feat(openchallenges): model input data types of challenges with EDAM

[tschaffter]

Closes #2551

Changelog

• model Challenge.inputDataTypes as an array of EdamData objects
• remove the endpoint used to explore the collection of custom input data types
• add README.md to the folder src/main/resources/db to share notes about how data are imported from CSV files

Future Work

• Remove dummy input data type (another PR), keeping them in this PR for the sake of testing
• Create a facet to explore used EDAM input data types

Preview

Search using the full-text search field

One challenge annotated with "Resource type" (http://edamontology.org/data_0005)

Searching with EDAM preferred name:

Searching with short EDAM class ID:

Searching with full EDAM class ID:

Challenge.inputDataTypes is now an array of EDAM Data objects

http://localhost:8085/v1/challenges/1

{
  "id": 1,
  "slug": "network-topology-and-parameter-inference",
  "name": "Network Topology and Parameter Inference",
  "headline": "Optimize methods to estimate biology model parameters",
  "description": "Participants are asked to develop and/or apply optimization methods, including the selection of the most informative experiments, to accurately estimate parameters and predict outcomes of perturbations in Systems Biology models.",
  "doi": "",
  "status": "completed",
  "platform": {
    "id": 1,
    "slug": "synapse",
    "name": "Synapse"
  },
  "websiteUrl": "https://www.synapse.org/#!Synapse:syn2821735",
  "avatarUrl": "",
  "incentives": [
    "publication"
  ],
  "submissionTypes": [
    "prediction_file"
  ],
  "inputDataTypes": [
    {
      "classId": "http://edamontology.org/data_0005",
      "preferredLabel": "Resource type"
    }
  ],
  "categories": [],
  "startDate": "2012-06-01",
  "endDate": "2012-10-01",
  "starredCount": 2,
  "operation": null,
  "createdAt": "2023-11-15T22:40:15Z",
  "updatedAt": "2024-03-04T18:31:19Z"
}

Example of challenge with input data type indexed in Elasticsearch

http://localhost:9200/openchallenges-challenge-000001/_search?q=(name:Network%20Topology%20and%20Parameter%20Inference)&size=1

Notes

ES indexed values may be a single objects or an array

Note

What is describe below is not an issue. It is simply how ES index data. The property returned by the OC Challenge Service will still always be an array.

The property Challenge.inputDataTypes takes an array as value when the challenge has multiple types. However, this property takes the value of a single object when its has a single type. This property must always be an array.

"id","challenge_id","edam_concept_id","created_at"
"1","1","1","2023-06-23 00:00:00"

http://localhost:9200/openchallenges-challenge-000001/_search?q=(name:Network%20Topology%20and%20Parameter%20Inference)&size=1

          "input_data_types": {
            "class_id": "http://edamontology.org/data_0005",
            "preferred_label": "Resource type"
          },

vs

"id","challenge_id","edam_concept_id","created_at"
"1","1","1","2023-06-23 00:00:00"
"2","1","2","2023-06-23 00:00:00"

http://localhost:9200/openchallenges-challenge-000001/_search?q=(name:Network%20Topology%20and%20Parameter%20Inference)&size=1

          "input_data_types": [
            {
              "class_id": "http://edamontology.org/data_0005",
              "preferred_label": "Resource type"
            },
            {
              "class_id": "http://edamontology.org/data_0007",
              "preferred_label": "Tool"
            }
          ],

cc: @vpchung @mdsage1 @gaiaandreoletti

[vpchung]

Works on my end - thanks!

[sonarqubecloud]

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

[sonarqubecloud]

Quality Gate passed for 'openchallenges-challenge-service'

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
41.8% Duplication on New Code

See analysis details on SonarCloud

[sonarqubecloud]

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

[sonarqubecloud]

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