Feature/400

Makefile

@@ -58,8 +58,7 @@ run-dev: migrate
 run-staging: migrate
 	make run-django-staging & \
 	make run-celery & \
-	make run-celery-beat & \
-	make run-virgo-staging
+	make run-celery-beat
 
 django-migrate: migrations migrate
 
@@ -85,7 +84,7 @@ run-celery:
 	celery -A scidash.main worker -l info --concurrency=5 --maxtasksperchild=20
 
 run-celery-beat:
-	celery -A scidash.main beat -l info --scheduler django_celery_beat.schedulers:DatabaseScheduler
+	celery -A scidash.main beat -l info --scheduler django_celery_beat.schedulers:DatabaseScheduler --pidfile=
 
 run-virgo-staging:
 	/bin/bash /opt/virgo/bin/startup.sh

requirements.in

@@ -13,3 +13,4 @@ celery[redis]
 django-celery-beat
 django-celery-results
 django-db-logger
+git+git://github.com/ddelpiano/neuronunit@4.0.0#egg=neuronunit

requirements.txt

@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile
 # To update, run:
 #
-#    pip-compile 
+#    pip-compile
 #
 amqp==2.4.2               # via kombu
 asgiref==2.3.2            # via channels
@@ -27,6 +27,7 @@ django==1.11.7
 djangorestframework-jwt==1.11.0
 djangorestframework==3.7.1
 drf-writable-nested==0.5.1
+git+git://github.com/ddelpiano/neuronunit@4.0.0#egg=neuronunit
 hyperlink==18.0.0         # via twisted
 idna==2.8                 # via hyperlink
 incremental==17.5.0       # via twisted

scidash/sciunittests/migrations/0046_auto_20190827_0221.py

@@ -0,0 +1,38 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.7 on 2019-12-11 01:56
+from __future__ import unicode_literals
+
+import datetime
+import django.contrib.postgres.fields.jsonb
+from django.db import migrations, models
+import scidash.sciunittests.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('sciunittests', '0045_auto_20190712_1041'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='testclass',
+            name='default_params',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, encoder=scidash.sciunittests.models.JSONEncoder, null=True),
+        ),
+        migrations.AlterField(
+            model_name='scoreinstance',
+            name='timestamp',
+            field=models.DateTimeField(default=datetime.datetime.today),
+        ),
+        migrations.AlterField(
+            model_name='testinstance',
+            name='timestamp',
+            field=models.DateTimeField(auto_now=True),
+        ),
+        migrations.AlterField(
+            model_name='testsuite',
+            name='timestamp',
+            field=models.DateTimeField(default=datetime.datetime.today),
+        ),
+    ]

scidash/sciunittests/views.py

@@ -17,16 +17,10 @@ def get(self, request, *args, **kwargs):
             day=current_date.day
         )
 
-        three_month_ago = current_date_iso - three_month_period
-        six_month_ago = three_month_ago - three_month_period
-        nine_month_ago = six_month_ago - three_month_period
-        tvelwe_month_ago = nine_month_ago - three_month_period
-
         acceptable_period = None
 
-        for period in [
-            three_month_ago, six_month_ago, nine_month_ago, tvelwe_month_ago
-        ]:
+        for quarter in range(1, s.SCIDASH_INITIAL_SEARCH_QUARTERS + 1):
+            period = current_date_iso - quarter*three_month_period
             count = ScoreInstance.objects.filter(
                 timestamp__gte=period, timestamp__lt=current_date_iso
             ).count()
@@ -36,7 +30,7 @@ def get(self, request, *args, **kwargs):
                 break
 
         if acceptable_period is None:
-            acceptable_period = tvelwe_month_ago
+            acceptable_period = period
 
         return Response(
             {

service/deployment/docker-compose.yml

@@ -4,21 +4,29 @@ services:
   scidash-redis:
     image: redis
     expose:
-        - "6379"
+        - 6379
   scidash-postgres:
     image: metacell/scidash_db:latest
     expose:
-        - "5432"
+        - 5432
     volumes:
         - ./database:/var/lib/postgresql/
-  scidash:
-    image: metacell/scidash:latest
+  scidash-virgo:
+    image: metacell/scidash_virgo:v1.0.0
+    expose:
+        - 8080
     mem_reservation: 5120m
     mem_limit: 10240m
-    priviliged: true
+    privileged: true
     shm_size: 512M
-    expose:
-        - "8000"
     depends_on:
         - scidash-redis
         - scidash-postgres
+  scidash:
+    image: metacell/scidash:latest
+    ports:
+        - 8000:8000
+    depends_on:
+        - scidash-redis
+        - scidash-postgres
+        - scidash-virgo

service/docker/Dockerfile-scidash

@@ -1,6 +1,6 @@
-FROM metacell/scidash_virgo:v1.0.0
+FROM python:3.6
 
-USER root 
+USER root
 
 # BUILD VARIABLES
 ARG ROOT=/
@@ -9,47 +9,45 @@ ARG NRN_SYMLINK=/Applications/NEURON-7.6/nrn/
 ARG DOTENV_FILE=env-docker
 ARG STATIC_DIR=$APP_DIR/scidash/static
 ARG GEPPETTO_DIR=$STATIC_DIR/org.geppetto.frontend/src/main/webapp
-ARG SCIDASH_BRANCH=4.0.1
+ARG SCIDASH_BRANCH=feature/400
 ENV SERVER_HOME $APP_DIR/virgo-tomcat-server
 
-WORKDIR $ROOT
+RUN useradd -ms /bin/bash developer
+ENV HOME /home/developer
 
-#COPYING PROJECT
-WORKDIR $APP_DIR
-RUN git clone -b $SCIDASH_BRANCH https://github.com/MetaCell/scidash
+WORKDIR $ROOT
 
 # INSTALLING REQUIREMENTS
-RUN apt-get install -y curl wget lsof
+RUN apt-get install -y curl wget
 RUN curl -sL https://deb.nodesource.com/setup_9.x | bash
 RUN apt-get update && apt-get -y install nodejs
+RUN curl https://www.npmjs.com/install.sh | sh
+
+#COPYING PROJECT
+WORKDIR $APP_DIR
+RUN git clone -b $SCIDASH_BRANCH https://github.com/MetaCell/scidash
 
-WORKDIR /nrn
-RUN chown -R developer ./
 
 WORKDIR $APP_DIR/scidash
-RUN pip install virtualenv 
+RUN pip install virtualenv
 RUN virtualenv venv-py -p python3.6
-WORKDIR /usr/local/nrn/src/nrnpython
-RUN python setup.py install
 
 WORKDIR $APP_DIR/scidash
 RUN make install-backend-with-env
-RUN make install-sciunit-neuronunit
 RUN make install-frontend
 
 WORKDIR $GEPPETTO_DIR
 RUN ls -la
 RUN npm run build-dev-noTest
 
 WORKDIR $APP_DIR/scidash
-RUN rm -rf .git &&\ 
-    rm -rf static/org.geppetto.frontend/.git &&\ 
+RUN rm -rf .git &&\
+    rm -rf static/org.geppetto.frontend/.git &&\
     rm -rf static/org.geppetto.frontend/extension/geppetto-scidash/.git &&\
     rm -rf sciunit/.git &&\
     rm -rf neuronunit/.git
 RUN chown -R developer ./
 RUN cp ./service/dotenv/scidash_env .env
 
 USER developer
-
 CMD ./service/scripts/run.sh

service/docker/Dockerfile-virgo

@@ -14,6 +14,7 @@ ARG SCIDASH_BRANCH=development
 WORKDIR /
 RUN useradd -ms /bin/bash developer
 ENV HOME /home/developer
+RUN printf "\ndeb http://deb.debian.org/debian/ sid main\n" >> /etc/apt/sources.list
 RUN apt-get update && \
     apt-get install -y openjdk-8-jdk && \
     apt-get install -y ant && \
@@ -80,14 +81,14 @@ RUN ls -l /usr/local/nrn/
 
 # -== INSTALL VIRGO ==-
 RUN mkdir $VIRGO_DIR
-RUN apt-get install curl
+RUN apt-get -y install curl
 RUN curl -L 'http://www.eclipse.org/downloads/download.php?file=/virgo/release/VP/3.7.2.RELEASE/virgo-tomcat-server-3.7.2.RELEASE.zip&r=1' > virgo.zip
 RUN unzip virgo.zip
 RUN cp -r ./virgo-tomcat-server-3.7.2.RELEASE/* $VIRGO_DIR
 RUN rm $VIRGO_DIR/configuration/java-server.profile
 RUN cp /git/scidash/service/geppetto/java-server.profile $VIRGO_DIR/configuration/
 RUN rm $VIRGO_DIR/configuration/tomcat-server.xml
-RUN cp /git/scidash/service/geppetto/tomcat-server.xml $VIRGO_DIR/configuration/
+RUN cat /git/scidash/service/geppetto/tomcat-server.xml | sed 's/127.0.0.1/0.0.0.0/' > $VIRGO_DIR/configuration/tomcat-server.xml
 RUN chmod u+x $VIRGO_DIR/bin/*.sh
 ENV SERVER_HOME $VIRGO_DIR
 RUN chmod 777 -R $VIRGO_DIR

service/dotenv/env-docker

@@ -12,6 +12,12 @@ STATIC_DIR=static
 
 REDIS_URL=redis://scidash-redis:6379
 
-GEPPETTO_SERVLET_URL='ws://localhost:8080/org.geppetto.frontend/GeppettoServlet'
-GEPPETTO_BASE_URL='http://localhost:8080/org.geppetto.frontend/geppetto'
-BASE_PROJECT_FILES_HOST='http://localhost:8000/static/projects/'
+# for localhost
+# GEPPETTO_HOST=localhost
+# for docker
+GEPPETTO_HOST=scidash-virgo
+GEPPETTO_PORT=8080
+GEPPETTO_SERVLET_URL=ws://${GEPPETTO_HOST}:${GEPPETTO_PORT}/org.geppetto.frontend/GeppettoServlet
+GEPPETTO_BASE_URL=http://${GEPPETTO_HOST}:${GEPPETTO_PORT}/org.geppetto.frontend/geppetto
+
+BASE_PROJECT_FILES_HOST='http://scidash:8000/static/projects/'

service/dotenv/scidash_env

@@ -12,6 +12,12 @@ REDIS_URL=redis://scidash-redis:6379
 STATIC_URL='/static/'
 STATIC_DIR='static'
 
-# GEPPETTO_SERVLET_URL='ws://scidash-virgo:8080/org.geppetto.frontend/GeppettoServlet'
-# GEPPETTO_BASE_URL='http://scidash-virgo:8080/org.geppetto.frontend/geppetto'
-# BASE_PROJECT_FILES_HOST='http://scidash-virgo:8000/static/projects/'
+# for localhost
+# GEPPETTO_HOST=localhost
+# for docker
+GEPPETTO_HOST=scidash-virgo
+GEPPETTO_PORT=8080
+GEPPETTO_SERVLET_URL=ws://${GEPPETTO_HOST}:${GEPPETTO_PORT}/org.geppetto.frontend/GeppettoServlet
+GEPPETTO_BASE_URL=http://${GEPPETTO_HOST}:${GEPPETTO_PORT}/org.geppetto.frontend/geppetto
+
+BASE_PROJECT_FILES_HOST='http://scidash:8000/static/projects/'

service/geppetto/GeppettoConfiguration.json

@@ -1,7 +1,7 @@
 {
 	"_README": "http://docs.geppetto.org/en/latest/build.html",
 	"contextPath": "org.geppetto.frontend",
-	"useSsl": true,
+	"useSsl": false,
 	"embedded": false,
 	"embedderURL": ["/"],
 	"rootRedirect": "",

service/geppetto/tomcat-server.xml

@@ -27,7 +27,7 @@
   <Listener className="org.apache.catalina.security.SecurityListener" />
 
   <Service name="Catalina">
-    <Connector address="127.0.0.1" port="8080"
+    <Connector address="0.0.0.0" port="8080"
                protocol="org.apache.coyote.http11.Http11NioProtocol"
                connectionTimeout="20000" enableLookups="false" redirectPort="8443" />
 

service/scripts/db-create-psql.sh

@@ -1,17 +1,8 @@
 #!/bin/bash
 
-psql -d template1 -c 'create extension hstore;'
-
-psql <<EOF
-\x
-DROP DATABASE IF EXISTS scidash;
-CREATE DATABASE scidash;
-\c scidash;
-
-REVOKE ALL PRIVILEGES ON DATABASE scidash FROM scidash_admin;
-DROP USER IF EXISTS scidash_admin;
-CREATE USER scidash_admin WITH PASSWORD 'scidash_local_password';
-
-GRANT ALL PRIVILEGES ON DATABASE scidash TO scidash_admin;
-ALTER USER scidash_admin CREATEDB
-EOF
+cd /tmp
+git clone https://github.com/ddelpiano/scidash-artifacts
+cd scidash-artifacts/database
+gunzip `ls | head -n 1`
+pg_restore --clean -d scidash `ls *db | head -n 1`
+cd -

service/scripts/db-create-psql.sh.bak

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+psql -d template1 -c 'create extension hstore;'
+
+psql <<EOF
+\x
+DROP DATABASE IF EXISTS scidash;
+CREATE DATABASE scidash;
+\c scidash;
+
+REVOKE ALL PRIVILEGES ON DATABASE scidash FROM scidash_admin;
+DROP USER IF EXISTS scidash_admin;
+CREATE USER scidash_admin WITH PASSWORD 'scidash_local_password';
+
+GRANT ALL PRIVILEGES ON DATABASE scidash TO scidash_admin;
+ALTER USER scidash_admin CREATEDB
+EOF