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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,158 @@ | ||
| import httpx | ||
| import pytest | ||
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| from app.api import utility as util | ||
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| def test_get_instances_endpoint_with_vocab_lookup( | ||
| test_app, | ||
| monkeypatch, | ||
| set_test_credentials, | ||
| ): | ||
| """ | ||
| Given a GET request to /assessments/ (attribute with an external vocabulary lookup file available), | ||
| test that the endpoint correctly returns graph instances as prefixed term URIs and their human-readable labels | ||
| (where found), and excludes term URIs with unrecognized namespaces with a warning. | ||
| """ | ||
| # TODO: Since these mock HTTPX response JSONs are so similar (and useful), | ||
| # we could refactor their creation out into a function. | ||
| mock_response_json = { | ||
| "head": {"vars": ["termURL"]}, | ||
| "results": { | ||
| "bindings": [ | ||
| { | ||
| "termURL": { | ||
| "type": "uri", | ||
| "value": "https://www.cognitiveatlas.org/task/id/tsk_U9gDp8utahAfO", | ||
| } | ||
| }, | ||
| { | ||
| "termURL": { | ||
| "type": "uri", | ||
| "value": "https://www.cognitiveatlas.org/task/id/not_found_id", | ||
| } | ||
| }, | ||
| { | ||
| "termURL": { | ||
| "type": "uri", | ||
| "value": "https://www.notanatlas.org/task/id/tsk_alz5hjlUXp4WY", | ||
| } | ||
| }, | ||
| ] | ||
| }, | ||
| } | ||
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| def mock_httpx_post(**kwargs): | ||
| return httpx.Response(status_code=200, json=mock_response_json) | ||
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| monkeypatch.setattr(httpx, "post", mock_httpx_post) | ||
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| with pytest.warns( | ||
| UserWarning, | ||
| match="does not come from a vocabulary recognized by Neurobagel", | ||
| ): | ||
| with test_app: | ||
| response = test_app.get("/assessments/") | ||
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| assert response.json() == { | ||
| "nb:Assessment": [ | ||
| { | ||
| "TermURL": "cogatlas:tsk_U9gDp8utahAfO", | ||
| "Label": "Pittsburgh Stress Battery", | ||
| }, | ||
| {"TermURL": "cogatlas:not_found_id", "Label": None}, | ||
| ] | ||
| } | ||
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| def test_get_instances_endpoint_without_vocab_lookup( | ||
| test_app, monkeypatch, set_test_credentials | ||
| ): | ||
| """ | ||
| Given a GET request to /pipelines/ (attribute without a vocabulary lookup file available), | ||
| test that the endpoint correctly returns the found graph instances as prefixed term URIs with empty label fields. | ||
| """ | ||
| # Ensure that the API knows about some fake ontologies (with no vocabulary lookup files) | ||
| monkeypatch.setattr( | ||
| util, | ||
| "CONTEXT", | ||
| { | ||
| "cko": "https://www.coolknownontology.org/task/id/", | ||
| "ako": "https://www.awesomeknownontology.org/vocab/", | ||
| }, | ||
| ) | ||
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| mock_response_json = { | ||
| "head": {"vars": ["termURL"]}, | ||
| "results": { | ||
| "bindings": [ | ||
| { | ||
| "termURL": { | ||
| "type": "uri", | ||
| "value": "https://www.coolknownontology.org/task/id/trm_123", | ||
| } | ||
| }, | ||
| { | ||
| "termURL": { | ||
| "type": "uri", | ||
| "value": "https://www.coolknownontology.org/task/id/trm_234", | ||
| } | ||
| }, | ||
| ] | ||
| }, | ||
| } | ||
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| def mock_httpx_post(**kwargs): | ||
| return httpx.Response(status_code=200, json=mock_response_json) | ||
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| monkeypatch.setattr(httpx, "post", mock_httpx_post) | ||
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| response = test_app.get("/pipelines/") | ||
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| assert response.json() == { | ||
| "nb:Pipeline": [ | ||
| {"TermURL": "cko:trm_123", "Label": None}, | ||
| {"TermURL": "cko:trm_234", "Label": None}, | ||
| ] | ||
| } | ||
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| @pytest.mark.parametrize( | ||
| "attribute, expected_vocab_name, expected_namespace_pfx", | ||
| [ | ||
| ("assessments", "Cognitive Atlas Tasks", "cogatlas"), | ||
| ("diagnoses", "SNOMED CT", "snomed"), | ||
| ], | ||
| ) | ||
| def test_get_vocab_endpoint( | ||
| test_app, | ||
| monkeypatch, | ||
| set_test_credentials, | ||
| attribute, | ||
| expected_vocab_name, | ||
| expected_namespace_pfx, | ||
| ): | ||
| """ | ||
| Given a GET request to the /vocab subpath for a specific attribute router, | ||
| test that the endpoint returns a JSON object containing the correct vocabulary name, | ||
| namespace info, and term-label mappings for the attribute. | ||
| """ | ||
| # Ensure a temporary vocab term-label lookup file is available for the attribute | ||
| mock_term_labels = { | ||
| "trm_1234": "Generic Vocabulary Term 1", | ||
| "trm_2345": "Generic Vocabulary Term 2", | ||
| } | ||
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| def mock_load_json(path): | ||
| return mock_term_labels | ||
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| monkeypatch.setattr(util, "load_json", mock_load_json) | ||
| response = test_app.get(f"/{attribute}/vocab") | ||
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| assert response.status_code == 200 | ||
| assert response.json() == { | ||
| "vocabulary_name": expected_vocab_name, | ||
| "namespace_url": util.CONTEXT[expected_namespace_pfx], | ||
| "namespace_prefix": expected_namespace_pfx, | ||
| "term_labels": mock_term_labels, | ||
| } |
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