Merge pull request #1302 from PathwayCommons/development

3.0.1

Author: jvwong

Dockerfile

@@ -2,9 +2,15 @@
 # https://nodejs.org/en/docs/guides/nodejs-docker-webapp/
 # https://github.com/nodejs/docker-node
 
-# Node.js base image 
+# Node.js base image
 FROM node:8
 
+# default NODE_ENV for building the app (clientside JS etc.)
+ARG NODE_ENV=production
+
+# default NODE_ENV for running the server
+ENV NODE_ENV=production
+
 # Create an unprivileged user w/ home directory
 RUN groupadd appuser \
   && useradd --gid appuser --shell /bin/bash --create-home appuser
@@ -17,18 +23,19 @@ WORKDIR /home/appuser/app
 COPY . /home/appuser/app
 
 # Install app dependencies
-RUN npm install
+# Note: must be development so that dev deps are installed
+RUN NODE_ENV=development npm install
 
-# Build project 
+# Build project
 RUN npm run clean
 RUN npm run build
 
 # Expose port
 EXPOSE 3000
 
-# Change ownership of the app to the unprivileged user 
+# Change ownership of the app to the unprivileged user
 RUN chown appuser:appuser -R /home/appuser/app
-USER appuser 
+USER appuser
 
 # Run the command that starts the app
 CMD npm start

README.md

@@ -3,60 +3,52 @@
 
 ## Required software
 
-- [Node.js](https://nodejs.org/en/) >=6.3.0
+- [Node.js](https://nodejs.org/en/) >=8.11.2
 - [RethinkDB](https://www.rethinkdb.com/) >=2.3.6
-- [Chromium](https://www.chromium.org/Home)
+
 ## Running the App Locally
-1.  Start rethinkdb by typing this command in your terminal
-```
-rethinkdb
-```
-2. Install the project dependencies by typing:
-```
-npm install
-```
 
-3.  Run the project using one of the defined package scripts:
+1. Install the project dependencies by typing:
+    ```
+    npm install
+    ```
 
-For development:
-```
-npm run watch
-```
+2.  Run the project using one of the defined package scripts:
 
-For a production build:
-```
-npm run build-prod
-npm run start
-```
+    For development:
+    ```
+    npm run watch
+    ```
+
+    For a production build:
+    ```
+    npm run build-prod
+    npm run start
+    ```
 
 ## Configuration
 
 The following environment variables can be used to configure the server:
 
-- `NODE_ENV` : the environment mode, either `production` or `development` (default)
-- `PC_URL` : root Pathway Commons URL (default: 'http://www.pathwaycommons.org/')
-- `FACTOID_URL` : the Factoid app URL (default: 'http://unstable.factoid.baderlab.org/')
-- `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.
+- `NODE_ENV`: the environment mode, either `production` or `development` (default)
+- `PORT`: the port on which the server runs (default 3000)
+- `PC_URL`: root Pathway Commons URL (default: 'http://www.pathwaycommons.org/')
+- `NCBI_API_KEY`: NCBI E-Utilities API key ([read more](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/))
+- `FACTOID_URL`: the Factoid app URL (default: 'http://unstable.factoid.baderlab.org/')
 
 ### 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 (don't forget to set PC_URL),
 then the file `src/server/graph-generation/biopax-metadata/generic-physical-entity-map.json`
-needs to be updated. Also, purge the RethinkDb db tables or simply switch the database.
+needs to be updated.
 
-The following script downloads and processes physical_entities.json.gz file from Pathway Commons:
+Use the script
 ```sh
 cd src/scripts/generic-entity-mapping/
-PC_VERSION=v10 sh update.sh
+PC_VERSION=v11 sh update.sh
 ```
-(PC_VERSION should be set to the name of a sub-directory in `www.pathwaycommons.org/archives/PC2/`)
+to refresh `physical_entities.json.gz` from the path `www.pathwaycommons.org/archives/PC2/<PC_VERSION>/` in Pathway Commons.
 
 ## Run targets
 
@@ -69,6 +61,7 @@ PC_VERSION=v10 sh update.sh
 - `npm run watch` : watch mode (debug mode enabled, autorebuild, autoreload)
 - `npm test` : run tests
 - `npm run lint` : lint the project
+- `npm run ci` : run the tests and lint at once
 
 
 ## Running via Docker
@@ -79,13 +72,13 @@ Build the container.  Here, `app-ui` is used as the container name.
 
 ```
 cd app-ui
-docker build --build-arg "NODE_ENV=production" -t app-ui .
+docker build --build-arg NODE_ENV=production -t app-ui .
 ```
 
 Run the container:
 
 ```
-docker run -it -p 12345:3000 -u "node" -e "NODE_ENV=production" --name "app-ui" app-ui
+docker run -it --rm -p 12345:3000 -e "NODE_ENV=production" --name "app-ui" app-ui
 ```
 
 Notes:
@@ -104,13 +97,13 @@ Notes:
 
 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:
+To run the GitHub master 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`.
 
 Notes:
 - References:
@@ -119,16 +112,16 @@ Notes:
 
 ## Testing
 
-All files `/test` will be run by [Mocha](https://mochajs.org/).  You can `npm test` to run all tests, or you can run `mocha -g specific-test-name` (prerequisite: `npm install -g mocha`) to run specific tests.
+All files `/test` will be run by [Mocha](https://mochajs.org/).  You can `npm test` to run all tests, or you can run `npm run test ./test/path/to/test` to run specific tests.
 
 [Chai](http://chaijs.com/) is included to make the tests easier to read and write.
 
 
-## Devloping a feature and making a pull request
+## Developing a feature and making a pull request
 
 Students who work on the repo should follow these instructions for each feature that they work on:
 
-1. Initial prepartion (only needed once)
+1. Initial preparation (only needed once)
     1. [Make a fork on Github](https://github.com/PathwayCommons/app-ui#fork-destination-box) (if you haven't already) under your personal account
     1. Check out the fork repo: `git clone https://github.com/myusername/app-ui.git`
     1. Change the directory to the project: `cd app-ui`

docker-compose.yml

@@ -1,14 +1,11 @@
 version: '3'
 services:
   webapp:
-    image: pathwaycommons/app-ui:development
+    image: pathwaycommons/app-ui:master
     container_name: appui_webapp
     ports:
-      - "9090:3000" 
+      - "9090:3000"
     environment:
-      host: "db"
-  db:
-    container_name: appui_db
-    image: rethinkdb:2.3.6
-    ports:
-      - "8020:8080" 
+      NODE_ENV: "production"
+      PC_URL: "http://www.pathwaycommons.org/"
+      FACTOID_URL: "http://factoid.baderlab.org/"

src/client/common/components/error-message.js

@@ -5,7 +5,17 @@ const { Link } = require('react-router-dom');
 
 class ErrorMessage extends React.Component {
   render(){
-    const logo = this.props.logo ? h(Link, { to: { pathname: `/`}, target: '_blank' }, [ h('div.pc-logo')]): null;
+    const logo = this.props.logo
+      ? h( Link, { to: { pathname: `/`}, target: '_blank' }, [
+          h('div.error-branding', [
+            h('div.pc-logo'),
+            h('div.error-branding-descriptor', [
+              h('h2.error-subtitle', 'Pathway Commons'),
+              h('h1.error-title', 'Search')
+            ])
+          ])
+      ])
+      : null;
 
     const title = h('h1.error-message-title',
       this.props.title !== undefined ? this.props.title : 'An error occurred' );
@@ -21,8 +31,8 @@ class ErrorMessage extends React.Component {
     ]);
 
     return  h('div.error-message-container', [
-      logo,
       h('div.error-message', [
+        logo,
         title,
         body,
         footer

src/client/features/enrichment/index.js

@@ -77,7 +77,7 @@ class Enrichment extends React.Component {
     if( networkEmpty ) {
       errorMessage = h(ErrorMessage, { title: 'No results to display.', body: 'Try different genes in your search.' , footer: null, logo: true } );
     } else if( error instanceof TimeoutError ) {
-      errorMessage = h( ErrorMessage, { title: 'This is taking longer that we expected', body: 'Try again later.', logo: true } );
+      errorMessage = h( ErrorMessage, { title: 'This is taking longer than expected', body: 'Try again later.', logo: true } );
     } else if( error ) {
       errorMessage = h( ErrorMessage, { logo: true } );
     }

src/client/features/interactions/index.js

@@ -77,7 +77,7 @@ class Interactions extends React.Component {
     if( networkEmpty ) {
       errorMessage = h(ErrorMessage, { title: 'No interactions to display.', body: 'Try different genes in your search.' , footer: null, logo: true } );
     } else if( error instanceof TimeoutError ) {
-      errorMessage = h( ErrorMessage, { title: 'This is taking longer that we expected', body: 'Try again later.', logo: true } );
+      errorMessage = h( ErrorMessage, { title: 'This is taking longer than expected', body: 'Try again later.', logo: true } );
     } else if( error ) {
       errorMessage = h( ErrorMessage, { logo: true } );
     }

src/client/features/search/index.js

@@ -121,7 +121,7 @@ class Search extends React.Component {
     if( this.props.notFoundError ) {
       errorMessage = h( ErrorMessage, { title: 'We couldn\'t find the resource you are looking for', body: 'Check the location and try again.' } );
     } else if( this.state.error instanceof TimeoutError ) {
-      errorMessage = h( ErrorMessage, { title: 'This is taking longer that we expected', body: 'Try again later.' }  );
+      errorMessage = h( ErrorMessage, { title: 'This is taking longer than expected', body: 'Try again later.' }  );
     } else if( this.state.error ) {
       errorMessage = h( ErrorMessage );
     }

src/server/external-services/gprofiler/gprofiler.js

@@ -8,7 +8,7 @@ const { GPROFILER_URL } = require('../../../config');
 const logger = require('../../logger');
 const { cachePromise } = require('../../cache');
 
-
+const GPROFILER_GOST_URL = GPROFILER_URL + 'index.cgi';
 const GPROFILER_DEFAULT_OPTS = {
   output: 'mini',
   organism: 'hsapiens',
@@ -106,7 +106,7 @@ const rawEnrichment = (query, opts) => {
     } );
 
 
-    fetch(GPROFILER_URL, { method: 'post', body: qs.stringify(gProfilerOpts)})
+    fetch(GPROFILER_GOST_URL, { method: 'post', body: qs.stringify(gProfilerOpts)})
       .then( res => res.text() )
       .then( gprofilerRes =>  parseGProfilerResponse( gprofilerRes ) )
       .then( pathwayInfo => resolve( pathwayInfo ) )

src/styles/common/error-message.css

@@ -3,16 +3,44 @@
   justify-content: center;
   align-items: center;
   flex-direction: row;
+  margin: 1.5em;
 
   & .pc-logo {
     background-image: url("../image/pc_logo_dark.svg");
     background-repeat: no-repeat;
-    height: 5em;
-    width: 5em;
-    padding: 0px 10px 0px 0px;
+    height: 3em;
+    width: 3em;
+    padding: 0;
   }
 }
 
+.error-branding {
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  height: 100%;
+  padding-right: 0.5em;
+  margin-bottom: 1em;
+}
+
+.error-branding-descriptor {
+  margin-left: 0.5em;
+}
+
+.error-title {
+  margin: 0;
+  line-height: 1em;
+  color: var(--dark-base-colour);
+  font-size: 2em;
+}
+
+.error-subtitle {
+  margin: 0;
+  line-height: 1em;
+  color: var(--dark-base-colour);
+  font-size: 0.75em;
+}
+
 .error-message {
   display: flex;
   justify-content: center;