TCIA Adapter #121
TCIA Adapter #121
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The style in this PR agrees with This formatting comment was generated automatically by a script in uc-cdis/wool. |
Please find the detailed integration test report here Please find the ci env pod logs here |
tests/test_agg_mds_tcia_adapter.py
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| field_mappings = { |
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We need PatientID, EthnicGroup, Patient Sex and SeriesCount also in the final fields
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This is just tests. Though, I have added the fields for clarification.
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Thanks for adding the fields. I had requested it to align with CTDS guidelines, but as long as it works reliably, I’m okay to proceed.
| assert get_metadata( | ||
| "tcia", "http://test/ok", filters=filters, mappings=field_mappings | ||
| ) == { | ||
| "study_id_1": { |
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On some level this is how the subject metadata coming out of adapter should be
{
"_guid_type": "TCIA_promethueus_subject_metadata",
"gen3_discovery": {
"tags": [
{
"name": "TCIA",
"category": "Data Source"
},
{
"name": "path:PatientSex",
"category": "gender"
},
{
"name": "path:EthnicGroup",
"category": "race"
}
],
"authz": "",
"gender": "path:PatientSex",
"commons": "",
"data_source": "TCIA",
"apollo_id": "path:PatientID",
"_unique_id": "path:StudyInstanceUID",
"subject_id": "path:StudyInstanceUID",
"year_of_birth" : datetime.datetime.now().year - path:PatientAge.replace("Y" , ""), (convert age to year of birth)
"gender" : "path:PatientSex",
"race" : "path:EthnicGroup",
"_series_count" : "path:SeriesCount",
"study_title": "path:StudyDescription",
"program_name": "path:Collection",
}
}
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This is just tests. From what I see it has the same structure to what you provided.
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Appreciate that. My request was to meet the testing standards, but looking at time crunch, if it works as required, I’m fine moving forward
tests/test_agg_mds_tcia_adapter.py
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| @respx.mock | ||
| def test_get_metadata_tcia(): | ||
| tcia_response = """ |
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This TCIA response only test for subject level metadata. For study-level metadata coming from this URL I think the mapping should be like this
{
"_guid_type": "TCIA_promethueus_study_metadata",
"gen3_discovery": {
"tags": [
{
"name": "TCIA",
"category": "Data Source"
}
],
"authz": "",
"_unique_id": "path:SeriesInstanceUID",
"commons": "",
"data_source": "TCIA",
"apollo_id": "path:PatientID",
"short_name": "path:ProtocolName",
"study_description" : "path:SeriesDescription",
"program_name": "path:Collection",
"subject_id": "path:StudyInstanceUID",
"series_number" : "path:SeriesNumber",
"image_count": "path:ImageCount",
"study_url": "path:CollectionURI",
}
}
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I have added the part for study-level to the tests.
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Please find the ci env pod logs here |
tests/test_agg_mds_tcia_adapter.py
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| ] | ||
| """ | ||
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| field_mappings = { |
There was a problem hiding this comment.
This is just tests. Though, I have added the fields for clarification.
tests/test_agg_mds_tcia_adapter.py
Outdated
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| @respx.mock | ||
| def test_get_metadata_tcia(): | ||
| tcia_response = """ |
There was a problem hiding this comment.
I have added the part for study-level to the tests.
Please find the detailed integration test report here Please find the ci env pod logs here |
Please find the detailed integration test report here Please find the ci env pod logs here |
|
Please find the ci env pod logs here |
Please find the detailed integration test report here Please find the ci env pod logs here |
Link to JIRA ticket if there is one: PROM-168
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