#412 Create django tests to test connection to the Java backend

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+plugins =
+    django_coverage_plugin
+omit =
+    venv/*
+    static/*
+    */migrations/*

.flake8

@@ -1,3 +1,3 @@
 [flake8]
 max-line-length = 79
-exclude = .git,__pycache__,build,dist,.tox,*/migrations/*,env,__init__.py,settings.py,*/node_modules/*,routing.py
+exclude = .git,__pycache__,build,dist,.tox,*/migrations/*,env,venv,__init__.py,settings.py,*/node_modules/*,routing.py

.gitignore

@@ -39,9 +39,8 @@ MANIFEST
 pip-log.txt
 pip-delete-this-directory.txt
 
-# Unit test / coverage reports
+# Unit tests / coverage reports
 htmlcov/
-.tox/
 .coverage
 .coverage.*
 .cache

.travis.yml

@@ -5,7 +5,7 @@ node_js:
 install:
   - npm install jest@24.8.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
 script:
-  - echo -e "Trigger python unit testing in here when they will be ready" || true
+  - echo -e "python unit/integration testing running in geppetto-scidash travis" || true
 after_success:
   - echo $TRAVIS_BRANCH
   - echo $TRAVIS_PULL_REQUEST

Makefile

@@ -1,3 +1,10 @@
+
+VENV:=$(shell if [ -d "venv" ]; then echo "venv/bin/"; else echo ""; fi)
+PYTHON:=$(VENV)python3
+PIP:=$(VENV)/bin/pip
+MANAGE:="manage.py"
+MANAGECMD=$(PYTHON) $(MANAGE)
+
 install: create-db install-sciunit-neuronunit install-frontend install-backend
 	@echo "==========================="
 	@echo "=        Finished         ="
@@ -63,19 +70,19 @@ run-staging: migrate
 django-migrate: migrations migrate
 
 migrations:
-	./manage.py makemigrations
+	$(MANAGECMD) makemigrations
 
 migrate:
-	./manage.py migrate
+	$(MANAGECMD) migrate
 
 superuser:
-	./manage.py createsuperuser
+	$(MANAGECMD) createsuperuser
 
 run-django:
-	./manage.py runserver
+	$(MANAGECMD) runserver
 
 run-django-staging:
-	python3.6 manage.py runserver --insecure 0.0.0.0:8000
+	$(MANAGECMD) runserver --insecure 0.0.0.0:8000
 
 run-frontend:
 	cd static/org.geppetto.frontend/src/main/webapp/; npm run build-dev-noTest:watch;
@@ -89,6 +96,18 @@ run-celery-beat:
 run-virgo-staging:
 	/bin/bash /opt/virgo/bin/startup.sh
 
+manage/%:
+	$(MANAGECMD) $*
+
+run-tests: run-django-tests
+
+run-django-tests:
+	$(MANAGECMD) test
+
+coverage:
+	coverage run $(MANAGE) test
+	coverage report -m
+
 lint: flake8-lint isort-lint yapf-lint
 
 format: yapf-format isort-format

README.md

@@ -1,3 +1,5 @@
+[![Build Status](https://img.shields.io/travis/MetaCell/scidash/master.svg?style=flat-square&label=master)](https://travis-ci.org/MetaCell/scidash)
+[![Build Status](https://img.shields.io/travis/MetaCell/scidash/development.svg?style=flat-square&label=develop)](https://travis-ci.org/MetaCell/scidash)
 <p align="center">
   <img src="http://scidash.github.io/assets/scidash-text.png" alt="SciDash logo"/>
 </p>

requirements-dev.txt

@@ -1,3 +1,6 @@
 flake8
 yapf
 isort
+coverage
+django_coverage_plugin
+pip-tools

requirements.in

@@ -1,5 +1,5 @@
-psycopg2
 django==1.11.23
+psycopg2==2.7.7
 channels==2.1.2
 djangorestframework==3.7.1
 drf-writable-nested
@@ -14,3 +14,4 @@ django-celery-beat
 django-celery-results
 django-db-logger
 git+git://github.com/ddelpiano/neuronunit@4.0.0#egg=neuronunit
+wheel==0.33.6

requirements.txt

@@ -2,45 +2,24 @@
 # This file is autogenerated by pip-compile
 # To update, run:
 #
-#    pip-compile
+#    pip-compile requirements.in
 #
-airspeed==0.5.4dev-20150515
-allensdk==0.14.5
 amqp==2.4.2               # via kombu
-apipkg==1.5               # via execnet
-argparse==1.4.0           # via scoop
 asgiref==2.3.2            # via channels
-asteval==0.9.18           # via lmfit
 async-timeout==3.0.1      # via asgiref
-attrs==19.1.0             # via automat, jsonschema, twisted
+attrs==19.1.0             # via automat, twisted
 autobahn==19.3.3          # via daphne
 automat==0.7.0            # via twisted
-backcall==0.1.0           # via ipython
-backports.tempfile==1.0
-backports.weakref==1.0.post1  # via backports.tempfile
-beautifulsoup4==4.8.2     # via bs4
 billiard==3.5.0.5         # via celery
-bleach==3.1.0             # via nbconvert
-git+https://github.com/russelljjarvis/BluePyOpt@scidash#egg=bluepyopt-9999
-bokeh==1.4.0              # via dask
-bs4==0.0.1
-cachetools==0.8.0         # via airspeed
 celery[redis]==4.2.2
-cerberus==1.3.2
-certifi==2019.11.28       # via requests
 channels==2.1.2
-chardet==3.0.4            # via requests
-click==7.0                # via distributed
-cloudpickle==1.2.2        # via dask, distributed
 constantly==15.1.0        # via twisted
-cycler==0.10.0            # via matplotlib
-cypy==0.2.0
 daphne==2.2.5             # via channels
-dask[complete]==2.9.1     # via distributed
+dask[complete]==2.9.0     # via distributed
 deap==1.3.0
 decorator==4.4.1          # via ipyparallel, ipython, networkx, traitlets, validators
 defusedxml==0.6.0         # via nbconvert
-distributed==2.9.1        # via dask
+distributed==2.9.0        # via dask
 django-celery-beat==1.4.0
 django-celery-results==1.0.4
 django-db-logger==0.1.7
@@ -53,26 +32,17 @@ django==1.11.23
 djangorestframework-jwt==1.11.0
 djangorestframework==3.7.1
 drf-writable-nested==0.5.1
-efel==3.0.70
-elephant==0.4.1
-entrypoints==0.3          # via nbconvert
-execnet==1.7.1
-fsspec==0.6.2             # via dask
-future==0.18.2            # via allensdk
-gitdb2==2.0.6             # via gitpython
-gitpython==3.0.5
-greenlet==0.4.15          # via scoop
-h5py==2.10.0              # via allensdk
-heapdict==1.0.1           # via zict
+git+git://github.com/ddelpiano/neuronunit@4.0.0#egg=neuronunit
 hyperlink==18.0.0         # via twisted
 idna==2.8                 # via hyperlink, requests
 igor==0.3
 imageio==2.6.1            # via scikit-image
+importlib-metadata==1.3.0  # via jsonschema
 incremental==17.5.0       # via twisted
 ipykernel==5.1.3          # via ipyparallel
 ipyparallel==6.2.4
 ipython-genutils==0.2.0   # via ipyparallel, nbformat, traitlets
-ipython==7.11.1           # via ipykernel, ipyparallel
+ipython==7.10.2           # via ipykernel, ipyparallel
 jedi==0.15.2              # via ipython
 jinja2==2.10.3            # via allensdk, bokeh, nbconvert
 jsonschema==3.2.0         # via nbformat
@@ -89,6 +59,7 @@ lxml==4.4.2               # via libneuroml
 markupsafe==1.1.1         # via jinja2
 matplotlib==3.1.2         # via allensdk, scikit-image
 mistune==0.8.4            # via nbconvert
+more-itertools==8.0.2     # via zipp
 msgpack==0.6.2            # via distributed
 nbconvert==5.6.1
 nbformat==4.4.0           # via nbconvert
@@ -106,54 +77,33 @@ partd==1.1.0              # via dask
 patsy==0.5.1              # via statsmodels
 pexpect==4.7.0            # via ipython
 pickleshare==0.7.5        # via ipython
-pillow==7.0.0             # via bokeh, imageio, scikit-image
+pillow==6.2.1             # via bokeh, imageio, scikit-image
 prompt-toolkit==3.0.2     # via ipython
 psutil==5.6.7             # via distributed
 psycopg2==2.7.7
-ptyprocess==0.6.0         # via pexpect
-pygments==2.5.2           # via ipython, nbconvert
 pyhamcrest==1.9.0         # via twisted
 pyjwt==1.7.1              # via djangorestframework-jwt
 pylems==0.4.9.3
 git+https://github.com/rgerkin/pyneuroml@master#egg=pyneuroml-9999
 pynn==0.9.5
-pynrrd==0.4.2             # via allensdk
+pynrrd==0.4.1             # via allensdk
 pyparsing==2.4.6          # via matplotlib, packaging
 pyrsistent==0.15.6        # via jsonschema
 python-crontab==2.3.6     # via django-celery-beat
-python-dateutil==2.8.0    # via bokeh, ipyparallel, jupyter-client, matplotlib, pandas, python-crontab
-pytz==2018.9              # via celery, django, django-timezone-field, pandas
-pywavelets==1.1.1         # via scikit-image
-pyyaml==5.2               # via bokeh, dask, distributed
-pyzmq==18.1.1             # via ipyparallel, jupyter-client, scoop
-quantities==0.12.1        # via elephant, neo, pynn
+python-dateutil==2.8.0    # via python-crontab
+pytz==2018.9              # via celery, django, django-timezone-field
 redis==2.10.6             # via celery
-requests-toolbelt==0.9.1  # via allensdk
-requests==2.22.0          # via allensdk, requests-toolbelt
 rest-framework-cache==0.1
-scikit-image==0.16.2      # via allensdk
-scipy==1.4.1              # via allensdk, elephant, lmfit, scikit-image, statsmodels
-git+https://github.com/scidash/sciunit@dev#egg=sciunit-9999
-scoop==0.7.1.1
-simpleitk==1.2.4          # via allensdk
-simplejson==3.17.0        # via allensdk
-six==1.12.0               # via airspeed, allensdk, autobahn, automat, bleach, bokeh, cycler, django-extensions, efel, elephant, h5py, jsonschema, libneuroml, packaging, patsy, pyhamcrest, pyrsistent, python-dateutil, traitlets, txaio, validators
-smmap2==2.0.5             # via gitdb2
-sortedcontainers==2.1.0   # via distributed
-soupsieve==1.9.5          # via beautifulsoup4
-statsmodels==0.10.2       # via allensdk
-tblib==1.6.0              # via distributed
-testpath==0.4.4           # via nbconvert
-toolz==0.10.0             # via dask, distributed, partd
-tornado==6.0.3            # via bokeh, distributed, ipykernel, ipyparallel, jupyter-client
-traitlets==4.3.3          # via ipykernel, ipyparallel, ipython, jupyter-client, jupyter-core, nbconvert, nbformat
+six==1.12.0               # via autobahn, automat, django-extensions, pyhamcrest, python-dateutil, txaio
 twisted==18.9.0           # via daphne
 txaio==18.8.1             # via autobahn
-uncertainties==3.1.2      # via lmfit
-urllib3==1.25.7           # via requests
-validators==0.14.1
 vine==1.3.0               # via amqp
-wcwidth==0.1.8            # via prompt-toolkit
+wcwidth==0.1.7            # via prompt-toolkit
 webencodings==0.5.1       # via bleach
+wheel==0.33.6
 zict==1.0.0               # via distributed
+zipp==0.6.0               # via importlib-metadata
 zope.interface==4.6.0     # via twisted
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

scidash/general/serializers.py

@@ -1,4 +1,4 @@
-from rest_framework import serializers
+from rest_framework import serializers, fields
 
 from scidash.general.models import Tag
 
@@ -7,3 +7,48 @@ class TagSerializer(serializers.ModelSerializer):
     class Meta:
         model = Tag
         fields = ('name', )
+
+
+class SerializerWritableMethodField(fields.ModelField):
+    """
+    A writable (ModelField base) SerializerMethodField that get its
+    representation from calling a method on the parent serializer class. The
+    method called will be of the form "get_{field_name}", and should take a
+    single argument, which is the object being serialized.
+
+    For example:
+
+    class ExampleSerializer(self):
+        class_name = SciDashSerializerWritableMethodField(
+                model_field=TestClass()._meta.get_field('class_name'))
+
+        def get_class_name(self, obj):
+            return ...  # Calculate some data to return.
+    """
+
+    def __init__(self, method_name=None, **kwargs):
+        self.method_name = method_name
+        super(SerializerWritableMethodField, self).__init__(**kwargs)
+
+    def bind(self, field_name, parent):
+        # In order to enforce a consistent style, we error if a redundant
+        # 'method_name' argument has been used. For example:
+        # my_fld = serializer.SerializerMethodField(method_name='get_my_fld')
+        default_method_name = 'get_{field_name}'.format(field_name=field_name)
+        assert self.method_name != default_method_name, (
+            "It is redundant to specify `%s` on SerializerMethodField '%s' in "
+            "serializer '%s', because it is the same as the default method "
+            "name. Remove the `method_name` argument." %
+            (self.method_name, field_name, parent.__class__.__name__)
+        )
+
+        # The method name should default to `get_{field_name}`.
+        if self.method_name is None:
+            self.method_name = default_method_name
+
+        super(SerializerWritableMethodField, self).bind(
+            field_name, parent)
+
+    def to_representation(self, value):
+        method = getattr(self.parent, self.method_name)
+        return method(value)

scidash/general/tests/test_geppetto_servlet.py

@@ -0,0 +1,15 @@
+from django.test import TestCase
+
+from pygeppetto_gateway.base import GeppettoServletManager
+
+
+class GeppettoServletTest(TestCase):
+    @classmethod
+    def setUpClass(cls):
+        super(GeppettoServletTest, cls).setUpClass()
+        cls.servlet_manager = GeppettoServletManager()
+
+    def test_ws_address(self):
+        self.assertEqual(
+            self.servlet_manager.host,
+            "ws://scidash-virgo:8080/org.geppetto.frontend/GeppettoServlet")

scidash/sciunitmodels/tests/test_data/score_object.json

@@ -1,11 +1,29 @@
 {
-  "score_class": {"class_name": "ZScore", "url": "http://test-url.for/not-spaming-data/in-database"},
+  "score_class": {
+    "class_name": "ZScore",
+    "url": "http://test-url.for/not-spaming-data/in-database"
+  },
   "hash_id": "111",
   "model_instance": {
     "model_class": {
       "class_name": "ReducedModel",
       "url": "http://test-url.for/not-spaming-data/in-database",
+      "import_path": "neuronunit.models.static.StaticModel",
+      "memo": null,
+      "extra_capabilities": [],
       "capabilities": [
+        {
+          "class_name": "ReceivesSquareCurrent"
+        },
+        {
+          "class_name": "ProducesActionPotentials"
+        },
+        {
+          "class_name": "ProducesSpikes"
+        },
+        {
+          "class_name": "ProducesMembranePotential"
+        },
         {
           "class_name": "CanBeReduced"
         }
@@ -25,16 +43,18 @@
   "test_instance": {
     "description": null,
     "hash_id": "111",
-    "test_suites": [{
-      "hash": "testhash",
-      "name": "ReducedSuite"
-    }],
+    "test_suites": [
+      {
+        "hash": "testhash",
+        "name": "ReducedSuite"
+      }
+    ],
     "test_class": {
       "class_name": "MyTest",
       "url": "http://test-url.for/not-spaming-data/in-database"
     },
     "observation": {
-      "mean":"8",
+      "mean": "8",
       "std": "3",
       "url": ""
     },