V1.0.0

.eslintrc.json

@@ -8,6 +8,7 @@
   },
   "extends": "eslint:recommended",
   "parserOptions": {
+    "ecmaVersion": 8,
     "ecmaFeatures": {
       "jsx": true
     }

.gitignore

@@ -4,9 +4,10 @@ node_modules
 build
 .DS_Store
 *.log
-package-lock.json
 rethinkdb_data/*
 src/scripts/pathways/*
 src/scripts/sbgn/*
 src/scripts/jsonld/*
 .vscode/*
+/.idea/
+/nohup.out

.travis.yml

@@ -1,8 +1,14 @@
+dist: trusty
 language: node_js
 node_js:
-  - "6"
-  - "7"
   - "8"
   - "stable"
-sudo: false
-script: npm run test
+script: npm run test:travis
+sudo: required
+before_install:
+  - sudo apt-get -qq update
+  - source /etc/lsb-release && echo "deb http://download.rethinkdb.com/apt $DISTRIB_CODENAME main" | sudo tee /etc/apt/sources.list.d/rethinkdb.list
+  - wget -qO- https://download.rethinkdb.com/apt/pubkey.gpg | sudo apt-key add -
+  - sudo apt-get update
+  - sudo apt-get install rethinkdb
+  - rethinkdb &

Dockerfile

@@ -2,24 +2,33 @@
 # https://nodejs.org/en/docs/guides/nodejs-docker-webapp/
 # https://github.com/nodejs/docker-node
 
-# v6 is the latest LTS
-FROM node:6
+# Node.js base image 
+FROM node:8
+
+# Create an unprivileged user w/ home directory
+RUN groupadd appuser \
+  && useradd --gid appuser --shell /bin/bash --create-home appuser
 
 # Create app directory
-RUN mkdir -p /usr/src/app
-WORKDIR /usr/src/app
+RUN mkdir -p /home/appuser/app
+WORKDIR /home/appuser/app
 
 # Bundle app
-COPY . /usr/src/app
+COPY . /home/appuser/app
 
 # Install app dependencies
 RUN npm install
 
 # Build project 
-# RUN npm run build
+RUN npm run clean
+RUN npm run build
 
 # Expose port
 EXPOSE 3000
 
+# Change ownership of the app to the unprivileged user 
+RUN chown appuser:appuser -R /home/appuser/app
+USER appuser 
+
 # Run the command that starts the app
 CMD npm start

README.md

@@ -1,4 +1,4 @@
-# app-ui
+# Pathway Commons App(s)
 
 
 ## Required software
@@ -19,7 +19,7 @@ npm install
 
 For development:
 ```
-npm run watch
+npm run watch 
 ```
 
 For a production build:
@@ -33,14 +33,28 @@ npm run start
 The following environment variables can be used to configure the server:
 
 - `NODE_ENV` : the environment mode, either `production` or `development` (default)
+- `PC_URL` : actual Pathway Commons web service endpoint URL (default: 'http://www.pathwaycommons.org/pc2/')
 - `PORT` : the port on which the server runs (default 3000)
 
 ### Configure RethinkDB
  1. Download [RethinkDB](https://www.rethinkdb.com/docs/install/)
  2. Start your RethinkDB server by following the steps [here](https://www.rethinkdb.com/docs/start-a-server/)
  3. Go to `src/server/database/config.js`  and modify the ip field to match your server address
- 4. Start the project : `npm run start` or `npm run watch`, then the server will auto create all the required tables for you.
+ 4. Start the project : `npm run start` or `npm run watch`, then the server will auto create all the required tables for you. 
 
+### Switching Pathway Commons Versions (release/other)
+
+If Pathway Commons data and files have been updated since this app's last built and run,
+or you simply want to connect to a different PC2 instance (and set PC_URL environment variable), 
+then the file `src/server/graph-generation/generic-physical-entities/generic-physical-entity-map.json` 
+needs to be updated. Also, purge the RethinkDb db tables or simply switch the database.
+
+The following script downloads and processes physical_entities.json.gz file from Pathway Commons:
+```sh
+cd src/scripts/generic-entity-mapping/
+PC_VERSION=v10 sh update.sh
+```
+(PC_VERSION should be set to the name of a sub-directory in `www.pathwaycommons.org/archives/PC2/`) 
 
 ## Run targets
 
@@ -86,15 +100,15 @@ Notes:
 
 ### Run image hosted on Docker Hub using Docker Compose
 
-Pathway Commons maintains a [Docker Hub](https://hub.docker.com/) image for [app-ui](https://hub.docker.com/r/pathwaycommons/app-ui/) that is automatically built each time a commit is pushed to GitHub.
+Pathway Commons maintains a [Docker Hub](https://hub.docker.com/) image for [app-ui](https://hub.docker.com/r/pathwaycommons/app-ui/) that is automatically built each time a commit is pushed to GitHub. 
 
 To run the GitHub development branch:
 
 ```sh
 docker-compose --file docker-compose.yml up --detach
 ```
 
-Access the app instance at port `9090`.The default configuration declared in `docker-compose.yml` also runs a [rethinkdb](https://hub.docker.com/_/rethinkdb/) image; access the UI at port `8020`.
+Access the app instance at port `9090`.The default configuration declared in `docker-compose.yml` also runs a [rethinkdb](https://hub.docker.com/_/rethinkdb/) image; access the UI at port `8020`. 
 
 Notes:
 - References:
@@ -145,7 +159,7 @@ Students who work on the repo should follow these instructions for each feature
         1. Using the console: `git checkout name-of-feature`, `git merge development`
         1. Using GitUp:
             1. Make sure your `HEAD` is the newest commit of your feature branch: Right-click the latest commit on `name-of-feature` branch and select `Checkout "name-of-feature" Branch`
-            1. Right-click the latest commit of the `development` branch and select `Merge into Current Branch`
+            1. Right-click the latest commit of the `development` branch and select `Merge into Current Branch` 
 1. Push your commits to GitHub:
     1. Note: You can push as often as you'd like so that your code is backed up on GitHub.  You *must* push everything before you make a pull request.
     1. Using the console: `git push`
@@ -166,3 +180,4 @@ Students who work on the repo should follow these instructions for each feature
   1. For a breaking API change, run `npm version major.`
   1. For a specific version number (e.g. 1.2.3), run `npm version 1.2.3`.
 1. Push the release: `git push origin --tags`
+

ci.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+# This is a helper script to set up a very simple CI dev/testing server.  It can
+# be used with `cron` in order to set up regular builds, e.g. for every 15 minutes:
+#
+# `crontab -e`
+# 
+# @reboot /home/username/rethinkdb.sh > /home/username/rethinkdb.log
+# */15 * * * * /home/username/master.sh > /home/username/master.log
+#
+# To use this script, create a script per server instance, e.g. `master.sh`:
+#
+# #!/bin/bash
+#
+# # Mandatory repo/branch conf
+# export REPO=https://github.com/PathwayCommons/factoid.git
+# export BRANCH=master
+#
+# # Project-specific env vars
+# export PORT=3000
+# 
+# ./ci.sh
+
+JOB_NAME=$BRANCH
+WORKSPACE=/home/`whoami`/$JOB_NAME
+WORKSPACE_TMP=/tmp/$JOB_NAME
+
+rm -rf $WORKSPACE_TMP
+mkdir -p $WORKSPACE_TMP
+cd $WORKSPACE_TMP
+
+# get the repo
+git clone $REPO $WORKSPACE_TMP
+git checkout $BRANCH
+
+# build
+npm install
+npm run clean
+
+export NODE_ENV=production
+
+npm run build
+
+# stop the old screen session
+screen -X -S $JOB_NAME quit || echo "No screen session to stop"
+
+# swap out old workspace with new one
+mkdir -p /tmp/rm
+mv $WORKSPACE /tmp/rm/$JOB_NAME || echo "No old workspace to move"
+mv $WORKSPACE_TMP $WORKSPACE
+
+# start the server in a screen session
+screen -d -m -S $JOB_NAME npm start
+
+# delete the old workspace files
+rm -rf /tmp/rm/$JOB_NAME || echo "No old workspace to delete"
+

docker-compose.yml

@@ -1,17 +1,14 @@
-version: '2'
+version: '3'
 services:
   webapp:
-    image: pathwaycommons/app-ui:latest
+    image: pathwaycommons/app-ui:development
     container_name: appui_webapp
     ports:
-      - "3000:3000" 
+      - "9090:3000" 
     environment:
-      ip: "db"      
-    links:
-      - db
+      host: "db"
   db:
     container_name: appui_db
     image: rethinkdb:2.3.6
     ports:
-      - "8080:8080"   
-      - "28015:28015"   
+      - "8020:8080"