A command-line tool to generate SBGN images for PC pathways

.gitignore

@@ -13,3 +13,5 @@ src/scripts/jsonld/*
 /nohup.out
 src/*.gmt
 downloads/*
+public/img/pathways/*
+!/**/.gitkeep

Dockerfile.syblars

@@ -0,0 +1,36 @@
+FROM node:14.21.3
+
+# Environment variables
+ENV NODE_OPTIONS=--max_old_space_size=8192
+
+# 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 /home/appuser/app
+
+# Copy in source code
+RUN cd /home/appuser/app && git clone https://github.com/iVis-at-Bilkent/syblars.git
+WORKDIR /home/appuser/app/syblars
+
+# Install app dependencies
+# Puppeteer requirements
+RUN wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - \
+    && sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list' \
+    && apt-get update \
+    && apt-get install -y google-chrome-stable fonts-ipafont-gothic fonts-wqy-zenhei fonts-thai-tlwg fonts-kacst fonts-freefont-ttf libxss1 libxtst6 gconf-service libasound2 libatk1.0-0 libatk-bridge2.0-0 libc6 libcairo2 libcups2 libdbus-1-3 libexpat1 libfontconfig1 libgcc1 libgconf-2-4 libgdk-pixbuf2.0-0 libglib2.0-0 libgtk-3-0 libnspr4 libpango-1.0-0 libpangocairo-1.0-0 libstdc++6 libx11-6 libx11-xcb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxext6 libxfixes3 libxi6 libxrandr2 libxrender1 libxss1 libxtst6 ca-certificates fonts-liberation libappindicator1 libnss3 lsb-release xdg-utils wget \
+    --no-install-recommends
+
+RUN npm clean-install
+
+# Expose port
+EXPOSE 3000
+
+# Change ownership of the app to the unprivileged user
+RUN chown appuser:appuser -R /home/appuser/app
+USER appuser
+
+# set server start as entry point
+ENTRYPOINT npm run start
+

README.md

@@ -36,6 +36,8 @@ The following environment variables can be used to configure the server (also do
 - `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/')
+- `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`)
 
 ## Run targets
 
@@ -66,7 +68,7 @@ docker build --build-arg NODE_ENV=production -t app-ui .
 Run the container:
 
 ```
-docker run -it --rm -p 12345:3000 -e "NODE_ENV=production" --name "app-ui" app-ui
+docker run -it --rm -p 3000:3000 -e "NODE_ENV=production" --name "app-ui" app-ui
 ```
 
 Notes:
@@ -93,25 +95,15 @@ PC repository on Docker Hub).
 To run the app using the pathwaycommons/app-ui:master image, execute:
 
 ```sh
-docker-compose up -d
+docker-compose up -d webapp
 ```
 
-Access the app instance at port `9090` (can be specified in the docker-compose.yml).
+Access the app instance at port `3000` (can be specified in the docker-compose.yml).
 
 Notes:
 - References:
   - [Getting started with Docker Compose](https://docs.docker.com/compose/gettingstarted/)
 
-### Custom build/rebuild/run with Docker Compose
-
-Create .env file in this directory and define there yours: NODE_ENV, PC_URL, FACTOID_URL, PORT options;
-execute:
-
-```sh
-docker-compose -f dev-compose.yml build
-docker-compose -f dev-compose.yml up -d
-```
-
 
 ## Testing
 
@@ -121,6 +113,26 @@ 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.
 
 
+## Scripts
+
+### Command line tools
+
+The `scripts/cli.js` file contains app-ui command line tools:
+  - `source`: Download and extract a file to `downloads` folder
+  - `snapshot`: Generate PNG images for pathways listed in a PC GMT-formatted file
+    - 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`:
+
+```sh
+$ docker-compose up -d syblars
+$ SERVER_FETCH_TIMEOUT="60000" node src/scripts/cli.js snapshot --file PathwayCommons12.All.hgnc.gmt
+```
+NB: The default timeout of fetch is normally quite brief (5 seconds).
+
+In this way, images will be served via expressJS at `img/pathways/:id`, where `id` is the pathway URI with anything that is not a letter (a-z) or digit (0-9) is replaced with underscores (`_`).
+
 ## 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:

docker-compose.yml

@@ -32,6 +32,14 @@ services:
       FACTOID_URL:
     networks:
       - app-ui-network
+  syblars:
+    image: pathwaycommons/syblars:${SYBLARS_IMAGE_TAG:-latest}
+    restart: unless-stopped
+    container_name: syblars
+    ports:
+      - "${SYBLARS_PORT:-9090}:3000"
+    networks:
+      - app-ui-network
 
 networks:
   app-ui-network:

package.json

@@ -94,13 +94,15 @@
     "winston": "^2.4.0"
   },
   "devDependencies": {
+    "async-retry": "^1.3.3",
     "babel-core": "^6.26.0",
     "babel-loader": "^7.1.2",
     "babel-plugin-transform-async-to-generator": "^6.24.1",
     "babel-polyfill": "^6.26.0",
     "babel-preset-env": "^1.6.0",
     "babel-preset-react": "^6.24.1",
     "chai": "^4.1.2",
+    "commander": "^11.1.0",
     "cross-env": "^5.0.5",
     "cssnano": "^3.10.0",
     "echo-cli": "^1.0.8",

src/config.js

@@ -15,6 +15,8 @@ let defaults = {
   UNIPROT_API_BASE_URL: 'https://www.ebi.ac.uk/proteins/api',
   DOI_BASE_URL: 'https://doi.org/',
   ORCID_BASE_URL: 'https://orcid.org/',
+  SBGN_IMG_SERVICE_BASE_URL: 'http://localhost:9090/',
+  SBGN_IMG_PATH: 'public/img/pathways',
   PC_IMAGE_CACHE_MAX_SIZE: 10000,
   PC_CACHE_MAX_SIZE: 1000,
   PUB_CACHE_MAX_SIZE: 1000000,