neurobagel / neurobagel/api

Split subject-level data list in API response into imaging and phenotypic session arrays

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someday
Dominant language
Python
Stars
7
Forks
10
Avg merge
4d 1h
Merged PRs (30d)
8

Description

Current response:

[
  {
    "dataset_uuid": "http://neurobagel.org/vocab/e0c7d08c-edcc-4c2a-816a-306878ed7be2",
    "dataset_name": "BIDS synthetic",
    "dataset_portal_uri": "https://github.com/bids-standard/bids-examples",
    "dataset_total_subjects": 5,
    "records_protected": false,
    "num_matching_subjects": 5,
    "subject_data": [
      {
        "sub_id": "sub-01",
        "session_id": "ses-01",
        "num_phenotypic_sessions": 2,
        "num_imaging_sessions": 2,
        "session_type": "http://neurobagel.org/vocab/ImagingSession",
        "age": null,
        "sex": null,
        "diagnosis": [
          null
        ],
        "subject_group": null,
        "assessment": [
          null
        ],
        "image_modal": [
          "http://purl.org/nidash/nidm#T1Weighted",
          "http://purl.org/nidash/nidm#FlowWeighted"
        ],
        "session_file_path": "/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01"
      },
      {
        "sub_id": "sub-01",
        "session_id": "ses-01",
        "num_phenotypic_sessions": 2,
        "num_imaging_sessions": 2,
        "session_type": "http://neurobagel.org/vocab/PhenotypicSession",
        "age": 34.1,
        "sex": "http://purl.bioontology.org/ontology/SNOMEDCT/248152002",
        "diagnosis": [
          null
        ],
        "subject_group": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C94342",
        "assessment": [
          "https://www.cognitiveatlas.org/task/id/trm_57964b8a66aed",
          "https://www.cognitiveatlas.org/task/id/tsk_4a57abb949ece"
        ],
        "image_modal": [
          null
        ],
        "session_file_path": null
      },

Motivations for keeping this response:

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

No source file, test, or entry point is named in the issue. Start by locating the API response assembly that produces subject_data, then confirm the response separates imaging and phenotypic sessions into distinct arrays and add or update coverage for the revised shape.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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