Upgrade master for release 5

.coveragerc

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

.dockerignore

@@ -0,0 +1,6 @@
+venv
+tmp
+**/*/node_modules
+pygeppetto-django
+static/org.geppetto.frontend
+service/docker

.env

@@ -1,11 +1,29 @@
 DEVELOPMENT=1
 PRODUCTION=0
 
-DB_HOST='localhost'
+DB_HOST=scidash-postgres
 DB_PORT=5432
-DB_NAME='scidash'
+DB_NAME=scidash
+DB_USER=scidash_admin
+DB_PASSWORD=scidash_local_password
 
-REDIS_URL='redis://'
+STATIC_URL=/static/
+STATIC_DIR=static
 
-STATIC_URL='/static/'
-STATIC_DIR='static'
+REDIS_URL=redis://scidash-redis:6379
+
+# 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://172.21.0.1:8000/static/projects/'
+
+DEBUG=True
+# ToDo: change in development sentry dsn
+SENTRY_DSN="https://ccf48f7877bc4fb5a4cca74bdd193feb@sentry.io/1955654" # base of all errors
+SENTRY_SYS_DSN="https://ccf48f7877bc4fb5a4cca74bdd193feb@sentry.io/1955654" # system/infra errors
+SENTRY_APP_DSN="https://81d007aa741d46ada0741f1a4f1cfd1c@sentry.io/2069800" # application errors

.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
@@ -120,3 +119,6 @@ static/models/*
 virgo-tomcat-server/*
 virgo-tomcat-server/work/*
 celerybeat.pid
+
+.devcontainer
+tmp

.project

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>scidash</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+	</buildSpec>
+	<natures>
+	</natures>
+</projectDescription>

.travis.yml

@@ -0,0 +1,20 @@
+language: node_js
+sudo: required
+node_js:
+  - "9"
+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 "python unit/integration testing running in geppetto-scidash travis" || true
+after_success:
+  - echo $TRAVIS_BRANCH
+  - echo $TRAVIS_PULL_REQUEST
+  - echo $TRAVIS_PULL_REQUEST_BRANCH
+  - if [ "${TRAVIS_PULL_REQUEST}" != "false" ]; then
+      bash $TRAVIS_BUILD_DIR/service/scripts/trigger-travis.sh --branch $TRAVIS_PULL_REQUEST_BRANCH Metacell geppetto-scidash  $TRAVIS_ACCESS_TOKEN ;
+      echo "I am in the first condition, so I am evaluating";
+    else
+      bash $TRAVIS_BUILD_DIR/service/scripts/trigger-travis.sh --branch $TRAVIS_BRANCH Metacell geppetto-scidash  $TRAVIS_ACCESS_TOKEN ;
+      echo "I am in the second condition";
+    fi
+  - cat /tmp/travis-request-output*

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         ="
@@ -19,7 +26,7 @@ install-frontend:
 	@echo "==========================="
 	@echo "=    Install frontend     ="
 	@echo "==========================="
-	@./service/scripts/install-frontend.sh
+	@./service/scripts/install-frontend.sh $(ARGS)
 
 codefresh-install-frontend:
 	@echo "==========================="
@@ -37,7 +44,7 @@ install-backend-with-env:
 	@echo "==========================="
 	@echo "=    Install backend      ="
 	@echo "==========================="
-	@./service/scripts/install-backend.sh -v
+	@./service/scripts/install-backend.sh -v $(ARGS)
 
 create-db:
 	@echo "==========================="
@@ -63,19 +70,20 @@ 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
+	cp ./service/dotenv/dev_env .env
+	$(MANAGECMD) runserver --insecure 0.0.0.0:8000
 
 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 +97,23 @@ 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
+
+run-coverage:
+	coverage run $(MANAGE) test
+
+coverage-badge: run-coverage
+	coverage-badge -o coverage.svg -f
+
+coverage: run-coverage
+	coverage report -m
+
 lint: flake8-lint isort-lint yapf-lint
 
 format: yapf-format isort-format
@@ -140,3 +165,5 @@ push-scidash-db:
 	@echo "=  Push scidash db image  ="
 	@echo "==========================="
 	@./service/scripts/push-image-scidash-db.sh
+%:
+    @: