Enable pheno level session for response and query

[alyssadai]

This issue is to address two things:

• The query tool can send requests for # of pheno and imaging sessions according to the new query variables:

https://github.com/neurobagel/federation-api/blob/771b1a2fd21030ee3a6fe1a8bc6c37db401a8fd1/app/api/models.py#L20-L21

• Query tool can understand the new response model from the API:

https://github.com/neurobagel/api/blob/c5c6222f77995e1b723e5ac24f7041151556b458/app/api/models.py#L13-L24

Steps:

• update query UI for # of imaging sessions
• add query UI for # of pheno sessions
• add tests to check that this is correctly mapped to new query parameters
• add test to ensure the tool creates the correct participant.tsv files when given the new API response with session_type:

[
  {
    "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_matching_phenotypic_sessions": 2,
        "num_matching_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_matching_phenotypic_sessions": 2,
        "num_matching_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
      },
      ...
]

• add capacity to receive response with new session_type parameter / make that test pass

[rmanaem]

Blocked by neurobagel/planning#96

[rmanaem]

Unblocked since neurobagel/planning#96 has been addressed

[surchs]

@alyssadai do you have an example response from the API that includes session_type? mainly for testing purposes

[alyssadai]

Here you go @surchs:

[
  {
    "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_matching_phenotypic_sessions": 2,
        "num_matching_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_matching_phenotypic_sessions": 2,
        "num_matching_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
      },
      ...
]

[surchs]

Thanks a lot @alyssadai !

[alyssadai]

Blocked until #97 is reviewed to avoid messy rebasing

[rmanaem]

DatasetID	SubjectID	SessionID	SessionType	Age	Sex	Diagnosis	Assessment	SessionFilePath	NumPhenotypicSessions	NumImagingSessions	Modality
http://neurobagel.org/vocab/e0c7d08c-edcc-4c2a-816a-306878ed7be2	sub-01	ses-01	http://neurobagel.org/vocab/ImagingSession	null	null	null	null	/data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01	1	1	[http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted]
http://neurobagel.org/vocab/e0c7d08c-edcc-4c2a-816a-306878ed7be2	sub-01	ses-01	http://neurobagel.org/vocab/PhenotypicSession	34.1	http://purl.bioontology.org/ontology/SNOMEDCT/248152002	null	[https://www.cognitiveatlas.org/task/id/trm_57964b8a66aed, https://www.cognitiveatlas.org/task/id/tsk_4a57abb949ece]	null	1	1	null

[surchs]

🚀 Issue was released in v0.2.0 🚀