[text analytics] assertions

sdk/textanalytics/azure-ai-textanalytics/CHANGELOG.md

@@ -12,6 +12,8 @@
 
 - Add property `normalized_text` to `HealthcareEntity`. This property is a normalized version of the `text` property that already
 exists on the `HealthcareEntity`
+- Add property `assertion` onto `HealthcareEntity`. This contains assertions about the entity itself, i.e. if the entity represents a diagnosis,
+is this diagnosis conditional on a symptom?
 
 ## 5.1.0b5 (2021-02-10)
 

sdk/textanalytics/azure-ai-textanalytics/README.md

@@ -477,6 +477,11 @@ for idx, doc in enumerate(docs):
             for data_source in entity.data_sources:
                 print("......Entity ID: {}".format(data_source.entity_id))
                 print("......Name: {}".format(data_source.name))
+        if entity.assertion is not None:
+            print("...Assertion:")
+            print("......Conditionality: {}".format(entity.assertion.conditionality))
+            print("......Certainty: {}".format(entity.assertion.certainty))
+            print("......Association: {}".format(entity.assertion.association))
     for relation in doc.entity_relations:
         print("Relation of type: {} has the following roles".format(relation.relation_type))
         for role in relation.roles:

sdk/textanalytics/azure-ai-textanalytics/azure/ai/textanalytics/__init__.py

@@ -45,7 +45,9 @@
     HealthcareEntityRelationRoleType,
 )
 from ._paging import AnalyzeHealthcareEntitiesResult
-from ._generated.v3_1_preview_4.models import RelationType as HealthcareEntityRelationType
+from ._generated.v3_1_preview_4.models import (
+    RelationType as HealthcareEntityRelationType,
+)
 
 __all__ = [
     'TextAnalyticsApiVersion',

sdk/textanalytics/azure-ai-textanalytics/azure/ai/textanalytics/_models.py

@@ -498,6 +498,11 @@ class HealthcareEntity(DictMixin):
     :ivar str category: Entity category, see the following link for health's named
         entity types: https://aka.ms/text-analytics-health-entities
     :ivar str subcategory: Entity subcategory.
+    :ivar assertion: Contains various assertions about this entity. For example, if
+        an entity is a diagnosis, is this diagnosis 'conditional' on a symptom?
+        Are the doctors 'certain' about this diagnosis? Is this diagnosis 'associated'
+        with another diagnosis?
+    :vartype assertion: ~azure.ai.textanalytics.HealthcareEntityAssertion
     :ivar int length: The entity text length.  This value depends on the value
         of the `string_index_type` parameter specified in the original request, which is
         UnicodeCodePoints by default.
@@ -515,18 +520,29 @@ def __init__(self, **kwargs):
         self.normalized_text = kwargs.get("normalized_text", None)
         self.category = kwargs.get("category", None)
         self.subcategory = kwargs.get("subcategory", None)
+        self.assertion = kwargs.get("assertion", None)
         self.length = kwargs.get("length", None)
         self.offset = kwargs.get("offset", None)
         self.confidence_score = kwargs.get("confidence_score", None)
         self.data_sources = kwargs.get("data_sources", [])
 
     @classmethod
     def _from_generated(cls, healthcare_entity):
+        assertion = None
+        try:
+            if healthcare_entity.assertion:
+                assertion = HealthcareEntityAssertion._from_generated(  # pylint: disable=protected-access
+                    healthcare_entity.assertion
+                )
+        except AttributeError:
+            assertion = None
+
         return cls(
             text=healthcare_entity.text,
             normalized_text=healthcare_entity.name,
             category=healthcare_entity.category,
             subcategory=healthcare_entity.subcategory,
+            assertion=assertion,
             length=healthcare_entity.length,
             offset=healthcare_entity.offset,
             confidence_score=healthcare_entity.confidence_score,
@@ -539,18 +555,58 @@ def __hash__(self):
         return hash(repr(self))
 
     def __repr__(self):
-        return "HealthcareEntity(text={}, normalized_text={}, category={}, subcategory={}, length={}, offset={}, "\
-        "confidence_score={}, data_sources={})".format(
+        return "HealthcareEntity(text={}, normalized_text={}, category={}, subcategory={}, assertion={}, length={}, "\
+        "offset={}, confidence_score={}, data_sources={})".format(
             self.text,
             self.normalized_text,
             self.category,
             self.subcategory,
+            repr(self.assertion),
             self.length,
             self.offset,
             self.confidence_score,
             repr(self.data_sources),
         )[:1024]
 
+class HealthcareEntityAssertion(DictMixin):
+    """Contains various assertions about a `HealthcareEntity`.
+
+    For example, if an entity is a diagnosis, is this diagnosis 'conditional' on a symptom?
+    Are the doctors 'certain' about this diagnosis? Is this diagnosis 'associated'
+    with another diagnosis?
+
+    :ivar str conditionality: Describes whether the healthcare entity it's on is conditional on another entity.
+        For example, "If the patient has a fever, he has pneumonia", the diagnosis of pneumonia
+        is 'conditional' on whether the patient has a fever. Possible values are "hypothetical" and
+        "conditional".
+    :ivar str certainty: Describes how certain the healthcare entity it's on is. For example,
+        in "The patient may have a fever", the fever entity is not 100% certain, but is instead
+        "positivePossible". Possible values are "positive", "positivePossible", "neutralPossible",
+        "negativePossible", and "negative".
+    :ivar str association: Describes whether the healthcare entity it's on is the subject of the document, or
+        if this entity describes someone else in the document. For example, in "The subject's mother has
+        a fever", the "fever" entity is not associated with the subject themselves, but with the subject's
+        mother. Possible values are "subject" and "other".
+    """
+
+    def __init__(self, **kwargs):
+        self.conditionality = kwargs.get("conditionality", None)
+        self.certainty = kwargs.get("certainty", None)
+        self.association = kwargs.get("association", None)
+
+    @classmethod
+    def _from_generated(cls, healthcare_assertion):
+        return cls(
+            conditionality=healthcare_assertion.conditionality,
+            certainty=healthcare_assertion.certainty,
+            association=healthcare_assertion.association,
+        )
+
+    def __repr__(self):
+        return "HealthcareEntityAssertion(conditionality={}, certainty={}, association={})".format(
+            self.conditionality, self.certainty, self.association
+        )
+
 
 class HealthcareEntityDataSource(DictMixin):
     """

sdk/textanalytics/azure-ai-textanalytics/samples/async_samples/sample_analyze_healthcare_entities_async.py

@@ -88,6 +88,11 @@ async def analyze_healthcare_entities_async(self):
                     for data_source in entity.data_sources:
                         print("......Entity ID: {}".format(data_source.entity_id))
                         print("......Name: {}".format(data_source.name))
+                if entity.assertion is not None:
+                    print("...Assertion:")
+                    print("......Conditionality: {}".format(entity.assertion.conditionality))
+                    print("......Certainty: {}".format(entity.assertion.certainty))
+                    print("......Association: {}".format(entity.assertion.association))
             for relation in doc.entity_relations:
                 print("Relation of type: {} has the following roles".format(relation.relation_type))
                 for role in relation.roles:

sdk/textanalytics/azure-ai-textanalytics/samples/sample_analyze_healthcare_entities.py

@@ -84,6 +84,11 @@ def analyze_healthcare_entities(self):
                     for data_source in entity.data_sources:
                         print("......Entity ID: {}".format(data_source.entity_id))
                         print("......Name: {}".format(data_source.name))
+                if entity.assertion is not None:
+                    print("...Assertion:")
+                    print("......Conditionality: {}".format(entity.assertion.conditionality))
+                    print("......Certainty: {}".format(entity.assertion.certainty))
+                    print("......Association: {}".format(entity.assertion.association))
             for relation in doc.entity_relations:
                 print("Relation of type: {} has the following roles".format(relation.relation_type))
                 for role in relation.roles:

sdk/textanalytics/azure-ai-textanalytics/tests/recordings/test_analyze_healthcare.test_healthcare_assertion.yaml

@@ -0,0 +1,109 @@
+interactions:
+- request:
+    body: '{"documents": [{"id": "0", "text": "Baby not likely to have Meningitis.",
+      "language": "en"}]}'
+    headers:
+      Accept:
+      - application/json, text/json
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      Content-Length:
+      - '93'
+      Content-Type:
+      - application/json
+      User-Agent:
+      - azsdk-python-ai-textanalytics/5.1.0b6 Python/3.9.1 (macOS-10.13.6-x86_64-i386-64bit)
+    method: POST
+    uri: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs?stringIndexType=UnicodeCodePoint
+  response:
+    body:
+      string: ''
+    headers:
+      apim-request-id:
+      - 982d8d11-7c5e-41cc-afb4-3a0a39cf7e5b
+      date:
+      - Thu, 04 Mar 2021 17:06:40 GMT
+      operation-location:
+      - https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs/40590cb7-4fa0-4ce8-afed-19b16395bd65
+      strict-transport-security:
+      - max-age=31536000; includeSubDomains; preload
+      transfer-encoding:
+      - chunked
+      x-content-type-options:
+      - nosniff
+      x-envoy-upstream-service-time:
+      - '355'
+    status:
+      code: 202
+      message: Accepted
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      User-Agent:
+      - azsdk-python-ai-textanalytics/5.1.0b6 Python/3.9.1 (macOS-10.13.6-x86_64-i386-64bit)
+    method: GET
+    uri: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs/40590cb7-4fa0-4ce8-afed-19b16395bd65
+  response:
+    body:
+      string: '{"jobId":"40590cb7-4fa0-4ce8-afed-19b16395bd65","lastUpdateDateTime":"2021-03-04T17:06:40Z","createdDateTime":"2021-03-04T17:06:40Z","expirationDateTime":"2021-03-05T17:06:40Z","status":"notStarted","errors":[]}'
+    headers:
+      apim-request-id:
+      - fb188517-edcf-402f-9d1e-3d1fe1c757e7
+      content-type:
+      - application/json; charset=utf-8
+      date:
+      - Thu, 04 Mar 2021 17:06:45 GMT
+      strict-transport-security:
+      - max-age=31536000; includeSubDomains; preload
+      transfer-encoding:
+      - chunked
+      x-content-type-options:
+      - nosniff
+      x-envoy-upstream-service-time:
+      - '179'
+    status:
+      code: 200
+      message: OK
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      User-Agent:
+      - azsdk-python-ai-textanalytics/5.1.0b6 Python/3.9.1 (macOS-10.13.6-x86_64-i386-64bit)
+    method: GET
+    uri: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs/40590cb7-4fa0-4ce8-afed-19b16395bd65
+  response:
+    body:
+      string: '{"jobId":"40590cb7-4fa0-4ce8-afed-19b16395bd65","lastUpdateDateTime":"2021-03-04T17:06:48Z","createdDateTime":"2021-03-04T17:06:40Z","expirationDateTime":"2021-03-05T17:06:40Z","status":"succeeded","errors":[],"results":{"documents":[{"id":"0","entities":[{"offset":0,"length":4,"text":"Baby","category":"Age","confidenceScore":0.89,"links":[{"dataSource":"UMLS","id":"C0021270"},{"dataSource":"AOD","id":"0000005273"},{"dataSource":"CCPSS","id":"0030805"},{"dataSource":"CHV","id":"0000006675"},{"dataSource":"DXP","id":"U002089"},{"dataSource":"LCH","id":"U002421"},{"dataSource":"LCH_NW","id":"sh85066022"},{"dataSource":"LNC","id":"LA19747-7"},{"dataSource":"MDR","id":"10021731"},{"dataSource":"MSH","id":"D007223"},{"dataSource":"NCI","id":"C27956"},{"dataSource":"NCI_FDA","id":"C27956"},{"dataSource":"NCI_NICHD","id":"C27956"},{"dataSource":"SNOMEDCT_US","id":"133931009"}]},{"offset":24,"length":10,"text":"Meningitis","category":"Diagnosis","confidenceScore":1.0,"assertion":{"certainty":"negative"},"links":[{"dataSource":"UMLS","id":"C0025289"},{"dataSource":"AOD","id":"0000006185"},{"dataSource":"BI","id":"BI00546"},{"dataSource":"CCPSS","id":"1018016"},{"dataSource":"CCSR_10","id":"NVS001"},{"dataSource":"CHV","id":"0000007932"},{"dataSource":"COSTAR","id":"478"},{"dataSource":"CSP","id":"2042-5301"},{"dataSource":"CST","id":"MENINGITIS"},{"dataSource":"DXP","id":"U002543"},{"dataSource":"HPO","id":"HP:0001287"},{"dataSource":"ICD10","id":"G03.9"},{"dataSource":"ICD10AM","id":"G03.9"},{"dataSource":"ICD10CM","id":"G03.9"},{"dataSource":"ICD9CM","id":"322.9"},{"dataSource":"ICPC2ICD10ENG","id":"MTHU048434"},{"dataSource":"ICPC2P","id":"N71002"},{"dataSource":"LCH","id":"U002901"},{"dataSource":"LCH_NW","id":"sh85083562"},{"dataSource":"LNC","id":"LP20756-0"},{"dataSource":"MDR","id":"10027199"},{"dataSource":"MEDCIN","id":"31192"},{"dataSource":"MEDLINEPLUS","id":"324"},{"dataSource":"MSH","id":"D008581"},{"dataSource":"NANDA-I","id":"02899"},{"dataSource":"NCI","id":"C26828"},{"dataSource":"NCI_CPTAC","id":"C26828"},{"dataSource":"NCI_CTCAE","id":"E11458"},{"dataSource":"NCI_FDA","id":"2389"},{"dataSource":"NCI_NCI-GLOSS","id":"CDR0000471780"},{"dataSource":"NCI_NICHD","id":"C26828"},{"dataSource":"OMIM","id":"MTHU005994"},{"dataSource":"PSY","id":"30660"},{"dataSource":"RCD","id":"X000H"},{"dataSource":"SNM","id":"M-40000"},{"dataSource":"SNMI","id":"DA-10010"},{"dataSource":"SNOMEDCT_US","id":"7180009"},{"dataSource":"WHO","id":"0955"}]}],"relations":[],"warnings":[]}],"errors":[],"modelVersion":"2021-01-11"}}'
+    headers:
+      apim-request-id:
+      - 30f0264a-61c1-4137-92bb-747ed9ca8e15
+      content-type:
+      - application/json; charset=utf-8
+      date:
+      - Thu, 04 Mar 2021 17:06:51 GMT
+      strict-transport-security:
+      - max-age=31536000; includeSubDomains; preload
+      transfer-encoding:
+      - chunked
+      x-content-type-options:
+      - nosniff
+      x-envoy-upstream-service-time:
+      - '224'
+    status:
+      code: 200
+      message: OK
+version: 1

sdk/textanalytics/azure-ai-textanalytics/tests/recordings/test_analyze_healthcare_async.test_healthcare_assertion.yaml

@@ -0,0 +1,53 @@
+interactions:
+- request:
+    body: '{"documents": [{"id": "0", "text": "Baby not likely to have Meningitis.",
+      "language": "en"}]}'
+    headers:
+      Accept:
+      - application/json, text/json
+      Content-Length:
+      - '93'
+      Content-Type:
+      - application/json
+      User-Agent:
+      - azsdk-python-ai-textanalytics/5.1.0b6 Python/3.9.1 (macOS-10.13.6-x86_64-i386-64bit)
+    method: POST
+    uri: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs?stringIndexType=UnicodeCodePoint
+  response:
+    body:
+      string: ''
+    headers:
+      apim-request-id: 90f5a116-0d67-4ca0-bdf2-ead5e23bcca7
+      date: Thu, 04 Mar 2021 17:06:51 GMT
+      operation-location: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs/e3f9abec-0960-4602-b4af-f91991dccb57
+      strict-transport-security: max-age=31536000; includeSubDomains; preload
+      transfer-encoding: chunked
+      x-content-type-options: nosniff
+      x-envoy-upstream-service-time: '188'
+    status:
+      code: 202
+      message: Accepted
+    url: https://westus2.api.cognitive.microsoft.com//text/analytics/v3.1-preview.4/entities/health/jobs?stringIndexType=UnicodeCodePoint
+- request:
+    body: null
+    headers:
+      User-Agent:
+      - azsdk-python-ai-textanalytics/5.1.0b6 Python/3.9.1 (macOS-10.13.6-x86_64-i386-64bit)
+    method: GET
+    uri: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs/e3f9abec-0960-4602-b4af-f91991dccb57
+  response:
+    body:
+      string: '{"jobId":"e3f9abec-0960-4602-b4af-f91991dccb57","lastUpdateDateTime":"2021-03-04T17:06:52Z","createdDateTime":"2021-03-04T17:06:51Z","expirationDateTime":"2021-03-05T17:06:51Z","status":"succeeded","errors":[],"results":{"documents":[{"id":"0","entities":[{"offset":0,"length":4,"text":"Baby","category":"Age","confidenceScore":0.89,"links":[{"dataSource":"UMLS","id":"C0021270"},{"dataSource":"AOD","id":"0000005273"},{"dataSource":"CCPSS","id":"0030805"},{"dataSource":"CHV","id":"0000006675"},{"dataSource":"DXP","id":"U002089"},{"dataSource":"LCH","id":"U002421"},{"dataSource":"LCH_NW","id":"sh85066022"},{"dataSource":"LNC","id":"LA19747-7"},{"dataSource":"MDR","id":"10021731"},{"dataSource":"MSH","id":"D007223"},{"dataSource":"NCI","id":"C27956"},{"dataSource":"NCI_FDA","id":"C27956"},{"dataSource":"NCI_NICHD","id":"C27956"},{"dataSource":"SNOMEDCT_US","id":"133931009"}]},{"offset":24,"length":10,"text":"Meningitis","category":"Diagnosis","confidenceScore":1.0,"assertion":{"certainty":"negative"},"links":[{"dataSource":"UMLS","id":"C0025289"},{"dataSource":"AOD","id":"0000006185"},{"dataSource":"BI","id":"BI00546"},{"dataSource":"CCPSS","id":"1018016"},{"dataSource":"CCSR_10","id":"NVS001"},{"dataSource":"CHV","id":"0000007932"},{"dataSource":"COSTAR","id":"478"},{"dataSource":"CSP","id":"2042-5301"},{"dataSource":"CST","id":"MENINGITIS"},{"dataSource":"DXP","id":"U002543"},{"dataSource":"HPO","id":"HP:0001287"},{"dataSource":"ICD10","id":"G03.9"},{"dataSource":"ICD10AM","id":"G03.9"},{"dataSource":"ICD10CM","id":"G03.9"},{"dataSource":"ICD9CM","id":"322.9"},{"dataSource":"ICPC2ICD10ENG","id":"MTHU048434"},{"dataSource":"ICPC2P","id":"N71002"},{"dataSource":"LCH","id":"U002901"},{"dataSource":"LCH_NW","id":"sh85083562"},{"dataSource":"LNC","id":"LP20756-0"},{"dataSource":"MDR","id":"10027199"},{"dataSource":"MEDCIN","id":"31192"},{"dataSource":"MEDLINEPLUS","id":"324"},{"dataSource":"MSH","id":"D008581"},{"dataSource":"NANDA-I","id":"02899"},{"dataSource":"NCI","id":"C26828"},{"dataSource":"NCI_CPTAC","id":"C26828"},{"dataSource":"NCI_CTCAE","id":"E11458"},{"dataSource":"NCI_FDA","id":"2389"},{"dataSource":"NCI_NCI-GLOSS","id":"CDR0000471780"},{"dataSource":"NCI_NICHD","id":"C26828"},{"dataSource":"OMIM","id":"MTHU005994"},{"dataSource":"PSY","id":"30660"},{"dataSource":"RCD","id":"X000H"},{"dataSource":"SNM","id":"M-40000"},{"dataSource":"SNMI","id":"DA-10010"},{"dataSource":"SNOMEDCT_US","id":"7180009"},{"dataSource":"WHO","id":"0955"}]}],"relations":[],"warnings":[]}],"errors":[],"modelVersion":"2021-01-11"}}'
+    headers:
+      apim-request-id: 40cc7792-e2e3-4722-beac-485880adb432
+      content-type: application/json; charset=utf-8
+      date: Thu, 04 Mar 2021 17:06:56 GMT
+      strict-transport-security: max-age=31536000; includeSubDomains; preload
+      transfer-encoding: chunked
+      x-content-type-options: nosniff
+      x-envoy-upstream-service-time: '151'
+    status:
+      code: 200
+      message: OK
+    url: https://westus2.api.cognitive.microsoft.com/text/analytics/v3.1-preview.4/entities/health/jobs/e3f9abec-0960-4602-b4af-f91991dccb57
+version: 1

sdk/textanalytics/azure-ai-textanalytics/tests/test_analyze_healthcare.py

@@ -384,11 +384,22 @@ def test_normalized_text(self, client):
             polling_interval=self._interval(),
         ).result())
 
-        # currently just testing it has that attribute.
-        # have an issue to update https://github.com/Azure/azure-sdk-for-python/issues/17072
-
         assert all([
             e for e in result[0].entities if hasattr(e, "normalized_text")
         ])
+
         histologically_entity = list(filter(lambda x: x.text == "histologically", result[0].entities))[0]
-        assert histologically_entity.normalized_text == "Histology Procedure"
+        assert histologically_entity.normalized_text == "Histology Procedure"
+
+    @GlobalTextAnalyticsAccountPreparer()
+    @TextAnalyticsClientPreparer()
+    def test_healthcare_assertion(self, client):
+        result = list(client.begin_analyze_healthcare_entities(
+            documents=["Baby not likely to have Meningitis."]
+        ).result())
+
+        # currently can only test certainty
+        # have an issue to update https://github.com/Azure/azure-sdk-for-python/issues/17088
+        meningitis_entity = next(e for e in result[0].entities if e.text == "Meningitis")
+        assert meningitis_entity.assertion.certainty == "negative"
+