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Merge pull request #172 from WengLab-InformaticsResearch/deprecate_oxo
Deprecate oxo
2 parents 95a8895 + cc87b03 commit b7e4e72

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Lines changed: 200 additions & 190 deletions

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‎cohd/cohd_flask.conf‎

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DEPLOYMENT_ENV = 'ITRB-CI' # Expected values: ITRB-CI, ITRB-TEST, or ITRB-PROD
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DEBUG = False
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CACHE_TYPE = 'filesystem'
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CACHE_TYPE = 'FileSystemCache'
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CACHE_DEFAULT_TIMEOUT = 3600
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CACHE_DIR = 'flask_cache'
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CACHE_THRESHOLD = 100000

‎cohd/cohd_oas3.yaml‎

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@@ -41,7 +41,7 @@ info:
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[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki)
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[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy)
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[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets)
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version: 5.0.0
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version: 5.1.0
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title: Columbia Open Health Data (COHD) API
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contact:
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name: Casey Ta
@@ -669,10 +669,15 @@ paths:
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example: "SNOMED"
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/omop/xrefToOMOP:
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get:
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deprecated: true
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tags:
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- OMOP
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summary: Cross-reference from an ontology to OMOP standard concepts using the Ontology Xref Service
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description: >-
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This endpoint has been deprecated. COHD is now using Translator SRI services to map from OMOP to Biolink model.
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Also, the OxO API has been producing internal server errors in some circumstances for several months. This
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endpoint is currently still available but may not function correctly.
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Attempts to map a concept from an external ontology to an OMOP standard concept ID using the EMBL-EBI Ontology Xref Service (OxO): https://www.ebi.ac.uk/spot/oxo/index. This method attempts to use OxO to map from the original ontology to an intermediate ontology that is included in OMOP (ICD9CM, ICD10CM, SNOMEDCT, and MeSH), then uses the OMOP mappings to the standard concepts. Multiple mappings may be returned. Results are sorted by total_distance (OxO distance + OMOP distance) in ascending order.
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parameters:
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- name: curie
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example: 2
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/omop/xrefFromOMOP:
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get:
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deprecated: true
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tags:
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- OMOP
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summary: Cross-reference from an ontology to OMOP standard concepts using the Ontology Xref Service
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description: >-
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This endpoint has been deprecated. COHD is now using Translator SRI services to map from OMOP to Biolink model.
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Also, the OxO API has been producing internal server errors in some circumstances for several months. This
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endpoint is currently still available but may not function correctly.
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Attempts to map a concept from an external ontology to an OMOP standard concept ID using the EMBL-EBI Ontology Xref Service (OxO): https://www.ebi.ac.uk/spot/oxo/index. This method maps from the OMOP standard concept to an intermediate vocabulary included is OxO (ICD9CM, ICD10CM, SNOMEDCT, and MeSH), then uses the OxO API to map to other ontologies. Multiple mappings may be returned. Results are sorted by total_distance (OxO distance + OMOP distance) in ascending order.
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parameters:
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- name: concept_id

‎cohd/test_unit_tests.py‎

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@@ -272,84 +272,84 @@ def test_omop_vocab_to_oxo_prefix():
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omop_xref.omop_vocab_to_oxo_prefix('MeSH') == 'MeSH'
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def test_oxo_search():
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""" Tests omop_xref.oxo_search
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Uses oxo_search to make multiple requests to OxO and checks that the results have the expected formats, expected
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number of search results (i.e., one search result for each CURIE queried), and checks how the number of mappings
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compare across different calls with different parameter settings (i.e., more mappings when larger distances are
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used).
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Returns
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-------
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No return value. Asserts will be triggered upon failure.
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"""
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oxo_response_keys = ['_links', '_embedded', 'page']
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# Check oxo_search with a known CURIE that should produce matches
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json = omop_xref.oxo_search(['DOID:8398'], distance=2)
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# Check the general response format
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assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# Searched for 1 CURIE, expect searchResults with length 1
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assert len(json['_embedded']['searchResults']) == 1
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# Check that the query produced a response, but don't verify the mappings themselves
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# Keep track of the number of results for comparison against following queries
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comparison_length = len(json['_embedded']['searchResults'][0]['mappingResponseList'])
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# Sleep for 2 seconds so we don't overload OxO
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sleep(2)
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# Check oxo_search with a known CURIE with a shorter distance and check that there are fewer results
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json = omop_xref.oxo_search(['DOID:8398'], distance=1)
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# Check the general response format
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assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# Searched for 1 CURIE, expect searchResults with length 1
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assert len(json['_embedded']['searchResults']) == 1
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# Check that the query produced a response, but don't verify the mappings themselves
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# Keep track of the number of results for comparison against following queries
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) <= comparison_length
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# Sleep for 2 seconds so we don't overload OxO
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sleep(2)
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# Check oxo_search with a known CURIE with a longer distance and check that there are fewer results
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json = omop_xref.oxo_search(['DOID:8398'], distance=3)
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# Check the general response format
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assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# Searched for 1 CURIE, expect searchResults with length 1
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assert len(json['_embedded']['searchResults']) == 1
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# Check that the query produced a response, but don't verify the mappings themselves
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# Keep track of the number of results for comparison against following queries
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= comparison_length
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# Sleep for 2 seconds so we don't overload OxO
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sleep(2)
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# Check oxo_search with a known CURIE with a restricted mapping targets and check that there are fewer results
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json = omop_xref.oxo_search(['DOID:8398'], mapping_targets=['ICD10CM'], distance=2)
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# Check the general response format
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assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# Searched for 1 CURIE, expect searchResults with length 1
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assert len(json['_embedded']['searchResults']) == 1
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# Check that the query produced a response, but don't verify the mappings themselves
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# Keep track of the number of results for comparison against following queries
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) <= comparison_length
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# Sleep for 2 seconds so we don't overload OxO
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sleep(2)
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# Check oxo_search with one valid CURIE and one fake CURIE
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json = omop_xref.oxo_search(['DOID:8398', 'DOID:83980000'], distance=1)
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# Check the general response format
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assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# Searched for 2 CURIEs, expect searchResults with length 2
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assert len(json['_embedded']['searchResults']) == 2
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# Check that the first query produced mappings and the second query produced no mappings
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assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) > 0 and \
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len(json['_embedded']['searchResults'][1]['mappingResponseList']) == 0
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# def test_oxo_search():
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# """ Tests omop_xref.oxo_search
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# Uses oxo_search to make multiple requests to OxO and checks that the results have the expected formats, expected
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# number of search results (i.e., one search result for each CURIE queried), and checks how the number of mappings
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# compare across different calls with different parameter settings (i.e., more mappings when larger distances are
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# used).
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#
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# Returns
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# -------
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# No return value. Asserts will be triggered upon failure.
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# """
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# oxo_response_keys = ['_links', '_embedded', 'page']
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#
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# # Check oxo_search with a known CURIE that should produce matches
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# json = omop_xref.oxo_search(['DOID:8398'], distance=2)
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# # Check the general response format
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# assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# # Searched for 1 CURIE, expect searchResults with length 1
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# assert len(json['_embedded']['searchResults']) == 1
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# # Check that the query produced a response, but don't verify the mappings themselves
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# # Keep track of the number of results for comparison against following queries
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# comparison_length = len(json['_embedded']['searchResults'][0]['mappingResponseList'])
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#
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# # Sleep for 2 seconds so we don't overload OxO
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# sleep(2)
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#
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# # Check oxo_search with a known CURIE with a shorter distance and check that there are fewer results
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# json = omop_xref.oxo_search(['DOID:8398'], distance=1)
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# # Check the general response format
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# assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# # Searched for 1 CURIE, expect searchResults with length 1
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# assert len(json['_embedded']['searchResults']) == 1
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# # Check that the query produced a response, but don't verify the mappings themselves
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# # Keep track of the number of results for comparison against following queries
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) <= comparison_length
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#
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# # Sleep for 2 seconds so we don't overload OxO
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# sleep(2)
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#
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# # Check oxo_search with a known CURIE with a longer distance and check that there are fewer results
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# json = omop_xref.oxo_search(['DOID:8398'], distance=3)
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# # Check the general response format
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# assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# # Searched for 1 CURIE, expect searchResults with length 1
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# assert len(json['_embedded']['searchResults']) == 1
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# # Check that the query produced a response, but don't verify the mappings themselves
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# # Keep track of the number of results for comparison against following queries
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= comparison_length
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#
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# # Sleep for 2 seconds so we don't overload OxO
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# sleep(2)
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#
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# # Check oxo_search with a known CURIE with a restricted mapping targets and check that there are fewer results
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# json = omop_xref.oxo_search(['DOID:8398'], mapping_targets=['ICD10CM'], distance=2)
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# # Check the general response format
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# assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# # Searched for 1 CURIE, expect searchResults with length 1
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# assert len(json['_embedded']['searchResults']) == 1
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# # Check that the query produced a response, but don't verify the mappings themselves
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) >= 0
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# # Keep track of the number of results for comparison against following queries
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) <= comparison_length
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#
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# # Sleep for 2 seconds so we don't overload OxO
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# sleep(2)
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#
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# # Check oxo_search with one valid CURIE and one fake CURIE
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# json = omop_xref.oxo_search(['DOID:8398', 'DOID:83980000'], distance=1)
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# # Check the general response format
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# assert json is not None and isinstance(json, dict) and all(k in json for k in oxo_response_keys)
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# # Searched for 2 CURIEs, expect searchResults with length 2
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# assert len(json['_embedded']['searchResults']) == 2
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# # Check that the first query produced mappings and the second query produced no mappings
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# assert len(json['_embedded']['searchResults'][0]['mappingResponseList']) > 0 and \
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# len(json['_embedded']['searchResults'][1]['mappingResponseList']) == 0
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def test_xref_best_from():

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