Scout: Make Matchmaker matches page more compact

[northwestwitch]

Not it looks like this:

You get a bit lost in the results.

Perhaps it's enough is the matching patients are foldable

[northwestwitch]

I'm thinking about a way to simulate an environment to help you fix this one @moedarrah.

To give you an idea how real pages with MatchMaker results look like we need to:

• [x] Grant you permissions to use MatchMaker on stage and then you'll have access to a case with matches.
• [ ] Develop locally connecting Scout to a local image of the MatchMaker

[northwestwitch]

@moedarrah now it should work for you to use the MatchMaker. You can check this case here: https://scout-stage.scilifelab.se/cust101/A1383. Click on the MatchMaker link on the sidebar of the case:

From there you can see past matches.

[northwestwitch]

I've fixed the port issue in the MatchMaker, you should be able to connect it to your local scout following these steps:

Running the MatchMaker demo app:

• git clone https://github.com/Clinical-Genomics/patientMatcher.git
• cd patientMatcher
• docker-compose up

Fixing Scout to connect to the MatchMaker -from within Scout repo:
Edit scout/server/config.py by adding these lines:

MME_ACCEPTS = "application/vnd.ga4gh.matchmaker.v1.0+json"
MME_URL = "http://localhost:9020"
MME_TOKEN = "custom_token"

Granting your local user access over the MatchMaker feature
From another terminal, while the Scout docker-compose still runs
docker-compose -f docker-compose-dev.yml run scout-cli scout --host mongodb --demo update user -u [email protected] -r mme_submitter

[northwestwitch]

I've just figured out why sending the patient from docker Scout to Docker PatientMatcher doesn't work! It's because if you tell Scout container that the PatientMatcher has address 127.0.0.1:9020 then it will send the request to its own localhost (inside the container) and not the localhost of your machine. I think it's an easy fix. OMG all this stuff! 🙄

[northwestwitch]

I've spent some time on the issue from the comment above, but I've realized that is actually quite complicated, because if you tell the Scout docker-compose to use localhost instead of the internal network, then it's using it also for the database connection, resulting in all mongodb-related things not to work.

Perhaps it can be done, but I think the easiest just for the sake of creating an environment for testing this PR, would be to actually merge the docker-compose files from Scout and from PatientMatcher to have everything into 1.

You could try to do that @moedarrah and see what comes out. If you have everything in the same file then it shouldn't be a problem any more to send requests out of the container.

[moedarrah]

I will test it!

[northwestwitch]

Here is a docker-compose file that combines Scout and PatientMatcher. I've added also the command the grants the MatchMaker permission to the Scout user so it should create a complete test environment for Scout connected to the MatchMaker:

version: '3'
# usage:
# sudo docker-compose up
services:
  mongodb:
    # Lightweight Docker image for MongoDB which makes it easy to create:
    # - admin
    # - database
    # - database user with password
    # when the container is first launched.
    image: vepo/mongo
    container_name: mongo
    networks:
      - custom-net
    environment:
      - AUTH=y
      - ADMIN_USER=root
      - ADMIN_PASS=admin123
      - APPLICATION_DATABASE=pmatcher
      - APPLICATION_USER=pmUser
      - APPLICATION_PASS=pmPassword
    ports:
      - '27013:27017'
    expose:
      - '27017'

  pmatcher-cli:
    container_name: pmatcher-cli
    image: clinicalgenomics/patientmatcher
    environment:
      MONGODB_HOST: mongodb
      PMATCHER_CONFIG: '/home/worker/app/patientMatcher/patientMatcher/instance/config.py'
    depends_on:
      - mongodb
    networks:
      - custom-net
    command: bash -c "pmatcher add client -id test_client -token custom_token -url custom_url && pmatcher add demodata --ensembl_genes"

  pmatcher-web:
    container_name: pmatcher-web
    image: clinicalgenomics/patientmatcher
    environment:
      MONGODB_HOST: mongodb
      PMATCHER_CONFIG: '/home/worker/app/patientMatcher/patientMatcher/instance/config.py'
    depends_on:
      - mongodb
    networks:
      - custom-net
    ports:
      - '9020:9020'
    expose:
      - '9020'
    command: bash -c 'pmatcher run --host 0.0.0.0 -p 9020'

  scout-cli:
    build: .
    container_name: scout-cli
    command: bash -c "
      scout --host mongodb setup demo
      && scout --host mongodb --demo update user -u [email protected] -r mme_submitter"
    volumes:
      - ./scout:/home/worker/app/scout
      - ./volumes/scout/data:/home/worker/data
    depends_on:
      - mongodb
    networks:
      - custom-net

  scout-web:
    build: .
    container_name: scout-web
    expose:
      - '5000'
    ports:
      - '5000:5000'
    command: scout --host mongodb --demo serve --host 0.0.0.0
    volumes:
      - ./scout:/home/worker/app/scout
      - ./volumes/scout/data:/home/worker/data
    depends_on:
      - mongodb
      - pmatcher-web
    networks:
      - custom-net

networks:
  custom-net:
    driver: bridge
    ipam:
      driver: default
      config:
        - subnet: 172.21.0.0/24

To make it work you should modify the scout config file by adding the following lines:

MME_ACCEPTS = "application/vnd.ga4gh.matchmaker.v1.0+json"
MME_URL = "http://pmatcher-web:9020"
MME_TOKEN = "custom_token"

Tadaaa:

[moedarrah]

It works!