Expanded code system preference lists

Author: dogversioning

cumulus_library/studies/core/builder_condition.py

@@ -54,6 +54,9 @@ def denormalize_codes(self):
                 "http://snomed.info/sct",
                 "http://hl7.org/fhir/sid/icd-10-cm",
                 "http://hl7.org/fhir/sid/icd-9-cm",
+                "urn:oid:1.2.840.114350.1.13.71.2.7.2",
+                "urn:oid:1.2.840.114350.1.13.71.2.7.4",
+                "http://terminology.hl7.org/CodeSystem/data-absent-reason",
             ],
         )
         self.queries.append(

cumulus_library/studies/core/builder_encounter.py

@@ -40,6 +40,9 @@ def denormalize_codes(self, schema, cursor):
                     "http://terminology.hl7.org/CodeSystem/v2-0004",
                     "urn:oid:2.16.840.1.113883.4.642.3.248",
                     "http://snomed.info/sct",
+                    "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/71",
+                    "urn:oid:1.2.840.114350.1.13.71.2.7.10",
+                    "urn:oid:1.2.840.114350.1.13.71.2.7.2",
                 ],
                 "has_data": False,
             },
@@ -51,6 +54,8 @@ def denormalize_codes(self, schema, cursor):
                     "http://terminology.hl7.org/CodeSystem/service-type",
                     "urn:oid:2.16.840.1.113883.4.642.3.518",
                     "http://snomed.info/sct",
+                    "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/34",
+                    "urn:oid:1.2.840.114350.1.13.71.2.7.10",
                 ],
                 "has_data": False,
             },
@@ -61,6 +66,8 @@ def denormalize_codes(self, schema, cursor):
                 "code_systems": [
                     "http://terminology.hl7.org/CodeSystem/v3-ActPriority",
                     "http://snomed.info/sct",
+                    "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/3",
+                    "urn:oid:1.2.840.114350.1.13.71.2.7.10",
                 ],
                 "has_data": False,
             },
@@ -71,6 +78,10 @@ def denormalize_codes(self, schema, cursor):
                 "code_systems": [
                     "http://terminology.hl7.org/CodeSystem/v3-ActPriority",
                     "http://snomed.info/sct",
+                    "http://hl7.org/fhir/sid/icd-10-cm",
+                    "http://hl7.org/fhir/sid/icd-9-cm",
+                    "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/nomenclature",
+                    "urn:oid:1.2.840.114350.1.13.71.2.7.2",
                 ],
                 "has_data": False,
             },

cumulus_library/studies/discovery/code_detection.py

@@ -8,7 +8,7 @@
 class CodeDetectionBuilder(base_table_builder.BaseTableBuilder):
     display_text = "Selecting unique code systems..."
 
-    def _check_coding_against_db(code_source, schema, cursor):
+    def _check_coding_against_db(self, code_source, schema, cursor):
         """selects the appropriate DB query to run"""
 
         if code_source["is_array"]:

cumulus_library/template_sql/codeable_concept_denormalize.sql.jinja

@@ -21,7 +21,7 @@ CREATE TABLE {{ target_table }} AS (
         {%- endif %}
         {%- if filter_priority %}
         WHERE
-            u.codeable_concept.system = '{{ system }}'
+            u.codeable_concept.system LIKE '{{ system }}%'
         {%- endif %}
     ), --noqa: LT07
     {%- endfor %}

cumulus_library/template_sql/sql_utils.py

@@ -28,8 +28,9 @@ class CodeableConceptConfig:
     :param source_id: the id field to use in the new table (default: 'id')
     :param filter_priority: If true, will use code systems to select a single code,
       in preference order, for use as a display value.
-    :param code_systems: a list of systems, in preference order, for selecting data
-      for filtering. This should not be set if filter_priority is false.
+    :param code_systems: a list of strings matching the start of the systems field,
+      in preference order, for selecting data for filtering. This should not be set
+      if filter_priority is false.
     """
 
     column_name: str
@@ -50,7 +51,7 @@ class ExtensionConfig:
     :param target_table: the name of the table to create
     :param target_col_prefix: the string to prepend code/display column names with
     :param fhir_extension: the URL of the FHIR resource to select
-    :param code_systems: a list of codes, in preference order, to use to select data
+    :param ext_systems: a list of codes, in preference order, to use to select data
     :param is_array: a boolean indicating if the targeted field is an array type
     """
 

tests/test_templates.py

@@ -77,7 +77,7 @@ def test_codeable_concept_denormalize_filter_creation():
             source AS s,
             UNNEST(s.code_col.coding) AS u (codeable_concept)
         WHERE
-            u.codeable_concept.system = 'http://snomed.info/sct'
+            u.codeable_concept.system LIKE 'http://snomed.info/sct%'
     ), --noqa: LT07
 
     system_code_col_1 AS (
@@ -91,7 +91,7 @@ def test_codeable_concept_denormalize_filter_creation():
             source AS s,
             UNNEST(s.code_col.coding) AS u (codeable_concept)
         WHERE
-            u.codeable_concept.system = 'http://hl7.org/fhir/sid/icd-10-cm'
+            u.codeable_concept.system LIKE 'http://hl7.org/fhir/sid/icd-10-cm%'
     ), --noqa: LT07
 
     union_table AS (