Merge pull request #133 from MetaCell/feature/130

Feature/130

Author: filippomc

.dockerignore

@@ -10,4 +10,7 @@ netpyne
 Dockerfile
 Dockerfile_base
 Dockerfile_dev
-netpyne_workspace
+netpyne_workspace
+webapp/node_modules
+webapp/build
+webapp/geppetto-client

.gitignore

@@ -9,6 +9,12 @@ netpyne/
 org.geppetto.frontend.jupyter/
 *.ipynb
 init.py
+webapp/node_modules
+webapp/geppetto-client
+webapp/build
+tests
+netpyne_workspace
+Dockerfile_mini
 npm*
 .vscode
 app.log

.gitmodules

@@ -1,76 +1,14 @@
 language: python
 os: linux
-sudo: false
 dist: trusty
-bundler_args: --retry 5
 node_js:
   - "7"
 env:
   global:
     secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
-before_install:
-- sudo apt-get install -y xserver-xorg-dev libxext-dev libxi-dev
-install:
-- git clone --quiet  https://github.com/MetaCell/geppetto-netpyne.git
-- cd geppetto-netpyne
-- if [ `git branch -a | egrep "remotes/origin/${TRAVIS_BRANCH}"` ]; then git checkout $TRAVIS_BRANCH ; else echo "Branch $TRAVIS_BRANCH does not exist for the dependent bundle, checking out development ..." && git checkout development; fi
-- cd ..
-- npm install --silent -g phantomjs
-- npm install --silent -g casperjs
-- npm install --silent -g slimerjs
-- npm install --silent -g gl
-python:
-  - "2.7"
-  - "3.5"
-edge: true
 notifications:
   slack: metacell:5ALSeoP88DqIhORUJvxE56sq
 services:
-  - docker
-addons:
-  firefox: "58.0"
-  apt:
-    packages:
-    - mesa-utils
-    - xvfb
-    - libgl1-mesa-dri
-    - libglapi-mesa
-    - libosmesa6
-
-before_script:
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
-  - export SLIMERJSLAUNCHER=/home/travis/firefox-58.0/firefox/firefox
-  - export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/
-    
+  - docker  
 script:
-  - travis_retry docker build -t="netpyne-ui" --build-arg branch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .
-  - travis_retry docker run  -t -dit --name=netpyne-ui_container -h localhost -p 8888:8888 netpyne-ui:latest
-  - cd $TRAVIS_BUILD_DIR/ && ls
-  - cd geppetto-netpyne && ls
-  - cd tests
-  - bash utilities/netpyne-server-status.sh
-  - sleep 30
-  - http_status=$(curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'})
-  - echo "$http_status"
-  - while [ "$http_status" == "404" ]; do
-      echo "Restart run";
-      echo "Printing logs for debugging purposes";
-      docker stop $(docker ps -a -q);
-      docker rm $(docker ps -a -q);
-      docker run  -t -dit --name=netpyne-ui_container -h localhost -p 8888:8888 netpyne-ui:latest
-      bash utilities/netpyne-server-status.sh
-      sleep 30;
-      http_status=$(curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'})
-      echo "Done restarting";
-      echo "$http_status";
-    done;
-  - http_status=$(curl -s -I $1 http://localhost:28081 | grep HTTP/1.1 | awk {'print $2'})
-  - echo "$http_status";
-  - "curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'}"
-  - firefox --version
-  - travis_retry xvfb-run -a --server-args="-screen 0 1024x768x24"  casperjs test netpyne-tests.js --host=http://localhost:8888/ --engine=slimerjs
-  - python -c "import fcntl; fcntl.fcntl(1, fcntl.F_SETFL, 0)"
-  - docker logs -t netpyne-ui_container
-  - docker stop $(docker ps -a -q)
-  - docker rm $(docker ps -a -q)
+  - travis_retry docker build -t="netpyne-ui" --build-arg branch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .

.travis.yml

@@ -124,7 +124,7 @@ steps:
       - CHART_NAME=jupyterhub
       - RELEASE_NAME=${{RELEASE_NAME}}
       - KUBE_CONTEXT=geppetto-cluster@metacellllc
-      - NAMESPACE=netpyne
+      - NAMESPACE=${{NAMESPACE}}
       - TILLER_NAMESPACE=kube-system
       - CHART_VERSION=0.9.0-beta.4
       - 'CHART_REPO_URL=https://jupyterhub.github.io/helm-chart/'

k8s/cf.yaml

@@ -69,19 +69,11 @@ def main(argv):
 # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip
 # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./')
 clone_repo(project='openworm',
-           repo_name='org.geppetto.frontend',
-           folder='geppetto',
-           default_branch='feature/127',
-           cwdp='netpyne_ui/',
+           repo_name='geppetto-client',
+           folder='geppetto-client',
+           default_branch='feature/178',
+           cwdp='webapp/',
            recursive=False,
-           destination_folder='geppetto'
-)
-
-clone_repo(project='MetaCell',
-           repo_name='geppetto-netpyne',
-           folder='geppetto-netpyne',
-           default_branch='development',
-           cwdp='netpyne_ui/geppetto/src/main/webapp/extensions/'
 )
 
 branch = None
@@ -106,15 +98,12 @@ def main(argv):
     subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout)
 subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js')
 
-print("Enabling Geppetto NetPyNE Extension ...")
-geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.copyme.json')
-copyfile(geppetto_configuration, './netpyne_ui/geppetto/src/main/webapp/GeppettoConfiguration.json')
 
 # Installing and building
 print("NPM Install and build for Geppetto Frontend  ...")
 with open('npm_frontend_log', 'a') as stdout:
-    subprocess.call(['npm', 'install'], cwd='./netpyne_ui/geppetto/src/main/webapp/', stdout=stdout)
-subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
+    subprocess.call(['npm', 'install'], cwd='webapp/', stdout=stdout)
+subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='webapp/')
 
 print("Installing jupyter_geppetto python package ...")
 subprocess.call(['python3', '-m', 'pip', 'install', '-e', '.'], cwd='./org.geppetto.frontend.jupyter')

netpyne_ui/geppetto

@@ -0,0 +1,9 @@
+etc/*
+node/*
+build/*
+META-INF/*
+**/tests/casperjs/**/*.js
+**/tests/jest-puppeteer/**/*.js
+**/*min.js
+geppetto-client/**
+node_modules/**

utilities/install.py

@@ -0,0 +1,19 @@
+module.exports = {
+  extends: [
+    "./node_modules/@geppettoengine/geppetto-client/.eslintrc.js",
+    "plugin:jest/recommended"
+  ],
+  plugins: ["jest"],
+  globals: {
+    page: true,
+    browser: true,
+    context: true,
+    jestPuppeteer: true,
+    acnet2: true,
+    c302: true,
+    pvdr: true,
+    net1: true,
+    CanvasContainer: true,
+    patchRequire: true
+  }
+};

webapp/.eslintignore

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