fix: retrieve spelling corrections

ibm_whcs_sdk/annotator_for_clinical_data/annotator_for_clinical_data_v1.py

@@ -3756,7 +3756,7 @@ class ContainerAnnotation(object):
     :attr list[Section] sections: (optional)
     :attr list[NluEntities] nlu_entities: (optional)
     :attr list[Relations] relations: (optional)
-    :attr list[SpellingCorrection]: (optional)
+    :attr list[SpellingCorrection] spelling_corrections: (optional)
     :attr list[SpellCorrectedText] spell_corrected_text: (optional)
     :attr list[Temporal] temporal_spans: (optional)
     :attr list[Annotation] lines: (optional)
@@ -3805,7 +3805,7 @@ def __init__(self, allergy_ind=None, allergy_medication_ind=None, attribute_valu
         :param list[Section] sections: (optional)
         :param list[NluEntities] nlu_entities: (optional)
         :param list[Relations] relations: (optional)
-        :param list[SpellingCorrection] spelling_correction: (optional)
+        :param list[SpellingCorrection] spelling_corrections: (optional)
         :param list[SpellCorrectedText] spell_corrected_text: (optional)
         :param list[Temporal] temporal_spans: (optional)
         :param list[Annotation] lines: (optional)

ibm_whcs_sdk/annotator_for_clinical_data/tests/common/test_spell_correction.py → ibm_whcs_sdk/annotator_for_clinical_data/tests/common/test_spelling_correction.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-# Copyright 2018 IBM All Rights Reserved.
+# Copyright 2018, 2021 IBM All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -16,7 +16,7 @@
 
 from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_suggestion as ts
 
-class TestSpellCorrectionAnnotation(object):
+class TestSpellingCorrection(object):
 
     @staticmethod
     def test_spelling_correction(annotation_list=None):
@@ -26,4 +26,4 @@ def test_spelling_correction(annotation_list=None):
                 assert annotation.end > annotation.begin
                 assert annotation.covered_text is not None
                 for suggestion in annotation.suggestions:
-                    ts.TestSuggestion.test_spelling_suggestion(suggestion)
+                    ts.TestSuggestion.test_spelling_suggestions(suggestion)

ibm_whcs_sdk/annotator_for_clinical_data/tests/common/test_unstructured_container.py

@@ -30,7 +30,7 @@
 from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_section as tsec
 from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_nlu_entities as tne
 from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_relation as tr
-#import tests.functional.test_spell_correction as tsc
+from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_spelling_correction as tsc
 from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_spell_corrected_text as tsct
 from ibm_whcs_sdk.annotator_for_clinical_data.tests.common import test_temporal_span as tts
 
@@ -97,6 +97,8 @@ def test_unstructured_container(data=None):
                 tne.TestNluEntitiesAnnotation.test_nlu_entities(data.nlu_entities)
             if data.relations is not None:
                 tr.TestRelationAnnotation.test_relation_annotation(data.relations)
+            if data.spelling_corrections is not None:
+                tsc.TestSpellingCorrection.test_spelling_correction(data.spelling_corrections)
             if data.spell_corrected_text is not None:
                 tsct.TestSpellCorrectedText.test_spell_corrected_text(data.spell_corrected_text)
             if data.temporal_spans is not None:

ibm_whcs_sdk/annotator_for_clinical_data/tests/integration/test_acd_analyze_apis.py

@@ -26,7 +26,7 @@
 IAMURL = CONFIG.get('settings', 'iam_url')
 VERSION = CONFIG.get('settings', 'version')
 LEVEL = CONFIG.get('settings', 'logging_level')
-DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True)
+DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True')
 FLOW = CONFIG.get('settings', 'flow')
 
 ACD = wh.AnnotatorForClinicalDataV1(

ibm_whcs_sdk/annotator_for_clinical_data/tests/integration/test_acd_annotator_apis.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-# Copyright 2018 IBM All Rights Reserved.
+# Copyright 2018, 2021 IBM All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@
 IAMURL = CONFIG.get('settings', 'iam_url')
 VERSION = CONFIG.get('settings', 'version')
 LEVEL = CONFIG.get('settings', 'logging_level')
-DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True)
+DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True')
 
 ACD = wh.AnnotatorForClinicalDataV1(
     authenticator=IAMAuthenticator(apikey=APIKEY, url=IAMURL, disable_ssl_verification=DISABLE_SSL),

ibm_whcs_sdk/annotator_for_clinical_data/tests/integration/test_acd_flows_apis.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-# Copyright 2018 IBM All Rights Reserved.
+# Copyright 2018, 2021 IBM All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@
 IAMURL = CONFIG.get('settings', 'iam_url')
 VERSION = CONFIG.get('settings', 'version')
 LEVEL = CONFIG.get('settings', 'logging_level')
-DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True)
+DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True')
 FLOW = CONFIG.get('settings', 'flow')
 
 ACD = wh.AnnotatorForClinicalDataV1(
@@ -64,7 +64,7 @@ def test_get_bad_flows_id():
 
 def test_create_flow():
     test_elementList = []
-    test_anno = wh.Annotator(name = 'concept_detection')
+    test_anno = wh.Annotator(name = 'concept_detection', parameters = {"include_optional_fields": ["medical_codes", "source_vocabularies"]})
     test_flowEntry = wh.FlowEntry(annotator=test_anno)
     test_elementList.append(test_flowEntry)
     test_flow = wh.Flow(elements = test_elementList, async_ = False)

ibm_whcs_sdk/annotator_for_clinical_data/tests/integration/test_acd_health_check.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-# Copyright 2018 IBM All Rights Reserved.
+# Copyright 2018, 2021 IBM All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@
 IAMURL = CONFIG.get('settings', 'iam_url')
 VERSION = CONFIG.get('settings', 'version')
 LEVEL = CONFIG.get('settings', 'logging_level')
-DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True)
+DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True')
 
 ACD = wh.AnnotatorForClinicalDataV1(
     authenticator=IAMAuthenticator(apikey=APIKEY, url=IAMURL, disable_ssl_verification=DISABLE_SSL),

ibm_whcs_sdk/annotator_for_clinical_data/tests/integration/test_acd_profiles_apis.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-# Copyright 2018 IBM All Rights Reserved.
+# Copyright 2018, 2021 IBM All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@
 IAMURL = CONFIG.get('settings', 'iam_url')
 VERSION = CONFIG.get('settings', 'version')
 LEVEL = CONFIG.get('settings', 'logging_level')
-DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True)
+DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True')
 PROFILE = CONFIG.get('settings', 'profile')
 
 ACD = wh.AnnotatorForClinicalDataV1(

ibm_whcs_sdk/annotator_for_clinical_data/tests/integration/test_delete_user_data.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-# Copyright 2018 IBM All Rights Reserved.
+# Copyright 2018, 2021 IBM All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@
 IAMURL = CONFIG.get('settings', 'iam_url')
 VERSION = CONFIG.get('settings', 'version')
 LEVEL = CONFIG.get('settings', 'logging_level')
-DISABLE_SSL = CONFIG.get('settings', 'disable_ssl')
+DISABLE_SSL = (CONFIG.get('settings', 'disable_ssl')=='True')
 PROFILE = CONFIG.get('settings', 'profile')
 
 ACD = wh.AnnotatorForClinicalDataV1(