feat(openchallenges): filter EDAM concepts by sections

[tschaffter]

Closes #2633

Description

Update the challenge service to enable the user to query EDAM concepts associated to one or more EDAM concept topics (e.g. operation, data, format, etc.).

Two solutions were considered to index concept section values in Elasticsearch:

1. Dynamically generate the section value from the class ID.
   • E.g. http://edamontology.org/format_1478 => format
   • E.g. http://edamontology.org/data_1 => data
   • There are two outlier concepts that get their section value set to null:
     • http://www.geneontology.org/formats/oboInOwl#ObsoleteClass => null
     • http://www.w3.org/2002/07/owl#DeprecatedClass => null
2. Generate concept section values as described above but store these values in a new column of the EDAM concept table.

I went with Solution 1 because the data model is not modified and there is no need to add (~duplicated) data to the SQL DB.

cc: @rrchai @gaiaandreoletti

Changelog

• update the API description to include the sections search query parameters
• index a new property named section in Elasticsearch whose value is dynamically generated from the concept class ID
• update the custom repository for searching EDAM concept by sections
• update the API client for Angular

Preview

Search with the challenge service

List the EDAM concepts that belong to the "data" or "format" section.

GET {{basePath}}/edamConcepts?sections=data,format
HTTP/1.1 200
{
  "number": 0,
  "size": 100,
  "totalElements": 2221,
  "totalPages": 23,
  "hasNext": true,
  "hasPrevious": false,
  "edamConcepts": [
    {
      "id": 1567,
      "classId": "http://edamontology.org/format_1478",
      "preferredLabel": "PDBML"
    },
    {
      "id": 1557,
      "classId": "http://edamontology.org/format_1436",
      "preferredLabel": "TreeBASE format"
    },
...

Elasticsearch queries used to explore EDAM concepts during development

Check that the property section is indexes by Elasticsearch:

http://localhost:9200/openchallenges-edam-concept-000001

Check the value of section for a few documents:

http://localhost:9200/openchallenges-edam-concept-000001/_search

Find all the concepts that belong to the "data" section with ES:

http://localhost:9200/openchallenges-edam-concept-000001/_search?q=section:data

[sonarcloud[bot]]

Quality Gate passed for 'openchallenges-app'

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud

[sonarcloud[bot]]

Quality Gate passed for 'openchallenges-challenge-service'

Issues
0 New issues
3 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[sonarcloud[bot]]

Quality Gate passed for 'openchallenges-organization-service'

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud

[sonarcloud[bot]]

Quality Gate passed for 'openchallenges-image-service'

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud