await tutorial_3a_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(tutorial_3a_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await tutorial_3a_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(tutorial_3a_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await tutorial_3a_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await tutorial_3a_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser3.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await tutorial_3a_page.on("dialog", dialog => + dialog.accept()); + + await tutorial_3a_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await tutorial_3a_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_3a_page.waitForTimeout(PAGE_WAIT) + await tutorial_3a_page.click(selectors.FILE_TAB_SELECTOR) + await tutorial_3a_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_3a_page.waitForTimeout(PAGE_WAIT) + await tutorial_3a_page.click(selectors.NEW_FILE_SELECTOR) + await tutorial_3a_page.waitForTimeout(PAGE_WAIT) + await tutorial_3a_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_3a_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_3a_page.waitForTimeout(PAGE_WAIT * 2) + + await tutorial_3a_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await tutorial_3a_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Create and Simulate network', async () => { + + await tutorial_3a_page.waitForTimeout(PAGE_WAIT * 2) + await tutorial_3a_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #3a') + + await tutorial_3a_page.waitForTimeout(PAGE_WAIT) + await tutorial_3a_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { visible: true }) + + await tutorial_3a_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.TUTORIAL_3A_SELECTOR, { visible: true }) + await tutorial_3a_page.click(selectors.TUTORIAL_3A_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.E_CELL_TYPE_SELECTOR) + await tutorial_3a_page.waitForSelector(selectors.I_CELL_TYPE_SELECTOR) + await tutorial_3a_page.waitForTimeout(PAGE_WAIT) + + await tutorial_3a_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await tutorial_3a_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3a_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await tutorial_3a_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await tutorial_3a_page.waitForTimeout(PAGE_WAIT * 3) + + await tutorial_3a_page.waitForSelector(selectors.THREE_D_REP_SELECTOR, { timeout: TIMEOUT }) + + console.log('... taking snapshot ...'); + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#3a Network' + }); + await tutorial_3a_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3a_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3a_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3a_page.click(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + + console.log('Simulate network') + + await tutorial_3a_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await tutorial_3a_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 10 }) + + + }); + + + it('Connections Plot', async () => { + + await tutorial_3a_page.waitForTimeout(PAGE_WAIT * 2); + await tutorial_3a_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Connections Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Connections Plot' + }); + + }); + + it('2D Net Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View 2D Net Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT * 3); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: '2D Net Plot' + }); + }); + + it('Cell Traces Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Cell Traces Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Cell Traces Plot' + }); + }); + + it('Raster Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Raster Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Raster Plot' + }); + }); + + it('Spike Hist Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Spike Hist Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Spike Hist Plot' + }); + }); + + it('LFP Time Series Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.LFP_TS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.LFP_TS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP Time Series Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Time Series Plot' + }); + }); + + it('LFP PSD Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.LFP_PSD_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.LFP_PSD_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP PSD Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP PSD Plot' + }); + }); + + it('LFP Spectrogram Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.LFP_SPECTOGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.LFP_SPECTOGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP Spectrogram Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT * 5); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Spectrogram Plot' + }); + }); + + it('Granger Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Granger Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Granger Plot' + }); + }); + + it('RxD concentration plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.RXD_CONCENTRATION_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.RXD_CONCENTRATION_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View RxD concentration plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'RxD concentration plot' + }); + }); + + it('Rate Spectogram Plot', async () => { + await tutorial_3a_page.waitForSelector(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + // await tutorial_3a_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3a_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + // await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_3a_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3a_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + console.log('View Rate Spectogram Plot ...') + await tutorial_3a_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3a_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Rate Spectogram Plot' + }); + }); +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/Tut#3b_smoke.test.js b/tests/frontend/e2e/tests/Tut#3b_smoke.test.js new file mode 100644 index 00000000..da3b28b6 --- /dev/null +++ b/tests/frontend/e2e/tests/Tut#3b_smoke.test.js @@ -0,0 +1,340 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(3000000); +let browser3b; +let tutorial_3b_page; + + +describe('Tutorial #3b for Smoke Testing', () => { + + beforeAll(async () => { + browser3b = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + tutorial_3b_page = await browser3b.newPage(); + await tutorial_3b_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await tutorial_3b_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await tutorial_3b_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(tutorial_3b_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await tutorial_3b_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(tutorial_3b_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await tutorial_3b_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await tutorial_3b_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser3b.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await tutorial_3b_page.on("dialog", dialog => + dialog.accept()); + + await tutorial_3b_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await tutorial_3b_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_3b_page.waitForTimeout(PAGE_WAIT) + await tutorial_3b_page.click(selectors.FILE_TAB_SELECTOR) + await tutorial_3b_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_3b_page.waitForTimeout(PAGE_WAIT) + await tutorial_3b_page.click(selectors.NEW_FILE_SELECTOR) + await tutorial_3b_page.waitForTimeout(PAGE_WAIT) + await tutorial_3b_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_3b_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 2) + + await tutorial_3b_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await tutorial_3b_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Create and Simulate network', async () => { + + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 2) + await tutorial_3b_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #3b') + + await tutorial_3b_page.waitForTimeout(PAGE_WAIT) + await tutorial_3b_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.TUTORIAL_3B_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.TUTORIAL_3B_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.E_CELL_TYPE_SELECTOR) + await tutorial_3b_page.waitForSelector(selectors.I_CELL_TYPE_SELECTOR) + await tutorial_3b_page.waitForTimeout(PAGE_WAIT) + + await tutorial_3b_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await tutorial_3b_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3b_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await tutorial_3b_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 3) + + await tutorial_3b_page.waitForSelector(selectors.THREE_D_REP_SELECTOR) + + console.log('... taking snapshot ...'); + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#3b Network' + }); + await tutorial_3b_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3b_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3b_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3b_page.click(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Simulate network') + + await tutorial_3b_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await tutorial_3b_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + + }); + + + it('Connections Plot', async () => { + + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 2); + await tutorial_3b_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Connections Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Connections Plot' + }); + + }); + + it('2D Net Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View 2D Net Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 3); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: '2D Net Plot' + }); + }); + + it('Cell Traces Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Cell Traces Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Cell Traces Plot' + }); + }); + + it('Raster Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Raster Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Raster Plot' + }); + }); + + it('Spike Hist Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Spike Hist Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Spike Hist Plot' + }); + }); + + it('LFP Time Series Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.LFP_TS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.LFP_TS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP Time Series Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Time Series Plot' + }); + }); + + it('LFP PSD Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.LFP_PSD_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.LFP_PSD_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP PSD Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 2); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP PSD Plot' + }); + }); + + it('LFP Spectrogram Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.LFP_SPECTOGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.LFP_SPECTOGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP Spectrogram Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 5); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Spectrogram Plot' + }); + }); + + it('Granger Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Granger Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT * 2); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Granger Plot' + }); + }); + + it('RxD concentration plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.RXD_CONCENTRATION_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.RXD_CONCENTRATION_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View RxD concentration plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'RxD concentration plot' + }); + }); + + it('Rate Spectogram Plot', async () => { + await tutorial_3b_page.waitForSelector(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_3b_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + // await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_3b_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3b_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + console.log('View Rate Spectogram Plot ...') + await tutorial_3b_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3b_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Rate Spectogram Plot' + }); + }); + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/Tut#3c_smoke.test.js b/tests/frontend/e2e/tests/Tut#3c_smoke.test.js new file mode 100644 index 00000000..6c2b68fd --- /dev/null +++ b/tests/frontend/e2e/tests/Tut#3c_smoke.test.js @@ -0,0 +1,329 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(3000000); +let browser3c; +let tutorial_3c_page; + + +describe('Tutorial #3c for Smoke Testing', () => { + + beforeAll(async () => { + browser3c = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + tutorial_3c_page = await browser3c.newPage(); + await tutorial_3c_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await tutorial_3c_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await tutorial_3c_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(tutorial_3c_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await tutorial_3c_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(tutorial_3c_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await tutorial_3c_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await tutorial_3c_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser3c.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await tutorial_3c_page.on("dialog", dialog => + dialog.accept()); + + await tutorial_3c_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await tutorial_3c_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_3c_page.waitForTimeout(PAGE_WAIT) + await tutorial_3c_page.click(selectors.FILE_TAB_SELECTOR) + await tutorial_3c_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_3c_page.waitForTimeout(PAGE_WAIT) + await tutorial_3c_page.click(selectors.NEW_FILE_SELECTOR) + await tutorial_3c_page.waitForTimeout(PAGE_WAIT) + await tutorial_3c_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_3c_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_3c_page.waitForTimeout(PAGE_WAIT * 2) + + await tutorial_3c_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await tutorial_3c_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Create and Simulate network', async () => { + + await tutorial_3c_page.waitForTimeout(PAGE_WAIT * 2) + await tutorial_3c_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #3c') + + await tutorial_3c_page.waitForTimeout(PAGE_WAIT) + await tutorial_3c_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.TUTORIAL_3C_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.TUTORIAL_3C_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.E_CELL_TYPE_SELECTOR) + await tutorial_3c_page.waitForSelector(selectors.I_CELL_TYPE_SELECTOR) + await tutorial_3c_page.waitForTimeout(PAGE_WAIT) + + await tutorial_3c_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await tutorial_3c_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3c_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await tutorial_3c_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await tutorial_3c_page.waitForTimeout(PAGE_WAIT * 3) + + await tutorial_3c_page.waitForSelector(selectors.THREE_D_REP_SELECTOR) + + console.log('... taking snapshot ...'); + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#3c Network' + }); + + //there is a bug related to 'Model' > 'Simulate Network' + // await page.click( MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + //reason why the tests are using the simulate button on the top right + await tutorial_3c_page.click(selectors.SIMULATE_TOP_RIGHT_BUTTON_SELECTOR, { timeout: TIMEOUT }); + // await page.click( SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + console.log('Simulate network') + + await tutorial_3c_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await tutorial_3c_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + + }); + + + it('Connections Plot', async () => { + + await tutorial_3c_page.waitForTimeout(PAGE_WAIT * 2); + await tutorial_3c_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Connections Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Connections Plot' + }); + + }); + + it('2D Net Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View 2D Net Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT * 3); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: '2D Net Plot' + }); + }); + + it('Cell Traces Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Cell Traces Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Cell Traces Plot' + }); + }); + + it('Raster Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Raster Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Raster Plot' + }); + }); + + it('Spike Hist Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Spike Hist Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Spike Hist Plot' + }); + }); + + it('LFP Time Series Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.LFP_TS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.LFP_TS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP Time Series Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Time Series Plot' + }); + }); + + it('LFP PSD Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.LFP_PSD_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.LFP_PSD_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP PSD Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP PSD Plot' + }); + }); + + it('LFP Spectrogram Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.LFP_SPECTOGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.LFP_SPECTOGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View LFP Spectrogram Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT * 3); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'LFP Spectrogram Plot' + }); + }); + + it('Granger Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.GRANGER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Granger Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Granger Plot' + }); + }); + + + it('Rate Spectogram Plot', async () => { + await tutorial_3c_page.waitForSelector(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + // await tutorial_3c_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3c_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + // await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_3c_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_3c_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + console.log('View Rate Spectogram Plot ...') + await tutorial_3c_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_3c_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Rate Spectogram Plot' + }); + }); + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/Tut#4_smoke.test.js b/tests/frontend/e2e/tests/Tut#4_smoke.test.js new file mode 100644 index 00000000..dc0a3051 --- /dev/null +++ b/tests/frontend/e2e/tests/Tut#4_smoke.test.js @@ -0,0 +1,265 @@ +//IMPORTS: +import 'expect-puppeteer'; +import puppeteer from 'puppeteer'; +import { click } from './utils'; +import { toMatchImageSnapshot } from 'jest-image-snapshot' +expect.extend({ toMatchImageSnapshot }) +const path = require('path'); +var scriptName = path.basename(__filename, '.js'); +import * as selectors from './selectors' + + +//PAGE INFO: +const baseURL = process.env.url || 'https://test.netpyne.metacell.us/' +const PAGE_WAIT = 3000; +const TIMEOUT = 60000; + +//SNAPSHOT: +const SNAPSHOT_OPTIONS = { + customSnapshotsDir: `./tests/snapshots/${scriptName}`, + comparisonMethod: 'ssim', + failureThresholdType: 'percent', + failureThreshold: 0.5 +}; + + +let r = (Math.random() + 1).toString(36).substring(2); + +//USERS: +const USERNAME = `TestUser${r}` +const PASSWORD = 'testpassword' + + +//TESTS: + +jest.setTimeout(3000000); +let browser4; +let tutorial_4_page; + + +describe('Tutorial #4 for Smoke Testing', () => { + + beforeAll(async () => { + browser4 = await puppeteer.launch( + { + headless: 'new', + args: ['--no-sandbox', '--disable-setuid-sandbox'], + defaultViewport: { + width: 1300, + height: 1024 + }, + } + ); + tutorial_4_page = await browser4.newPage(); + await tutorial_4_page.goto(baseURL); + if (baseURL.includes('test.netpyne.metacell.us')) { + console.log('Logging in as test user ...') + await tutorial_4_page.waitForSelector(selectors.LOGIN_PAGE_SELECTOR); + await tutorial_4_page.waitForSelector(selectors.USERNAME_SELECTOR) + await expect(tutorial_4_page) + .toFill(selectors.USERNAME_SELECTOR, USERNAME, { timeout: TIMEOUT }); + + await tutorial_4_page.waitForSelector(selectors.PASSWORD_SELECTOR) + await expect(tutorial_4_page) + .toFill(selectors.PASSWORD_SELECTOR, PASSWORD, { timeout: TIMEOUT }); + + await tutorial_4_page.click(selectors.LOGIN_BUTTON_SELECTOR) + // Wait for initial loading spinner to disappear + await tutorial_4_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + console.log('Logged in successfully') + } + }); + + afterAll(async () => { + // Close the browser instance after all tests have run + await browser4.close(); + }); + + it('Open new page', async () => { + + console.log('Opening a new NetPyNE page') + + await tutorial_4_page.on("dialog", dialog => + dialog.accept()); + + await tutorial_4_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 6, visible: true }) + await tutorial_4_page.waitForSelector(selectors.FILE_TAB_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_4_page.waitForTimeout(PAGE_WAIT) + await tutorial_4_page.click(selectors.FILE_TAB_SELECTOR) + await tutorial_4_page.waitForSelector(selectors.NEW_FILE_SELECTOR, { timeout: PAGE_WAIT * 3 }) + await tutorial_4_page.waitForTimeout(PAGE_WAIT) + await tutorial_4_page.click(selectors.NEW_FILE_SELECTOR) + await tutorial_4_page.waitForTimeout(PAGE_WAIT) + await tutorial_4_page.waitForSelector(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_4_page.click(selectors.CONFIRM_NEW_PAGE_SELECTOR) + await tutorial_4_page.waitForTimeout(PAGE_WAIT * 2) + + await tutorial_4_page.waitForFunction(() => { + let el = document.querySelector('#loading-spinner'); + return el == null || el.clientHeight === 0; + }, { timeout: TIMEOUT }); + + await tutorial_4_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT * 10 }) + + console.log('Page opened successfully') + + }) + + + it('Create and Simulate network', async () => { + + await tutorial_4_page.waitForTimeout(PAGE_WAIT * 2) + await tutorial_4_page.waitForSelector(selectors.SELECT_CELL_BUTTON_SELECTOR, { timeout: TIMEOUT }) + + console.log('Tutorial #4') + + await tutorial_4_page.waitForTimeout(PAGE_WAIT) + await tutorial_4_page.waitForSelector(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.TUTORIALS_BUTTON_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.TUTORIAL_4_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.TUTORIAL_4_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.PYR_2_CELL_SELECTOR) + await tutorial_4_page.waitForTimeout(PAGE_WAIT) + + await tutorial_4_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR) + await tutorial_4_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_4_page.waitForSelector(selectors.CREATE_NETWORK_SELECTOR) + await tutorial_4_page.click(selectors.CREATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Create network') + + await tutorial_4_page.waitForTimeout(PAGE_WAIT * 3) + + await tutorial_4_page.waitForSelector(selectors.THREE_D_REP_SELECTOR) + + console.log('... taking snapshot ...'); + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Tutorial#4 Network' + }); + await tutorial_4_page.waitForSelector(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_4_page.click(selectors.MODEL_BUTTON_SELECTOR, { timeout: TIMEOUT }); + await tutorial_4_page.waitForSelector(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + await tutorial_4_page.click(selectors.SIMULATE_NETWORK_SELECTOR, { timeout: TIMEOUT }); + + console.log('Simulate network') + + await tutorial_4_page.waitForSelector(selectors.SIMULATION_PAGE_SELECTOR, { timeout: TIMEOUT * 2 }); + + await tutorial_4_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT * 3 }) + + + }); + + + it('Connections Plot', async () => { + + await tutorial_4_page.waitForTimeout(PAGE_WAIT * 2); + await tutorial_4_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Connections Plot ...') + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Connections Plot' + }); + + }); + + it('2D Net Plot', async () => { + await tutorial_4_page.waitForSelector(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.TWO_D_NET_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View 2D Net Plot ...') + await tutorial_4_page.waitForTimeout(PAGE_WAIT * 3); + + console.log('... taking snapshot ...'); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: '2D Net Plot' + }); + }); + + it('Cell Traces Plot', async () => { + await tutorial_4_page.waitForSelector(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.CELL_TRACES_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Cell Traces Plot ...') + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Cell Traces Plot' + }); + }); + + it('Raster Plot', async () => { + await tutorial_4_page.waitForSelector(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.RASTER_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Raster Plot ...') + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Raster Plot' + }); + }); + + it('Spike Hist Plot', async () => { + await tutorial_4_page.waitForSelector(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.SPIKE_HIST_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + console.log('View Spike Hist Plot ...') + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Spike Hist Plot' + }); + }); + + + it('Rate Spectogram Plot', async () => { + await tutorial_4_page.waitForSelector(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + // await tutorial_4_page.waitForTimeout(PAGE_WAIT); + // await tutorial_4_page.waitForSelector(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_4_page.click(selectors.CONNECTIONS_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + + // await tutorial_4_page.click(selectors.RATE_SPECTROGRAM_PLOT_SELECTOR, { timeout: TIMEOUT }) + // await tutorial_4_page.waitForSelector(selectors.CANVAS_SELECTOR, { timeout: TIMEOUT }) + + console.log('View Rate Spectogram Plot ...') + await tutorial_4_page.waitForTimeout(PAGE_WAIT); + + console.log('... taking snapshot ...'); + expect(await tutorial_4_page.screenshot()) + .toMatchImageSnapshot({ + ...SNAPSHOT_OPTIONS, + customSnapshotIdentifier: 'Rate Spectogram Plot' + }); + }); + +}); \ No newline at end of file diff --git a/tests/frontend/e2e/tests/selectors.js b/tests/frontend/e2e/tests/selectors.js new file mode 100644 index 00000000..ad70c467 --- /dev/null +++ b/tests/frontend/e2e/tests/selectors.js @@ -0,0 +1,106 @@ + +export const BASE_PAGE_SELECTOR = '.NetPyNE-root-1' +export const TUTORIALS_BUTTON_SELECTOR = 'button[id = "Examples"]' +export const MODEL_BUTTON_SELECTOR = 'button[id="Model"]' +export const CREATE_NETWORK_SELECTOR = 'li[id="Create network"]' +export const CREATE_AND_SIMULATE_NETWORK_SELECTOR = 'li[id="Create and simulate network"]' +export const SIMULATE_NETWORK_SELECTOR = 'li[id="Simulate network"]' +export const SIMULATE_TOP_RIGHT_BUTTON_SELECTOR = 'div[class="MuiButtonGroup-root MuiButtonGroup-contained"]' +export const SIMULATION_PAGE_SELECTOR = 'canvas' +export const CONNECTIONS_PLOT_SELECTOR = 'div[title=\"Connections Plot\"][role=button]' +export const LOGIN_PAGE_SELECTOR = '#login-main'; +export const USERNAME_SELECTOR = '#username_input'; +export const PASSWORD_SELECTOR = '#password_input'; +export const LOGIN_BUTTON_SELECTOR = '#login_submit'; +export const SELECT_CELL_BUTTON_SELECTOR = '#selectCellButton'; +export const TUTORIAL_1_SELECTOR = "li[id='Tut 1: Simple cell network']"; +export const TUTORIAL_2_SELECTOR = "li[id='Tut 2: Detailed cell network']" +export const TUTORIAL_3A_SELECTOR = "li[id='Tut 3a: Multiscale network (low IP3)']" +export const TUTORIAL_3B_SELECTOR = "li[id='Tut 3b: Multiscale network (high IP3)']" +export const TUTORIAL_3C_SELECTOR = "li[id='Tut 3c: Multiscale network (no RxD)']" +export const TUTORIAL_4_SELECTOR = "li[id='Tut 4: Simple oscillatory network']" +export const PYR_CELL_SELECTOR = '#pyr'; +export const PYR_2_CELL_SELECTOR = '#PYR' +export const INT_CELL_SELECTOR = '#INT' +export const E_CELL_TYPE_SELECTOR = '#E' +export const I_CELL_TYPE_SELECTOR = '#I' +export const CONFIGURATION_TAB_SELECTOR = 'div[title="Configuration"]'; +export const RECORDING_CONFIGURATION_TAB_SELECTOR = '#configRecord'; +export const TRACES_TO_RECORD_SELECTOR = `div[title="Dict of traces to record (default: {} ; example: {'V_soma': {'sec':'soma','loc':0.5,'var':'v'} })."]`; +export const DIPOLE_LFPYKIT_SELECTOR = `#simConfigrecordDipole`; +export const DISABLED_EEG_PLOT_SELECTOR = 'div[title="EEG plot"][aria-disabled="true"]'; +export const DISABLED_DIPOLE_PLOT_SELECTOR = 'div[title="Dipole plot"][aria-disabled="true"]'; +export const SIMULATE_BUTTON_SELECTOR = 'div[class="MuiButtonGroup-root MuiButtonGroup-contained"]'; +export const RASTER_PLOT_SELECTOR = 'div[title="Raster plot"][aria-disabled="false"]'; +export const EEG_PLOT_SELECTOR = 'div[title="EEG plot"][aria-disabled="false"]'; +export const DIPOLE_PLOT_SELECTOR = 'div[title="Dipole plot"][aria-disabled="false"]'; +export const GRANGER_PLOT_SELECTOR = 'div[title=\"Granger Plot\"][role=button]' +export const TWO_D_NET_PLOT_SELECTOR = 'div[title=\"2D Net Plot\"][role=button]' +export const CELL_TRACES_PLOT_SELECTOR = 'div[title=\"Cell traces\"][role=button]' +export const SPIKE_HIST_PLOT_SELECTOR = 'div[title=\"Spike Hist Plot\"][role=button]' +export const RATE_SPECTROGRAM_PLOT_SELECTOR = 'div[title=\"Rate Spectrogram Plot\"][role=button]' +export const RXD_CONCENTRATION_PLOT_SELECTOR = 'div[title=\"RxD concentration plot\"][role=button]' +export const LFP_TS_PLOT_SELECTOR = 'div[title=\"LFP Time Series Plot\"][role=button]' +export const LFP_PSD_PLOT_SELECTOR = 'div[title=\"LFP PSD Plot\"][role=button]' +export const LFP_SPECTOGRAM_PLOT_SELECTOR = 'div[title=\"LFP Spectrogram Plot\"][role=button]' +export const CANVAS_SELECTOR = 'canvas'; +export const THREE_D_REP_SELECTOR = 'div[title="3D Representation"][aria-disabled="false"]' +export const DISABLED_RASTER_PLOT_SELECTOR = 'div[title="Raster plot"][aria-disabled="true"]' +export const EXPERIMENT_MANAGER_TAB_SELECTOR = 'div[title="Experiment Manager"]' +export const CREATE_NEW_EXPERIMENT_SELECTOR = 'button[class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textPrimary"]' +export const CREATE_NEW_EXPERIMENT_POPUP_SELECTOR = 'h2[class="MuiTypography-root MuiTypography-h6"]' +export const CONFIRM_SELECTOR = '#confirmDeletion' +export const EXPERIMENT_NAME_SELECTOR = '#experiment-name' +export const PARAMETER_SELECTION_SELECTOR = '#undefined-combo-box-demo' +export const FROM_VALUE_SELECTOR = '#undefined-from' +export const TO_VALUE_SELECTOR = '#undefined-to' +export const STEP_VALUE_SELECTOR = '#undefined-step' +export const CREATE_EXPERIMENT_BUTTON_SELECTOR = 'button[class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary"]' +export const EXPERIMENT_TABLE_HEADER_SELECTOR = 'th[class="MuiTableCell-root MuiTableCell-body"]' +// export const SIMULATE_POPUP_SELECTOR = 'div[class="MuiBox-root MuiBox-root-185 wrap"]' +export const SIMULATE_POPUP_SELECTOR = '.MuiDialogContent-root > .MuiBox-root.custom-radio > :nth-child(2) > div' + +export const CONFIRM_SIMULATE_SELECTOR = '#appBarPerformActionButton' +export const CONFIRM_EXPERIMENT_STARTED_SELECTOR = 'button[class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary"]' +// export const SIMULATION_LOADER_SELECTOR = 'div[class = "MuiBox-root MuiBox-root-186 MuiChip-icon MuiChipLoader"]' +export const SIMULATION_LOADER_SELECTOR = '.MuiTableCell-root.MuiTableCell-body.experimentTableCell.MuiTableCell-alignLeft > div > .MuiChipLoader ' +export const BACK_TO_EDIT_SELECTOR = 'span[class="MuiButton-startIcon MuiButton-iconSizeMedium"]' +export const CELL_TYPES_TAB_SELECTOR = 'div[title="Cell Types"]' +export const EXPERIMENT_TABLE_SELECTOR = 'table[class="MuiTable-root"]' +export const CREATED_EXPERIMENT_SELECTOR = 'button[class="MuiButtonBase-root MuiButton-root MuiButton-text"]' +export const EXPERIMENT_CONDIIONS_ROW_SELECTOR = 'tr[class = "MuiTableRow-root MuiTableRow-head"]' +export const EDIT_EXPERIMENT_BACK_SELECTOR = '.editExperimentBack > svg' +export const INDIVIDUAL_EXPERIMENT_ROW_SELECTOR = 'tr[class="MuiTableRow-root"]' +export const FILE_TAB_SELECTOR = '#File' +export const NEW_FILE_SELECTOR = '#New' +export const CONFIRM_NEW_PAGE_SELECTOR = '#appBarPerformActionButton' +export const CONTROL_PANEL_TAB_SELECTOR = 'div[title="Control Panel"]' +export const NETWORKS_IN_CONTROL_PANEL_SELECTOR = 'ul[role="tree"]' +export const NETWORK_ITEMS_CONTROL_PANEL_SELECTOR = 'li[role="treeitem"]' +export const COLOR_CONTROL_BUTTONS_SELECTOR = 'button[class="MuiButtonBase-root MuiIconButton-root"]' +export const COLOR_RECT_SELECTOR = 'rect[rx="5"]' +export const CONTROL_PANEL_NETWORK_ROWS_SELECTOR = 'div[class = "MuiTypography-root MuiTreeItem-label MuiTypography-body1"]' +export const CONTROL_PANEL_TABLE_SELECTOR = 'div[class="MuiGrid-root MuiGrid-container MuiGrid-justify-content-xs-space-between"]' +export const CONTROL_PANEL_FILTER_SELECTOR = 'input[class="MuiInputBase-input MuiOutlinedInput-input"]' +export const FILE_SYSTEM_SELECTOR = '.ReactVirtualized__Grid__innerScrollContainer' +export const LEVEL_UP_SELECTOR ='.fa-level-up' +export const FOLDERS_SELECTOR ='div[class = "rst__rowContents rst__rowContentsDragDisabled"]' +export const SELECT_BUTTON_SELECTOR ='#browserAccept' +export const E_RULE_SELECTOR ='#Erule' +export const NETWORK_CREATION_MENU_BUTTON_SELECTOR ='button[aria-label="select merge strategy"]' +export const NETWORK_CREATION_MENU_ITEMS_SELECTOR ='#split-button-menu > li' +export const NETWORK_CREATION_BUTTON_SELECTOR ='div[aria-label="split button"]' +export const POPULATIONS_TAB_SELECTOR ='div[title="Populations"]' +export const SAVE_MENU_SELECTOR ='h2[class="MuiTypography-root MuiTypography-h6"]' +export const PATH_INPUT_SELECTOR ='input[class="MuiInputBase-input MuiFilledInput-input MuiInputBase-inputAdornedStart MuiFilledInput-inputAdornedStart"]' +export const SAVE_BUTTON_SELECTOR ='#appBarPerformActionButton' +export const EXPORT_OPTIONS_SELECTOR ='ul[class="MuiList-root MuiList-padding"]' +export const CHECKBOX_OPTION_SELECTOR ='input[type="checkbox"]' +export const PYTHON_CONSOLE_TAB_SELECTOR ='div[title="Python"]' +export const PYTHON_CONSLE_SELECTOR ='#pythonConsoleOutput' +export const PYTHON_CONSOLE_FRAME_SELECTOR ='#pythonConsoleFrame' +export const MAIN_PYTHON_APP_SELECTOR ='#ipython-main-app' +export const PYTHON_CELL_SELECTOR ='div.inner_cell' +export const PYTHON_OUTPUT_SELECTOR ='div[class="output_subarea output_text output_stream output_stdout"]' +export const PYTHON_FIRST_OUTPUT_SELECTOR ='div[class="output_subarea output_text output_result"]' + diff --git a/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/Dipole Plot-snap.png b/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/Dipole Plot-snap.png new file mode 100644 index 00000000..e3106138 Binary files /dev/null and b/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/Dipole Plot-snap.png differ diff --git a/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/EEG Plot-snap.png b/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/EEG Plot-snap.png new file mode 100644 index 00000000..28eca622 Binary files /dev/null and b/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/EEG Plot-snap.png differ diff --git a/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/Tutorial#1 Network-snap.png b/tests/frontend/e2e/tests/snapshots/EEG_and_Dipole_Tut#1.test/Tutorial#1 Network-snap.png new file mode 100644 index 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mode 100644 index 00000000..1709b831 Binary files /dev/null and b/tests/frontend/e2e/tests/snapshots/Tut#4_smoke.test/Spike Hist Plot-snap.png differ diff --git a/tests/frontend/e2e/tests/snapshots/Tut#4_smoke.test/Tutorial#4 Network-snap.png b/tests/frontend/e2e/tests/snapshots/Tut#4_smoke.test/Tutorial#4 Network-snap.png new file mode 100644 index 00000000..55eeb91e Binary files /dev/null and b/tests/frontend/e2e/tests/snapshots/Tut#4_smoke.test/Tutorial#4 Network-snap.png differ diff --git a/utilities/install.py b/utilities/install.py index 8075fb79..1830adc0 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -13,13 +13,16 @@ PYGEPPETTO = 'https://github.com/openworm/pygeppetto.git' NETPYNE = 'https://github.com/Neurosim-lab/netpyne.git' WORKSPACE = 'https://github.com/Neurosim-lab/netpyne_workspace' +META = 'https://github.com/MetaCell/geppetto-meta/' ROOT_DIR = os.path.join(HERE, os.pardir) DEPS_DIR = os.path.join(ROOT_DIR, 'src') WEBAPP_DIR = os.path.join(ROOT_DIR, 'webapp') JUPYTER_DIR = 'jupyter-geppetto' +PYGEPPETTO_DIR = 'pygeppetto' NETPYNE_DIR = 'netpyne' +META_DIR = 'geppetto-meta' WORKSPACE_DIR = 'workspace' @@ -34,7 +37,7 @@ def cprint(string): def execute(cmd, cwd='.', *args, **kwargs): exit_code = subprocess.call(cmd, cwd=cwd, *args, **kwargs) if exit_code != 0: - raise SystemExit('Error installing NetPyNE-UI') + raise SystemExit(f'Error installing NetPyNE-UI - Command {cmd} failed with code {exit_code} in directory {cwd}') # by default clones branch (which can be passed as a parameter python install.py branch test_branch) @@ -46,13 +49,22 @@ def clone(repository, folder=None, branch_or_tag=None, cwdp=DEPS_DIR, recursive= if folder and os.path.exists(os.path.join(cwdp, folder)): print(f'Skipping clone of {repository}: folder exists') else: + exit_code = 0 if recursive: - subprocess.call(['git', 'clone', '--recursive', repository], cwd=cwdp) + exit_code = subprocess.call(['git', 'clone', '--recursive', repository], cwd=cwdp) else: if folder: - subprocess.call(['git', 'clone', repository, folder], cwd=cwdp) + exit_code = subprocess.call(['git', 'clone', repository, folder], cwd=cwdp) else: - subprocess.call(['git', 'clone', repository], cwd=cwdp) + exit_code = subprocess.call(['git', 'clone', repository], cwd=cwdp) + + if exit_code != 0: + raise SystemExit(f'Failed to clone repository {repository} into {folder}') + + if not os.path.exists(os.path.join(cwdp, folder, '.git')): + print(f'Skipping checkout of {repository}: folder is not a git repository') + return + if branch_or_tag: checkout(folder, branch_or_tag, cwdp) @@ -63,7 +75,9 @@ def checkout(folder, branch_or_tag, cwdp): print(f'Checking out {branch_or_tag}') try: + subprocess.call(['git', 'fetch'], cwd=newPath) subprocess.call(['git', 'checkout', branch_or_tag], cwd=newPath) + subprocess.call(['git', 'pull', 'origin', branch_or_tag], cwd=newPath) except Exception as e: logging.error('Cannot checkout branch or tag %s on %s', branch_or_tag, folder, exc_info=True) @@ -72,57 +86,54 @@ def compile_mod(): execute(['nrnivmodl', os.path.join(WORKSPACE_DIR, 'mod')], cwd=ROOT_DIR) -def main(netpyne_branch, workspace_branch, pygeppetto_branch=None, jupyter_geppetto_branch=None, skipNpm=False, - skipTest=False, development=False): +def main(netpyne_branch, workspace_branch, geppetto_branch=None, skipNpm=False, + skipTest=False, development=False): cprint("Installing requirements") execute(cmd=['pip', 'install', '-r', 'requirements.txt'], cwd=ROOT_DIR) + cprint("Installing UI python package...") + execute(cmd=['pip', 'install', '-e', '.', '--no-deps'], cwd=ROOT_DIR) if not os.path.exists(DEPS_DIR): os.mkdir(DEPS_DIR) - - if development: + if geppetto_branch: + if geppetto_branch.replace(" ", "") is '': + geppetto_branch = 'development' + os.chdir(DEPS_DIR) + cprint("Installing geppetto-meta") + clone(repository=META, folder=META_DIR, branch_or_tag=geppetto_branch) + # installing pygeppetto + cprint("Installing pygeppetto") + execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, META_DIR, PYGEPPETTO_DIR)) + # installing jupyter geppetto + cprint("Installing jupyter geppetto") + execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR)) + # installing core dependencies + execute(cmd=['pip', 'install', '-e', '.'], cwd=ROOT_DIR) + if netpyne_branch: + if netpyne_branch.replace(" ", "") is '': + netpyne_branch = 'development' os.chdir(DEPS_DIR) - cprint("Installing netpyne") clone(repository=NETPYNE, branch_or_tag=netpyne_branch) execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, NETPYNE_DIR)) - # install pygeppetto - cprint("Installing pygeppetto") - clone(repository=PYGEPPETTO, - folder='pygeppetto', - branch_or_tag=pygeppetto_branch - ) - execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, 'pygeppetto')) - - # install jupyter geppetto - cprint("Installing org.geppetto.frontend.jupyter") - clone(repository=JUPYTER, - folder=JUPYTER_DIR, - branch_or_tag=jupyter_geppetto_branch - ) - - execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, JUPYTER_DIR)) - execute(cmd=['pip', 'install', '-e', '.'], cwd=ROOT_DIR) - else: - # install requirements - cprint("Installing UI python package...") - execute(cmd=['pip', 'install', '-e', '.', '--no-deps'], cwd=ROOT_DIR) os.chdir(ROOT_DIR) - cprint("Cloning workspace") - clone(repository=WORKSPACE, branch_or_tag=workspace_branch, folder=WORKSPACE_DIR, cwdp=ROOT_DIR) - cprint("Compiling workspace modules") - compile_mod() + if workspace_branch: + cprint("Cloning workspace") + clone(repository=WORKSPACE, branch_or_tag=workspace_branch, folder=WORKSPACE_DIR, cwdp=ROOT_DIR) + cprint("Compiling workspace modules") + #compile_mod() - if not skipNpm and os.path.exists(os.path.join(DEPS_DIR, JUPYTER_DIR)): + if not skipNpm and os.path.exists(os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR)): cprint("Building Jupyter Geppetto extension...") - execute(cmd=['npm', 'ci'], cwd=os.path.join(DEPS_DIR, JUPYTER_DIR, 'js')) + execute(cmd=['npm', 'ci'], cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR, 'js')) execute(cmd=['npm', 'run', 'build-dev' if development else 'build'], - cwd=os.path.join(DEPS_DIR, JUPYTER_DIR, 'js')) + cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR, 'js')) + execute(cmd=['jupyter', 'nbextension', 'uninstall', 'jupyter_geppetto']) execute(cmd=['jupyter', 'nbextension', 'install', '--py', '--symlink', '--sys-prefix', 'jupyter_geppetto']) execute(cmd=['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'jupyter_geppetto']) execute(cmd=['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'widgetsnbextension']) @@ -160,6 +171,7 @@ def main(netpyne_branch, workspace_branch, pygeppetto_branch=None, jupyter_geppe _ = config['NotebookApp']['tornado_settings'] except KeyError: config['NotebookApp']['tornado_settings'] = {} + config['NotebookApp']['tornado_settings']['headers'] = { 'Content-Security-Policy': "frame-ancestors 'self' http: https: http://localhost:8081 *" } config['NotebookApp']['tornado_settings']['gzip'] = True f.seek(0) json.dump(config, f, indent=4, sort_keys=True) @@ -173,12 +185,27 @@ def main(netpyne_branch, workspace_branch, pygeppetto_branch=None, jupyter_geppe cprint("Installing test libraries") execute(cmd=['pip', 'install', '-r', 'requirements-test.txt'], cwd=ROOT_DIR) cprint("Testing NetPyNE") - # execute("python -m unittest netpyne_ui.tests.netpyne_model_interpreter_test".split()) + execute("python -m pytest tests".split()) cprint("Installing client packages") if not skipNpm: - execute(cmd=['npm', 'install' if development else 'ci'], cwd=WEBAPP_DIR) - execute(cmd=['npm', 'run', 'build-dev'], cwd=WEBAPP_DIR) + if geppetto_branch: + # install geppetto meta + if os.path.exists(os.path.join(WEBAPP_DIR, '.yalc')): + execute(cmd=['rm', '-rf', '.yalc'], cwd=WEBAPP_DIR) + execute(cmd=['ln', '-s', os.path.expanduser('~') + '/.yalc', '.yalc'], cwd=WEBAPP_DIR) + else: + execute(cmd=['ln', '-s', os.path.expanduser('~') + '/.yalc', '.yalc'], cwd=WEBAPP_DIR) + execute(cmd=['ls'], cwd=WEBAPP_DIR) + execute(cmd=['bash', 'geppetto_ui.sh'], cwd=WEBAPP_DIR) + execute(cmd=['yarn'], cwd=WEBAPP_DIR) + execute(cmd=['yarn', 'run', 'build-dev'], cwd=WEBAPP_DIR) + execute(cmd=['cp', 'package.bak', 'package.json'], cwd=WEBAPP_DIR) + else: + # install jupyter geppetto + cprint("Installing geppetto ui, client and core dependecies") + execute(cmd=['yarn', 'install', '--immutable'], cwd=WEBAPP_DIR) + execute(cmd=['yarn', 'run', 'build'], cwd=WEBAPP_DIR) if __name__ == "__main__": @@ -196,27 +223,22 @@ def main(netpyne_branch, workspace_branch, pygeppetto_branch=None, jupyter_geppe help='Install for development.') parser.add_argument('--netpyne', '-vn', dest='netpyne_version', action="store", - default=os.getenv('NETPYNE_VERSION', 'development'), + default=os.getenv('NETPYNE_VERSION', None), help='Specify NetPyNE library branch or tag.') parser.add_argument('--workspace', '-vw', dest='workspace_version', action="store", default=os.getenv('WORKSPACE_VERSION', 'master'), help='Specify workspace branch or tag.') - parser.add_argument('--pygeppetto', '-vp', dest='pygeppetto_version', action="store", - default=os.getenv('PYGEPPETTO_VERSION', 'development'), + parser.add_argument('--geppetto', '-vp', dest='geppetto_version', action="store", + default=os.getenv('GEPPETTO_VERSION', None), help='Specify Pygeppetto library branch or tag (only for dev build).') - parser.add_argument('--jupyter_geppetto', '-vj', dest='jupyter_geppetto_version', action="store", - default=os.getenv('JUPYTER_GEPPETTO_VERSION', 'development'), - help='Specify Jupyter Geppetto library branch or tag (only for dev build).') - args = parser.parse_args(sys.argv[1:]) print('Install arguments:\n', args) main(skipNpm=args.skipNpm, skipTest=args.skipTest, development=args.development, - netpyne_branch=args.netpyne_version, - workspace_branch=args.workspace_version, - pygeppetto_branch=args.pygeppetto_version, - jupyter_geppetto_branch=args.jupyter_geppetto_version - ) + netpyne_branch=args.netpyne_version, + workspace_branch=args.workspace_version, + geppetto_branch=args.geppetto_version, + ) diff --git a/webapp/.eslintignore b/webapp/.eslintignore index 1d81b61d..f38f43ea 100644 --- a/webapp/.eslintignore +++ b/webapp/.eslintignore @@ -6,4 +6,5 @@ META-INF/* **/tests/jest-puppeteer/**/*.js **/*min.js geppetto-client/** -node_modules/** \ No newline at end of file +node_modules/** +webpack.*.js diff --git a/webapp/.eslintrc.js b/webapp/.eslintrc.js index f95a2637..7add959b 100644 --- a/webapp/.eslintrc.js +++ b/webapp/.eslintrc.js @@ -10,7 +10,52 @@ module.exports = { // Tweak some rules to our preferences 'space-before-function-paren': ['error', 'always'], + 'react/prop-types': 1, 'no-console': 0, + 'import/extensions': 0, + 'max-len': ['warn', { code: 140 }], + 'no-eval': 1, + eqeqeq: 1, + 'no-plusplus': 1, + 'react/destructuring-assignment': 1, + 'no-param-reassign': 1, + 'vars-on-top': 1, + 'no-use-before-define': 1, + 'no-unused-vars': 1, + 'import/no-unresolved': 1, + 'import/named': 1, + 'react/jsx-props-no-spreading': 1, + 'no-nested-ternary': 1, + 'no-return-assign': 1, + 'react/no-array-index-key': 1, + 'react/sort-comp': 1, + 'consistent-return': 1, + 'import/prefer-default-export': 1, + 'react/no-unused-state': 1, + 'jsx-a11y/alt-text': 1, + 'no-restricted-syntax': 1, + 'no-underscore-dangle': 1, + 'no-restricted-globals': 1, + camelcase: 1, + 'max-classes-per-file': 1, + 'jsx-a11y/click-events-have-key-events': 1, + 'jsx-a11y/no-static-element-interactions': 1, + 'prefer-destructuring': 1, + 'no-redeclare': 1, + 'import/no-webpack-loader-syntax': 1, + 'global-require': 1, + 'default-case': 1, + 'react/prefer-stateless-function': 1, + 'block-scoped-var': 1, + 'no-var': 1, + 'no-shadow': 1, + 'react/no-did-update-set-state': 1, + 'react/no-string-refs': 1, + 'no-multi-assign': 1, + 'guard-for-in': 1, + 'no-unused-expressions': 1, + 'no-control-regex': 1, + 'no-loop-func': 1, }, globals: { page: true, @@ -23,6 +68,18 @@ module.exports = { CanvasContainer: true, patchRequire: true, window: true, + document: true, + $: true, + IPython: true, + fetch: true, + Blob: true, + FormData: true, + Event: true, + jQuery: true, + define: true, + // geppetto + Instances: true, GEPPETTO: true, + IPython: true, }, }; diff --git a/webapp/GeppettoConfiguration.json b/webapp/GeppettoConfiguration.json index 54e3cc20..f5b97848 100644 --- a/webapp/GeppettoConfiguration.json +++ b/webapp/GeppettoConfiguration.json @@ -1,11 +1,12 @@ { "_README" : "http://docs.geppetto.org/en/latest/build.html", "contextPath": "org.geppetto.frontend", - "useSsl": false, - "embedded": false, + "useSsl": true, + "embedded": true, "embedderURL": ["/"], "rootRedirect":"", "noTest": false, + "customSplash": "geppetto/build/static/splash.gif", "extensions": { "geppetto-default/ComponentsInitialization": false, "geppetto-netpyne/ComponentsInitialization": true diff --git a/webapp/Main.js b/webapp/Main.js index c48f0ca9..e1663bf1 100644 --- a/webapp/Main.js +++ b/webapp/Main.js @@ -1,39 +1,48 @@ -global.jQuery = require('jquery'); -global.GEPPETTO_CONFIGURATION = require('./GeppettoConfiguration.json'); - -jQuery(() => { - require('geppetto-client-initialization'); - const ReactDOM = require('react-dom'); - const React = require('react'); - const { MuiThemeProvider } = require('@material-ui/core/styles'); - const { NetPyNE } = require('./components'); - - const theme = require('./theme').default; - - const { Provider } = require('react-redux'); - const configureStore = require('./redux/store').default; - - require('./css/netpyne.less'); - require('./css/material.less'); - require('./css/traceback.less'); - require('./css/flexlayout.less'); - require('./css/tree.less'); +import React from 'react'; +import ReactDOM from 'react-dom'; +import { Provider } from 'react-redux'; +import { MuiThemeProvider } from '@material-ui/core/styles'; +import * as Sentry from '@sentry/react'; +import { CaptureConsole } from '@sentry/integrations'; +import { LoadingSpinner } from '@metacell/geppetto-meta-client/components'; +import { NetPyNE } from './components'; +import theme from './theme'; +import store from './redux/store'; +import '@metacell/geppetto-meta-ui/flex-layout/style/dark.css'; - const store = configureStore(); - - ReactDOM.render( -

- - - - - - -
, - document.querySelector('#mainContainer'), - ); - - GEPPETTO.G.setIdleTimeOut(-1); - GEPPETTO.Resources.COLORS.DEFAULT = '#6f54aa'; - GEPPETTO.trigger(GEPPETTO.Events.Show_spinner, 'Initialising NetPyNE'); -}); +global.GEPPETTO_CONFIGURATION = require('./GeppettoConfiguration.json'); +const { initGeppetto } = require('@metacell/geppetto-meta-client/GEPPETTO'); + +if (process.env.NODE_ENV === 'production') { + Sentry.init({ + dsn: 'https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6', + integrations: [ + new CaptureConsole({ + levels: ['error'], + }), + ], + tracesSampleRate: 1.0, + }); +} + +window.$ = Array; // TODO Temporary fix -- remove upon https://github.com/MetaCell/geppetto-meta/issues/380 +initGeppetto(); +require('./css/netpyne.less'); +require('./css/material.less'); +require('./css/traceback.less'); +require('./css/flexlayout.less'); +require('./css/tree.less'); + +ReactDOM.render( +
+ + + + + + +
, + document.querySelector('#mainContainer'), +); + +GEPPETTO.Resources.COLORS.DEFAULT = '#6f54aa'; diff --git a/webapp/Utils.js b/webapp/Utils.js index 33d82062..da39c01c 100644 --- a/webapp/Utils.js +++ b/webapp/Utils.js @@ -1,13 +1,14 @@ +import * as Sentry from '@sentry/react'; + import { execPythonMessage, evalPythonMessage, -} from '@geppettoengine/geppetto-client/js/communication/geppettoJupyter/GeppettoJupyterUtils'; -import React from 'react'; +} from './components/general/GeppettoJupyterUtils'; const Utils = { getAvailableKey (model, prefix) { - if (model == undefined) { + if (model === undefined) { return prefix; } // Get New Available ID @@ -23,24 +24,65 @@ const Utils = { return id; }, - getMetadataField (key, field) { - if (key == undefined) { - return; + captureSentryException (e) { + if (process.env.NODE_ENV == 'production') + Sentry.captureException(e); + console.error(e); + }, + + /** + * Retrieves the metadata object for the passed `key`. + * + * A specific attributes can be selected by passing `field`. + * + * The algorithm will iteratively test the key for each nesting in metadata. + * + * Example key: `netParams.popParams.E.numCells`. + * Since 'E' is not explicitly modeled in `netpyne.metadata` + * this algorithm implements additional logic to skip certain levels. + * + * @param {*} key key of metadata path. + * @param {*} field specific object attribute. + * @returns metadata object or specific attribute. + */ + getMetadataField (key, field = null) { + if (key === undefined) { + return null; } + let currentObject; let nextObject = window.metadata; - key.split('.') - .forEach((item) => { + let skipped = false; + + // eslint-disable-next-line no-restricted-syntax + for (const item of key.split('.')) { + if (currentObject != null && currentObject?.container === true && !(item in nextObject)) { + if (skipped) { + return null; + } + + // skip the list element, e.g. "E"! + // console.debug(`Skip ${item} at ${nextObject.label}`); + skipped = true; + } else { + skipped = false; + if (item in nextObject) { currentObject = nextObject[item]; if ('children' in currentObject) { nextObject = currentObject.children; } } else { - currentObject = undefined; + currentObject = null; } - }); - return (currentObject == undefined) ? currentObject : currentObject[field]; + } + } + + if (currentObject) { + return field ? currentObject[field] : currentObject; + } + + return null; }, getHTMLType (key) { @@ -113,7 +155,13 @@ const Utils = { return modelFields; }, + asEscapedString (value) { + return value.replace(/\\/g, '\\\\').replace(/"/g, '\\"') + }, + renameKey (path, oldValue, newValue, callback) { + oldValue = oldValue.replace(/\\/g, '\\\\').replace(/"/g, '\\"'); + newValue = newValue.replace(/\\/g, '\\\\').replace(/"/g, '\\"'); this.execPythonMessage(`netpyne_geppetto.rename("${path}","${oldValue}","${newValue}")`) .then((response) => { callback(response, newValue); @@ -132,7 +180,7 @@ const Utils = { return name; }, - // FIXME: Hack to remove scaped chars (\\ -> \ and \' -> ') manually + // FIXME: Hack to remove escaped chars (\\ -> \ and \' -> ') manually convertToJSON (data) { if (typeof data === 'string' || data instanceof String) { return JSON.parse(data.replace(/\\\\/g, '\\') @@ -147,20 +195,23 @@ const Utils = { getErrorResponse (data) { const parsedData = this.convertToJSON(data); - if (parsedData.type && parsedData.type == 'ERROR') { + if (parsedData && parsedData.type && parsedData.type === 'ERROR') { const error = { details: parsedData.details }; if (Object.prototype.hasOwnProperty.call(parsedData, 'message')) { error.message = parsedData.message; } else if (Object.prototype.hasOwnProperty.call(parsedData, 'websocket')) { error.message = parsedData.websocket; } + if (Object.prototype.hasOwnProperty.call(parsedData, 'additional_info')) { + error.additionalInfo = parsedData.additional_info ; + } return error; } return null; }, handleUpdate (updateCondition, newValue, originalValue, context, componentName) { - if ((updateCondition) && (newValue != originalValue)) { + if ((updateCondition) && (newValue !== originalValue)) { /* * if the new value has been changed by the function Utils.nameValidation means that the name convention * has not been respected, so we need to open the dialog and inform the user. @@ -171,10 +222,10 @@ const Utils = { errorDetails: `Leading digits or whitespaces are not allowed in ${componentName} names.`, }); return true; - } if ((updateCondition) && (newValue == originalValue)) { + } if ((updateCondition) && (newValue === originalValue)) { context.setState({ currentName: newValue }); return true; - } if (!(updateCondition) && (newValue == originalValue)) { + } if (!(updateCondition) && (newValue === originalValue)) { context.setState({ currentName: newValue, errorMessage: 'Error', @@ -182,7 +233,7 @@ const Utils = { } is already used in this model, please pick another name.`, }); return false; - } if (!(updateCondition) && (newValue != originalValue)) { + } if (!(updateCondition) && (newValue !== originalValue)) { context.setState({ currentName: newValue, errorMessage: 'Error', @@ -192,8 +243,22 @@ const Utils = { } }, + formatDate (timestamp) { + const date = new Date(timestamp); + return date?.toLocaleString(); + }, + execPythonMessage, evalPythonMessage, + + flatten (obj, path = '') { + if (!(obj instanceof Object)) return { [path.replace(/\.$/g, '')]: obj }; + + return Object.keys(obj) + .reduce((output, key) => (obj instanceof Array + ? { ...output, ...Utils.flatten(obj[key], `${path.slice(0, -1)}[${key}].`) } + : { ...output, ...Utils.flatten(obj[key], `${path + key}.`) }), {}); + }, }; export default Utils; diff --git a/webapp/api/experiments.js b/webapp/api/experiments.js new file mode 100644 index 00000000..568df62e --- /dev/null +++ b/webapp/api/experiments.js @@ -0,0 +1,17 @@ +import Utils from 'root/Utils'; + +export const getExperiments = () => Utils.evalPythonMessage('netpyne_geppetto.experiments.get_experiments', []); + +export const getExperiment = (name) => Utils.evalPythonMessage('netpyne_geppetto.experiments.get_experiment', [name]); +export const removeExperiment = (name) => Utils.evalPythonMessage('netpyne_geppetto.experiments.remove_experiment', [name]); +export const addExperiment = (experiment) => Utils.evalPythonMessage('netpyne_geppetto.experiments.add_experiment', [experiment]); +export const editExperiment = (name, experiment) => Utils.evalPythonMessage('netpyne_geppetto.experiments.edit_experiment', + [name, experiment]); + +export const getParameters = () => Utils.evalPythonMessage('netpyne_geppetto.getModelAsJson', []); +export const getModelSpecification = (name, trial) => Utils.evalPythonMessage('netpyne_geppetto.experiments.get_model_specification', + [name, trial]); + +export const getRunConfiguration = () => Utils.evalPythonMessage('netpyne_geppetto.get_run_configuration', []); +export const editRunConfiguration = (runConfig) => Utils.evalPythonMessage('netpyne_geppetto.edit_run_configuration', + [runConfig]); diff --git a/webapp/api/hooks.js b/webapp/api/hooks.js new file mode 100644 index 00000000..365d9684 --- /dev/null +++ b/webapp/api/hooks.js @@ -0,0 +1,30 @@ +import { useEffect, useRef } from 'react'; + +/** + * Interval hook taken from: https://overreacted.io/making-setinterval-declarative-with-react-hooks/ + * + * @param callback + * @param delay + */ +const useInterval = (callback, delay) => { + const savedCallback = useRef(); + + // Remember the latest callback. + useEffect(() => { + savedCallback.current = callback; + }, [callback]); + + // Set up the interval. + useEffect(() => { + function tick () { + savedCallback.current(); + } + + if (delay !== null) { + const id = setInterval(tick, delay); + return () => clearInterval(id); + } + }, [delay]); +}; + +export default useInterval; diff --git a/webapp/babel.config.js b/webapp/babel.config.js index e7772fc3..0ba8b437 100644 --- a/webapp/babel.config.js +++ b/webapp/babel.config.js @@ -4,6 +4,8 @@ module.exports = { '@babel/preset-env', { targets: { node: 'current' } }, ], + '@babel/preset-typescript', + '@babel/preset-react', ], plugins: [ '@babel/plugin-proposal-class-properties', diff --git a/webapp/components/NetPyNE.js b/webapp/components/NetPyNE.js index 932dbbc7..e61b6b1b 100644 --- a/webapp/components/NetPyNE.js +++ b/webapp/components/NetPyNE.js @@ -8,11 +8,13 @@ import { LayoutManager, Drawer, Dialog, + ConfirmationDialog, + LaunchDialog, + TutorialObserver, } from 'netpyne/components'; - -import Utils from '../Utils'; - -import { EDIT_WIDGETS } from '../constants'; +import { openDialog } from '../redux/actions/general'; +// import { execPythonMessage } from './general/GeppettoJupyterUtils'; +import { replayAll } from './general/CommandRecorder'; const styles = ({ zIndex }) => ({ root: { @@ -29,7 +31,7 @@ const styles = ({ zIndex }) => ({ }, topbar: { position: 'relative', - zIndex: zIndex.drawer + 1, + zIndex: zIndex.drawer, }, content: { flexGrow: 1, @@ -40,97 +42,177 @@ const styles = ({ zIndex }) => ({ noGrow: { flexGrow: 0 }, }); -const TIMEOUT = 10000; class NetPyNE extends React.Component { - openPythonCallDialog (event) { - const payload = { - errorMessage: event.evalue, - errorDetails: event.traceback.join('\n'), - }; - this.props.pythonCallErrorDialogBox(payload); - } - - addMetadataToWindow (data) { - console.log('Initialising NetPyNE Tabs'); - window.metadata = data.metadata; - window.currentFolder = data.currentFolder; - window.isDocker = data.isDocker; - window.pythonConsoleLoaded = true; - window.tuts = data.tuts; + constructor (props) { + super(props); + this.openPythonCallDialog = this.openPythonCallDialog.bind(this); + this.kernelRestartState = { + state: "idle", + kernelID: undefined, + crashLoop: false + } } componentDidMount () { GEPPETTO.on(GEPPETTO.Events.Error_while_exec_python_command, this.openPythonCallDialog, this); - this.props.setDefaultWidgets(); - - GEPPETTO.on('jupyter_geppetto_extension_ready', (data) => { - const project = { - id: 1, - name: 'Project', - experiments: [{ - id: 1, - name: 'Experiment', - status: 'DESIGN', - }], - }; - GEPPETTO.Manager.loadProject(project, false); - GEPPETTO.Manager.loadExperiment(1, [], []); - - let responded = false; - Utils.execPythonMessage('from netpyne_ui.netpyne_geppetto import netpyne_geppetto'); - Utils.evalPythonMessage('netpyne_geppetto.getData', []) - .then((response) => { - responded = true; - - GEPPETTO.trigger(GEPPETTO.Events.Show_spinner, 'Loading NetPyNE-UI'); - const metadata = Utils.convertToJSON(response); - this.addMetadataToWindow(metadata); - this.props.setWidgets(EDIT_WIDGETS); - this.props.modelLoaded(); - GEPPETTO.trigger(GEPPETTO.Events.Hide_spinner); - }); - - setTimeout(() => { - if (!responded) { - GEPPETTO.trigger(GEPPETTO.Events.Show_spinner, 'Reloading Python Kernel'); - IPython.notebook.restart_kernel({ confirm: false }) - .then(() => window.location.reload()); + + const { + setDefaultWidgets, + } = this.props; + + setDefaultWidgets(); + + + + // Logic for kernel reinit + const handleKernelRestart = ({ detail: { kernel, type } }) => { + switch (this.kernelRestartState.state) { + case "restarting": + if (type === "kernel_ready" || type === "kernel_autorestarting") { + console.log("Replaying all commands since the beginning of the session") + replayAll(this.kernelRestartState.kernelID) + this.kernelRestartState = { + ...this.kernelRestartState, + state: "idle", + kernelID: undefined, + } + } + case "idle": + if (type === "kernel_connected") { + console.log("Kernel is connecting/starting, being init") + this.kernelRestartState = { + ...this.kernelRestartState, + state: "init", + kernelID: kernel.id + } + } + else if (type === "kernel_autorestarting") { + console.log("Kernel restart event caught, trying to re-init the current model") + this.kernelRestartState = { + ...this.kernelRestartState, + state: "restarting", + kernelID: kernel.id + } + if (!this.kernelRestartState.crashLoop) { + this.props.dispatchAction(openDialog({ + title: "Kernel restart", + message: "An action occured that made the kernel restart. We are reloading your model and all the actions you applied on it." + })) + } + } + else if (type === "kernel_restarting") { + console.log("Kernel restart, perhaps it's a special restart?") + this.kernelRestartState = { + ...this.kernelRestartState, + state: "special_restart", + kernelID: kernel.id + } + } + case "init": + if (type === "kernel_ready") { + console.log("Kernel properly initialized") + this.kernelRestartState = { + ...this.kernelRestartState, + state: "idle", + kernelID: undefined, + } + } + case "special_restart": + if (type == "kernel_autorestarting") { + console.log("Kernel autorestart after a start, we might not have the ready event, we force it then") + replayAll(this.kernelRestartState.kernelID) + this.kernelRestartState = { + ...this.kernelRestartState, + state: 'restarting', + kernelID: kernel.id, + } + } else { + console.log("Regular restart detected") + this.kernelRestartState = { + ...this.kernelRestartState, + state: 'idle', + kernelID: undefined, + } + } + } + } + window.addEventListener('kernelstatus', handleKernelRestart) + + // Dedicated code to handle crash loops + const kernelRestartLoopHandler = ( ) => { + if (!this.kernelRestartState.crashLoop) { + this.props.dispatchAction(openDialog({ + title: "Kernel restart loop stabilization", + message: "One of your actions triggered a kernel restart loop. We are trying to identify the faulty command and to restore your model until this point. Close this window and wait for the kernel stabilization notification." + })) + } else { + clearTimeout(this.kernelRestartState.crashLoop) + } + const taskID = setTimeout((_this) => { + this.props.dispatchAction(openDialog({ + title: "Kernel restart loop stabilized", + message: "The kernel is now stabilized." + })); + this.kernelRestartState = { + ...this.kernelRestartState, + crashLoop: false } - }, TIMEOUT); - }); + }, 8000, this) + this.kernelRestartState = { + ...this.kernelRestartState, + crashLoop: taskID + } + } + window.addEventListener('kernelRestartLoop', kernelRestartLoopHandler) } componentWillUnmount () { GEPPETTO.off(GEPPETTO.Events.Error_while_exec_python_command, this.openPythonCallDialog, this); } + openPythonCallDialog (event) { + if (event?.evalue && event?.traceback) { + this.props.pythonCallErrorDialogBox({ + errorMessage: event.evalue, + errorDetails: event.traceback.join('\n'), + }); + } else { + this.props.pythonCallErrorDialogBox({ + errorMessage: event.data.response.evalue, + errorDetails: event.data.response.traceback.join('\n'), + }); + } + } + render () { const { classes } = this.props; - if (!this.props.modelLoaded) { - return ''; - } + const Layout = LayoutManager(); return ( -
-
-
- -
- - - - + +
+
+
+ +
+ + + + + + + + - - - - - + +
+ + + +
- - -
+ ); } } diff --git a/webapp/components/definition/cellRules/NetPyNECellRules.js b/webapp/components/definition/cellRules/NetPyNECellRules.js index adc161a4..cfcb944b 100644 --- a/webapp/components/definition/cellRules/NetPyNECellRules.js +++ b/webapp/components/definition/cellRules/NetPyNECellRules.js @@ -86,6 +86,7 @@ export default class NetPyNECellRules extends React.Component { handleNewCellRule (defaultCellRules) { const key = Object.keys(defaultCellRules)[0]; const value = defaultCellRules[key]; + // eslint-disable-next-line react/no-access-state-in-setstate const model = { ...this.state.value }; // Get New Available ID @@ -337,6 +338,8 @@ export default class NetPyNECellRules extends React.Component { } componentDidUpdate (prevProps, prevState) { + if (this.props.commands !== prevProps.commands) + this.forceUpdate(); // we need to check if any of the three entities have been renamed and if that's the case change the state for the selection variable const newCellRuleName = this.hasSelectedCellRuleBeenRenamed( prevState, @@ -483,7 +486,7 @@ export default class NetPyNECellRules extends React.Component { if (page === 'main') { event.preventDefault(); this.setState({ anchorEl: event.currentTarget }); - // this.handleNewCellRule({ 'CellType': { 'conds':{}, 'secs':{} } }); + // this.handleNewCellRule({ CellType: { conds: {}, secs: {} } }); } else if (page === 'sections') { this.handleNewSection({ Section: { @@ -608,6 +611,7 @@ export default class NetPyNECellRules extends React.Component { name, ]) .then((response) => { + // eslint-disable-next-line react/no-access-state-in-setstate const model = this.state.value; delete model[this.state.selectedCellRule].secs[ this.state.selectedSection @@ -627,6 +631,7 @@ export default class NetPyNECellRules extends React.Component { name, ]) .then((response) => { + // eslint-disable-next-line react/no-access-state-in-setstate const model = this.state.value; delete model[this.state.selectedCellRule].secs[name]; this.setState({ @@ -804,6 +809,7 @@ export default class NetPyNECellRules extends React.Component { break; } default: { + break; } } return 'undefined'; diff --git a/webapp/components/definition/cellRules/SelectCellTemplate.js b/webapp/components/definition/cellRules/SelectCellTemplate.js index ff38d6cd..628b4ebe 100644 --- a/webapp/components/definition/cellRules/SelectCellTemplate.js +++ b/webapp/components/definition/cellRules/SelectCellTemplate.js @@ -1,12 +1,14 @@ import React, { Component } from 'react'; import Menu from '@material-ui/core/Menu'; import MenuItem from '@material-ui/core/MenuItem'; +import { connect } from 'react-redux'; +import { runControlledStep } from '../../../redux/actions/tutorials'; import Fab from '@material-ui/core/Fab'; import Tooltip from '../../general/Tooltip'; import Utils from '../../../Utils'; -export default class NetPyNENewPlot extends React.Component { +class NetPyNENewPlot extends React.Component { constructor (props) { super(props); this.handleClick = this.handleSelection.bind(this); @@ -14,6 +16,10 @@ export default class NetPyNENewPlot extends React.Component { this.state = { anchorEl: null }; } + componentDidMount() { + //this.props.dispatch(runControlledStep({ tourStep: 1 })); + } + handleButtonClick = (event) => { // This prevents ghost click. event.preventDefault(); @@ -42,8 +48,11 @@ export default class NetPyNENewPlot extends React.Component { handleButtonClick, anchorEl, clearAnchorEl, + tourRunning } = this.props; + const displayMenu = Boolean(anchorEl); + return (
@@ -52,6 +61,7 @@ export default class NetPyNENewPlot extends React.Component { style={{ width: 40, height: 40, + borderRadius: '50%', }} color={page == 'main' ? 'primary' : 'secondary'} onClick={(event) => handleButtonClick(event)} @@ -70,7 +80,7 @@ export default class NetPyNENewPlot extends React.Component { clearAnchorEl()} @@ -79,7 +89,6 @@ export default class NetPyNENewPlot extends React.Component { id="emptyCellTemplate" key="Empty" value="Empty" - onClick={() => this.handleSelection('Empty')} > Empty cell @@ -117,3 +126,11 @@ export default class NetPyNENewPlot extends React.Component { ); } } + +const mapStateToProps = (state) => { + return { + tourRunning: state.tutorial.tourRunning + }; +}; + +export default connect(mapStateToProps)(NetPyNENewPlot); diff --git a/webapp/components/definition/cellRules/sections/NetPyNESection.js b/webapp/components/definition/cellRules/sections/NetPyNESection.js index 67f7dc2c..ce33e805 100644 --- a/webapp/components/definition/cellRules/sections/NetPyNESection.js +++ b/webapp/components/definition/cellRules/sections/NetPyNESection.js @@ -276,7 +276,6 @@ export default class NetPyNESection extends React.Component { showLabels style={{ borderRadius: '4px' }} value={this.state.selectedIndex} - showLabels > {bottomNavigationItems} diff --git a/webapp/components/definition/cellRules/sections/mechanisms/NetPyNEMechanism.js b/webapp/components/definition/cellRules/sections/mechanisms/NetPyNEMechanism.js index e2691c70..20195872 100644 --- a/webapp/components/definition/cellRules/sections/mechanisms/NetPyNEMechanism.js +++ b/webapp/components/definition/cellRules/sections/mechanisms/NetPyNEMechanism.js @@ -37,7 +37,7 @@ export default class NetPyNEMechanism extends React.Component { name={name} model={`${tag}['${name}']`} label={name} - realType="float" + realType="func" /> )); diff --git a/webapp/components/definition/configuration/NetPyNESimConfig.js b/webapp/components/definition/configuration/NetPyNESimConfig.js index f71a26fb..919fae00 100644 --- a/webapp/components/definition/configuration/NetPyNESimConfig.js +++ b/webapp/components/definition/configuration/NetPyNESimConfig.js @@ -11,20 +11,22 @@ import { GridLayout, } from 'netpyne/components'; +const CONFIG_SECTIONS = { + GENERAL: 'General', + SAVE_CONFIGURATION: 'SaveConfiguration', + RECORD: 'Record', + NET_PARAMS: 'netParams', +}; + class NetPyNESimConfig extends React.Component { constructor (props) { super(props); this.state = { - model: props.model, selectedIndex: 0, - sectionId: 'General', + sectionId: CONFIG_SECTIONS.GENERAL, }; } - UNSAFE_componentWillReceiveProps (nextProps) { - this.setState({ model: nextProps.model }); - } - select = (index, sectionId) => this.setState({ selectedIndex: index, sectionId, @@ -34,7 +36,7 @@ class NetPyNESimConfig extends React.Component { let contentLeft =
; let contentRight =
; const { classes } = this.props; - if (this.state.sectionId == 'General') { + if (this.state.sectionId === CONFIG_SECTIONS.GENERAL) { contentLeft = (
@@ -69,19 +71,6 @@ class NetPyNESimConfig extends React.Component { - - - - - - -
); contentRight = ( @@ -172,7 +161,7 @@ class NetPyNESimConfig extends React.Component {
); - } else if (this.state.sectionId == 'SaveConfiguration') { + } else if (this.state.sectionId === CONFIG_SECTIONS.SAVE_CONFIGURATION) { contentLeft = (
@@ -254,7 +243,7 @@ class NetPyNESimConfig extends React.Component {
); - } else if (this.state.sectionId == 'Record') { + } else if (this.state.sectionId === CONFIG_SECTIONS.RECORD) { contentLeft = (
@@ -288,6 +277,14 @@ class NetPyNESimConfig extends React.Component { + + + + + + + + + + + + + + + + + + + + +
); - } else if (this.state.sectionId == 'netParams') { + } else if (this.state.sectionId === CONFIG_SECTIONS.NET_PARAMS) { contentLeft = (
@@ -405,28 +435,28 @@ class NetPyNESimConfig extends React.Component { > } onClick={() => this.select(0, 'General')} /> } onClick={() => this.select(1, 'Record')} /> } onClick={() => this.select(2, 'SaveConfiguration')} /> } onClick={() => this.select(3, 'netParams')} @@ -443,7 +473,6 @@ class NetPyNESimConfig extends React.Component { } const styles = ({ - shape, spacing, }) => ({ root: { @@ -462,6 +491,7 @@ const styles = ({ maxHeight: `calc(100vh - ${spacing(27)}px)`, overflowY: 'auto', }, + option: { color: 'white' }, }); export default withStyles(styles)(NetPyNESimConfig); diff --git a/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js b/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js index 7dd3c1d5..587f3b00 100644 --- a/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js +++ b/webapp/components/definition/connectivity/NetPyNEConnectivityRule.js @@ -198,12 +198,9 @@ export default class NetPyNEConnectivityRule extends React.Component { `netParams.connParams['${this.props.name}']['synMech']` } fullWidth + multiple method="netpyne_geppetto.getAvailableSynMech" - postProcessItems={(pythonData, selected) => pythonData.map((name) => ( - - {name} - - ))} + postProcessItems={this.postProcessMenuItems} /> diff --git a/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js b/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js index b1992425..d1b3b5ca 100644 --- a/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js +++ b/webapp/components/definition/connectivity/NetPyNEConnectivityRules.js @@ -34,7 +34,7 @@ export default class NetPyNEConnectivityRules extends Component { this.handleRenameChildren = this.handleRenameChildren.bind(this); } - handleToggle = () => this.setState({ drawerOpen: !this.state.drawerOpen }); + handleToggle = () => this.setState((prevState) => ({ drawerOpen: !prevState.drawerOpen })); selectPage (page) { this.setState({ page }); @@ -55,6 +55,7 @@ export default class NetPyNEConnectivityRules extends Component { // Get Key and Value const key = Object.keys(defaultConnectivityRules)[0]; const value = defaultConnectivityRules[key]; + // eslint-disable-next-line react/no-access-state-in-setstate const model = { ...this.state.value }; // Get New Available ID @@ -102,6 +103,8 @@ export default class NetPyNEConnectivityRules extends Component { } componentDidUpdate (prevProps, prevState) { + if (this.props.commands !== prevProps.commands) + this.forceUpdate(); // we need to check if any of the three entities have been renamed and if that's the case change the state for the selection variable const newConnectivityRuleName = this.hasSelectedConnectivityRuleBeenRenamed( prevState, @@ -246,7 +249,7 @@ export default class NetPyNEConnectivityRules extends Component { /> )); - var selectedConnectivityRule = undefined; + var selectedConnectivityRule; if ( this.state.selectedConnectivityRule !== undefined && Object.keys(model) diff --git a/webapp/components/definition/plots/NetPyNEInclude.js b/webapp/components/definition/plots/NetPyNEInclude.js index 07d36fcf..fbf7b8c6 100644 --- a/webapp/components/definition/plots/NetPyNEInclude.js +++ b/webapp/components/definition/plots/NetPyNEInclude.js @@ -67,11 +67,12 @@ export default class NetPyNEInclude extends Component { let answer = ''; if (include.exclusive) { return `${include.exclusive} -- ${data.gids} cells -- all NetStims`; - } if (include.groups.indexOf('allCells') > -1) { + } + if (include.groups.indexOf('allCells') > -1) { if (include.groups.indexOf('allNetStims') == -1) { return `allCells -- ${data.gids} cells`; } - return `${'all' + ' -- '}${data.gids} cells -- all NetStims`; + return `all -- ${data.gids} cells -- all NetStims`; } include.groups.forEach((group) => { if (group != 'allNetStims') { @@ -171,15 +172,15 @@ export default class NetPyNEInclude extends Component { }); if ((open || this.state.mainPopoverOpen) && !(open && this.state.mainPopoverOpen)) { - this.setState({ + this.setState((prevState) => ({ mainPopoverOpen: open, secondPopoverOpen: clone, - anchorEl: target || this.state.anchorEl, - }); + anchorEl: target || prevState.anchorEl, + })); } if (!open) { this.sendToPython(); - this.setState({ label: this.whoIsIncluded(this.state.include, this.state.data) }); + this.setState((prevState) => ({ label: this.whoIsIncluded(prevState.include, prevState.data) })); } }; @@ -195,11 +196,10 @@ export default class NetPyNEInclude extends Component { }); if (!this.checkEqual(clone, this.state.secondPopoverOpen)) { - this.setState({ + this.setState((prevState) => ({ secondPopoverOpen: clone, - anchorEl2: target || this.state.anchorEl, - }); - } else { + anchorEl2: target || prevState.anchorEl, + })); } }; @@ -318,6 +318,7 @@ export default class NetPyNEInclude extends Component { }; handleSecondaryMenusClick = (group, name, item) => { + // eslint-disable-next-line react/no-access-state-in-setstate const clone = { ...this.state.include }; if (group == 'gids') { clone[group].indexOf(item) == -1 ? clone[group].push(item) : clone[group].splice(clone[group].indexOf(item), 1); @@ -330,7 +331,6 @@ export default class NetPyNEInclude extends Component { if (clone.groups.indexOf(name) > -1) { // when selecting individuals, remove population selection clone.groups.splice(clone.groups.indexOf(name), 1); } - } else { } clone.exclusive = false; if (clone.groups.indexOf('allCells') > -1 && name != 'allNetStims') { @@ -342,7 +342,8 @@ export default class NetPyNEInclude extends Component { IsSecondaryMenuChecked = (group, name, index) => { if (group == 'gids') { return this.state.include[group].indexOf(index) > -1; - } if (group == 'popids') { + } + if (group == 'popids') { if (name in this.state.include[group]) { return this.state.include[group][name].indexOf(index) > -1; } diff --git a/webapp/components/definition/plots/NetPyNENewPlot.js b/webapp/components/definition/plots/NetPyNENewPlot.js index f6df1ee7..648cf1d2 100644 --- a/webapp/components/definition/plots/NetPyNENewPlot.js +++ b/webapp/components/definition/plots/NetPyNENewPlot.js @@ -28,7 +28,7 @@ export default class NetPyNENewPlot extends React.Component { return (
- + @@ -101,6 +101,13 @@ export default class NetPyNENewPlot extends React.Component { > Granger Causality Plot + this.handleClick('plotRateSpectrogram')} + > + Rate Spectrogram Plot +
); diff --git a/webapp/components/definition/plots/NetPyNEPlots.js b/webapp/components/definition/plots/NetPyNEPlots.js index cf9ecb02..0ffeb385 100644 --- a/webapp/components/definition/plots/NetPyNEPlots.js +++ b/webapp/components/definition/plots/NetPyNEPlots.js @@ -10,6 +10,7 @@ import PlotRaster from './plotTypes/PlotRaster'; import PlotTraces from './plotTypes/PlotTraces'; import PlotGranger from './plotTypes/PlotGranger'; import PlotRatePSD from './plotTypes/PlotRatePSD'; +import PlotRateSpectrogram from './plotTypes/PlotRateSpectrogram' import PlotSpikeHist from './plotTypes/PlotSpikeHist'; import PlotSpikeStats from './plotTypes/PlotSpikeStats'; import NetPyNENewPlot from './NetPyNENewPlot'; @@ -29,6 +30,11 @@ export default class NetPyNEPlots extends React.Component { this.handleNewPlot = this.handleNewPlot.bind(this); } + componentDidUpdate (prevProps, prevState) { + if (this.props.commands !== prevProps.commands) + this.forceUpdate(); + } + selectPlot (plot) { this.setState({ selectedPlot: plot }); } @@ -123,6 +129,9 @@ export default class NetPyNEPlots extends React.Component { case 'granger': selectedPlot = ; break; + case 'plotRateSpectrogram': + selectedPlot = ; + break; } return ( diff --git a/webapp/components/definition/plots/plotTypes/PlotRateSpectrogram.js b/webapp/components/definition/plots/plotTypes/PlotRateSpectrogram.js new file mode 100644 index 00000000..2c78b0e0 --- /dev/null +++ b/webapp/components/definition/plots/plotTypes/PlotRateSpectrogram.js @@ -0,0 +1,116 @@ +import React, { Component } from 'react'; +import Box from '@material-ui/core/Box'; +import { + NetPyNEInclude, + NetPyNEField, + SelectField, + NetPyNECheckbox, + NetPyNETextField, +} from 'netpyne/components'; +import TimeRange from '../TimeRange'; + +export default class PlotRateSpectrogram extends React.Component { + constructor (props) { + super(props); + this.state = { checked: false }; + this.handleCheckChange = this.handleCheckChange.bind(this); + } + + handleCheckChange = (event, isCheck) => { + this.setState({ Checked: isCheck }); + }; + + render () { + const tag = 'simConfig.analysis[\'plotRateSpectrogram\']'; + return ( + + + + + + + + + + + + + + + + + + + + + + + + + + + + {/* + + + + + + + + + + + + + + + + + + */} + + ); + } +} diff --git a/webapp/components/definition/populations/Dimensions.js b/webapp/components/definition/populations/Dimensions.js index 798f42ab..2bb72455 100644 --- a/webapp/components/definition/populations/Dimensions.js +++ b/webapp/components/definition/populations/Dimensions.js @@ -6,9 +6,9 @@ import Box from '@material-ui/core/Box'; import InputLabel from '@material-ui/core/InputLabel'; import FormControl from '@material-ui/core/FormControl'; - import { NetPyNEField, + ListComponent, NetPyNETextField, } from 'netpyne/components'; import Utils from '../../../Utils'; @@ -44,6 +44,10 @@ class DimensionsComponent extends Component { label: 'Grid spacing', value: 'gridSpacing', }, + { + label: 'Cell List', + value: 'cellsList', + }, ]; } @@ -52,7 +56,6 @@ class DimensionsComponent extends Component { this.updateLayout(); } } - componentWillUnmount () { this.mounted = false; } @@ -74,8 +77,8 @@ class DimensionsComponent extends Component { updateLayout () { const requests = this.popDimensionsOptions.map((popDimensionsOption) => // FIXME Better to wrap calls rather than directly accessing objects - Utils - .evalPythonMessage(`'${popDimensionsOption.value}' in netpyne_geppetto.netParams.popParams['${this.state.modelName}']`)); + // eslint-disable-next-line implicit-arrow-linebreak + Utils.evalPythonMessage(`'${popDimensionsOption.value}' in netpyne_geppetto.netParams.popParams['${this.state.modelName}']`)); // Get population dimension by asking each for each key Promise.all(requests) @@ -108,6 +111,7 @@ class DimensionsComponent extends Component { render () { const { classes } = this.props; + return (
@@ -139,22 +143,29 @@ class DimensionsComponent extends Component { this.state.dimension != undefined && this.state.dimension != '' && ( - - { - this.props.updateCards(); - }} + realType="list(dict)" /> - + ) : ( + + { + this.props.updateCards(); + }} + /> + + )} ) } diff --git a/webapp/components/definition/populations/NetPyNEPopulation.js b/webapp/components/definition/populations/NetPyNEPopulation.js index fa6061dd..a163db61 100644 --- a/webapp/components/definition/populations/NetPyNEPopulation.js +++ b/webapp/components/definition/populations/NetPyNEPopulation.js @@ -1,25 +1,35 @@ -import React from 'react'; +import React, { useState } from 'react'; import TextField from '@material-ui/core/TextField'; -import { BottomNavigation, BottomNavigationAction } from '@material-ui/core'; +import { BottomNavigation, BottomNavigationAction, Grid, Switch, Typography } from '@material-ui/core'; import FontIcon from '@material-ui/core/Icon'; import Box from '@material-ui/core/Box'; import Dialog from '@material-ui/core/Dialog/Dialog'; import Button from '@material-ui/core/Button'; import MenuItem from '@material-ui/core/MenuItem'; +import IconButton from '@material-ui/core/IconButton'; +import Icon from '@material-ui/core/Icon'; import DialogActions from '@material-ui/core/DialogActions'; import DialogContent from '@material-ui/core/DialogContent'; import DialogContentText from '@material-ui/core/DialogContentText'; import DialogTitle from '@material-ui/core/DialogTitle'; + import { withStyles } from '@material-ui/core/styles'; import { Dimensions, NetPyNEField, NetPyNECoordsRange, NetPyNESelectField, + NetPyNETextField, + ListComponent, + Tooltip, } from 'netpyne/components'; import Utils from '../../../Utils'; +import Checkbox from '../../general/Checkbox'; +import { vars } from '../../../theme'; +import { BASE_PATH } from '../../general/NetPyNEIcons'; +import { evalPythonMessage, execPythonMessage } from '../../general/GeppettoJupyterUtils'; const styles = ({ spacing }) => ({ fields: { @@ -28,8 +38,16 @@ const styles = ({ spacing }) => ({ }, }); +const { textColor, primaryColor, experimentLabelColor } = vars; +const newPulseObject = { + start: 0, + end: 0, + rate: 0, + noise: 0, +}; + class NetPyNEPopulation extends React.Component { - constructor (props) { + constructor(props) { super(props); this.state = { currentName: props.name, @@ -37,15 +55,38 @@ class NetPyNEPopulation extends React.Component { sectionId: 'General', errorMessage: undefined, errorDetails: undefined, + startParam: 'start', + model: undefined }; + + this.updateModel() + } + + updateModel = async (componentName) => { + const name = componentName ? componentName : this.props.name; + const command = `utils.convertToJS(netpyne_geppetto.netParams.popParams['${name}'])` + const response = await execPythonMessage(command) + this.setState({ model: response }) } - UNSAFE_componentWillReceiveProps (nextProps) { + UNSAFE_componentWillReceiveProps(nextProps) { this.setState({ currentName: nextProps.name, selectedIndex: 0, sectionId: 'General', }); + this.updateModel(nextProps.name) + } + + shouldComponentUpdate(nextProps, nextState) { + return ( + this.state.model == undefined + || this.state.currentName != nextState.currentName + || this.state.cellModelFields != nextState.cellModelFields + || this.state.sectionId != nextState.sectionId + || this.state.selectedIndex != nextState.selectedIndex + || this.state.model != nextState.model + ); } getModelParameters = () => { @@ -88,26 +129,16 @@ class NetPyNEPopulation extends React.Component { } modelParameters.push( } - onClick={() => select(3, 'CellList')} + key="Stimulation" + label="Stimulation" + icon={} + onClick={() => select(4, 'Stimulation')} />, ); return modelParameters; }; - shouldComponentUpdate (nextProps, nextState) { - return ( - this.state.model == undefined - || this.state.currentName != nextState.currentName - || this.state.cellModelFields != nextState.cellModelFields - || this.state.sectionId != nextState.sectionId - || this.state.selectedIndex != nextState.selectedIndex - ); - } - handleRenameChange = (event) => { const storedValue = this.props.name; const newValue = Utils.nameValidation(event.target.value); @@ -137,7 +168,7 @@ class NetPyNEPopulation extends React.Component { } }; - triggerUpdate (updateMethod) { + triggerUpdate(updateMethod) { // common strategy when triggering processing of a value change, delay it, every time there is a change we reset if (this.updateTimer != undefined) { clearTimeout(this.updateTimer); @@ -145,7 +176,7 @@ class NetPyNEPopulation extends React.Component { this.updateTimer = setTimeout(updateMethod, 1000); } - postProcessMenuItems (pythonData, selected) { + postProcessMenuItems(pythonData, selected) { return pythonData.map((name) => ( { + this.updateModel() + } + + changeCellPattern = (newValue) => { + if (!newValue) { + execPythonMessage(`del netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern']`) + } + else { + execPythonMessage(`netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern'] = {} +netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern']['type'] = '${newValue}'`) + } + this.updateModel() + } + + handleStartMaxChange = (newValue) => { + const maxIsSet = !(!newValue || newValue === '') + if (maxIsSet) { + const command = ` +pattern = netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern'] +pattern['start'], pattern['startMin'] = -1, pattern.get('start', '')` + execPythonMessage(command) + } else { + const command = ` +pattern = netpyne_geppetto.netParams.popParams['${this.props.name}']['spikePattern'] +pattern['start'] = pattern['startMin'] +del pattern['startMin']` + execPythonMessage(command) + } + + this.setState({ + startParam: maxIsSet ? "startMin" : "start" + }) + } + + rhythmicLayout = () => { + return <> + + Start + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + } + + evokedLayout = () => { + return <> + + + + + + + + + + + + + + } + + poissonLayout = () => { + return <> + + + + + + + + + + + } + + gaussLayout = () => { + return <> + + + + + + + + } + + changeStimulationPatternLayout = (pattern) => { + const patternKey = `${pattern}Layout`; + if (!(patternKey in this)) { + return <> + } + return this[patternKey]() + } + + addAnotherPulse = () => { + const command = ` +pulse = {'start': 0, 'end': 0, 'rate': 0, 'noise': 0} +netpyne_geppetto.netParams.popParams['${this.props.name}'].setdefault('pulses', []).append(pulse) +pulse` + execPythonMessage(command).then((_) => { + this.updateModel() + }) + }; + + removePulse = (index) => { + const command = ` +netpyne_geppetto.netParams.popParams['${this.props.name}']['pulses'].pop(${index})` + execPythonMessage(command).then((_) => { + this.updateModel() + }) + } + + displayPulses = () => { + if (!this.state.model || !this.state.model.pulses) { + return <> + } + return this.state.model.pulses.map((pulse, index) => ( + + + this.removePulse(index)}> + + + + + + + + + + + + + + + + + + + + + + + + {/* + this.removePulse(index)} > + + + */} + )) + } + + cellStimulationLayout = () => { + if (!this.state.model) { + return <> + } + if (!["VecStim", "NetStim"].includes(this.state.model.cellModel)) { + return <> + } + return <> + + + + + + + + + Spiking Pulse + + + {this.displayPulses()} + + + + + + + + + + + + + {/* + + */} + + + + + + + {this.changeStimulationPatternLayout(this.state.model?.spikePattern?.type)} + + + + } + + render() { + const { classes } = this.props; const dialogPop = this.state.errorMessage != undefined ? ( @@ -204,6 +599,7 @@ class NetPyNEPopulation extends React.Component {
); - } else if (this.state.sectionId == 'CellList') { + } else if (this.state.sectionId == 'Stimulation') { var content = ( -
Option to provide individual list of cells. Coming soon ...
+ + {/* + + + + + Override stimulation + + Stimulation is automatically set to the same configurations as the VectStim’s stimulation that has been set in ‘Stim. Sources’ + + + + */} + + + + + {this.cellStimulationLayout()} + + {/* + + + + */} + ); } else { var content =
{this.state.cellModelFields}
; diff --git a/webapp/components/definition/populations/NetPyNEPopulations.js b/webapp/components/definition/populations/NetPyNEPopulations.js index 07e4d08a..14a65022 100644 --- a/webapp/components/definition/populations/NetPyNEPopulations.js +++ b/webapp/components/definition/populations/NetPyNEPopulations.js @@ -33,7 +33,7 @@ export default class NetPyNEPopulations extends React.Component { this.handleRenameChildren = this.handleRenameChildren.bind(this); } - handleToggle = () => this.setState({ drawerOpen: !this.state.drawerOpen }); + handleToggle = () => this.setState((prevState) => ({ drawerOpen: !prevState.drawerOpen })); hasSelectedPopulationBeenRenamed (prevState, currentState) { const currentModel = prevState.value; @@ -145,6 +145,7 @@ export default class NetPyNEPopulations extends React.Component { // Get Key and Value const key = Object.keys(defaultPopulationValues)[0]; const value = defaultPopulationValues[key]; + // eslint-disable-next-line react/no-access-state-in-setstate const model = { ...this.state.value }; // Get New Available ID @@ -247,7 +248,7 @@ export default class NetPyNEPopulations extends React.Component { /> )); - var selectedPopulation = undefined; + var selectedPopulation; if ( this.state.selectedPopulation !== undefined && Object.keys(model) diff --git a/webapp/components/definition/stimulationSources/NetPyNEStimulationSource.js b/webapp/components/definition/stimulationSources/NetPyNEStimulationSource.js index a7a56383..0efdd557 100644 --- a/webapp/components/definition/stimulationSources/NetPyNEStimulationSource.js +++ b/webapp/components/definition/stimulationSources/NetPyNEStimulationSource.js @@ -16,9 +16,15 @@ import { NetPyNEField, NetPyNETextField, ListComponent, + NetPyNESelectField } from 'netpyne/components'; import Utils from '../../../Utils'; import Select from '../../general/Select'; +import Checkbox from '../../general/Checkbox'; +import { Grid, Typography } from '@material-ui/core'; +import { vars } from '../../../theme'; + +const { textColor, primaryColor, experimentLabelColor } = vars; const styles = ({ spacing }) => ({ selectField: { @@ -26,7 +32,11 @@ const styles = ({ spacing }) => ({ width: '100%', }, }); - +const newPulseObject = { + start: null, + end: null, + noise: null, +}; class NetPyNEStimulationSource extends React.Component { constructor (props) { super(props); @@ -35,6 +45,9 @@ class NetPyNEStimulationSource extends React.Component { sourceType: 'NetStim', errorMessage: undefined, errorDetails: undefined, + pulses: [{ + ...newPulseObject, + }], }; this.stimSourceTypeOptions = [ { type: 'NetStim' }, @@ -144,6 +157,13 @@ class NetPyNEStimulationSource extends React.Component { this.props.updateCards(); } + addAnotherPulse = () => { + this.setState((prevState) => ({ + ...prevState, // Spread the current state to retain other properties + pulses: [...prevState.pulses, { ...newPulseObject }], // Push the new object into the 'pulses' array + })); + }; + render () { const { classes } = this.props; const dialogPop = this.state.errorMessage != undefined ? ( @@ -417,6 +437,163 @@ class NetPyNEStimulationSource extends React.Component { return ( + {/* + + + + + + + + + + Spiking Pulse / Rate + + + { this.state.pulses.map((pulse, index) => ( + + + + + + + + + + ) + )} + + + + + + + + + + + + + + + + + + + + + + Start + + + + + + + + + + + + + + */}
{ const storedValue = this.props.name; @@ -147,7 +150,7 @@ export default class NetPyNEStimulationTarget extends React.Component { }; postProcessMenuItems = (pythonData, selectedStimSourceName) => { - if ((selectedStimSourceName != Object) & (selectedStimSourceName != '')) { + if ((selectedStimSourceName != Object) && (selectedStimSourceName != '')) { this.isStimSourceTypeNetStim(selectedStimSourceName); } return pythonData.map((name) => ( diff --git a/webapp/components/definition/stimulationTargets/NetPyNEStimulationTargets.js b/webapp/components/definition/stimulationTargets/NetPyNEStimulationTargets.js index 27a1d5a7..afb4e7f9 100644 --- a/webapp/components/definition/stimulationTargets/NetPyNEStimulationTargets.js +++ b/webapp/components/definition/stimulationTargets/NetPyNEStimulationTargets.js @@ -50,6 +50,7 @@ export default class NetPyNEStimulationTargets extends Component { }; const key = Object.keys(defaultStimulationTargets)[0]; const value = defaultStimulationTargets[key]; + // eslint-disable-next-line react/no-access-state-in-setstate const model = { ...this.state.value }; const StimulationTargetId = Utils.getAvailableKey(model, key); const newStimulationTarget = { @@ -93,6 +94,8 @@ export default class NetPyNEStimulationTargets extends Component { } componentDidUpdate (prevProps, prevState) { + if (this.props.commands !== prevProps.commands) + this.forceUpdate(); const newStimulationTargetName = this.hasSelectedStimulationTargetBeenRenamed( prevState, this.state, @@ -275,6 +278,7 @@ export default class NetPyNEStimulationTargets extends Component { overflow: 'visible', display: 'flex', justifyContent: 'center', + borderRadius: '50%', }} > Target diff --git a/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRule.js b/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRule.js new file mode 100644 index 00000000..75a89c04 --- /dev/null +++ b/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRule.js @@ -0,0 +1,541 @@ +import React from 'react'; +import TextField from '@material-ui/core/TextField'; +import FontIcon from '@material-ui/core/Icon'; +import { BottomNavigation, BottomNavigationAction } from '@material-ui/core'; +import Dialog from '@material-ui/core/Dialog/Dialog'; +import Button from '@material-ui/core/Button'; +import DialogActions from '@material-ui/core/DialogActions'; +import DialogContent from '@material-ui/core/DialogContent'; +import DialogContentText from '@material-ui/core/DialogContentText'; +import DialogTitle from '@material-ui/core/DialogTitle'; +import MenuItem from '@material-ui/core/MenuItem'; +import Box from '@material-ui/core/Box'; + +import { + NetPyNESelectField, + NetPyNEField, + NetPyNETextField, + ListComponent, + NetPyNECoordsRange, +} from 'netpyne/components'; +import Select from 'netpyne/components/general/Select'; +import Utils from '../../../Utils'; + +export default class NetPyNESubCellsConnectivityRule extends React.Component { + constructor (props) { + super(props); + this.state = { + currentName: props.name, + selectedIndex: 0, + sectionId: 'General', + errorMessage: undefined, + errorDetails: undefined, + type: undefined, + density: undefined, + coord: undefined, + }; + + this.postProcessDensity = this.postProcessDensity.bind(this); + } + + refreshComponent () { + // get initial values + Utils.evalPythonMessage(`netpyne_geppetto.netParams.subConnParams["${ + this.props.name + }"]`) + .then((response) => { + if ((typeof response === 'object') && (response.density)) { + this.setState({ type: response.density.type, density: response.density }); // splitting so it fires update + } + }); + } + + componentDidUpdate (prevProps, prevState) { + if (JSON.stringify(prevProps.model) != JSON.stringify(this.props.model)) this.refreshComponent(); + } + + componentDidMount () { + this.refreshComponent(); + } + + handleRenameChange = (event) => { + const storedValue = this.props.name; + const newValue = Utils.nameValidation(event.target.value); + const updateCondition = this.props.renameHandler(newValue); + const triggerCondition = Utils.handleUpdate( + updateCondition, + newValue, + event.target.value, + this, + 'ConnectionRule', + ); + + if (triggerCondition) { + this.triggerUpdate(() => { + // Rename the population in Python + Utils.renameKey( + 'netParams.subConnParams', + storedValue, + newValue, + (response, newValue) => { + this.renaming = false; + }, + ); + this.renaming = true; + }); + } + }; + + triggerUpdate (updateMethod) { + // common strategy when triggering processing of a value change, delay it, every time there is a change we reset + // eslint-disable-next-line eqeqeq + if (this.updateTimer !== undefined) { + clearTimeout(this.updateTimer); + } + this.updateTimer = setTimeout(updateMethod, 1000); + } + + select = (index, sectionId) => this.setState({ + selectedIndex: index, + sectionId, + }); + + getBottomNavigationAction (index, sectionId, label, icon, id) { + return ( + } + onClick={() => this.select(index, sectionId)} + /> + ); + } + + postProcessMenuItems (pythonData, selected) { + return pythonData.map((name) => ( + -1} + value={name} + > + {name} + + )); + } + + postProcessDensity (pythonData, selected) { + // TODO: the following line is a hack to handle the pythoncontrolledcapab that sometime return an array and sometime a string + if (typeof selected === 'string' || selected instanceof String) { + this.handleDensity(selected); + } else if (Array.isArray(selected) && selected.length > 0) { + this.handleDensity(selected[selected.length - 1]); + } + return pythonData.map((name) => ( + -1} + value={name} + > + {name} + + )); + } + + UNSAFE_componentWillReceiveProps (nextProps) { + this.setState({ currentName: nextProps.name, type: nextProps.model.density }); + } + + handleDensity (value) { + this.setState({ type: value }); + Utils.execPythonMessage( + `netpyne_geppetto.netParams.subConnParams['${this.props.name}']['density'] = { 'type': '${value}' }`, + ); + } + + handleCoord (value) { + this.setState({ coord: value }); + if (value === 'cartesian') { + Utils.execPythonMessage( + `netpyne_geppetto.netParams.subConnParams['${this.props.name}']['density']['coord'] = '${value}'`, + ); + Utils.execPythonMessage('netpyne_geppetto.netParams.defineCellShapes = True'); + } else { + Utils.execPythonMessage('netpyne_geppetto.netParams.defineCellShapes = False'); + Utils.execPythonMessage( + `del netpyne_geppetto.netParams.subConnParams['${this.props.name}']['density']['coord']`, + ); + } + } + + densityExtraFun () { + switch (this.state.type) { + case '2DMap': + case '1DMap': + Utils.execPythonMessage('netpyne_geppetto.netParams.defineCellShapes = True'); + return ( + <> + + + + {this.state.type === '2DMap' + ? ( + + + + ) : <>} + + + + + + + + + ); + case 'distance': + Utils.execPythonMessage('netpyne_geppetto.netParams.defineCellShapes = False'); + return ( + <> + + + + + + + + + + + + + + ); + default: + Utils.execPythonMessage('netpyne_geppetto.netParams.defineCellShapes = False'); + } + } + + render () { + const densityExtras = this.densityExtraFun(); + const dialogPop = this.state.errorMessage !== undefined ? ( + + + {this.state.errorMessage} + + + + {this.state.errorDetails} + + + + + + + ) : undefined; + + if (this.state.sectionId === 'General') { + var content = ( + + + + + + + pythonData.map((name) => ( + + {name} + + ))} + /> + + + + + + + + + + + {densityExtras} + + {dialogPop} + + ); + } else if (this.state.sectionId === 'Pre Conditions') { + var content = ( + + + + + + + + + + + + + + + + ); + } else if (this.state.sectionId === 'Post Conditions') { + var content = ( + + + + + + + + + + + + + + + + ); + } + + // Generate Menu + let index = 0; + const bottomNavigationItems = []; + bottomNavigationItems.push( + this.getBottomNavigationAction( + index++, + 'General', + 'General', + 'fa-bars', + 'generalConnTab', + ), + ); + bottomNavigationItems.push( + this.getBottomNavigationAction( + index++, + 'Pre Conditions', + 'Pre-synaptic cells conditions', + 'fa-caret-square-o-left', + 'preCondsConnTab', + ), + ); + bottomNavigationItems.push( + this.getBottomNavigationAction( + index++, + 'Post Conditions', + 'Post-synaptic cells conditions', + 'fa-caret-square-o-right', + 'postCondsConnTab', + ), + ); + + return ( +
+ + {bottomNavigationItems} + + {content} +
+ ); + } + + handleChange = (event, index, values) => this.setState({ values }); +} diff --git a/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js b/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js new file mode 100644 index 00000000..b828eced --- /dev/null +++ b/webapp/components/definition/subcellConnectivity/NetPyNESubcellsConnectivityRules.js @@ -0,0 +1,320 @@ +import React, { Component } from 'react'; +import Dialog from '@material-ui/core/Dialog/Dialog'; + +import Button from '@material-ui/core/Button'; +import { NetPyNEThumbnail, GridLayout, Filter } from 'netpyne/components'; +import Box from '@material-ui/core/Box'; +import Utils from '../../../Utils'; +import NetPyNEHome from '../../general/NetPyNEHome'; +import NetPyNEAddNew from '../../general/NetPyNEAddNew'; + +import NetPyNEConnectivityRule from './NetPyNESubcellsConnectivityRule'; + +import RulePath from '../../general/RulePath'; +import Accordion from '../../general/ExpansionPanel'; + +export default class NetPyNESubCellsConnectivityRules extends Component { + constructor (props) { + super(props); + this.state = { + drawerOpen: false, + selectedConnectivityRule: undefined, + deletedConnectivityRule: undefined, + page: 'main', + errorMessage: undefined, + errorDetails: undefined, + filterValue: null, + }; + + this.selectPage = this.selectPage.bind(this); + + this.selectConnectivityRule = this.selectConnectivityRule.bind(this); + this.handleNewConnectivityRule = this.handleNewConnectivityRule.bind(this); + + this.handleRenameChildren = this.handleRenameChildren.bind(this); + } + + handleToggle = () => this.setState((prevState) => ({ drawerOpen: !prevState.drawerOpen })); + + selectPage (page) { + this.setState({ page }); + } + + /* Method that handles button click */ + selectConnectivityRule (connectivityRule) { + this.setState({ selectedConnectivityRule: connectivityRule }); + } + + handleNewConnectivityRule () { + const defaultConnectivityRules = { + ConnectivityRule: { + preConds: {}, + postConds: {}, + }, + }; + // Get Key and Value + const key = Object.keys(defaultConnectivityRules)[0]; + const value = defaultConnectivityRules[key]; + // eslint-disable-next-line react/no-access-state-in-setstate + const model = { ...this.state.value }; + + // Get New Available ID + const connectivityRuleId = Utils.getAvailableKey(model, key); + const newConnectivityRule = { + name: connectivityRuleId, + ...value, + }; + // Create Cell Rule Client side + Utils.execPythonMessage( + `netpyne_geppetto.netParams.subConnParams["${ + connectivityRuleId + }"] = ${ + JSON.stringify(value)}`, + ); + model[connectivityRuleId] = newConnectivityRule; + // Update state + this.setState({ + value: model, + selectedConnectivityRule: connectivityRuleId, + }); + } + + hasSelectedConnectivityRuleBeenRenamed (prevState, currentState) { + const currentModel = prevState.value; + const model = currentState.value; + // deal with rename + if (currentModel != undefined && model != undefined) { + const oldP = Object.keys(currentModel); + const newP = Object.keys(model); + if (oldP.length == newP.length) { + // if it's the same lenght there could be a rename + for (let i = 0; i < oldP.length; i++) { + if (oldP[i] != newP[i]) { + if (prevState.selectedConnectivityRule != undefined) { + if (oldP[i] == prevState.selectedConnectivityRule) { + return newP[i]; + } + } + } + } + } + } + return undefined; + } + + componentDidUpdate (prevProps, prevState) { + // we need to check if any of the three entities have been renamed and if that's the case change the state for the selection variable + const newConnectivityRuleName = this.hasSelectedConnectivityRuleBeenRenamed( + prevState, + this.state, + ); + if (newConnectivityRuleName !== undefined) { + this.setState({ + selectedConnectivityRule: newConnectivityRuleName, + deletedConnectivityRule: undefined, + }); + } else if ( + prevState.value !== undefined + && Object.keys(prevState.value).length + !== Object.keys(this.state.value).length + ) { + /* + * logic into this if to check if the user added a new object from the python backend and + * if the name convention pass the checks, differently rename this and open dialog to inform. + */ + const model = this.state.value; + for (var m in model) { + if (prevState.value !== '' && !(m in prevState.value)) { + var newValue = Utils.nameValidation(m); + if (newValue != m) { + newValue = Utils.getAvailableKey(model, newValue); + model[newValue] = model[m]; + delete model[m]; + this.setState( + { + value: model, + errorMessage: 'Error', + errorDetails: + `Leading digits or whitespaces are not allowed in ConnectivityRule names.\n${ + m + } has been renamed ${ + newValue}`, + }, + () => { + Utils.renameKey( + 'netParams.subConnParams', + m, + newValue, + (response, newValue) => { + }, + ); + }, + ); + } + } + } + } + } + + shouldComponentUpdate (nextProps, nextState) { + const itemRenamed = this.hasSelectedConnectivityRuleBeenRenamed(this.state, nextState) + !== undefined; + let newItemCreated = false; + const selectionChanged = this.state.selectedConnectivityRule != nextState.selectedConnectivityRule; + const pageChanged = this.state.page != nextState.page; + const newModel = this.state.value == undefined; + if (!newModel) { + newItemCreated = Object.keys(this.state.value).length + != Object.keys(nextState.value).length; + } + const errorDialogOpen = this.state.errorDetails !== nextState.errorDetails; + const filterValueChanged = nextState.filterValue !== this.state.filterValue; + return ( + filterValueChanged + || newModel + || newItemCreated + || itemRenamed + || selectionChanged + || pageChanged + || errorDialogOpen + ); + } + + handleRenameChildren (childName) { + childName = childName.replace(/\s*$/, ''); + const childrenList = Object.keys(this.state.value); + for (let i = 0; childrenList.length > i; i++) { + if (childName === childrenList[i]) { + return false; + } + } + return true; + } + + getCopyPath () { + const { + value: model, + selectedConnectivityRule, + } = this.state; + return ( + model + && model[selectedConnectivityRule] + && `netParams.subConnParams["${selectedConnectivityRule}"]` + ); + } + + render () { + const actions = [ + + + + + + + setTrialNumberErrorDialogOpen({ condition: false, number: 1 })} + textForDialog={{ + heading: 'Error - Number of conditions is too large', + content: `Please change your exploration parameters to + reduce the number of experimental conditions to less than 100. Last number of conditions: ${trialNumberErrorDialogOpen.number}`, + }} + /> + + ); +}; + +export default withStyles(useStyles)(ExperimentEdit); diff --git a/webapp/components/experiments/ExperimentEditStyle.js b/webapp/components/experiments/ExperimentEditStyle.js new file mode 100644 index 00000000..ca2bcbc8 --- /dev/null +++ b/webapp/components/experiments/ExperimentEditStyle.js @@ -0,0 +1,242 @@ +import { + bgDarkest, + bgLight, + bgRegular, + secondaryColor, + fontColor, + radius, + primaryColor, + experimentInputColor, + experimentFieldColor, + experimentSvgColor, + experimentLabelColor, + experimentAutocompleteBorder, + errorFieldBorder, +} from '../../theme'; + +/** + * Edit/Add view of a single Experiment. + * + * @return {JSX.Element} + * @constructor + */ +const useStyles = (theme) => ({ + root: { + '& .editExperimentContainer': { + '& .editExperimentContent': { + overflow: 'auto', + maxHeight: 'calc(100vh - 400px)', + '& .MuiTypography-body2': { + opacity: '0.54', + }, + }, + }, + '& .editExperimentBack': { + display: 'flex', + cursor: 'pointer', + paddingLeft: theme.spacing(1), + '& .MuiTypography-root': { + marginLeft: theme.spacing(1), + }, + }, + '& .editExperimentBreadcrumb': { + display: 'flex', + justifyContent: 'space-between', + alignItems: 'center', + '& .MuiButton-startIcon': { + marginRight: theme.spacing(0.4), + }, + }, + '& .editExperimentAutocomplete': { + '& .MuiInputLabel-outlined.MuiInputLabel-shrink': { + transform: 'translate(14px, 9px) scale(0.75)', + }, + '& .MuiAutocomplete-input': { + padding: '1rem 0.25rem 0.188rem', + }, + }, + '& .editExperimentList': { + display: 'flex', + marginBottom: theme.spacing(1), + width: '100%', + }, + '& .MuiTypography-body2': { + fontSize: '1rem', + }, + '& .editExperimentDefault': { + paddingLeft: theme.spacing(1), + overflow: 'auto', + }, + '& .editExperimentHead': { + paddingLeft: theme.spacing(1), + }, + '& .editExperimentGroup': { + background: bgDarkest, + borderRadius: theme.spacing(0.4), + padding: theme.spacing(2, 0), + '& .scrollbar': { + '&::-webkit-scrollbar-thumb': { + background: secondaryColor, + borderLeft: `${radius} solid ${bgDarkest}`, + borderRight: `${radius} solid ${bgDarkest}`, + }, + '&::-webkit-scrollbar': { + width: theme.spacing(2), + }, + }, + '& .editExperimentBreadcrumb': { + paddingLeft: '0.625rem', + }, + '& .editExperimentRow': { + paddingLeft: theme.spacing(4), + position: 'relative', + overflow: 'auto', + maxHeight: '25vh', + '&:before': { + background: bgLight, + content: '""', + height: '100%', + width: '0.125rem', + margin: 0, + display: 'block', + position: 'absolute', + left: '0.875rem', + }, + }, + '& .MuiFilledInput-root': { + background: experimentFieldColor, + }, + '& .MuiOutlinedInput-root': { + background: experimentFieldColor, + }, + }, + '& .MuiAutocomplete-root': { + width: '100% !important', + }, + '& .MuiPopover-root': { + '& .MuiPaper-root': { + '& .MuiList-root': { + '& .MuiMenuItem-gutters': { + paddingLeft: theme.spacing(2), + paddingRight: theme.spacing(2), + }, + }, + }, + }, + '& .MuiPopover-experiment': { + width: theme.spacing(14), + }, + '& .MuiFormControl-root': { + width: '100%', + }, + '& .MuiOutlinedInput-root': { + background: experimentInputColor, + }, + '& .MuiFilledInput-root': { + borderRadius: radius, + background: experimentInputColor, + border: '1px solid transparent', + '&.Mui-error': { + borderColor: errorFieldBorder, + boxShadow: '0 0 0 2px rgba(242, 69, 61, 0.2)', + }, + }, + '& .MuiOutlinedInput-notchedOutline': { + border: '0 !important', + }, + '& .MuiFilledInput-underline': { + '&:after, &:before': { + display: 'none', + }, + }, + '& .MuiFormLabel-root': { + fontWeight: 'normal', + color: fontColor, + opacity: '0.54', + '&.MuiInputLabel-shrink': { + color: experimentLabelColor, + opacity: '0.87', + }, + }, + '& .MuiTypography-colorPrimary': { + borderBottom: `${primaryColor} 1px solid`, + display: 'inline-flex', + color: primaryColor, + cursor: 'pointer', + marginLeft: theme.spacing(1), + '&:hover': { + textDecoration: 'none', + }, + '& .MuiSvgIcon-root': { + fontSize: '1rem', + marginTop: theme.spacing(0.4), + }, + }, + '& .editExperimentFooter': { + position: 'absolute', + left: 0, + bottom: 0, + right: 0, + display: 'flex', + justifyContent: 'flex-end', + alignItems: 'center', + background: bgRegular, + boxShadow: '0 -7px 13px -4px rgb(0, 0, 0, 0.6)', + padding: theme.spacing(2.5), + zIndex: 100, + '& .MuiButton-root': { + minWidth: theme.spacing(11), + padding: theme.spacing(0.4), + marginLeft: theme.spacing(1), + borderRadius: '2px', + cursor: 'pointer', + textTransform: 'uppercase', + }, + '& .MuiButton-textSecondary': { + color: fontColor, + }, + }, + '& .editExperimentWarning': { + paddingLeft: '0.625rem', + '& .MuiTypography-root': { + color: experimentLabelColor, + }, + '& .MuiTypography-caption': { + fontSize: '0.875rem', + }, + }, + '& .editExperimentField': { + '& .MuiFormControl-root': { + overflow: 'hidden', + '& .MuiFormLabel-root': { + whiteSpace: 'noWrap', + }, + }, + }, + '& .MuiFormHelperText-contained': { + marginLeft: 0, + }, + '& .MuiFormHelperText-root': { + fontSize: '0.875rem', + lineHeight: '100%', + }, + }, + popper: { + marginTop: -theme.spacing(1), + '& .MuiPaper-root': { + boxShadow: '0px 5px 5px -3px rgba(0, 0, 0, 0.2), 0px 8px 10px 1px rgba(0, 0, 0, 0.14), 0px 3px 14px 2px rgba(0, 0, 0, 0.12)', + borderRadius: `0 0 ${radius} ${radius}`, + borderTop: `1px solid ${experimentAutocompleteBorder}`, + }, + '& .MuiSvgIcon-root': { + color: experimentSvgColor, + }, + '& .MuiAutocomplete-option': { + paddingLeft: theme.spacing(2), + color: fontColor, + paddingRight: theme.spacing(1), + }, + }, +}); + +export default useStyles; diff --git a/webapp/components/experiments/ExperimentHelper.js b/webapp/components/experiments/ExperimentHelper.js new file mode 100644 index 00000000..d7902bc8 --- /dev/null +++ b/webapp/components/experiments/ExperimentHelper.js @@ -0,0 +1,137 @@ +import { REAL_TYPE } from '../../constants'; + +/** + * Converts a value based on `type` of the netpyne metadata `field`. + * + * @param {*} field metadata field of netpyne. + * @param {*} value value to be converted to proper type. + * @returns value converted to `type`. + */ +export const convertFieldValue = (field, value) => { + if (field == null) { + return value; + } + + switch (field.type) { + case REAL_TYPE.INT: + case REAL_TYPE.FLOAT: + case REAL_TYPE.FUNC: + return Number(value); + + case REAL_TYPE.STR: + return String(value); + + case REAL_TYPE.BOOL: + return Boolean(value); + + case REAL_TYPE_FLOAT: + return validLocale(value); + + default: + // .. handling of more types + // list(float), dict, list(list(float)), func + return value; + } +}; + +function getLocale() { + if (navigator.languages != undefined) + return navigator.languages[0]; + return navigator.language; +} +function validLocale(num) { + const locale = getLocale(); + return Intl.NumberFormat(locale).format(num); +} + +export const isValidValue = (value, type) => { + if (type == null) { + return false; + } + + let validate; + + switch (type) { + case REAL_TYPE.INT: + validate = (el) => el !== '' && !Number.isNaN(Number(el)) && Number.isInteger(Number(el)); + break; + + case REAL_TYPE.FLOAT: + validate = (el) => el !== '' && !Number.isNaN(Number(el)); + break; + + case REAL_TYPE.STR: + validate = (el) => String(el); + break; + + case REAL_TYPE.BOOL: + validate = (el) => Boolean(el); + break; + + case REAL_TYPE.FUNC: + // const valid = await Utils.evalPythonMessage('netpyne_geppetto.validateFunction', [el]); + validate = (el) => true; + break; + + default: + // .. handling of more types + // list(float), dict, list(list(float)), func + validate = (el) => false; + break; + } + + return validate(value); +}; + +export const getErrorText = (type) => { + switch (type) { + case REAL_TYPE.INT: + return 'Only integer values are allowed'; + + case REAL_TYPE.FLOAT: + return 'Float or int values allowed'; + + case REAL_TYPE.STR: + return 'Only string values are allowed'; + + case REAL_TYPE.BOOL: + return 'Only bool values (true|false) are allowed'; + + case REAL_TYPE.FUNC: + return 'Not a valid function'; + + default: + // .. handling of more types + // list(float), dict, list(list(float)), func + return 'Unkown error, field type is not supported'; + } +}; + +export const validateListParameter = (parameter) => { + let { values } = parameter; + const { field } = parameter; + + const validValue = values.every((element) => isValidValue(element, field?.type)); + if (validValue) { + values = values.map((el) => convertFieldValue(field, el)); + } + + return { + ...parameter, + values, + error: !validValue, + helperText: validValue ? '' : getErrorText(parameter.field.type), + }; +}; + +export const validateRangeParameter = (parameter, val, key) => { + const validValue = isValidValue(val, parameter.field ? parameter.field.type : null); + + return { + ...parameter, + [`${key}Val`]: val, + [key]: validValue ? convertFieldValue(parameter.field, val) : val, + [`${key}error`]: !validValue, + [`${key}helperText`]: validValue ? '' : getErrorText(parameter?.field?.type), + }; +}; diff --git a/webapp/components/experiments/ExperimentManager.js b/webapp/components/experiments/ExperimentManager.js new file mode 100644 index 00000000..26f0b033 --- /dev/null +++ b/webapp/components/experiments/ExperimentManager.js @@ -0,0 +1,63 @@ +import React, { useState } from 'react'; +import { Experiments, ExperimentEdit } from '../index'; + +import ViewExperiment from './ExperimentView'; +import JsonViewer from '../general/JsonViewer'; +import { EXPERIMENT_VIEWS } from '../../constants'; + +const ExperimentManager = (props) => { + const [editState, setEditState] = useState(false); + const [experimentName, setExperimentName] = useState(null); + const [trial, setTrial] = useState(null); + const [trialJSON, setTrialJSON] = useState(null); + const [view, setView] = useState(EXPERIMENT_VIEWS.list); + + + const viewHandler = () => { + switch (view) { + case EXPERIMENT_VIEWS.list: return ( + + ); + case EXPERIMENT_VIEWS.viewExperiment: return ( + + ); + case EXPERIMENT_VIEWS.jsonViewer: return ( + + ); + case EXPERIMENT_VIEWS.edit: return ( + + ); + + default: return ( + + ); + } + }; + return ( + <>{ viewHandler() } + ); +}; + +export default ExperimentManager; diff --git a/webapp/components/experiments/ExperimentRowFilter.js b/webapp/components/experiments/ExperimentRowFilter.js new file mode 100644 index 00000000..f24e7297 --- /dev/null +++ b/webapp/components/experiments/ExperimentRowFilter.js @@ -0,0 +1,201 @@ +import React from 'react'; +import { withStyles } from '@material-ui/core/styles'; +import { + Popover, + InputLabel, + MenuItem, + FormControl, + Select, + Link, + Box, + Grid, + TextField, + IconButton, +} from '@material-ui/core'; +import AddIcon from '@material-ui/icons/Add'; +import DeleteIcon from '@material-ui/icons/Delete'; +import { + fontColor, + primaryColor, + secondaryColor, + radius, + experimentGrey, + experimentInputColor, + experimentLabelColor, + errorFieldBorder, +} from '../../theme'; + +const useStyles = (theme) => ({ + root: { + '& .filter-row': { + display: 'flex', + alignItems: 'center', + '& .MuiGrid-root': { + paddingRight: theme.spacing(1), + flexGrow: 1, + }, + }, + '& .MuiSvgIcon-delete': { + borderRadius: theme.spacing(0.4), + alignSelf: 'center', + color: experimentGrey, + marginLeft: 'auto', + marginRight: 'auto', + padding: `${theme.spacing(0.6)}px ${theme.spacing(1)}px`, + '& svg': { + fontSize: '1.3rem', + }, + }, + '&.MuiPopover-filter': { + '& .MuiPopover-paper': { + '&::-webkit-scrollbar-thumb': { + background: secondaryColor, + height: '0.5rem', + borderRadius: '0.5rem', + }, + '&::-webkit-scrollbar': { + width: '0.5rem', + height: '0.5rem', + borderRadius: '0.5rem', + }, + }, + '& .popoverFormControl': { + width: '40rem', + padding: '1rem', + '& .MuiLink-root': { + color: primaryColor, + display: 'inline-flex', + alignItems: 'center', + fontSize: '1rem', + cursor: 'pointer', + borderBottom: `1px solid ${primaryColor}`, + '&:hover': { + textDecoration: 'none', + }, + '& .MuiSvgIcon-root': { + fontSize: '1.1rem', + marginRight: '0.15rem', + marginLeft: '-0.15rem', + }, + }, + '& .MuiOutlinedInput-root': { + background: experimentInputColor, + }, + '& .MuiFormControl-fullWidth': { + marginBottom: '0.5rem', + }, + '& .MuiFilledInput-root': { + borderRadius: radius, + background: experimentInputColor, + border: '1px solid transparent', + '&.Mui-error': { + borderColor: errorFieldBorder, + boxShadow: '0 0 0 2px rgba(242, 69, 61, 0.2)', + }, + }, + '& .MuiOutlinedInput-notchedOutline': { + border: '0 !important', + }, + '& .MuiFilledInput-underline': { + '&:after, &:before': { + display: 'none', + }, + }, + '& .MuiFormLabel-root': { + fontWeight: 'normal', + color: fontColor, + opacity: '0.54', + '&.MuiInputLabel-shrink': { + color: experimentLabelColor, + opacity: '0.87', + }, + }, + }, + }, + }, +}); + +const ExperimentRowFilter = (props) => { + const { + filter, + paramHeaders, + setParameterValue, + filterParameterChange, + anchorEl, + setAnchorEl, + classes, + addFilterRow, + removeFilter, + } = props; + + const open = Boolean(anchorEl); + const id = open ? 'simple-popover' : undefined; + const popoverhandleClose = () => { + setAnchorEl(null); + }; + + return ( + + + {filter.map((paramFilter, index) => ( + + + + + Parameter + + + + + + setParameterValue(e.target.value, index)} + /> + + + + removeFilter(index)}> + + + + ))} + + + + Add Filter + + + + + ); +}; + +export default withStyles(useStyles)(ExperimentRowFilter); diff --git a/webapp/components/experiments/ExperimentView.js b/webapp/components/experiments/ExperimentView.js new file mode 100644 index 00000000..c7208acd --- /dev/null +++ b/webapp/components/experiments/ExperimentView.js @@ -0,0 +1,662 @@ +import React, { useState, useEffect } from 'react'; +import { withStyles } from '@material-ui/core/styles'; +import PropTypes from 'prop-types'; +import { + Box, + Table, + TableBody, + Button, + IconButton, + TableCell, + TableHead, + TableRow, + TableSortLabel, + TableContainer, + Divider, + Typography, + TablePagination, +} from '@material-ui/core'; +import ArrowBackIcon from '@material-ui/icons/ArrowBack'; +import CodeIcon from '@material-ui/icons/Code'; +import ReplayIcon from '@material-ui/icons/Replay'; +import AssessmentIcon from '@material-ui/icons/Assessment'; +import ArrowDropDownIcon from '@material-ui/icons/ArrowDropDown'; +import FilterListIcon from '@material-ui/icons/FilterList'; +import { EXPERIMENT_TEXTS, EXPERIMENT_VIEWS } from 'root/constants'; +import DialogBox from 'root/components/general/DialogBox'; +import { useDispatch } from 'react-redux'; +import { viewExperimentResults, loadTrialModelSpec } from 'root/redux/actions/experiments'; +import * as ExperimentsApi from 'root/api/experiments'; +import Tooltip from 'root/components/general/Tooltip'; +import { + bgRegular, + bgDarker, + bgLight, + canvasBgLight, + bgInputs, + primaryColor, + experimentGrey, + secondaryColor, + fontColor, +} from '../../theme'; +import ExperimentRowFilter from './ExperimentRowFilter'; +import { stableSort, getComparator } from './utils'; +import Loader from '../general/Loader'; +import { EXPERIMENT_STATE } from '../../constants'; + +const useStyles = (theme) => ({ + table: { + minWidth: 650, + }, + sticky: { + position: 'sticky', + left: 0, + zIndex: 50, + }, + stickyRight: { + position: 'sticky', + right: 0, + textAlign: 'right', + '& .MuiSortIcon': { + display: 'none', + }, + }, + root: { + width: 'auto !important', + flexDirection: 'column', + marginLeft: -theme.spacing(1), + marginRight: -theme.spacing(1), + + '& .primary-loader': { + display: 'flex', + alignItems: 'center', + justifyContent: 'center', + flexDirection: 'column', + fontWeight: '500', + color: fontColor, + fontSize: '1rem', + height: '30rem', + }, + + '& .editExperiment-filter': { + display: 'flex', + alignItems: 'center', + + '& .MuiSvgIcon-replay': { + transform: 'rotate(-65deg)', + }, + '& .MuiButton-root': { + minWidth: 'inherit', + marginLeft: theme.spacing(1.2), + }, + }, + '& .MuiTablePagination-root': { + overflow: 'initial', + + '& .MuiTypography-body2': { + fontSize: '0.875rem', + }, + }, + '& .MuiTablePagination-select': { + fontSize: '0.875rem', + color: experimentGrey, + paddingTop: theme.spacing(0), + paddingBottom: theme.spacing(0), + }, + '& .MuiTablePagination-selectRoot': { + '& .MuiSelect-icon': { + color: experimentGrey, + }, + }, + '& .MuiTablePagination-actions': { + paddingRight: theme.spacing(3), + '& .MuiIconButton-root': { + padding: '0.25rem', + marginLeft: theme.spacing(2.6), + color: experimentGrey, + '&.Mui-disabled': { + opacity: 0.3, + }, + '&:hover': { + borderRadius: theme.spacing(0.4), + }, + }, + }, + '& .ViewExperimentHead': { + paddingLeft: theme.spacing(4), + paddingRight: theme.spacing(4), + display: 'flex', + justifyContent: 'space-between', + alignItems: 'center', + }, + '& .editExperiment-trials': { + display: 'flex', + alignItems: 'center', + justifyContent: 'flex-end', + background: bgDarker, + padding: theme.spacing(1, 4), + '& .MuiTypography-h5': { + fontSize: '1rem', + color: fontColor, + marginLeft: theme.spacing(1), + marginRight: theme.spacing(0.5), + }, + }, + '& .editExperimentBack': { + display: 'flex', + cursor: 'pointer', + '& .MuiTypography-root': { + marginLeft: theme.spacing(1), + }, + }, + '& .MuiTypography-body2': { + fontSize: '1rem', + }, + '& .MuiDivider-vertical': { + height: theme.spacing(4), + background: 'rgba(255, 255, 255, 0.3)', + }, + '& .MuiTableContainer-root': { + '&::-webkit-scrollbar-thumb': { + background: secondaryColor, + height: theme.spacing(0.8), + }, + '&::-webkit-scrollbar': { + width: theme.spacing(0.8), + height: theme.spacing(0.8), + }, + '& .MuiTableCell-root': { + padding: theme.spacing(1.4, 4), + '&:first-child': { + '& .MuiSortIcon': { + display: 'none', + }, + }, + }, + '& .MuiTableRow-colspan': { + '& .MuiTableCell-root': { + background: bgDarker, + padding: theme.spacing(1), + }, + '& .MuiBox-root': { + display: 'flex', + alignItems: 'center', + fontSize: '0.75rem', + fontWeight: '500', + color: experimentGrey, + '& .MuiSvgIcon-root': { + fontSize: '0.813rem', + marginRight: theme.spacing(1), + }, + }, + }, + '& .MuiTableCell-actions': { + display: 'flex', + alignItems: 'center', + justifyContent: 'flex-end', + '& .MuiIconButton-root': { + padding: '0.25rem', + marginLeft: theme.spacing(2.6), + color: experimentGrey, + '&:hover': { + borderRadius: theme.spacing(0.4), + }, + }, + '& .MuiDivider-root': { + marginLeft: theme.spacing(2.6), + }, + '& .MuiSvgIcon-assessment': { + color: primaryColor, + }, + '& .MuiSvgIcon-replay': { + fontSize: '1.2rem', + transform: 'rotate(-65deg)', + }, + }, + '& .MuiTableRow-head': { + '& .MuiTableSortLabel-icon': { + display: 'none', + }, + '& .MuiSortIcon': { + '&[direction="desc"]': { + transform: 'rotate(180deg)', + }, + }, + '& .MuiTableCell-root': { + background: bgLight, + color: experimentGrey, + fontWeight: '700', + whiteSpace: 'nowrap', + borderBottom: `1px solid ${bgInputs}`, + }, + }, + '& .MuiTableRow-root': { + '& .MuiTableCell-root': { + color: experimentGrey, + fontWeight: '700', + background: bgRegular, + fontSize: '0.875rem', + }, + }, + '& .MuiTableBody-root': { + '& .MuiTableCell-root': { + '&.MuiTableCell-paddingNone': { + color: canvasBgLight, + fontSize: '1rem', + fontWeight: '500', + }, + }, + }, + }, + }, +}); + +function EnhancedTableHead (props) { + const { + order, + orderBy, + onRequestSort, + classes, + paramHeaders, + experimentFinished, + } = props; + const createSortHandler = (property) => (event) => { + onRequestSort(event, property); + }; + + const headCells = [ + { + id: 'name', + numeric: false, + disablePadding: true, + label: 'EXPERIMENTAL CONDITIONS', + }, + ...paramHeaders, + ]; + + if (experimentFinished) { + headCells.push({ + id: 'status', + numeric: false, + disablePadding: false, + label: 'Actions', + }); + } + + return ( + + + {headCells.map((headCell, index) => ( + + + {headCell.label} + + + + ))} + + + ); +} + +EnhancedTableHead.propTypes = { + onRequestSort: PropTypes.func.isRequired, + order: PropTypes.oneOf(['asc', 'desc']).isRequired, + orderBy: PropTypes.string.isRequired, +}; + +const ExperimentView = (props) => { + const { + classes, + name, + setTrial, + setTrialJSON, + setView, + } = props; + const dispatch = useDispatch(); + const [order, setOrder] = useState('asc'); + const [orderBy, setOrderBy] = useState('name'); + const [tableRows, setTableRows] = useState([]); + const [filteredRows, setFilteredRows] = useState(tableRows); + const [experiment, setExperiment] = useState(null); + const [paramHeaders, setParamHeaders] = useState([]); + const [page, setPage] = useState(0); + const [rowsPerPage, setRowsPerPage] = useState(10); + const [loadResultsDialogOpen, setLoadResultsDialogOpen] = useState(false); + const [loadModelSpecDialogOpen, setLoadModelSpecDialogOpen] = useState(false); + const [selectedTrial, setSelectedTrial] = useState({ + experiment: null, + trial: null, + }); + const [loading, setLoading] = useState(false); + + const experimentFinished = experiment?.state === EXPERIMENT_STATE.SIMULATED || experiment?.state === EXPERIMENT_STATE.INSTANTIATED; + + const handleRequestSort = (event, property) => { + const isAsc = orderBy === property && order === 'asc'; + setOrder(isAsc ? 'desc' : 'asc'); + setOrderBy(property); + }; + + const [anchorEl, setAnchorEl] = useState(''); + const popoverhandleClick = (event) => { + setAnchorEl(event.currentTarget); + }; + + const filterObj = { + param: '', + value: '', + }; + const [filter, setFilter] = useState([filterObj]); + + const addFilterRow = () => { + setFilter([...filter, filterObj]); + }; + + const filterRows = (arr, criteria) => { + let count; + const filterWithoutEmpties = criteria.filter((f) => f.param && f.value); + if (filterWithoutEmpties.length > 0) { + // Helper function to loop through the filter criteria to find matching values + // Each filter criteria is treated as "AND" + const matchesFilter = (item) => { + count = 0; + // for filtering consider only those filter criterias where both parameter + // and value has been provided + filterWithoutEmpties.forEach((f) => { + if (Number(f.value) === item[f.param]) { + count += 1; + } + }); + // If TRUE, then the current item in the array meets all the filter criteria + return count === filterWithoutEmpties.length; + }; + return arr.filter((item) => matchesFilter(item)); + } + return arr; + }; + + const setParameterValue = (val, index) => { + const newFilter = [...filter]; + newFilter[index] = { + ...filter[index], + value: val, + }; + setPage(0); + setFilter(newFilter); + setFilteredRows(filterRows(tableRows, newFilter)); + }; + + const filterParameterChange = (val, index) => { + const newFilter = [...filter]; + newFilter[index] = { + param: val, + value: '', + }; + setFilter(newFilter); + }; + + useEffect(() => { + if (name) { + setLoading(true); + ExperimentsApi.getExperiment(name) + .then((exp) => { + setExperiment(exp); + if (exp?.trials.length > 0) { + if (exp?.trials[0].params.length > 0) { + setParamHeaders( + Object.keys(exp?.trials[0]?.params[0]) + .map((header) => ({ + id: header, + numeric: true, + disablePadding: false, + label: header, + })), + ); + } + + const rows = exp?.trials.map((trial, _) => ({ + id: trial.id, + name: trial.name, + ...trial.params.length > 0 ? trial.params[0] : [], + })); + + setTableRows(rows); + setFilteredRows(rows); + } + setLoading(false); + }) + .catch((error) => console.error(error)); + } + }, [name]); + + const openJsonViewer = (experiment, trial) => { + setLoading(true); + ExperimentsApi.getModelSpecification(experiment, trial.id) + .then((modelSpecification) => { + setTrialJSON(modelSpecification); + setTrial(trial.name); + setLoading(false); + setView(EXPERIMENT_VIEWS.jsonViewer); + }); + }; + + const handleChangePage = (event, newPage) => { + setPage(newPage); + }; + + const handleChangeRowsPerPage = (event) => { + setRowsPerPage(parseInt(event.target.value, 10)); + setPage(0); + }; + + const removeFilter = (filterIndex) => { + const newFilter = [...filter]; + newFilter.splice(filterIndex, 1); + setPage(0); + setFilter(newFilter); + setFilteredRows(filterRows(tableRows, newFilter)); + }; + + const openLoadResultsDialog = (experimentName, trial) => { + setSelectedTrial({ + experiment: experimentName, + trial, + }); + setLoadResultsDialogOpen(true); + }; + + const openLoadModelSpecificationDialog = (experimentName, trial) => { + setSelectedTrial({ + experiment: experimentName, + trial, + }); + setLoadModelSpecDialogOpen(true); + }; + + const onLoadResultsAction = (actionConfirmed) => { + if (actionConfirmed) { + dispatch(viewExperimentResults({ + name: selectedTrial.experiment, + trial: selectedTrial.trial, + })); + } + setSelectedTrial(null); + setLoadResultsDialogOpen(false); + }; + + const onLoadModelSpecificationAction = (actionConfirmed) => { + if (actionConfirmed) { + dispatch(loadTrialModelSpec({ + name: selectedTrial.experiment, + trial: selectedTrial.trial, + onlyModelSpecification: true, + })); + } + setSelectedTrial(null); + setLoadModelSpecDialogOpen(false); + }; + + return ( +
+ + + setView(EXPERIMENT_VIEWS.list)} /> + {experiment?.name} + +
+ {/* */} +
+ + {loading ? ( + + + Loading ... + + ) : ( + experiment?.trials && ( + <> + +
+ + +
+ + + + + + {stableSort(filteredRows, getComparator(order, orderBy)) + .slice(page * rowsPerPage, page * rowsPerPage + rowsPerPage) + .map((row) => ( + + + {row.name} + + {paramHeaders.map((header, index) => ( + + {row[header.label]} + + ))} + {experimentFinished && ( + + + + openLoadResultsDialog(experiment?.name, row)} + > + + + + + + openJsonViewer(experiment?.name, row)}> + + + + + openLoadModelSpecificationDialog(experiment?.name, row)}> + + + + + + )} + + ))} + +
+ + {filteredRows.length > 0 && ( + + )} + + + + + ) + )} +
+ ); +}; + +ExperimentView.propTypes = { + name: PropTypes.string.isRequired, + setTrial: PropTypes.func.isRequired, + setTrialJSON: PropTypes.func.isRequired, + setView: PropTypes.func.isRequired, +}; + +export default withStyles(useStyles)(ExperimentView); diff --git a/webapp/components/experiments/Experiments.js b/webapp/components/experiments/Experiments.js new file mode 100644 index 00000000..2df669eb --- /dev/null +++ b/webapp/components/experiments/Experiments.js @@ -0,0 +1,314 @@ +import React, { useEffect, useState } from 'react'; +import Box from '@material-ui/core/Box'; +import Table from '@material-ui/core/Table'; +import TableBody from '@material-ui/core/TableBody'; +import TableCell from '@material-ui/core/TableCell'; +import TableContainer from '@material-ui/core/TableContainer'; +import TableRow from '@material-ui/core/TableRow'; +import Paper from '@material-ui/core/Paper'; +import DeleteIcon from '@material-ui/icons/Delete'; +import EditIcon from '@material-ui/icons/Edit'; +import Chip from '@material-ui/core/Chip'; +import CancelRoundedIcon from '@material-ui/icons/CancelRounded'; +import FileCopyOutlinedIcon from '@material-ui/icons/FileCopyOutlined'; +import ChevronRightIcon from '@material-ui/icons/ChevronRight'; +import Button from '@material-ui/core/Button'; +import Typography from '@material-ui/core/Typography'; +import Divider from '@material-ui/core/Divider'; +import AddIcon from '@material-ui/icons/Add'; +import { + GridLayout, + +} from 'netpyne/components'; +import { withStyles } from '@material-ui/core/styles'; + +import Utils from '../../Utils'; +import { + EXPERIMENT_STATE, EXPERIMENT_TEXTS, EXPERIMENT_VIEWS, +} from '../../constants'; +import DialogBox from '../general/DialogBox'; +import { experimentGrey, experimentInputColor } from '../../theme'; + +const useStyles = (theme) => ({ + root: { + '& .scrollDiv': { + overflow: 'auto', + }, + '& .MuiTableContainer-root': { + maxHeight: 'calc(100% -60vh)', + overflow: 'auto', + '&::-webkit-scrollbar': { + height: theme.spacing(1), + }, + '& .MuiTable-root': { + '& .experimentHead': { + fontSize: '1rem', + }, + '& .experimentHeadIcon': { + fontSize: '1rem', + }, + '& .experimentDate': { + fontStyle: 'italic', + fontWeight: 300, + fontSize: '1rem', + color: experimentGrey, + whiteSpace: "nowrap" + }, + '& .experimentIcon': { + color: experimentGrey, + minWidth: 'auto', + '& .MuiSvgIcon-root': { + fontSize: '1.2rem', + }, + }, + '& .MuiChip-label': { + color: experimentGrey, + fontSize: ' 0.77rem', + fontWeight: 600, + }, + '& .MuiChip-root': { + background: experimentInputColor, + height: theme.spacing(3.2), + }, + '& .MuiChip-deleteIcon': { + marginRight: theme.spacing(0.4), + }, + '& .MuiTableCell-root': { + padding: theme.spacing(1, 2), + '&:nth-child(1)': { + width: '18.75rem', + '& button': { + maxWidth: '50vw', + justifyContent: 'inherit', + }, + '& h6': { + textOverflow: 'ellipsis', + whiteSpace: 'nowrap', + overflow: 'hidden', + }, + }, + '&:nth-child(2)': { + width: '9.375rem', + }, + }, + '& .MuiChip-icon': { + color: experimentGrey, + }, + '& .MuiDivider-vertical': { + height: theme.spacing(4), + background: 'rgba(255, 255, 255, 0.3)', + }, + '& .MuiTableCell-alignRight': { + width: theme.spacing(6), + paddingLeft: 0, + }, + '& .MuiTableCell-alignCenter': { + width: theme.spacing(6), + }, + }, + '& .MuiChipLoader': { + border: '3px solid rgba(196, 196, 196, 0.3)', + borderRadius: '50%', + borderTop: `3px solid ${experimentGrey}`, + width: theme.spacing(2.4), + height: theme.spacing(2.4), + animation: 'spin 2s linear infinite', + }, + }, + }, +}); + +const Experiments = (props) => { + const { + experiments, + classes, + setEditState, + setExperimentName, + cloneExperiment, + removeExperiment, + setView, + } = props; + + + + const [dialogOpen, setDialogOpen] = useState(false); + const [deleteDialogOpen, setDeleteDialogOpen] = useState(false); + const [cloneDialogOpen, setCloneDialogOpen] = useState(false); + const [actionExperimentName, setActionExperimentName] = useState(null); + + const deleteExperiment = (actionConfirmed) => { + if (actionConfirmed) { + removeExperiment(actionExperimentName); + + setDeleteDialogOpen(false); + + + } else { + setDeleteDialogOpen(false); + } + setActionExperimentName(null); + }; + + const viewExperiment = (name) => { + setEditState(false); + setExperimentName(name); + setView(EXPERIMENT_VIEWS.viewExperiment); + }; + + const createExperimentScreen = (actionConfirmed) => { + setDialogOpen(false); + setEditState(false); + setExperimentName(null); + setView(!actionConfirmed ? EXPERIMENT_VIEWS.list : EXPERIMENT_VIEWS.edit); + }; + + const openEditExperiment = (name) => { + setExperimentName(name); + setView(EXPERIMENT_VIEWS.edit); + setEditState(true); + }; + + const openCloneDialog = (name) => { + setActionExperimentName(name); + setCloneDialogOpen(true); + }; + + const openDeleteDialog = (name) => { + setActionExperimentName(name); + setDeleteDialogOpen(true); + }; + + const onCloneExperimentAction = (actionConfirmed) => { + if (actionConfirmed) { + cloneExperiment(actionExperimentName); + } + setCloneDialogOpen(false); + setActionExperimentName(null); + }; + + return ( + <> + +
+ + + + + {experiments.sort((e1, e2) => new Date(e2.timestamp) - new Date(e1.timestamp)).map((experiment) => ( + + + + + + + {Utils.formatDate(experiment?.timestamp)} + + + + {( + [ + EXPERIMENT_STATE.PENDING, + EXPERIMENT_STATE.SIMULATING, + EXPERIMENT_STATE.INSTANTIATING, + ].includes(experiment?.state)) + ? ( + } + label={experiment?.state} + // deleteIcon={} + // onDelete={() => { + // }} + /> + ) + : ( + + )} + + + + + + + + + + + + ))} + +
+ + +
+ + + + + + + + + + + ); +}; + +export default withStyles(useStyles)(Experiments); diff --git a/webapp/components/experiments/ParameterMenu.js b/webapp/components/experiments/ParameterMenu.js new file mode 100644 index 00000000..533bb7e4 --- /dev/null +++ b/webapp/components/experiments/ParameterMenu.js @@ -0,0 +1,46 @@ +import React, { useState } from 'react'; +import IconButton from '@material-ui/core/IconButton'; +import Menu from '@material-ui/core/Menu'; +import MoreVertIcon from '@material-ui/icons/MoreVert'; +import MenuItem from '@material-ui/core/MenuItem'; + +const ParameterMenu = (props) => { + const { + parameter, index, removeFromGroup, addToGroup, removeParameter, + } = props; + const [anchorEl, setAnchorEl] = useState(null); + + const handleClick = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleClose = () => { + setAnchorEl(null); + }; + + return ( + <> + + + + + { parameter.inGroup + ? removeFromGroup(index)}>Remove from group + : addToGroup(index)}>Add to Group} + removeParameter(index, parameter)}>Delete + + + ); +}; + +export default ParameterMenu; diff --git a/webapp/components/experiments/processExperimentData.js b/webapp/components/experiments/processExperimentData.js new file mode 100644 index 00000000..ae101942 --- /dev/null +++ b/webapp/components/experiments/processExperimentData.js @@ -0,0 +1,56 @@ +import Utils from '../../Utils'; +import { getPythonTypeString } from './utils'; + +const REAL_TYPE = { + INT: 'int', + FLOAT: 'float', + BOOL: 'bool', + STR: 'str', + FUNC: 'func', + DICT: 'dict', + DICT_DICT: 'dict(dict)', +}; +const SUPPORTED_TYPES = [ + REAL_TYPE.INT, + REAL_TYPE.FLOAT, + REAL_TYPE.STR, + REAL_TYPE.BOOL, + REAL_TYPE.FUNC +]; + + + + + + +/** + * + * @param {*} params Netpyne parameters + * @returns map of flatten parameter name to the field spec from Netpyne metadata or inferred from the value + */ +export function getFlattenedParams(params) { + + const flattened = Utils.flatten(params); + function getFieldSpec(fieldKey) { + const metadataField = Utils.getMetadataField(fieldKey); + if(metadataField) { + return metadataField; + } + return { + type: getPythonTypeString(flattened[fieldKey]), + label: fieldKey.split(".").pop() + } + } + + const res = {}; + + for(const key in flattened) { + const field = getFieldSpec(key); + if(field && SUPPORTED_TYPES.includes(field.type)) { + res[key] = field + } + } + + return res; +} + diff --git a/webapp/components/experiments/utils.js b/webapp/components/experiments/utils.js new file mode 100644 index 00000000..b2e945d6 --- /dev/null +++ b/webapp/components/experiments/utils.js @@ -0,0 +1,41 @@ +import { REAL_TYPE } from '../../constants'; + +export function descendingComparator (a, b, orderBy) { + if (b[orderBy] < a[orderBy]) { + return -1; + } + if (b[orderBy] > a[orderBy]) { + return 1; + } + return 0; +} + +export function getComparator (order, orderBy) { + return order === 'desc' + ? (a, b) => descendingComparator(a, b, orderBy) + : (a, b) => -descendingComparator(a, b, orderBy); +} + +export function stableSort (array, comparator) { + const stabilizedThis = array.map((el, index) => [el, index]); + stabilizedThis.sort((a, b) => { + const order = comparator(a[0], b[0]); + if (order !== 0) return order; + return a[1] - b[1]; + }); + return stabilizedThis.map((el) => el[0]); +} + + +export function getPythonTypeString(obj) { + if(typeof obj == "number") { + return REAL_TYPE.FLOAT + } + if(typeof obj == "string") { + return REAL_TYPE.STR + } + if(typeof obj == "boolean") { + return REAL_TYPE.BOOL + } + return undefined; +} \ No newline at end of file diff --git a/webapp/components/general/AdapterComponent.js b/webapp/components/general/AdapterComponent.js index cdd8a5e2..b35336ed 100644 --- a/webapp/components/general/AdapterComponent.js +++ b/webapp/components/general/AdapterComponent.js @@ -27,6 +27,8 @@ export default class AdapterComponent extends Component { } componentDidUpdate (prevProps, prevState) { + if (this.props.commands !== prevProps.commands) + this.forceUpdate(); const newValue = this.props.convertFromPython(prevProps, prevState, this.props.value); if (newValue != undefined) { this.setState(newValue); @@ -49,7 +51,7 @@ export default class AdapterComponent extends Component { // Call to conversion function const newValue = this.props.convertToPython(this.state); - if (newValue != undefined && this.state.value != newValue) { + if (newValue != undefined && this.state.value != newValue && this.props.onChange) { this.props.onChange(null, null, newValue); } } diff --git a/webapp/components/general/Checkbox.js b/webapp/components/general/Checkbox.js index c7ba994b..4533b380 100644 --- a/webapp/components/general/Checkbox.js +++ b/webapp/components/general/Checkbox.js @@ -7,6 +7,10 @@ import FormControlLabel from '@material-ui/core/FormControlLabel'; import { bgLight } from '../../theme'; export default class Checkbox extends Component { + componentDidUpdate (prevProps, prevState) { + if (this.props.commands !== prevProps.commands) + this.forceUpdate(); + } render () { const { fullWidth, diff --git a/webapp/components/general/CommandRecorder.js b/webapp/components/general/CommandRecorder.js new file mode 100644 index 00000000..81bc975a --- /dev/null +++ b/webapp/components/general/CommandRecorder.js @@ -0,0 +1,103 @@ +import { KERNEL_HANDLING } from '../../constants'; +import { store } from '../../redux/actiondomainStore' +import { recordCommand, dropLastCommand, dropFromIndex } from '../../redux/actions/actiondomain'; +import { execPythonMessage, execPythonMessageWithoutRecording } from './GeppettoJupyterUtils'; + + +const registerKernelListeners = () => { + try { + if(IPython.notebook.kernel == null) { + console.warn("Kernel not initialized. Waiting to register kernel event listeners"); + setTimeout(registerKernelListeners, 500); + return; + } + } catch (error) { + console.warn("IPython not initialized. Waiting to register kernel event listeners"); + setTimeout(registerKernelListeners, 500); + return + } + + const notebook = IPython.notebook; + const handleKernelStatusChange = (event, data) => { + const kernelStatusEvent = new CustomEvent("kernelstatus", { + detail: { + "type": event.type, + ...data + }, + }); + window.dispatchEvent(kernelStatusEvent); + }; + + const handleExecutionRequest = (event, data) => { + if (data.content.netpyne_ui_triggered) { + return + } + const { kernel, content } = data; + record(kernel.id, content.code); + } + + // Kernel lifecycle requests + notebook.events.on('kernel_created.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_reconnecting.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_connected.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_starting.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_restarting.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_autorestarting.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_interrupting.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_disconnected.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_ready.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_killed.Kernel', handleKernelStatusChange); + notebook.events.on('kernel_dead.Kernel', handleKernelStatusChange); + + // Execution requests + notebook.events.on('execution_request.Kernel', handleExecutionRequest); +} +registerKernelListeners(); + + +const record = (kernelID, command) => { + store.dispatch(recordCommand(kernelID, command)) +} + +const TIMEFRAME = 10 * 1000; // 10s +let lastReplayTime = 0 + +const getCommands = (kernelID) => { + return [ + "from jupyter_geppetto import jupyter_geppetto", + "from jupyter_geppetto import utils", + "from netpyne_ui.netpyne_geppetto import netpyne_geppetto", + "netpyne_geppetto.deleteModel({})", + `netpyne_geppetto.loadFromIndexFile("${KERNEL_HANDLING.tmpModelPath}")`, + ...store.getState()[kernelID] + ] +} + +const replayAll = (kernelID, fromRec = false) => { + const currentTimestamp = Date.now(); + const commands = getCommands(kernelID); + + if (!fromRec && currentTimestamp - lastReplayTime < TIMEFRAME) { + const restartLoop = new CustomEvent("kernelRestartLoop", { + detail: { + "kernel": kernelID, + "state": "looping" + } + }); + window.dispatchEvent(restartLoop); + store.dispatch(dropLastCommand(kernelID)) + replayAll(kernelID, true) + return + } + + const lastCommand = commands.pop() // we drop the last command which is probably the faulty one + const script = commands.join('\n') + console.log("Playing", script) + console.log("Skipping last command", lastCommand) + lastReplayTime = currentTimestamp + execPythonMessageWithoutRecording(script).then(() => { + store.dispatch(dropLastCommand(kernelID)) + }) +} + +export { record, replayAll } \ No newline at end of file diff --git a/webapp/components/general/ConfirmationDialog.js b/webapp/components/general/ConfirmationDialog.js new file mode 100644 index 00000000..331f9442 --- /dev/null +++ b/webapp/components/general/ConfirmationDialog.js @@ -0,0 +1,75 @@ +import React from 'react'; +import Dialog from '@material-ui/core/Dialog/Dialog'; +import Button from '@material-ui/core/Button'; +import DialogActions from '@material-ui/core/DialogActions'; +import DialogContent from '@material-ui/core/DialogContent'; +import DialogTitle from '@material-ui/core/DialogTitle'; +import { withStyles } from '@material-ui/core/styles'; +import { PYTHON_CALL, LOAD_TUTORIAL } from '../../redux/actions/general'; + +const styles = () => ({ + cancel: { marginRight: 10 }, +}); + +class ConfirmationDialog extends React.Component { + constructor (props) { + super(props); + this.state = { hide: !this.props.open }; + } + + handleConfirmation = () => { + if (this.props.confirmationDialogOnConfirm) { + if (this.props.confirmationDialogOnConfirm.type === PYTHON_CALL) { + this.props.pythonCall(this.props.confirmationDialogOnConfirm.cmd, this.props.confirmationDialogOnConfirm.args); + } else if (this.props.confirmationDialogOnConfirm.type === LOAD_TUTORIAL) { + if (this.props.confirmationDialogOnConfirm.payload !== undefined) { + this.props.dispatchAction(this.props.confirmationDialogOnConfirm.action(this.props.confirmationDialogOnConfirm.payload)); + } else { + this.props.dispatchAction(this.props.confirmationDialogOnConfirm.action); + } + } + } + } + + render () { + const { + confirmationDialogOpen, + confirmationDialogTitle, + confirmationDialogMessage, + closeConfirmationDialog, + } = this.props; + + return ( + closeConfirmationDialog()} + > + {confirmationDialogTitle} + + {confirmationDialogMessage} + + + {this.props.confirmationDialogOnConfirm && } + + + + ); + } +} + +export default withStyles(styles)(ConfirmationDialog); diff --git a/webapp/components/general/ControlPanelTreeItem.js b/webapp/components/general/ControlPanelTreeItem.js new file mode 100644 index 00000000..0f9e6ba6 --- /dev/null +++ b/webapp/components/general/ControlPanelTreeItem.js @@ -0,0 +1,356 @@ +import * as React from 'react'; +import { makeStyles } from '@material-ui/core/styles'; +import Grid from '@material-ui/core/Grid'; +import Typography from '@material-ui/core/Typography'; +import Box from '@material-ui/core/Box'; +import IconButton from '@material-ui/core/IconButton'; +import TreeItem from '@material-ui/lab/TreeItem'; +import Visibility from '@material-ui/icons/Visibility'; +import VisibilityOff from '@material-ui/icons/VisibilityOff'; +import { ChromePicker } from 'react-color'; +import { useDispatch, useSelector } from 'react-redux'; +import { + experimentLabelColor, + bgDarker, + bgLight, + radius, +} from '../../theme'; +import { + RandomColorLensIcon, + SquareIcon, +} from './NetPyNEIcons'; +import { changeInstanceColor } from '../../redux/actions/general'; + +const useStyles = makeStyles((theme) => ({ + treeItem: { + '& .MuiTreeItem-iconContainer': { + marginRight: '5px', + }, + '& .MuiTreeItem-label': { + paddingTop: '2px', + paddingBottom: '2px', + paddingRight: '8px', + borderRadius: radius, + '&:hover': { + backgroundColor: '#333333', + }, + }, + }, + leafTreeItem: { + '& .MuiTreeItem-iconContainer': { + width: 0, + }, + }, + controls: { + '& .MuiIconButton-root': { + padding: '0 !important', + marginLeft: '0.5rem', + color: experimentLabelColor, + '&:hover': { + color: 'white', + }, + }, + }, + colorPickerBox: { + position: 'absolute', + top: '1.6rem', + right: '0', + height: '3rem', + }, + triangleIcon: { + marginBottom: '-7px', + color: bgDarker, + }, + colorPicker: { + position: 'absolute', + zIndex: 1000, + right: '0', + backgroundColor: `${bgDarker} !important`, + padding: '0.2rem', + '& label': { + color: '#ffffff !important', + fontFamily: 'Roboto, arial', + fontSize: '11px', + fontWeight: 400, + }, + '& input': { + backgroundColor: `${bgLight} !important`, + color: '#ffffff !important', + boxShadow: 'none !important', + fontFamily: 'Roboto, arial', + fontSize: '11px', + fontWeight: 400, + }, + '& svg': { + fill: '#ffffff !important', + }, + '& svg:hover': { + background: 'transparent !important', + }, + '& .hue-horizontal': { + borderRadius: '10px', + }, + '& :nth-child(2)': { + '& :nth-child(1)': { + '& :nth-child(2)': { + '& :nth-child(2)': { + '& :nth-child(1)': { + '& :nth-child(2)': { + borderRadius: '10px', + }, + }, + }, + }, + }, + }, + }, + activeColorPicker: { + '& path': { + fill: '#ffffff', + }, + }, +})); + +const ControlPanelTreeItem = (props) => { + const classes = useStyles(); + const dispatch = useDispatch(); + const [showColorPicker, setShowColorPicker] = React.useState(false); + const [isHoveredOver, setIsHoveredOver] = React.useState(false); + const [visibility, setVisibility] = React.useState(true); + const instances = useSelector((state) => state.general.instances); + const defaultColor = { + g: 0.50, + b: 0.60, + r: 1, + a: 1, + hex: "#FF7F99" + }; + + const getParent = (nodeId) => { + const insts = instances.filter((instance) => + nodeId.replace(instance.instancePath, '') !== nodeId && instance.instancePath.length < nodeId.length + ); + if (insts.length === 0) { + return null; + } + return insts.sort((a, b) => b.instancePath.length - a.instancePath.length)[0] + } + + const getColor = (nodeId) => { + const insts = instances.filter((instance) => instance.instancePath === nodeId); + const parent = getParent(nodeId); + // If there is no recorded parent, and there is no instances + if (!parent && insts.length === 0) { + return defaultColor; + } + // If there is a parent, but no instances, we take the color of the parent + if (insts.length === 0) { + return parent.color + } + const inst = insts[0] + // If the instance doesn't have children and have a color + if (props.children && props.children.length === 0 && insts.length > 0 && "color" in inst) { + return inst.color + } + // we check if all children have the same color + const children = instances.filter((instance) => instance.instancePath.startsWith(nodeId) && instance.instancePath !== nodeId); + // if we cannot find children (no color set for children) + if (children.length === 0) { + // if there is a color, we display it + if (inst.color) { + return inst.color + } + // if there is none (color not set) we take the default one + return defaultColor; + } + const color = children[0].color; + if (children.length > 1 && children.every(x => x.color && x.color.hex === color.hex)) { + return color + } + return { hex: "#989898" } + } + + const randomColor = () => { + const [r, g, b] = [Math.random() * 255, Math.random() * 255, Math.random() * 255]; + return { + r: parseFloat(r.toFixed(2)), + g: parseFloat(g.toFixed(2)), + b: parseFloat(b.toFixed(2)), + a: 1, + hex: "#" + (r >> 0).toString(16) + (g >> 0).toString(16) + (b >> 0).toString(16) + } + } + + const translateColor = (_color) => { + return { + r: _color.r / 255, + g: _color.g / 255, + b: _color.b / 255, + a: _color.a, + hex: _color.hex + } + } + + const handleLeafColorChange = (event, nodeId, colorGenerator) => { + const updateInstances = instances.filter((instance) => !instance.instancePath.startsWith(nodeId)); + updateInstances.push({ + instancePath: nodeId, + color: translateColor(colorGenerator()) + }); + dispatch(changeInstanceColor(updateInstances)); + } + + const handleContainerColorChange = (event, nodeId, colorGenerator) => { + event.stopPropagation(); + event.preventDefault(); + + const instance = window.Instances.getInstance(nodeId); + const childrenPaths = [...instance.getChildren()] + .map((instance) => instance.getInstancePath()); + const children = childrenPaths.filter((path) => path.startsWith(nodeId)); + const updateInstances = instances.filter((instance) => { + let condition = true; + children.forEach((child) => { + if (instance.instancePath.startsWith(child)) { + condition = false; + } + }); + return condition; + }); + children.forEach((child) => { + updateInstances.push({ + instancePath: child, + color: translateColor(colorGenerator()) + }); + }); + dispatch(changeInstanceColor(updateInstances)); + } + + const handleColorChange = (event, nodeId, colorGenerator) => { + if (props.children.length === 0) { + handleLeafColorChange(event, nodeId, colorGenerator); + return + } + handleContainerColorChange(event, nodeId, colorGenerator); + } + + const changeVisibility = (event, nodeId) => { + event.stopPropagation(); + event.preventDefault(); + const copiedInstances = instances.slice(); + let oldIndex = null; + let oldInstance = copiedInstances.find((pInstance, index) => { + if (pInstance.instancePath === nodeId) { + oldIndex = index; + return true; + } + return false; + }); + if (!oldInstance) { + oldInstance = { + instancePath: nodeId, + visibility: false, + }; + } else { + copiedInstances.splice(oldIndex, 1); + oldInstance.visibility = (oldInstance?.visibility !== undefined) ? !oldInstance.visibility : false; + } + + const newInstances = instances.map((instance) => { + if (!(instance.instancePath.startsWith(nodeId))) { + return instance; + } + const newInstance = instance; + newInstance.visibility = oldInstance.visibility; + return newInstance; + }); + + newInstances.push(oldInstance); + + dispatch(changeInstanceColor(newInstances)); + setVisibility(oldInstance.visibility); + }; + + const { + label, + type, + nodeId, + onNodeSelect, + onVisibilityClick, + children, + disableRandom, + ...other + } = props; + + return ( + setIsHoveredOver(true)} + onMouseLeave={() => { setIsHoveredOver(false); setShowColorPicker(false) }} + display="flex" + flexDirection="row" + justifyContent="space-between" + > + + + { + onNodeSelect(nodeId); + event.stopPropagation(); + event.preventDefault(); + }} + > + {label} + + + {type} + + {isHoveredOver + ? ( + <> + changeVisibility(event, nodeId)}> + { visibility ? : } + + handleColorChange(event, nodeId, randomColor)}> + + + + ) + : null} + { + event.stopPropagation(); + event.preventDefault(); + setShowColorPicker(true) + }}> + + + + {showColorPicker && isHoveredOver + ? ( + setShowColorPicker(false)} + > + { + handleColorChange(event, nodeId, () => {return {...color.rgb, hex: color.hex}}); + }} + /> + + ) : null + } + + + )} + > + {children} + + ); +}; + +export default ControlPanelTreeItem; diff --git a/webapp/components/general/DeleteDialogBox.js b/webapp/components/general/DeleteDialogBox.js deleted file mode 100644 index 23ff6fac..00000000 --- a/webapp/components/general/DeleteDialogBox.js +++ /dev/null @@ -1,63 +0,0 @@ -/** - * Tabbed Drawer resizable component - * It uses the components DrawerButton and Rnd to create a resizable Tabbed Drawer. - * - * @author Dario Del Piano - * @author Adrian Quintana - */ - -import React from 'react'; -import Dialog from '@material-ui/core/Dialog'; -import Button from '@material-ui/core/Button'; - -import DialogActions from '@material-ui/core/DialogActions'; -import DialogContent from '@material-ui/core/DialogContent'; -import DialogContentText from '@material-ui/core/DialogContentText'; -import DialogTitle from '@material-ui/core/DialogTitle'; - -export default class DeleteDialogBox extends React.Component { - constructor (props) { - super(props); - this.state = { - open: props.open, - response: false, - }; - } - - componentDidUpdate (prevProps, prevState) { - if (prevProps.open != this.props.open) { - this.setState({ open: this.props.open }); - } - } - - render () { - return ( - - {`Delete ${this.props.textForDialog}`} - - - {`Do you want to remove ${this.props.textForDialog} ?`} - - - - - - - - ); - } -} diff --git a/webapp/components/general/Dialog.js b/webapp/components/general/Dialog.js index 6f2c413b..c133d28a 100644 --- a/webapp/components/general/Dialog.js +++ b/webapp/components/general/Dialog.js @@ -1,18 +1,11 @@ import React from 'react'; -import Button from '@material-ui/core/Button'; import MuiDialog from '@material-ui/core/Dialog'; -import DialogActions from '@material-ui/core/DialogActions'; -import DialogContent from '@material-ui/core/DialogContent'; -import Typography from '@material-ui/core/Typography'; -import DialogTitle from '@material-ui/core/DialogTitle'; -import Paper from '@material-ui/core/Paper'; -import Box from '@material-ui/core/Box'; -import Link from '@material-ui/core/Link'; -import Icon from '@material-ui/core/Icon'; +import { Button,DialogActions, DialogContent, DialogTitle, DialogContentText } from '@material-ui/core'; +import { Typography, Paper, Box, Link, Icon } from '@material-ui/core'; import { withStyles } from '@material-ui/core/styles'; import { secondaryColor, bgLight } from '../../theme'; -import logo_netpyne from '../../static/netpyne-logo_white.png'; -import logo_metacell from '../../static/metacell_new.png'; +import logoNetpyne from '../../static/netpyne-logo_white.png'; +import logoMetaCell from '../../static/metacell_new.png'; const styles = (theme) => ({ paper: { @@ -23,18 +16,24 @@ const styles = (theme) => ({ const AboutContent = withStyles(styles)(({ classes }) => ( - + - - NetPyNE-UI v0.7.0 - + + NetPyNE-UI v1.1.0 + + + NetPyNE v1.0.6 + + + NEURON v8.2.2 + NetPyNE is a Python package to facilitate the development, simulation, parallelization, and analysis of biological neuronal networks using the - NEURON simulator. Checkout our + NEURON simulator. Check out our {' '} eLife paper. @@ -58,7 +57,10 @@ const AboutContent = withStyles(styles)(({ classes }) => ( - NetPyNE-UI is being developed in collaboration with: + NetPyNE-UI is being developed by the State University of New York Downstate ( + Dura-Bernal Lab + ) + in collaboration with: ( width: 150, padding: '10px', }} - src={logo_metacell} + src={logoMetaCell} /> @@ -125,18 +127,32 @@ const ContributeContent = withStyles(styles)(({ classes }) => ( )); + + +const titleContentMapping = { + Contribute: , + About: +} + export default function Dialog ({ open, title, message, handleClose, }) { + const selectMessageContent = () => { + if (title in titleContentMapping) { + return titleContentMapping[title] + } + return {message} + } return (
{title} - {title === 'Contribute' ? : } + {/* {title === 'Contribute' ? : } */} + {selectMessageContent()} + + + + ); + } +} diff --git a/webapp/components/general/ExpansionPanel.js b/webapp/components/general/ExpansionPanel.js index f8cf2708..76b6807d 100644 --- a/webapp/components/general/ExpansionPanel.js +++ b/webapp/components/general/ExpansionPanel.js @@ -10,7 +10,10 @@ import Tooltip from './Tooltip'; const styles = ({ spacing }) => ({ button: { marginRight: 0 } }); class NetPyNEAccordion extends Component { - state = { expanded: false }; + constructor (props) { + super(props); + this.state = { expanded: false }; + } render () { const { @@ -24,7 +27,7 @@ class NetPyNEAccordion extends Component { this.setState({ expanded: !this.state.expanded }), + onClick: () => this.setState((prevState) => ({ expanded: !prevState.expanded })), className: classes.button, }} expandIcon={( diff --git a/webapp/components/general/ExperimentControlPanel.js b/webapp/components/general/ExperimentControlPanel.js new file mode 100644 index 00000000..8f0aee4e --- /dev/null +++ b/webapp/components/general/ExperimentControlPanel.js @@ -0,0 +1,191 @@ +/* eslint-disable no-nested-ternary */ +import * as React from 'react'; +import { useDispatch, useSelector } from 'react-redux'; +import { makeStyles } from '@material-ui/core/styles'; +import Box from '@material-ui/core/Box'; +import Typography from '@material-ui/core/Typography'; +import TextField from '@material-ui/core/TextField'; +import TreeView from '@material-ui/lab/TreeView'; +import ControlPanelTreeItem from './ControlPanelTreeItem'; +import { experimentLabelColor } from '../../theme'; +import { MODEL_STATE } from '../../constants'; +import { selectInstances } from '../../redux/actions/general'; +import { TreeItemArrowRightIcon, TreeItemArrowDownIcon } from './NetPyNEIcons'; + +const useStyles = makeStyles(() => ({ + root: { + '& ul': { + position: 'relative', + '&::before': { + content: '""', + height: 'calc(100% - 1.1rem)', + width: '0.0625rem', + position: 'absolute', + left: '-0.65rem', + borderRadius: '3.125rem', + top: '0rem', + backgroundImage: 'url("data:image/svg+xml,%3Csvg width=\'1\' height=\'8\' viewBox=\'0 0 1 8\' fill=\'none\' xmlns=\'http://www.w3.org/2000/svg\'%3E%3Cpath d=\'M0 0H1V8H0V0Z\' fill=\'%23989898\'/%3E%3C/svg%3E")', + backgroundRepeat: 'repeat', + }, + '& .MuiTreeItem-root': { + position: 'relative', + '&::before': { + content: '""', + height: '0.875rem', + width: '1.4375rem', + backgroundImage: 'url("data:image/svg+xml,%3Csvg width=\'12\' height=\'6\' viewBox=\'0 0 12 6\' fill=\'none\' xmlns=\'http://www.w3.org/2000/svg\'%3E%3Cpath d=\'M6 6C2.68629 6 0 3.31371 0 0H1C1 2.80391 3.19609 5 6 5V6Z\' fill=\'%23989898\'/%3E%3Cpath d=\'M6 5H11.5C11.7761 5 12 5.22386 12 5.5C12 5.77614 11.7761 6 11.5 6H6V5Z\' fill=\'%23989898\'/%3E%3C/svg%3E")', + position: 'absolute', + top: '0.5rem', + backgroundRepeat: 'no-repeat', + left: '-0.65rem', + }, + '&::after': { + content: '""', + height: '0.0625rem', + borderRadius: '3.125rem', + width: '0.5rem', + backgroundColor: '#ffffff', + position: 'absolute', + left: '0', + top: '1.0625rem', + display: 'none', + }, + '&:hover': { + background: 'transparent', + }, + '&:focus > .MuiTreeItem-content': { + backgroundColor: 'transparent', + }, + }, + }, + }, + header: { + '& .MuiTypography-root': { + color: experimentLabelColor, + fontWeight: 'bold', + }, + }, + svgContainer: { + fontSize: '12px', + width: '10px', + height: '10px', + }, +})); + +const ExperimentControlPanel = (props) => { + const classes = useStyles(); + const dispatch = useDispatch(); + const instances = useSelector((state) => state.general.instances); + const [filter, setFilter] = React.useState(''); + const onNodeSelect = (nodeId) => { + dispatch(selectInstances(instances, [nodeId])); + }; + const instancesMap = new Map(); + + const onVisibilityClick = (event, nodeId) => { + console.log(`Visibility of node with id of ${nodeId} clicked.`); + }; + + const traverseInstances = (instance) => { + if (instance.getPath().includes(filter)) { + instancesMap.set( + instance.getPath(), + ( + + ), + ); + } + + if (instance.getChildren() && instance.getChildren().length > 0) { + const children = instance.getChildren(); + for (let i = 0; i < children.length; i += 1) { + traverseInstances(children[i]); + } + } + }; + + const getFlatFilteredList = (instances) => { + instancesMap.clear(); + instances.forEach((instance) => traverseInstances(instance)); + + const flatList = []; + instancesMap.forEach((value, key) => { + if (value.key.includes(filter)) { + flatList.push(value); + } + }); + return flatList; + }; + + const getTreeItemsFromData = (treeItems) => treeItems.map((treeItemData) => { + let children = []; + if (treeItemData.getChildren() && treeItemData.getChildren().length > 0) { + children = getTreeItemsFromData(treeItemData.getChildren()); + } + + return ( + + {children} + + ); + }); + + return ( + <> + { + props.modelState === MODEL_STATE.INSTANTIATED || props.modelState === MODEL_STATE.SIMULATED + ? ( + window.Instances + ? ( + + setFilter(e.target.value)} /> + + Name + Type(s) + Controls + + } + defaultExpandIcon={} + > + {filter === '' + ? getTreeItemsFromData([window.Instances.getInstance('network')]) + : getFlatFilteredList([window.Instances.getInstance('network')])} + + + ) + : ( + +

Error: Should not happen. ModelState === INSTANTIATED but global Instances object is not defined.

+ + ) + ) + : ( + +

Model is not instantiated. Please instantiate a model to access the control panel.

+ + ) + } + + ); +}; + +export default ExperimentControlPanel; diff --git a/webapp/components/general/FileBrowser.js b/webapp/components/general/FileBrowser.js index cc45be66..c223d2b7 100644 --- a/webapp/components/general/FileBrowser.js +++ b/webapp/components/general/FileBrowser.js @@ -1,5 +1,4 @@ import React from 'react'; -import Tree from '@geppettoengine/geppetto-client/js/components/interface/tree/Tree'; import Button from '@material-ui/core/Button'; import { changeNodeAtPath, walk } from 'react-sortable-tree'; import Dialog from '@material-ui/core/Dialog'; @@ -10,6 +9,7 @@ import DialogContent from '@material-ui/core/DialogContent'; import { Tooltip } from 'netpyne/components'; import IconButton from '@material-ui/core/IconButton'; import Icon from '@material-ui/core/Icon'; +import Tree from './tree/Tree'; import Utils from '../../Utils'; import { bgLight, fontColor } from '../../theme'; @@ -20,17 +20,24 @@ export default class FileBrowser extends React.Component { this.handleClickVisualize = this.handleClickVisualize.bind(this); this.state = {}; + this.tree; + if (this.props.open) { + this.getDirList([], undefined, this.props.startDir); + } } - getDirList (treeData, rowInfo) { + getDirList (treeData, rowInfo, startDir = '') { if (rowInfo != undefined) { var { path } = rowInfo.node; } else { var path = ''; } + if (!startDir) { + startDir = ''; + } Utils - .evalPythonMessage('netpyne_geppetto.getDirList', [path, this.props.exploreOnlyDirs, this.props.filterFiles]) + .evalPythonMessage('netpyne_geppetto.getDirList', [path, this.props.exploreOnlyDirs, this.props.filterFiles, startDir]) .then((dirList) => { if (treeData != [] && treeData.length > 0) { rowInfo.node.children = dirList; @@ -50,13 +57,13 @@ export default class FileBrowser extends React.Component { } else { this.setState({ selection: rowInfo.node }); } - this.refs.tree.updateTreeData(newTreeData); + this.tree.updateTreeData(newTreeData); }); } handleClickVisualize (event, rowInfo) { if (rowInfo.node.load == false) { - this.getDirList(this.refs.tree.state.treeData, rowInfo); + this.getDirList(this.tree.state.treeData, rowInfo, this.props.startDir); } else if (this.props.exploreOnlyDirs || (rowInfo.node.children == undefined && rowInfo.node.load == undefined)) { this.setState({ selection: rowInfo.node }); } @@ -64,11 +71,11 @@ export default class FileBrowser extends React.Component { getSelectedFiles () { const nodes = {}; - if (!this.refs.tree) { + if (!this.tree) { return nodes; } walk({ - treeData: this.refs.tree.state.treeData, + treeData: this.tree.state.treeData, getNodeKey: ({ treeIndex }) => treeIndex, ignoreCollapsed: true, callback: (rowInfoIter) => { @@ -83,12 +90,12 @@ export default class FileBrowser extends React.Component { componentDidUpdate (prevProps, prevState) { if (prevProps.open == false && this.props.open) { - this.getDirList([]); + this.getDirList([], undefined, prevProps.startDir); } } handleMoveUp (reset = false) { - let path = this.refs.tree.state.treeData[0].path.split('/').slice(0, -2).join('/') || '/'; + let path = this.tree.state.treeData[0].path.split('/').slice(0, -2).join('/') || '/'; if (reset) { path = window.currentFolder; @@ -181,7 +188,7 @@ export default class FileBrowser extends React.Component { rowHeight={30} toggleMode={!!this.props.toggleMode} activateParentsNodeOnClick={this.props.exploreOnlyDirs} - ref="tree" + ref={(refElement) => this.tree = refElement} /> diff --git a/webapp/components/general/Filter.js b/webapp/components/general/Filter.js index 8f0b1924..f407a421 100644 --- a/webapp/components/general/Filter.js +++ b/webapp/components/general/Filter.js @@ -18,7 +18,10 @@ const styles = ({ spacing, shape }) => ({ listbox: { color: 'white', maxHeight: '20vh' }, }); class Filter extends Component { - state = { open: false } + constructor (props) { + super(props); + this.state = { open: false }; + } render () { const { @@ -31,7 +34,6 @@ class Filter extends Component { onClose={() => this.setState({ open: false })} onOpen={() => this.setState({ open: true })} className={classes.filter} - clearOnEscape autoComplete openOnFocus diff --git a/webapp/components/general/GeppettoJupyterUtils.js b/webapp/components/general/GeppettoJupyterUtils.js index 114a9f2c..276df8d0 100644 --- a/webapp/components/general/GeppettoJupyterUtils.js +++ b/webapp/components/general/GeppettoJupyterUtils.js @@ -1,16 +1,22 @@ +import { record as recordCommand } from './CommandRecorder'; + + const handle_output = function (data) { // data is the object passed to the callback from the kernel execution switch (data.msg_type) { case 'error': - GEPPETTO.CommandController.log('ERROR while executing a Python command:'); - GEPPETTO.CommandController.log(data.content.evalue.trim()); + console.log('ERROR while executing a Python command:'); + console.log(data.content.evalue.trim()); console.error('ERROR while executing a Python command:'); console.error(data.content.traceback); + if (data.content.evalue === "name 'utils' is not defined") { + execPythonMessage('from jupyter_geppetto import synchronization, utils, synchronization as jupyter_geppetto'); + execPythonMessage('from netpyne_ui.netpyne_geppetto import netpyne_geppetto'); + } + // dispatch(GeppettoActions.geppettoError); GEPPETTO.trigger(GEPPETTO.Events.Error_while_exec_python_command, data.content); - GEPPETTO.trigger(GEPPETTO.Events.Hide_spinner); break; case 'execute_result': - GEPPETTO.CommandController.log(data.content.data['text/plain'].trim(), true); try { var response = JSON.parse(data.content.data['text/plain'].replace(/^'(.*)'$/, '$1')); } catch (error) { @@ -22,27 +28,48 @@ const handle_output = function (data) { // FIXME break; default: - GEPPETTO.CommandController.log(data.content.text.trim(), true); + console.log(data.content.text.trim(), true); } }; -const execPythonMessage = function (command, callback = handle_output) { - GEPPETTO.CommandController.log(`Executing Python command: ${command}`, true); +const execPythonMessage = function (command, callback = handle_output, record = true) { const { kernel } = IPython.notebook; - const messageID = kernel.execute(command, { iopub: { output: callback } }, { silent: false, stop_on_error: true, store_history: true }); + if (record) { + recordCommand(kernel.id, command) + } + const messageID = kernel.execute( + command, + { + iopub: { output: callback } + }, + { + silent: false, + stop_on_error: true, + store_history: true, + netpyne_ui_triggered: true + }); + return new Promise((resolve, reject) => GEPPETTO.on(GEPPETTO.Events.Receive_Python_Message, (data) => { - if (data.id == messageID) { - resolve(data.response); + if (data.data.id == messageID) { + resolve(data.data.response); } })); }; -const evalPythonMessage = function (command, parameters, parse = true) { +const execPythonMessageWithoutRecording = function (command, callback = handle_output) { + return execPythonMessage(command, callback, false) +} + +const addslashes = function (str) { + return (str + '').replace(/[\\"']/g, '\\$&').replace(/\u0000/g, '\\0'); +} + +const evalPythonMessage = function (command, parameters, parse = true, record = true) { let parametersString = ''; if (parameters) { if (parameters.length > 0) { - parametersString = `(${parameters.map((parameter) => `utils.convertToPython('${JSON.stringify(parameter)}')`).join(',')})`; + parametersString = `(${parameters.map((parameter) => `utils.convertToPython('${addslashes(JSON.stringify(parameter))}')`).join(',')})`; } else { parametersString = '()'; } @@ -52,7 +79,7 @@ const evalPythonMessage = function (command, parameters, parse = true) { if (parse) { finalCommand = `utils.convertToJS(${finalCommand})`; } - return execPythonMessage(finalCommand, handle_output); + return execPythonMessage(finalCommand, handle_output, record); }; -export { execPythonMessage, evalPythonMessage }; +export { execPythonMessage, evalPythonMessage, execPythonMessageWithoutRecording }; diff --git a/webapp/components/general/HTMLViewer.js b/webapp/components/general/HTMLViewer.js index c078e83f..ca1bf4d1 100644 --- a/webapp/components/general/HTMLViewer.js +++ b/webapp/components/general/HTMLViewer.js @@ -1,9 +1,10 @@ import React, { Component, createRef } from 'react'; -import HTMLViewer - from '@geppettoengine/geppetto-client/js/components/interface/htmlViewer/HTMLViewer'; +import HTMLViewer from '@metacell/geppetto-meta-ui/html-viewer/HTMLViewer'; import { withStyles } from '@material-ui/core/styles'; +import { CircularProgress } from '@material-ui/core'; +import { primaryColor } from '../../theme'; const style = ({ palette }) => ({ container: { @@ -24,20 +25,16 @@ class CustomHTMLViewer extends Component { componentDidMount () { window.addEventListener('resize', this.delayedResize.bind(this)); - this.resizeIfNeeded(); - } - - componentWillUnmount () { - clearTimeout(this.timer); - window.removeEventListener('resize', this.delayedResize); + this.resizeIfNeeded(true); } componentDidUpdate () { - this.resizeIfNeeded(); + this.resizeIfNeeded(true); } - wasParentResized (dimensions) { - return dimensions.width !== this.dimensions.width || dimensions.height !== this.dimensions.height; + componentWillUnmount () { + clearTimeout(this.timer); + window.removeEventListener('resize', this.delayedResize); } getParentSize () { @@ -49,7 +46,11 @@ class CustomHTMLViewer extends Component { getSvgComponent () { // svg element - return this.containerRef.current.children[0].children[0].children[0]; + return this.containerRef?.current?.children[0]?.children[0]?.children[0]; + } + + wasParentResized (dimensions) { + return dimensions.width !== this.dimensions.width || dimensions.height !== this.dimensions.height; } adjustSVGSize () { @@ -64,10 +65,10 @@ class CustomHTMLViewer extends Component { } } - resizeIfNeeded () { + resizeIfNeeded (force = false) { const dimensions = this.getParentSize(); - if (dimensions !== false && this.wasParentResized(dimensions)) { + if ((dimensions !== false && this.wasParentResized(dimensions)) || (force)) { this.dimensions = dimensions; this.adjustSVGSize(); } @@ -78,7 +79,20 @@ class CustomHTMLViewer extends Component { } render () { - const { classes } = this.props; + const { classes, content } = this.props; + if (content === undefined) { + return ( + + ); + } return (
diff --git a/webapp/components/general/JsonViewer.js b/webapp/components/general/JsonViewer.js new file mode 100644 index 00000000..cf5164bb --- /dev/null +++ b/webapp/components/general/JsonViewer.js @@ -0,0 +1,126 @@ +import React from 'react'; +import ReactJson from 'react-json-view'; +import Breadcrumbs from '@material-ui/core/Breadcrumbs'; +import Typography from '@material-ui/core/Typography'; +import { withStyles } from '@material-ui/core/styles'; +import Button from '@material-ui/core/Button'; +import Box from '@material-ui/core/Box'; +import NavigateNextIcon from '@material-ui/icons/NavigateNext'; +import { + fontColor, + experimentLabelColor, + bgDarker, + bgDarkest, + primaryColor, +} from '../../theme'; +import { EXPERIMENT_VIEWS } from '../../constants'; + +const useStyles = (theme) => ({ + root: { + width: 'auto !important', + flexDirection: 'column', + backgroundColor: bgDarker, + padding: theme.spacing(2), + borderRadius: '0.25rem', + '& .MuiBreadcrumbs-separator': { + marginLeft: theme.spacing(0), + }, + '& .react-json-view': { + padding: theme.spacing(2), + overflow: 'auto', + borderRadius: '0.25rem', + '& span': { + opacity: 1, + }, + }, + '& .MuiBreadcrumbs-ol': { + paddingBottom: theme.spacing(2), + '& .MuiBreadcrumbs-li': { + '& a': { + color: experimentLabelColor, + fontSize: '1rem', + }, + '& p': { + color: fontColor, + fontSize: '1rem', + }, + }, + }, + '& .pageHeading': { + padding: `${theme.spacing(0.75)}px ${theme.spacing(1)}px ${theme.spacing(2)}px`, + height: theme.spacing(7), + color: fontColor, + fontSize: '1rem', + }, + }, +}); + +const JsonViewer = (props) => { + const { + baseTitle, classes, title, json, setView, + } = props; + + const theme = { + scheme: 'netPyneJsonViewer', + base00: bgDarkest, + base01: bgDarkest, + base02: '#4D4D4D', + base03: fontColor, + base04: fontColor, + base05: fontColor, + base06: fontColor, + base07: fontColor, + base08: fontColor, + base09: primaryColor, + base0A: fontColor, + base0B: primaryColor, + base0C: fontColor, + base0D: fontColor, + base0E: fontColor, + base0F: primaryColor, + }; + + const goBackToBase = () => { + setView(EXPERIMENT_VIEWS.viewExperiment); + }; + + return ( +
+ { baseTitle ? ( + } + aria-label="breadcrumb" + > + + {title} + + ) : ( + + {title} + + )} + +
+ ); +}; + +export default withStyles(useStyles)(JsonViewer); diff --git a/webapp/components/general/List.js b/webapp/components/general/List.js index 48af67ed..fbb2374e 100644 --- a/webapp/components/general/List.js +++ b/webapp/components/general/List.js @@ -34,6 +34,48 @@ class ListComponent extends Component { return this.props.realType == 'dict' || this.props.realType == 'dict(dict)'; } + isChildValidListOfDict(value) { + // check if valid - square bracket + var validBracket = value[0] == '[' && value[value.length - 1] == ']'; + if (!validBracket) { + return false; + } + try { + value = value.replace(/'([^']+)':/g, '"$1":').replace(/'/g, '"'); + const valueArray = JSON.parse(value); + let valid = true; + valueArray.forEach((element) => { + if (!this.isChildValidDict(JSON.stringify(element))) { + valid = false; + } + }); + return valid; + } catch (e) { + // if not parsable then false + return false; + } + } + + isChildValidDict(value) { + // validity of curly braces + var validBraces = value.indexOf('{') == 0 && value.indexOf('}') == value.length - 1; + if (!validBraces) { + return false; + } + + var valid = true; + + try { + // check if valid json after + value = value.replace(/'([^']+)':/g, '"$1":').replace(/'/g, '"'); + const valueArray = JSON.parse(value); + } catch (e) { + return false; + } + + return valid; + } + isValid (value) { switch (this.props.realType) { case 'list(float)': @@ -41,11 +83,12 @@ class ListComponent extends Component { break; case 'list(list(float))': var valid = true; - value.split(',').forEach((element) => { - if (!element.match(/^-?\d*(\.\d+)?$/)) { - valid = false; - } - }); + value.split(',') + .forEach((element) => { + if (!element.match(/^-?\d*(\.\d+)?$/)) { + valid = false; + } + }); if (value.endsWith(',')) { valid = false; } @@ -63,41 +106,45 @@ class ListComponent extends Component { valid = false; } else if ( (value.match(/{/g) || []).length != 1 - || (value.match(/}/g) || []).length != 1 + || (value.match(/}/g) || []).length != 1 ) { valid = false; } else if ( value.indexOf('{') > value.indexOf('}') - || !value.endsWith('}') + || !value.endsWith('}') ) { valid = false; } else { const subDict = value.match(/\{(.*?)\}/)[1]; if ( (subDict.match(/:/g) || []).length - 1 - != (subDict.match(/,/g) || []).length + != (subDict.match(/,/g) || []).length ) { valid = false; } else { - subDict.split(',').forEach((element) => { - if ( - (element.match(/:/g) || []).length != 1 - || element.startsWith(':') - || element.endsWith(':') - ) { - valid = false; - } - }); + subDict.split(',') + .forEach((element) => { + if ( + (element.match(/:/g) || []).length != 1 + || element.startsWith(':') + || element.endsWith(':') + ) { + valid = false; + } + }); const reminder = value.replace(`{${subDict}}`, ''); if ( (reminder.match(/:/g) || []).length != 1 - || !reminder.endsWith(':') + || !reminder.endsWith(':') ) { valid = false; } } } break; + case 'list(dict)': + valid = this.isChildValidListOfDict(value) || this.isChildValidDict(value); + break default: var valid = true; break; @@ -106,28 +153,36 @@ class ListComponent extends Component { } getErrorMessage () { - switch (this.props.realType) { + let message; + const { realType } = this.props; + switch (realType) { case 'list(float)': - var message = 'Only float numbers are allowed.'; + message = 'Only float numbers are allowed.'; break; case 'list(list(float))': - var message = 'Only comma separated float numbers are allowed.'; + message = 'Only comma separated float numbers are allowed.'; break; case 'dict': - var message = 'Key:Value pairs must be separated by colon : '; + message = 'Key:Value pairs must be separated by colon : '; break; case 'dict(dict)': - var message = 'Incorrect format. Example -> v_soma : { sec: soma, loc: 0.5, var: v}'; + message = 'Incorrect format. Example -> v_soma : { sec: soma, loc: 0.5, var: v}'; + break; + case 'list(dict)': + message = "Incorrect format. Example -> {'cellLabel':'gs21', 'x': 2}, or [{...}]"; break; default: - var message = 'No a valid value'; + message = 'Not a valid value'; break; } return message; } handleNewItemChange (event) { - this.setState({ newItemValue: event.target.value, newItemErrorText: '' }); + this.setState({ + newItemValue: event.target.value, + newItemErrorText: '', + }); } addChild () { @@ -165,6 +220,20 @@ class ListComponent extends Component { children[key][entry[0]] = entry[1]; }); break; + case 'list(dict)': + var newValue = this.state.newItemValue + if (this.isChildValidListOfDict(newValue)) { + newValue = newValue.replace(/'([^']+)':/g, '"$1":').replace(/'/g, '"'); + const valueArray = JSON.parse(newValue); + valueArray.forEach((element) => { + children.push(element); + }); + } else if (this.isChildValidDict(newValue)) { + newValue = newValue.replace(/'([^']+)':/g, '"$1":').replace(/"/g, "'").replace(/'/g, '"'); + const parsedNewValue = JSON.parse(newValue); + children.push(parsedNewValue); + } + break; default: var newValue = this.state.newItemValue; children.push(newValue); @@ -181,6 +250,8 @@ class ListComponent extends Component { const { children } = this.state; if (this.props.realType == 'dict' || this.props.realType == 'dict(dict)') { delete children[childIndex]; + } else if (this.props.realType == 'list(dict)') { + children.splice(childIndex, 1); } else { children.splice(childIndex, 1); } @@ -190,7 +261,10 @@ class ListComponent extends Component { convertToPython (children) { // Update State - this.setState({ children, newItemValue: '' }); + this.setState({ + children, + newItemValue: '', + }); if (this.props.realType == 'dict' || this.props.realType == 'dict(dict)') { var newValue = children; @@ -203,6 +277,9 @@ class ListComponent extends Component { case 'list(list(float))': var childConverted = JSON.parse(child); break; + case 'list(dict)': + var childConverted = child; + break; default: var childConverted = child; break; @@ -228,6 +305,9 @@ class ListComponent extends Component { ) { return typeof value === 'string' ? JSON.parse(value) : value; } + if (this.props.realType == 'list(dict)') { + return typeof value === 'string' ? JSON.parse(value) : value; + } if (!Array.isArray(value)) { value = [value]; } @@ -247,32 +327,40 @@ class ListComponent extends Component { } render () { - const childrenWithExtraProp = Object.keys(this.state.children).map( - (key, index) => { - key = key.toString(); - if (this.props.realType == 'dict') { - var value = `${key} : ${JSON.stringify(this.state.children[key])}`; - } else if (this.props.realType == 'dict(dict)') { - var value = `${key - }: ${ - JSON.stringify(this.state.children[key]) + const childrenWithExtraProp = Object.keys(this.state.children) + .map( + (key, index) => { + key = key.toString(); + if (this.props.realType == 'dict') { + var value = `${key} : ${JSON.stringify(this.state.children[key])}`; + } else if (this.props.realType == 'dict(dict)') { + var value = `${key + }: ${ + JSON.stringify(this.state.children[key]) + .replace(/["']/g, '') + .replace(/[:]/g, ': ') + .replace(/[,]/g, ', ')}`; + } + else if (this.props.realType == 'list(dict)') { + var value = `${JSON.stringify(this.state.children[key]) .replace(/["']/g, '') .replace(/[:]/g, ': ') .replace(/[,]/g, ', ')}`; - } else { - var value = this.state.children[key]; - } - return ( - this.removeChild(key)} - color="primary" - /> - ); - }, - ); + } + else { + var value = this.state.children[key]; + } + return ( + this.removeChild(key)} + color="primary" + /> + ); + }, + ); const { classes } = this.props; return ( @@ -282,12 +370,15 @@ class ListComponent extends Component { - + ({ + root: { + position: 'relative', + marginBottom: theme.spacing(1), + }, + bottom: { + color: fontColor, + }, + top: { + color: primaryColor, + animationDuration: '550ms', + position: 'absolute', + left: 0, + }, + circle: { + strokeLinecap: 'round', + }, +})); + +const CircularLoader = () => { + const classes = useStyles(); + + return ( +
+ + +
+ ); +}; + +export default CircularLoader; diff --git a/webapp/components/general/NetPyNEAddNew.js b/webapp/components/general/NetPyNEAddNew.js index 07757afb..3addeb47 100644 --- a/webapp/components/general/NetPyNEAddNew.js +++ b/webapp/components/general/NetPyNEAddNew.js @@ -30,6 +30,7 @@ class NetPyNEAddNew extends React.Component { id={this.props.id} className={classes.root} onClick={this.handleClick} + style={{ borderRadius: '50%' }} > diff --git a/webapp/components/general/NetPyNECoordsRange.js b/webapp/components/general/NetPyNECoordsRange.js index eacf42c4..0d35b5f9 100644 --- a/webapp/components/general/NetPyNECoordsRange.js +++ b/webapp/components/general/NetPyNECoordsRange.js @@ -9,46 +9,18 @@ import Utils from '../../Utils'; export default class NetPyNECoordsRange extends Component { constructor (props) { super(props); - this.state = { rangeType: undefined }; + this.state = { rangeType: undefined, rangeValue: [undefined, undefined] }; this._isMounted = false; } - triggerUpdate (updateMethod) { - // common strategy when triggering processing of a value change, delay it, every time there is a change we reset - if (this.updateTimer != undefined) { - clearTimeout(this.updateTimer); - } - this.updateTimer = setTimeout(updateMethod, 1000); - } - - componentDidUpdate (prevProps, prevState) { - if (this.props.name != prevProps.name) { - this.triggerUpdate(() => { - const message = `netpyne_geppetto.${this.props.model}['${this.props.name}']${(this.props.conds != undefined) ? `['${this.props.conds}']` : ''}`; - Utils - .evalPythonMessage(`[key in ${message} for key in ['${this.props.items[0].value}', '${this.props.items[1].value}']]`) - .then((response) => { - if (response[0] && this._isMounted === true) { - this.setState({ rangeType: this.props.items[0].value }); - } else if (response[1] && this._isMounted === true) { - this.setState({ rangeType: this.props.items[1].value }); - } else if (this._isMounted === true) { - this.setState({ rangeType: undefined }); - } - }); - }); - } else if (this.props.conds != prevProps.conds) { - this.updateLayout(); - } - } - componentDidMount () { this._isMounted = true; this.updateLayout(); } - updateLayout () { + componentDidUpdate (prevProps, prevState) { + if (this.props.name != prevProps.name) { const message = `netpyne_geppetto.${this.props.model}['${this.props.name}']${(this.props.conds != undefined) ? `['${this.props.conds}']` : ''}`; Utils .evalPythonMessage(`[key in ${message} for key in ['${this.props.items[0].value}', '${this.props.items[1].value}']]`) @@ -61,6 +33,52 @@ export default class NetPyNECoordsRange extends Component { this.setState({ rangeType: undefined }); } }); + } else if (this.props.conds != prevProps.conds) { + this.updateLayout(); + } + } + + updateLayout () { + const { + items, + model, + conds, + name, + } = this.props; + + const message = `netpyne_geppetto.${model}['${name}']${(conds !== undefined) + ? `['${conds}']` : ''}`; + const evalMessage = `[key in ${message} for key in ['${items[0].value}', '${items[1].value}']]` ; + + Utils + .evalPythonMessage(evalMessage) + .then((response) => { + + let rangeType = undefined ; + + if (response[0] && this._isMounted === true) { + rangeType = items[0].value ; + } else if (response[1] && this._isMounted === true) { + rangeType = items[1].value ; + } + + this.setState({ rangeType }); + + if (rangeType) + { + const pythonMessage = `netpyne_geppetto.${model}['${name}']['${conds}']['${this.state.rangeType}']` ; + + Utils + .evalPythonMessage(pythonMessage) + .then((response) => { + if (response && response.length > 0 ) { + this.setState({ rangeValue: response }); + }}); + } + else { + this.setState({ rangeValue: [undefined, undefined] }); + } + }); } createMenuItems = () => this.props.items.map((obj) => ( @@ -77,6 +95,73 @@ export default class NetPyNECoordsRange extends Component { this._isMounted = false; } + handleRangeTypeChange(event) { + const { + model, + conds, + name, + } = this.props; + + const rangeType = event.target.value ; + + if (this.state.rangeType && this.state.rangeType.length > 0) + { + const pyPath = `netpyne_geppetto.${model}['${name}']['${conds}']`; + const startLetter = String(this.state.rangeType)[0]; + const pythonMessageDelOpposite = `${pyPath} = {k: v for k, v in ${pyPath}.items() if not k.startswith('${startLetter}')}`; + Utils.execPythonMessage( + pythonMessageDelOpposite + ); + + const rangeValue = this.state.rangeValue ; + + if (!rangeValue.some(e => e === undefined)) + { + const pythonMessage = `netpyne_geppetto.${model}['${name}']['${conds}']['${rangeType}'] = [${rangeValue}]` ; + Utils.execPythonMessage( + pythonMessage + ); + } + } + + this.setState({ rangeType}) + } + + //preConds: pop, cellType, cellModel, x, y, z, xnorm, ynorm, znorm + handleCoordParamChange(index, newValue) { + const { + model, + conds, + name, + } = this.props; + + + if (newValue === '' || (/^\d+$/.test(newValue))) { + if (this.state.rangeType && this.state.rangeType.length > 0) + { + const pyPath = `netpyne_geppetto.${model}['${name}']['${conds}']`; + const startLetter = String(this.state.rangeType)[0]; + const pythonMessageDelOpposite = `${pyPath} = {k: v for k, v in ${pyPath}.items() if not k.startswith('${startLetter}')}`; + Utils.execPythonMessage( + pythonMessageDelOpposite + ); + } + + const rangeValue = this.state.rangeValue ; + rangeValue[index] = newValue ; + + if (!rangeValue.some(e => e === undefined)) + { + const pythonMessage = `netpyne_geppetto.${model}['${name}']['${conds}']['${this.state.rangeType}'] = [${rangeValue}]` ; + Utils.execPythonMessage( + pythonMessage + ); + } + + this.setState({ rangeValue }) + } + } + render () { if (this.props.conds != undefined) { var meta = `${this.props.model}.${this.props.conds}.${this.props.items[0].value}`; @@ -87,6 +172,10 @@ export default class NetPyNECoordsRange extends Component { } const min = `${this.props.id}MinRange`; const max = `${this.props.id}MaxRange`; + + const minVal = this.state.rangeValue[0]; + const maxVal = this.state.rangeValue[1]; + return (
@@ -94,7 +183,7 @@ export default class NetPyNECoordsRange extends Component { id={`${this.props.id}Select`} label="Range type" value={this.state.rangeType || ''} - onChange={(event) => this.setState({ rangeType: event.target.value })} + onChange={(event) => { this.handleRangeTypeChange(event); }} > {this.createMenuItems()} @@ -102,27 +191,8 @@ export default class NetPyNECoordsRange extends Component { {(this.state.rangeType != undefined) ? ( - { - if (!state[state.lastUpdated].toString() - .endsWith('.') - && ((!isNaN(parseFloat(state[min]))) && (!isNaN(parseFloat(state[max]))))) { - return [parseFloat(state[min]), parseFloat(state[max])]; - } - }} - convertFromPython={(prevProps, prevState, value) => { - if (value != undefined && prevProps.value != value && value != '') { - const output = {}; - output[min] = value[0]; - output[max] = value[1]; - return output; - } - }} - > - - - + { this.handleCoordParamChange(0, parseInt(e.target.value)) } } /> + { this.handleCoordParamChange(1, parseInt(e.target.value)) } } /> ) : null} diff --git a/webapp/components/general/NetPyNEField.js b/webapp/components/general/NetPyNEField.js index eb3bd89f..cc84e686 100644 --- a/webapp/components/general/NetPyNEField.js +++ b/webapp/components/general/NetPyNEField.js @@ -1,35 +1,21 @@ import React, { Component } from 'react'; -import Dialog from '@material-ui/core/Dialog'; -import Button from '@material-ui/core/Button'; import MenuItem from '@material-ui/core/MenuItem'; - -import DialogActions from '@material-ui/core/DialogActions'; -import DialogContent from '@material-ui/core/DialogContent'; -import DialogContentText from '@material-ui/core/DialogContentText'; -import DialogTitle from '@material-ui/core/DialogTitle'; import { Tooltip } from 'netpyne/components'; import Grid from '@material-ui/core/Grid'; import Box from '@material-ui/core/Box'; import Utils from '../../Utils'; +import { REAL_TYPE } from '../../constants'; export default class NetPyNEField extends Component { constructor (props) { super(props); - this.state = { openHelp: false }; + this.state = { open: false }; } - handleOpenHelp = (help) => { - this.setState({ openHelp: true, helpText: help }); - }; - - handleCloseHelp = () => { - this.setState({ openHelp: false }); - }; - setErrorMessage (value) { return new Promise((resolve, reject) => { - if (this.realType == 'func') { - if (value != '' && value != undefined) { + if (this.realType === REAL_TYPE.FUNC) { + if (value !== '' && value !== undefined) { Utils.evalPythonMessage('netpyne_geppetto.validateFunction', [ value, ]).then((response) => { @@ -42,7 +28,7 @@ export default class NetPyNEField extends Component { } else { resolve({ errorMsg: '' }); } - } else if (this.realType == 'float') { + } else if (this.realType === REAL_TYPE.FLOAT) { if (isNaN(value)) { resolve({ errorMsg: 'Only float allowed' }); } else { @@ -53,57 +39,32 @@ export default class NetPyNEField extends Component { } prePythonSyncProcessing (value) { - if (value == '') { - if (this.default != undefined) { + if (value === '') { + if (this.default !== undefined) { return this.default; } if ( !this.model.split('.')[0].startsWith('simConfig') || this.model.split('.')[1].startsWith('analysis') ) { - Utils.execPythonMessage(`del netpyne_geppetto.${this.model}`); + Utils.execPythonMessage(` + try: + del netpyne_geppetto.${this.model} + except KeyError: + ...`); } } return value; } + handleTooltip (action) { + this.setState({ open: action }); + } + render () { - const help = Utils.getMetadataField(this.props.id, 'help'); - if (help != undefined && help != '') { - const helpComponent = ( -
- -
-