encounter.sql

added support for encounter "type", "service", ""priority", "reasonCode" valueset.py added EncounterPriority and PatientClass count_core.py affects patient.sql (moved counts to count_core.sql) #31 #66
smart-on-fhir · Jul 5, 2023 · 221a855 · 221a855
1 parent f630f01
commit 221a855
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diff --git a/cumulus_library/schema/valueset.py b/cumulus_library/schema/valueset.py
@@ -13,7 +13,9 @@ class ValueSet(Enum):
     Ethnicity = "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
     DurationUnits = "http://hl7.org/fhir/valueset-duration-units.html"
     Units = "http://hl7.org/fhir/ValueSet/ucum-units"
-    EncounterCode = "http://hl7.org/fhir/v3/ActEncounterCode/vs.html"
+    PatientClass = 'http://terminology.hl7.org/CodeSystem/v2-0004'
+    EncounterCode = "http://terminology.hl7.org/ValueSet/v3-ActEncounterCode"
+    EncounterPriority = 'http://terminology.hl7.org/CodeSystem/v3-ActPriority'
     EncounterStatus = "http://hl7.org/fhir/ValueSet/encounter-status"
     EncounterType = "http://hl7.org/fhir/ValueSet/encounter-type"
     EncounterReason = "http://hl7.org/fhir/ValueSet/encounter-reason"

diff --git a/cumulus_library/studies/core/count_core.py b/cumulus_library/studies/core/count_core.py
@@ -0,0 +1,102 @@
+from typing import List
+from cumulus_library.schema import counts
+
+STUDY_PREFIX = 'core'
+
+def table(tablename: str, duration=None) -> str:
+    if duration:
+        return f'{STUDY_PREFIX}__{tablename}_{duration}'
+    else:
+        return f'{STUDY_PREFIX}__{tablename}'
+
+def count_patient():
+    view_name = table('count_patient')
+    from_table = table('patient')
+    cols = ['age', 'gender', 'race_display', 'ethnicity_display']
+
+    return counts.count_patient(view_name, from_table, cols)
+
+def count_encounter_demographics(duration=None):
+    view_name = table('count_encounter_demographics', duration)
+    from_table = table('encounter')
+
+    cols = [f'start_{duration}',
+            'enc_class_display',
+            'age_at_visit',
+            'gender',
+            'race_display',
+            'ethnicity_display']
+
+    return counts.count_encounter(view_name, from_table, cols)
+
+def _count_encounter_type(view_name, cols, duration):
+    """
+    Encounter Type information is for every visit, and therefore this
+    SQL should be precise in which fields to select (This is a BIG query).
+
+    :param view_name: name of the view from "core__encounter_type"
+    :param cols: from "core__encounter_type"
+    :param duration: None or ''month', 'year'
+    :return: SQL commands
+    """
+    view_name = table(view_name, duration)
+    from_table = table('encounter_type')
+
+    if duration:
+        cols.append(f'start_{duration}')
+
+    where = counts.where_clauses(min_subject=100)
+
+    return counts.count_encounter(view_name, from_table, cols, where)
+
+def count_encounter_type(duration=None):
+    cols = ['enc_class_display',
+            'enc_type_display',
+            'enc_service_display',
+            'enc_priority_display']
+    return _count_encounter_type('count_encounter_type', cols, duration)
+
+def count_encounter_enc_type(duration='month'):
+    cols = ['enc_class_display', 'enc_type_display']
+    return _count_encounter_type('count_encounter_enc_type', cols, duration)
+
+def count_encounter_service(duration='month'):
+    cols = ['enc_class_display', 'enc_service_display']
+    return _count_encounter_type('count_encounter_service', cols, duration)
+
+def count_encounter_priority(duration='month'):
+    cols = ['enc_class_display', 'enc_priority_display']
+    return _count_encounter_type('count_encounter_priority', cols, duration)
+
+def concat_view_sql(create_view_list: List[str]) -> str:
+    """
+    :param create_view_list: SQL prepared statements
+    :param filename: path to output file, default 'count.sql' in PWD
+    """
+    seperator = '-- ###########################################################'
+    concat = list()
+
+    for create_view in create_view_list:
+        concat.append(seperator + '\n'+create_view + '\n')
+
+    return '\n'.join(concat)
+
+def write_view_sql(view_list_sql: List[str], filename='count_core.sql') -> None:
+    """
+    :param view_list_sql: SQL prepared statements
+    :param filename: path to output file, default 'count_core.sql'
+    """
+    with open(filename, 'w') as fout:
+        fout.write(concat_view_sql(view_list_sql))
+
+
+if __name__ == '__main__':
+    write_view_sql([
+        count_patient(),
+        count_encounter_demographics('month'),
+        count_encounter_type(),
+        count_encounter_type('month'),
+        count_encounter_enc_type('month'),
+        count_encounter_service('month'),
+        count_encounter_priority('month'),
+    ])
diff --git a/cumulus_library/studies/core/count_core.sql b/cumulus_library/studies/core/count_core.sql
@@ -0,0 +1,132 @@
+-- ###########################################################
+CREATE or replace VIEW core__count_patient AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+
+        , age, gender, race_display, ethnicity_display        
+        FROM core__patient
+        group by CUBE
+        ( age, gender, race_display, ethnicity_display )
+    )
+    select
+          cnt_subject as cnt 
+        , age, gender, race_display, ethnicity_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+-- ###########################################################
+CREATE or replace VIEW core__count_encounter_demographics_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , start_month, enc_class_display, age_at_visit, gender, race_display, ethnicity_display        
+        FROM core__encounter
+        group by CUBE
+        ( start_month, enc_class_display, age_at_visit, gender, race_display, ethnicity_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , start_month, enc_class_display, age_at_visit, gender, race_display, ethnicity_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+-- ###########################################################
+CREATE or replace VIEW core__count_encounter_type AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , enc_class_display, enc_type_display, enc_service_display, enc_priority_display        
+        FROM core__encounter_type
+        group by CUBE
+        ( enc_class_display, enc_type_display, enc_service_display, enc_priority_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , enc_class_display, enc_type_display, enc_service_display, enc_priority_display
+    from powerset 
+    WHERE cnt_subject >= 100 
+    ORDER BY cnt desc;
+
+-- ###########################################################
+CREATE or replace VIEW core__count_encounter_type_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , enc_class_display, enc_type_display, enc_service_display, enc_priority_display, start_month        
+        FROM core__encounter_type
+        group by CUBE
+        ( enc_class_display, enc_type_display, enc_service_display, enc_priority_display, start_month )
+    )
+    select
+          cnt_encounter  as cnt 
+        , enc_class_display, enc_type_display, enc_service_display, enc_priority_display, start_month
+    from powerset 
+    WHERE cnt_subject >= 100 
+    ORDER BY cnt desc;
+
+-- ###########################################################
+CREATE or replace VIEW core__count_encounter_enc_type_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , enc_class_display, enc_type_display, start_month        
+        FROM core__encounter_type
+        group by CUBE
+        ( enc_class_display, enc_type_display, start_month )
+    )
+    select
+          cnt_encounter  as cnt 
+        , enc_class_display, enc_type_display, start_month
+    from powerset 
+    WHERE cnt_subject >= 100 
+    ORDER BY cnt desc;
+
+-- ###########################################################
+CREATE or replace VIEW core__count_encounter_service_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , enc_class_display, enc_service_display, start_month        
+        FROM core__encounter_type
+        group by CUBE
+        ( enc_class_display, enc_service_display, start_month )
+    )
+    select
+          cnt_encounter  as cnt 
+        , enc_class_display, enc_service_display, start_month
+    from powerset 
+    WHERE cnt_subject >= 100 
+    ORDER BY cnt desc;
+
+-- ###########################################################
+CREATE or replace VIEW core__count_encounter_priority_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , enc_class_display, enc_priority_display, start_month        
+        FROM core__encounter_type
+        group by CUBE
+        ( enc_class_display, enc_priority_display, start_month )
+    )
+    select
+          cnt_encounter  as cnt 
+        , enc_class_display, enc_priority_display, start_month
+    from powerset 
+    WHERE cnt_subject >= 100 
+    ORDER BY cnt desc;