8 cdc chronic disease requests

telemedicine visit valueset initial import #9 added more outpatient valusets from CMS165v11 AdultOutpatientEncounters valueset.py split *encounter* inclusion and exclusion into sets valueset.py split *rx medications* inclusion and exclusion steward: CMS165v11 AdvancedIllnessandFrailtyExclusionECQM inpatient now includes both acute and NON acute inpatient encounters. define_enc_observation are now exclusion criteria define_enc_edvisit are now exclusion criteria define_enc_icu are now exclusion criteria milestone: Encounter inclusion/exclusion criteria valusets from CMS165v11 and other sources, most commonly referencing NQF#0018 define_pregnancy: do not exclude pregnant patients define_esrd.sql end stage renal disease (exclude) define_frailty.sql frailty by device/dx/encounter (exclude) define_advanced_illness.sql very sick patients (exclude) organization: updating paths to prepare for valueset subdir moved VSAC files to "valueset" dir count low/high blood pressure from core__observation_vital_sign https://github.com/smart-on-fhir/cumulus-library/blob/f630f01ee2ad74ce90348213a80840a123f9c203/cumulus_library/studies/core/observation_vital_signs.sql#L18 using US CORE Profile tested against Cerner data. -- http://hl7.org/fhir/us/vitals/StructureDefinition/blood-pressure-panel -- --85354-9 Blood pressure panel with all children optional -- 8480-6 Systolic blood pressure -- 8462-4 Diastolic blood pressure performance improvements for buildings tables/counts. Athena is struggling to index this much data, so we build tables in steps. fixed table_bp.sql to join "observation_ref", much better SQL speed. count.py updated to ouput counts for htn__count_bp count.py now count by number of PATIENT (instead of encounters) table_bp.sql added race and ethnicity htn__dx defined (refactored from counts sql file) added support or htn__count_rx (optional) updated README.md * _htn__count_bp_month_ : BP (blood pressure) measures * _htn__count_dx_month_ : HTN diagnosis codes * _htn__count_rx_month_ : HTN blood pressure control meds scaled back what we count.py updated counts views. procedure and medication are optional and by default commented out. removed "order by cnt desc", will address in more detail later. smart-on-fhir/cumulus-library#71
smart-on-fhir · Jul 7, 2023 · b854c53 · b854c53
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diff --git a/README.md b/README.md
@@ -8,6 +8,49 @@ This definition attempts to "multi-solve" counting HTN cases for CDC and CMS use
 * CMS Quality Measures 
   * [Controlling High Blood Pressure CMS Quality #236 (NQF 0018)](https://docs.google.com/spreadsheets/d/1UTxg-MvAf0xMBI8dAw6SEF1cQduZqC330R-0MOAWli4/edit#gid=1986332053)
 
+-----
+**COUNT TABLES**
+
+Count number of patients per month matching criteria
+* _htn__count_bp_month_ : BP (blood pressure) measures
+* _htn__count_dx_month_ : HTN diagnosis codes 
+* _htn__count_rx_month_ : HTN blood pressure control meds
+
+
+
+| **htn__count_bp_month** | [Blood Pressure Panel](http://hl7.org/fhir/us/vitals/STU1/StructureDefinition-blood-pressure-panel.html)                         |
+|-------------------------|----------------------------------------------------------------------------------------------------------------------------------|
+| cnt                     | count number of patients                                                                                                         |
+| obs_month               | Month of BP observation                                                                                                          |
+| hypertension            | BP is 140/90 or higher (true or false)                                                                                           |           | 
+| hypotension             | BP is 90/60  or lower (true or false)                                                                                            |
+| enc_class_code          | [Encounter class](https://terminology.hl7.org/5.1.0/ValueSet-encounter-class.html) ambulatory, emergency, impatient, observation | 
+| gender                  | [female or male sex](http://hl7.org/fhir/ValueSet/administrative-gender)                                                         |
+| age_at_visit            | patient age at time of visit                                                                                                     |
+| race_display            | [CDC R5 race](http://hl7.org/fhir/us/core/StructureDefinition/us-core-race)                                                      |
+| ethnicity_display       | [Hispanic or Latino](http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity)                                          |
+
+| **htn__count_dx_month** | Hypertension diagnosis (ICD10-CM or SNOMED-CT)                                                                                   |
+|-------------------------|----------------------------------------------------------------------------------------------------------------------------------|
+| cnt                     | count number of patients                                                                                                         |
+| cond_month              | Month of HTN diagnosis                                                                                                           |
+| cond_display            | Display the label of HTN diagnosis                                                                                               |
+| cond_system_display     | SNOMED-CT or ICD-10-CM                                                                                                           |                                                                                                          |
+| enc_class_code          | [Encounter class](https://terminology.hl7.org/5.1.0/ValueSet-encounter-class.html) ambulatory, emergency, impatient, observation | 
+| gender                  | female or male sex                                                                                                               |
+| age_at_visit            | patient age at time of visit                                                                                                     |
+| race_display            | CDC R5 code                                                                                                                      |
+| ethnicity_display       | Hispanic or Latino                                                                                                               |
+
+
+| **htn__count_rx_month** | Blood Pressure Medications                                                                                 |
+|-------------------------|------------------------------------------------------------------------------------------------------------|
+| cnt                     | count number of patients                                                                                   |
+| authoredon_month        | Month of medication request                                                                                |
+| rx_display              | Display RXNORM drug label                                                                                  |
+| rx_category_code        | [inpatient, outpatient, or community](https://hl7.org/fhir/valueset-medicationrequest-admin-location.html) |                                                                                                          |
+
+
 -----
 
 **DIAGNOSIS**

diff --git a/cumulus_library_hypertension/htn/count.py b/cumulus_library_hypertension/htn/count.py
@@ -0,0 +1,82 @@
+from typing import List
+from cumulus_library.schema import counts
+
+STUDY_PREFIX = 'htn'
+
+def table(tablename: str, duration=None) -> str:
+    if duration:
+        return f'{STUDY_PREFIX}__{tablename}_{duration}'
+    else: 
+        return f'{STUDY_PREFIX}__{tablename}'
+
+def count_bp(duration=None):
+    view_name = table('count_bp', duration)
+    from_table = table('bp')
+    cols = ['hypertension', 'hypotension', 'enc_class_code',
+            'gender', 'age_at_visit', 'race_display', 'ethnicity_display']
+
+    if duration:
+        cols.append(f'obs_{duration}')
+
+    return counts.count_patient(view_name, from_table, cols)
+
+def count_dx(duration='month'):
+    view_name = table('count_dx', duration)
+    from_table = table('dx')
+    cols = [f'cond_{duration}',
+            'enc_class_code',
+            'gender', 'age_at_visit', 'race_display', 'ethnicity_display',
+            'cond_display', 'cond_system_display']
+    return counts.count_patient(view_name, from_table, cols)
+
+def count_rx(duration='month'):
+    view_name = table('count_rx', duration)
+    from_table = table('rx')
+    cols = ['category_code', 'rx_display']
+
+    if duration:
+        cols.append(f'authoredon_{duration}')
+
+    return counts.count_patient(view_name, from_table, cols)
+
+def count_procedure(duration=None):
+    view_name = table('count_procedure', duration)
+    from_table = table('procedure')
+    cols = ['enc_class_display', 'proc_display', 'proc_system']
+
+    if duration:
+        cols.append(f'enc_start_{duration}')
+
+    return counts.count_encounter(view_name, from_table, cols)
+
+def concat_view_sql(create_view_list: List[str]) -> str:
+    """
+    :param create_view_list: SQL prepared statements
+    """
+    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.sql') -> None:
+    """
+    :param view_list_sql: SQL prepared statements
+    :param filename: path to output file, default 'count.sql' in PWD
+    """
+    sql_optimizer = concat_view_sql(view_list_sql).replace('ORDER BY cnt desc', '')
+    with open(filename, 'w') as fout:
+        fout.write(sql_optimizer)
+
+
+if __name__ == '__main__':
+    write_view_sql([
+        count_bp(),
+        count_bp('month'),
+        count_dx('month'),
+        # count_rx('month'),          # TODO requires support for FHIR MedicationRequest
+        # count_procedure(),          # TODO requires support for FHIR Procedure
+        # count_procedure('month'),   # TODO requires support for FHIR Procedure
+    ])
diff --git a/cumulus_library_hypertension/htn/count.sql b/cumulus_library_hypertension/htn/count.sql
@@ -0,0 +1,113 @@
+-- ###########################################################
+CREATE or replace VIEW htn__count_bp AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+
+        , hypertension, hypotension, enc_class_code, gender, age_at_visit, race_display, ethnicity_display        
+        FROM htn__bp
+        group by CUBE
+        ( hypertension, hypotension, enc_class_code, gender, age_at_visit, race_display, ethnicity_display )
+    )
+    select
+          cnt_subject as cnt 
+        , hypertension, hypotension, enc_class_code, gender, age_at_visit, race_display, ethnicity_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ;
+
+-- ###########################################################
+CREATE or replace VIEW htn__count_bp_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+
+        , hypertension, hypotension, enc_class_code, gender, age_at_visit, race_display, ethnicity_display, obs_month        
+        FROM htn__bp
+        group by CUBE
+        ( hypertension, hypotension, enc_class_code, gender, age_at_visit, race_display, ethnicity_display, obs_month )
+    )
+    select
+          cnt_subject as cnt 
+        , hypertension, hypotension, enc_class_code, gender, age_at_visit, race_display, ethnicity_display, obs_month
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ;
+
+-- ###########################################################
+CREATE or replace VIEW htn__count_dx_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+
+        , cond_month, enc_class_code, gender, age_at_visit, race_display, ethnicity_display, cond_display, cond_system_display        
+        FROM htn__dx
+        group by CUBE
+        ( cond_month, enc_class_code, gender, age_at_visit, race_display, ethnicity_display, cond_display, cond_system_display )
+    )
+    select
+          cnt_subject as cnt 
+        , cond_month, enc_class_code, gender, age_at_visit, race_display, ethnicity_display, cond_display, cond_system_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ;
+
+-- ###########################################################
+--CREATE or replace VIEW htn__count_rx_month AS
+--    with powerset as
+--    (
+--        select
+--        count(distinct subject_ref)   as cnt_subject
+--
+--        , category_code, rx_display, authoredon_month
+--        FROM htn__rx
+--        group by CUBE
+--        ( category_code, rx_display, authoredon_month )
+--    )
+--    select
+--          cnt_subject as cnt
+--        , category_code, rx_display, authoredon_month
+--    from powerset
+--    WHERE cnt_subject >= 10
+--    ;
+
+-- ###########################################################
+--CREATE or replace VIEW htn__count_procedure AS
+--    with powerset as
+--    (
+--        select
+--        count(distinct subject_ref)   as cnt_subject
+--        , count(distinct encounter_ref)   as cnt_encounter
+--        , enc_class_display, proc_display, proc_system
+--        FROM htn__procedure
+--        group by CUBE
+--        ( enc_class_display, proc_display, proc_system )
+--    )
+--    select
+--          cnt_encounter  as cnt
+--        , enc_class_display, proc_display, proc_system
+--    from powerset
+--    WHERE cnt_subject >= 10
+--    ;
+
+-- ###########################################################
+--CREATE or replace VIEW htn__count_procedure_month AS
+--    with powerset as
+--    (
+--        select
+--        count(distinct subject_ref)   as cnt_subject
+--        , count(distinct encounter_ref)   as cnt_encounter
+--        , enc_class_display, proc_display, proc_system, enc_start_month
+--        FROM htn__procedure
+--        group by CUBE
+--        ( enc_class_display, proc_display, proc_system, enc_start_month )
+--    )
+--    select
+--          cnt_encounter  as cnt
+--        , enc_class_display, proc_display, proc_system, enc_start_month
+--    from powerset
+--    WHERE cnt_subject >= 10
+--    ;
diff --git a/cumulus_library_hypertension/htn/count_bp.sql b/cumulus_library_hypertension/htn/count_bp.sql
diff --git a/cumulus_library_hypertension/htn/count_dx.sql b/cumulus_library_hypertension/htn/count_dx.sql