diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8adabc8..3598833 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -21,6 +21,10 @@ repos: rev: v4.4.0 hooks: - id: check-yaml + - id: pretty-format-json + args: + - "--autofix" + - "--no-sort-keys" - repo: https://github.com/pycqa/isort rev: 5.12.0 diff --git a/app/api/crud.py b/app/api/crud.py index c628645..48a48b6 100644 --- a/app/api/crud.py +++ b/app/api/crud.py @@ -275,11 +275,11 @@ async def get_controlled_term_attributes() -> list: return results_list -async def get_term_labels_for_cogatlas( - term_labels_path: Path, +async def get_term_labels_for_vocab( + term_labels_path: Path, vocabulary_name: str, namespace_prefix: str ) -> VocabLabelsResponse: """ - Returns the term-label mappings along with the vocabulary namespace details for the Cognitive Atlas Task vocabulary. + Returns the term-label mappings along with the vocabulary namespace details for the specified vocabulary. Returns ------- @@ -288,8 +288,8 @@ async def get_term_labels_for_cogatlas( term_labels = util.load_json(term_labels_path) return VocabLabelsResponse( - vocabulary_name="Cognitive Atlas Tasks", - namespace_url=util.CONTEXT["cogatlas"], - namespace_prefix="cogatlas", + vocabulary_name=vocabulary_name, + namespace_url=util.CONTEXT[namespace_prefix], + namespace_prefix=namespace_prefix, term_labels=term_labels, ) diff --git a/app/api/models.py b/app/api/models.py index c4a9a18..b6417ba 100644 --- a/app/api/models.py +++ b/app/api/models.py @@ -69,6 +69,7 @@ class DataElementURI(str, Enum): """Data model for data element URIs that have available vocabulary lookups.""" assessment = "nb:Assessment" + diagnosis = "nb:Diagnosis" class VocabLabelsResponse(BaseModel): diff --git a/app/api/routers/attributes.py b/app/api/routers/attributes.py index 6462311..ddb2d49 100644 --- a/app/api/routers/attributes.py +++ b/app/api/routers/attributes.py @@ -12,9 +12,18 @@ async def get_term_labels_for_vocab( data_element_URI: DataElementURI, request: Request ): """When a GET request is sent, return a dict containing the name, namespace info, and all term ID-label mappings for the vocabulary of the specified variable.""" - if data_element_URI is DataElementURI.assessment: - return await crud.get_term_labels_for_cogatlas( - term_labels_path=request.app.state.cogatlas_term_lookup_path + # TODO: If/when more attribute options are supported, consider refactoring to use match/case (see https://peps.python.org/pep-0634/#the-match-statement) + if data_element_URI == DataElementURI.assessment: + return await crud.get_term_labels_for_vocab( + term_labels_path=request.app.state.cogatlas_term_lookup_path, + vocabulary_name="Cognitive Atlas Tasks", + namespace_prefix="cogatlas", + ) + if data_element_URI == DataElementURI.diagnosis: + return await crud.get_term_labels_for_vocab( + term_labels_path=request.app.state.snomed_term_lookup_path, + vocabulary_name="SNOMED CT", + namespace_prefix="snomed", ) @@ -28,8 +37,11 @@ async def get_terms( """ term_labels_path = None + # TODO: If/when more attribute options are supported, consider refactoring to use match/case (see https://peps.python.org/pep-0634/#the-match-statement) if data_element_URI == DataElementURI.assessment: term_labels_path = request.app.state.cogatlas_term_lookup_path + if data_element_URI == DataElementURI.diagnosis: + term_labels_path = request.app.state.snomed_term_lookup_path return await crud.get_terms(data_element_URI, term_labels_path) diff --git a/app/api/utility.py b/app/api/utility.py index dc27598..9d95051 100644 --- a/app/api/utility.py +++ b/app/api/utility.py @@ -373,7 +373,7 @@ def fetch_and_save_cogatlas(output_path: Path): Fetches the Cognitive Atlas vocabulary using its native Task API and writes term ID-label mappings to a temporary lookup file. If the API request fails, a backup copy of the vocabulary is used instead. - Saves a JSON with keys corresponding to Cognitive Atlas task IDs and values corresponding to human-readable task names). + Saves a JSON with keys corresponding to Cognitive Atlas task IDs and values corresponding to human-readable task names. Parameters ---------- @@ -381,18 +381,30 @@ def fetch_and_save_cogatlas(output_path: Path): File path to store output vocabulary lookup file. """ api_url = "https://www.cognitiveatlas.org/api/v-alpha/task?format=json" - response = httpx.get(url=api_url) - if response.is_success: - vocab = response.json() - else: + try: + response = httpx.get(url=api_url) + if response.is_success: + vocab = response.json() + else: + warnings.warn( + f""" + The API was unable to fetch the Cognitive Atlas task vocabulary (https://www.cognitiveatlas.org/tasks/a/) from the source and will default to using a local backup copy of the vocabulary instead. + + Details of the response from the source: + Status code {response.status_code} + {response.reason_phrase}: {response.text} + """ + ) + # Use backup copy of the raw vocabulary JSON + vocab = load_json(BACKUP_VOCAB_DIR / "cogatlas_task.json") + except httpx.NetworkError as exc: warnings.warn( - f""" - The API was unable to fetch the Cognitive Atlas task vocabulary (https://www.cognitiveatlas.org/tasks/a/) from the source and will default to using a local backup copy of the vocabulary instead. + f"""" + Fetching of the Cognitive Atlas task vocabulary (https://www.cognitiveatlas.org/tasks/a/) from the source failed due to a network error. + The API will default to using a local backup copy of the vocabulary instead. - Details of the response from the source: - Status code {response.status_code} - {response.reason_phrase}: {response.text} + Error: {exc} """ ) # Use backup copy of the raw vocabulary JSON @@ -401,3 +413,21 @@ def fetch_and_save_cogatlas(output_path: Path): term_labels = {term["id"]: term["name"] for term in vocab} with open(output_path, "w") as f: f.write(json.dumps(term_labels, indent=2)) + + +def create_snomed_term_lookup(output_path: Path): + """ + Reads in a file of disorder terms from the SNOMED CT vocabulary and writes term ID-label mappings to a temporary lookup file. + + Saves a JSON with keys corresponding to SNOMED CT IDs and values corresponding to human-readable term names. + + Parameters + ---------- + output_path : Path + File path to store output vocabulary lookup file. + """ + vocab = load_json(BACKUP_VOCAB_DIR / "snomedct_disorder.json") + + term_labels = {term["sctid"]: term["preferred_name"] for term in vocab} + with open(output_path, "w") as f: + f.write(json.dumps(term_labels, indent=2)) diff --git a/app/main.py b/app/main.py index f3ad141..f98e9b8 100644 --- a/app/main.py +++ b/app/main.py @@ -97,11 +97,16 @@ async def fetch_vocabularies_to_temp_dir(): app.state.vocab_dir = TemporaryDirectory() app.state.vocab_dir_path = Path(app.state.vocab_dir.name) + # TODO: Maybe store these paths in one dictionary on the app instance instead of separate variables? app.state.cogatlas_term_lookup_path = ( app.state.vocab_dir_path / "cogatlas_task_term_labels.json" ) + app.state.snomed_term_lookup_path = ( + app.state.vocab_dir_path / "snomedct_disorder_term_labels.json" + ) util.fetch_and_save_cogatlas(app.state.cogatlas_term_lookup_path) + util.create_snomed_term_lookup(app.state.snomed_term_lookup_path) @app.on_event("shutdown") diff --git a/tests/test_app_events.py b/tests/test_app_events.py index f70b010..5bc839e 100644 --- a/tests/test_app_events.py +++ b/tests/test_app_events.py @@ -108,6 +108,16 @@ def test_app_with_set_allowed_origins( ) +def test_stored_vocab_lookup_file_created_on_startup( + test_app, set_test_credentials +): + """Test that on startup, a non-empty temporary lookup file is created for term ID-label mappings for the locally stored SNOMED CT vocabulary.""" + with test_app: + term_labels_path = test_app.app.state.snomed_term_lookup_path + assert term_labels_path.exists() + assert term_labels_path.stat().st_size > 0 + + def test_external_vocab_is_fetched_on_startup( test_app, monkeypatch, set_test_credentials ): @@ -154,7 +164,7 @@ def test_failed_vocab_fetching_on_startup_raises_warning( test_app, monkeypatch, set_test_credentials ): """ - Tests that when a GET request to the Cognitive Atlas API fails (e.g., due to service being unavailable), + Tests that when a GET request to the Cognitive Atlas API has a non-success response code (e.g., due to service being unavailable), a warning is raised and that a term label lookup file is still created using a backup copy of the vocab. """ @@ -174,3 +184,25 @@ def mock_httpx_get(**kwargs): in str(warn.message) for warn in w ) + + +def test_network_error_on_startup_raises_warning( + test_app, monkeypatch, set_test_credentials +): + """ + Tests that when a GET request to the Cognitive Atlas API fails due to a network error (i.e., while issuing the request), + a warning is raised and that a term label lookup file is still created using a backup copy of the vocab. + """ + + def mock_httpx_get(**kwargs): + raise httpx.ConnectError("Some network error") + + monkeypatch.setattr(httpx, "get", mock_httpx_get) + + with pytest.warns(UserWarning) as w: + with test_app: + assert test_app.app.state.cogatlas_term_lookup_path.exists() + + assert any( + "failed due to a network error" in str(warn.message) for warn in w + ) diff --git a/tests/test_attributes.py b/tests/test_attributes.py index ecf51b1..1583572 100644 --- a/tests/test_attributes.py +++ b/tests/test_attributes.py @@ -195,23 +195,38 @@ def mock_httpx_post(**kwargs): ] -def test_get_attribute_vocab(test_app, monkeypatch, set_test_credentials): +@pytest.mark.parametrize( + "data_element_uri, expected_vocab_name, expected_namespace_pfx", + [ + ("nb:Assessment", "Cognitive Atlas Tasks", "cogatlas"), + ("nb:Diagnosis", "SNOMED CT", "snomed"), + ], +) +def test_get_attribute_vocab( + test_app, + monkeypatch, + set_test_credentials, + data_element_uri, + expected_vocab_name, + expected_namespace_pfx, +): """Given a GET request to the /attributes/{data_element_URI}/vocab endpoint, successfully returns a JSON object containing the vocabulary name, namespace info, and term-label mappings.""" + # Mock contents of a temporary term-label lookup file for a vocabulary mock_term_labels = { - "tsk_p7cabUkVvQPBS": "Generalized Self-Efficacy Scale", - "tsk_ccTKYnmv7tOZY": "Verbal Interference Test", + "trm_1234": "Generic Vocabulary Term 1", + "trm_2345": "Generic Vocabulary Term 2", } def mock_load_json(path): return mock_term_labels monkeypatch.setattr(util, "load_json", mock_load_json) - response = test_app.get("/attributes/nb:Assessment/vocab") + response = test_app.get(f"/attributes/{data_element_uri}/vocab") assert response.status_code == 200 assert response.json() == { - "vocabulary_name": "Cognitive Atlas Tasks", - "namespace_url": util.CONTEXT["cogatlas"], - "namespace_prefix": "cogatlas", + "vocabulary_name": expected_vocab_name, + "namespace_url": util.CONTEXT[expected_namespace_pfx], + "namespace_prefix": expected_namespace_pfx, "term_labels": mock_term_labels, } diff --git a/vocab/backup_external/snomedct_disorder.json b/vocab/backup_external/snomedct_disorder.json new file mode 100644 index 0000000..56d9edf --- /dev/null +++ b/vocab/backup_external/snomedct_disorder.json @@ -0,0 +1,27210 @@ +[ + { + "sctid": "10007009", + "preferred_name": "Coffin-Siris syndrome" + }, + { + "sctid": "1003374009", + "preferred_name": "Microlissencephaly" + }, + { + "sctid": "1003378007", + "preferred_name": "Optic nerve hypoplasia due to endocrine deficiency" + }, + { + "sctid": "1003380001", + "preferred_name": "6q16 microdeletion syndrome" + }, + { + "sctid": "1003422005", + "preferred_name": "Hypoplasia of optic nerve due to central nervous system malformation" + }, + { + "sctid": "1003429001", + "preferred_name": "Focal cortical dysplasia type IIa" + }, + { + "sctid": "1003430006", + "preferred_name": "Focal cortical dysplasia type IIb" + }, + { + "sctid": "1003434002", + "preferred_name": "Lipoma due to neurospinal dysraphism" + }, + { + "sctid": "1003444000", + "preferred_name": "Type 3 lissencephaly" + }, + { + "sctid": "1003445004", + "preferred_name": "Lumbosacral spina bifida aperta with hydrocephalus" + }, + { + "sctid": "1003447007", + "preferred_name": "Pelizaeus-Merzbacher disease null syndrome" + }, + { + "sctid": "1003448002", + "preferred_name": "Lumbosacral spina bifida aperta" + }, + { + "sctid": "1003461002", + "preferred_name": "Focal cortical dysplasia type II" + }, + { + "sctid": "1003462009", + "preferred_name": "Focal cortical dysplasia type Ib" + }, + { + "sctid": "1003463004", + "preferred_name": "Focal cortical dysplasia type I" + }, + { + "sctid": "1003464005", + "preferred_name": "Focal cortical dysplasia type Ia" + }, + { + "sctid": "1003465006", + "preferred_name": "Familial spinal neurofibromatosis" + }, + { + "sctid": "1003584006", + "preferred_name": "Hind brain laceration with open intracranial wound and loss of consciousness" + }, + { + "sctid": "1003881009", + "preferred_name": "Pelizaeus-Merzbacher disease in female carrier" + }, + { + "sctid": "100491000119103", + "preferred_name": "Myelopathy due to spinal stenosis of lumbar region" + }, + { + "sctid": "100511000119108", + "preferred_name": "Myelopathy co-occurrent and due to spinal stenosis of thoracic region" + }, + { + "sctid": "10068001", + "preferred_name": "Sensory somatic cortical disorder" + }, + { + "sctid": "100721000119109", + "preferred_name": "High grade astrocytoma of brain" + }, + { + "sctid": "100731000119107", + "preferred_name": "Low grade astrocytoma of brain" + }, + { + "sctid": "10082001", + "preferred_name": "Progressive rubella panencephalitis" + }, + { + "sctid": "100941000119100", + "preferred_name": "Epilepsy in mother complicating pregnancy" + }, + { + "sctid": "1010464002", + "preferred_name": "Agenesis of right hemisphere of cerebellum" + }, + { + "sctid": "1010465001", + "preferred_name": "Agenesis of left hemisphere of cerebellum" + }, + { + "sctid": "1010604007", + "preferred_name": "Ventriculomegaly due to developmental anomaly" + }, + { + "sctid": "1010630006", + "preferred_name": "X-linked complicated corpus callosum dysgenesis" + }, + { + "sctid": "1010642001", + "preferred_name": "Sporadic infantile bilateral striatal necrosis" + }, + { + "sctid": "1010643006", + "preferred_name": "Thoracolumbosacral spina bifida aperta" + }, + { + "sctid": "1010644000", + "preferred_name": "Spina bifida aperta of upper thoracic spine" + }, + { + "sctid": "1010663004", + "preferred_name": "Subcortical nodular heterotopia" + }, + { + "sctid": "101421000119107", + "preferred_name": "Dementia due to Parkinson's disease" + }, + { + "sctid": "101571000119107", + "preferred_name": "Ependymoma of cerebrum" + }, + { + "sctid": "10211000132109", + "preferred_name": "Perinatal depression" + }, + { + "sctid": "10277002", + "preferred_name": "Cerebellopontine angle syndrome" + }, + { + "sctid": "10278007", + "preferred_name": "Factitious purpura" + }, + { + "sctid": "10310006", + "preferred_name": "Open fracture of C1-C4 level with incomplete spinal cord lesion" + }, + { + "sctid": "10327003", + "preferred_name": "Cocaine-induced mood disorder" + }, + { + "sctid": "1032761000000105", + "preferred_name": "Intraventricular (nontraumatic) haemorrhage, grade 4, of fetus and newborn" + }, + { + "sctid": "10340008", + "preferred_name": "Isolated gonadotropin deficiency" + }, + { + "sctid": "10349009", + "preferred_name": "Multi-infarct dementia with delirium" + }, + { + "sctid": "103931000119102", + "preferred_name": "Hepatic coma due to hepatitis" + }, + { + "sctid": "10394003", + "preferred_name": "Friedreich's ataxia" + }, + { + "sctid": "104431000119107", + "preferred_name": "Lipomyelomeningocele" + }, + { + "sctid": "10481000119108", + "preferred_name": "Colloid brain cyst" + }, + { + "sctid": "104851000119103", + "preferred_name": "Postpartum major depression in remission" + }, + { + "sctid": "10491005", + "preferred_name": "Herpes zoster with meningitis" + }, + { + "sctid": "104981000119104", + "preferred_name": "Oligodendroglioma of cerebrum" + }, + { + "sctid": "1052243006", + "preferred_name": "Hemiparesis of left side of face" + }, + { + "sctid": "1052244000", + "preferred_name": "Hemiparesis of right side of face" + }, + { + "sctid": "1052326006", + "preferred_name": "Rachischisis partialis" + }, + { + "sctid": "10532003", + "preferred_name": "Primary degenerative dementia of the Alzheimer type, presenile onset, with depression" + }, + { + "sctid": "105421000119105", + "preferred_name": "Early onset Alzheimer's disease with behavioral disturbance" + }, + { + "sctid": "105451000119102", + "preferred_name": "Amnestic disorder associated with general medical condition" + }, + { + "sctid": "10575009", + "preferred_name": "Open fracture of vertebral column with spinal cord injury" + }, + { + "sctid": "10586006", + "preferred_name": "Occupation-related stress disorder" + }, + { + "sctid": "106015009", + "preferred_name": "Mental disorder AND/OR culture bound syndrome" + }, + { + "sctid": "106018006", + "preferred_name": "Hereditary degenerative disease of central nervous system" + }, + { + "sctid": "106021000119105", + "preferred_name": "Multi-infarct dementia due to atherosclerosis" + }, + { + "sctid": "106071000119106", + "preferred_name": "Secondary hypothalamic insufficiency" + }, + { + "sctid": "10649000", + "preferred_name": "Hyperpituitarism" + }, + { + "sctid": "10651001", + "preferred_name": "Temporal lobectomy behavior syndrome" + }, + { + "sctid": "1067201000000106", + "preferred_name": "Eating disorder co-occurrent with diabetes mellitus type 1" + }, + { + "sctid": "10677711000119101", + "preferred_name": "Encephalopathy due to Influenza A virus" + }, + { + "sctid": "10701000119109", + "preferred_name": "Refractory complex partial seizure with impairment of consciousness" + }, + { + "sctid": "10706006", + "preferred_name": "Tuberculosis of central nervous system" + }, + { + "sctid": "10736002", + "preferred_name": "Isolated thyroliberin deficiency" + }, + { + "sctid": "10741871000119101", + "preferred_name": "Alcohol dependence in pregnancy" + }, + { + "sctid": "10743001000119103", + "preferred_name": "Anxiety disorder in mother complicating childbirth" + }, + { + "sctid": "10749811000119108", + "preferred_name": "Obstetric anesthesia with central nervous system complication in childbirth" + }, + { + "sctid": "10750951000119106", + "preferred_name": "Epilepsy in mother complicating childbirth" + }, + { + "sctid": "10752641000119102", + "preferred_name": "Eclampsia with pre-existing hypertension in childbirth" + }, + { + "sctid": "10755041000119100", + "preferred_name": "Alcohol dependence in childbirth" + }, + { + "sctid": "107557061000119108", + "preferred_name": "Cerebrovascular accident due to embolism of bilateral anterior cerebral arteries" + }, + { + "sctid": "107561000119107", + "preferred_name": "Ependymoma of brain stem" + }, + { + "sctid": "107571000119101", + "preferred_name": "Oligodendroglioma of brain stem" + }, + { + "sctid": "107581000119103", + "preferred_name": "Astrocytoma of brain stem" + }, + { + "sctid": "10760421000119102", + "preferred_name": "Psychotic disorder in mother complicating childbirth" + }, + { + "sctid": "10760461000119107", + "preferred_name": "Psychotic disorder in mother complicating pregnancy" + }, + { + "sctid": "1078001000000105", + "preferred_name": "Haemorrhagic stroke" + }, + { + "sctid": "10783000", + "preferred_name": "Symptomatic pedophilia" + }, + { + "sctid": "10811121000119102", + "preferred_name": "Major depressive disorder in mother complicating childbirth" + }, + { + "sctid": "10811161000119107", + "preferred_name": "Major depressive disorder in mother complicating pregnancy" + }, + { + "sctid": "10811201000119102", + "preferred_name": "Mental disorder in mother complicating childbirth" + }, + { + "sctid": "1082451000119102", + "preferred_name": "Encephalitis due to Actinomyces" + }, + { + "sctid": "1082511000119102", + "preferred_name": "Hepatic coma due to acute hepatic failure" + }, + { + "sctid": "1082621000119108", + "preferred_name": "Hepatic coma due to alcoholic liver failure" + }, + { + "sctid": "10835871000119104", + "preferred_name": "Depressive disorder in mother complicating childbirth" + }, + { + "sctid": "1084061000000106", + "preferred_name": "Depressive personality disorder" + }, + { + "sctid": "1084741000119103", + "preferred_name": "Meningoencephalitis due to Blastomyces dermatitidis" + }, + { + "sctid": "1084801000119107", + "preferred_name": "Meningitis due to Sporothrix schenkii" + }, + { + "sctid": "1085091000119108", + "preferred_name": "Hepatic coma due to chronic hepatic failure" + }, + { + "sctid": "1085361000119104", + "preferred_name": "Meningitis due to Cytomegaloviral Mononucleosis" + }, + { + "sctid": "1086061000119109", + "preferred_name": "Diphtheria radiculomyelitis" + }, + { + "sctid": "1086471000000103", + "preferred_name": "Recurrent reactive depressive episodes, severe, with psychosis" + }, + { + "sctid": "1086661000000108", + "preferred_name": "Reactive depression, prolonged single episode" + }, + { + "sctid": "1086671000000101", + "preferred_name": "Reactive depression, single episode" + }, + { + "sctid": "1086681000000104", + "preferred_name": "Reactive depression, recurrent" + }, + { + "sctid": "1086691000000102", + "preferred_name": "Reactive depression, first episode" + }, + { + "sctid": "1086991000119103", + "preferred_name": "Gonococcal abscess of brain" + }, + { + "sctid": "1087451000000109", + "preferred_name": "Late onset alcohol-induced psychosis" + }, + { + "sctid": "1087461000000107", + "preferred_name": "Late onset substance-induced psychosis" + }, + { + "sctid": "1087471000000100", + "preferred_name": "Late onset substance-induced psychiatric disorder" + }, + { + "sctid": "1087481000000103", + "preferred_name": "Late onset cocaine-induced psychosis" + }, + { + "sctid": "1087491000000101", + "preferred_name": "Late onset LSD (lysergic acid diethylamide)-induced psychosis" + }, + { + "sctid": "10875004", + "preferred_name": "Severe mixed bipolar I disorder with psychotic features, mood-incongruent" + }, + { + "sctid": "1087501000000107", + "preferred_name": "Late onset cannabinoid-induced psychosis" + }, + { + "sctid": "1087511000000109", + "preferred_name": "Late onset amphetamine-induced psychosis" + }, + { + "sctid": "1089411000000104", + "preferred_name": "Cerebral infarction 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"preferred_name": "Epilepsy of infancy with migrating focal seizures" + }, + { + "sctid": "733198005", + "preferred_name": "Encephalopathy due to and following cardiopulmonary bypass" + }, + { + "sctid": "733199002", + "preferred_name": "Multifocal cerebral infarction due to and following procedure on cardiovascular system" + }, + { + "sctid": "733200004", + "preferred_name": "Superficial siderosis of central nervous system" + }, + { + "sctid": "73331006", + "preferred_name": "Hemimyelia" + }, + { + "sctid": "733417008", + "preferred_name": "Facial dysmorphism, macrocephaly, myopia, Dandy-Walker malformation syndrome" + }, + { + "sctid": "733418003", + "preferred_name": "Joubert syndrome with Jeune asphyxiating thoracic dystrophy" + }, + { + "sctid": "733419006", + "preferred_name": "Metaphyseal dysostosis, intellectual disability, conductive deafness syndrome" + }, + { + "sctid": "733422008", + "preferred_name": "Prion protein systemic amyloidosis" + }, + { + "sctid": "733452000", + 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