Merged from upstream; edited Dockerfile and Readme.

Author: IgorRodchenkov

.dockerignore

@@ -1,2 +1,4 @@
 node_modules
-npm-debug.log
+**/*.log
+build
+.idea

Dockerfile

@@ -11,8 +11,7 @@ WORKDIR /home/appuser/app
 # Bundle app
 COPY . /home/appuser/app
 
-# Install app dependencies
-# Note: here NODE_ENV env must be 'development' so that dev dependencies are installed
+# Here NODE_ENV must be 'development' so that all dependencies are installed
 RUN NODE_ENV=development npm ci
 
 # Bundle JS and CSS

README.md

@@ -2,7 +2,6 @@
 
 [![DOI](https://zenodo.org/badge/104936681.svg)](https://zenodo.org/badge/latestdoi/104936681)
 
-
 ## Required software
 
 - [Node.js](https://nodejs.org/en/) >=10.0.0 <11.0.0
@@ -24,7 +23,7 @@
     For a production build:
     ```
     npm run build-prod
-    npm run start
+    npm start
     ```
 
 ## Configuration
@@ -35,7 +34,7 @@ The following environment variables can be used to configure the server (also do
 - `PORT`: the port on which the server runs (default 3000)
 - `PC_URL`: Pathway Commons homepage URL (default: 'http://www.pathwaycommons.org/'; cPath2 service should be there available at /pc2/ path)
 - `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/')
+- `FACTOID_URL`: the Factoid app URL (default: 'https://biofactoid.org/')
 - `SBGN_IMG_SERVICE_BASE_URL`: URL for service that converts SBGN to an image (i.e. [Syblars](http://syblars.cs.bilkent.edu.tr/); default is `http://localhost:9090/`)
 - `SBGN_IMG_PATH`: cli tool `snapshot` output folder for images (default: `public/img/pathways`)
 
@@ -50,7 +49,7 @@ The following environment variables can be used to configure the server (also do
 - `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
+- `npm run ci` : run the tests and lint and build-prod at once
 
 
 ## Using Docker and Dockerfile
@@ -85,11 +84,11 @@ The `scripts/cli.js` file contains app-ui command line tools:
     - Requires an instance of [Syblars](http://syblars.cs.bilkent.edu.tr/) accessible at a location defined by the configuration variable `SBGN_IMG_SERVICE_BASE_URL` (see `docker-compose.yml` service `syblars`)
     - Images will be placed in directory `SBGN_IMG_PATH` (default: `public/img/pathways`)
 
-Usage: To generate a PNG of an SBGN representation for each pathway declared in the GMT file at `downloads/PathwayCommons12.All.hgnc.gmt`:
+Usage: To generate a PNG of an SBGN representation for each pathway declared in the GMT file at `downloads/pc-hgnc.gmt.gz`:
 
 ```sh
 $ docker-compose up -d syblars
-$ SERVER_FETCH_TIMEOUT="60000" node src/scripts/cli.js snapshot --file PathwayCommons12.All.hgnc.gmt
+$ SERVER_FETCH_TIMEOUT="60000" node src/scripts/cli.js snapshot --file pc-hgnc.gmt
 ```
 NB: The default timeout of fetch is normally quite brief (5 seconds).
 
@@ -100,7 +99,7 @@ In this way, images will be served via expressJS at `img/pathways/:id`, where `i
 Students who work on the repo should follow these instructions for each feature that they work on:
 
 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)
+    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`
@@ -116,7 +115,7 @@ Students who work on the repo should follow these instructions for each feature
         1. Select `Merge into Current Branch`
   1. Make a feature branch for the new feature or change you are working on.  Make sure to give your branch a clear, meaningful name.
       1. Using the console: `git checkout -b name-of-feature`
-      1. Using GitUp: Right click the `HEAD` commit (which should be the top commit of your local `development` branch),
+      1. Using GitUp: right-click the `HEAD` commit (which should be the top commit of your local `development` branch),
       then select `Create Branch...`
 1. Make commits as you're working on your feature:
     1. Using the console: `git commit -am "My descriptive commit message"`

src/server/db.js

@@ -3,7 +3,6 @@ const { DB_NAME, DB_HOST, DB_PORT, DB_CERT, DB_USER, DB_PASS } = require('../con
 const Promise = require('bluebird');
 let fs = require('fs');
 
-
 let db = {
   connect(){
     if( this.conn ){

src/server/index.js

@@ -22,7 +22,6 @@ cron.schedule(METADATA_CRON_SCHEDULE, () => {
 // make fetch() available as a global just like it is on the client side
 global.fetch = require('node-fetch');
 
-// const db = require('./db'); // for now disable db
 const logger = require('./logger');
 
 const app = express();