feat(openchallenges): create endpoint to search EDAM concepts

tschaffter commented 2 months ago

Closes #2608

Description

Add endpoints to the Challenge Service to explore EDAM concepts.

This endpoint will be used by the OC web app to enable users to filter challenges using selected EDAM concepts. The filtering of challenges using EDAM concepts will be implemented in another PR to keep this PR lean.

cc: @rrchai

Changelog

add the endpoint /edamConcepts to the API description
add the endpoint /edamConcepts to the challenge service
enable full-text search on EDAM concepts
update the OC API client for Angular
allow access to the new endpoint in the API gateway

Notes

For the new endpoint to be accessible via the API gateway, its config must be updated. See #2636.

Preview

List EDAM concepts:

GET {{basePath}}/edamConcepts
HTTP/1.1 200 

{
  "number": 0,
  "size": 100,
  "totalElements": 3473,
  "totalPages": 35,
  "hasNext": true,
  "hasPrevious": false,
  "edamConcepts": [
    {
      "id": 7,
      "classId": "http://edamontology.org/data_0831",
      "preferredLabel": "MeSH vocabulary"
    },
    {
      "id": 19,
      "classId": "http://edamontology.org/data_0851",
      "preferredLabel": "Sequence mask character"
    },

List the EDAM concepts that match the space-separated search terms "sequence":

GET {{basePath}}/edamConcepts?searchTerms=sequence
HTTP/1.1 200 

{
  "number": 0,
  "size": 100,
  "totalElements": 362,
  "totalPages": 4,
  "hasNext": true,
  "hasPrevious": false,
  "edamConcepts": [
    {
      "id": 805,
      "classId": "http://edamontology.org/data_2044",
      "preferredLabel": "Sequence"
    },
    {
      "id": 18,
      "classId": "http://edamontology.org/data_0850",
      "preferredLabel": "Sequence set"
    },
    {
      "id": 3073,
      "classId": "http://edamontology.org/topic_0158",
      "preferredLabel": "Sequence motifs"
    },

How to test

Remove all Docker artifacts: workspace-docker-stop && docker system prune -a
Build the OC images: openchallenges-build-images
Start the challenge service and its dependencies: nx serve-detach openchallenges-challenge-service
Try the EDAM example queries defined in apps/openchallenges/challenge-service/requests.http

tschaffter commented 2 months ago

I need to fix 9 issues identified by Sonar for the challenge service.