FHIR ValueSet(s) should enable wider support for CDC Pilot sites to use other codes for PCR tests, results, etc.

cumulus_library_covid/covid_symptom/count.py

@@ -0,0 +1,115 @@
+from typing import List
+from cumulus_library.schema import counts
+
+def table(tablename: str, duration=None, study_prefix='covid_symptom') -> str:
+    if duration:
+        return f'{study_prefix}__{tablename}_{duration}'
+    else: 
+        return f'{study_prefix}__{tablename}'
+
+def count_dx(duration='week'):
+    """
+    covid_symptom__count_dx_week
+    covid_symptom__count_dx_month
+    """
+    view_name = table('count_dx', duration)
+    from_table = table('dx')
+    cols = [f'cond_{duration}',
+            'enc_class_code',
+            'age_at_visit',
+            'ed_note',
+            'variant_era']
+    return counts.count_encounter(view_name, from_table, cols)
+
+def count_pcr(duration='week'):
+    """
+    covid_symptom__count_pcr_week
+    covid_symptom__count_pcr_month
+    """
+    view_name = table('count_pcr', duration)
+    from_table = table('pcr')
+    cols = [f'covid_pcr_{duration}',
+            'covid_pcr_result_display',
+            'variant_era',
+            'ed_note',
+            'age_at_visit',
+            'gender',
+            'race_display']
+    return counts.count_encounter(view_name, from_table, cols)
+
+def count_study_period(duration='month'):
+    """
+    covid_symptom__count_study_period_week
+    covid_symptom__count_study_period_month
+    covid_symptom__count_study_period_year
+    """
+    view_name = table('count_study_period', duration)
+    from_table = table('study_period')
+    cols = [f'start_{duration}',
+            'variant_era', 'start_month', 'ed_note',
+            'gender', 'age_group', 'race_display']
+    return counts.count_encounter(view_name, from_table, cols)
+
+def count_prevalence_ed(duration='month'):
+    view_name = table('count_prevalence_ed', duration)
+    from_table = table('prevalence_ed')
+    cols = [
+        'covid_dx',
+        'covid_icd10',
+        'covid_pcr_result',
+        'covid_symptom',
+        'symptom_icd10_display',
+        'variant_era',
+        'author_month',
+        'age_group']
+    return counts.count_encounter(view_name, from_table, cols)
+
+def count_symptom(duration='week'):
+    """
+    covid_symptom__count_symptom_week
+    covid_symptom__count_symptom_month
+    """
+    view_name = table('count_symptom', duration)
+    from_table = table('symptom')
+    cols = ['symptom_display',
+            'variant_era',
+            'author_week',
+            'age_group',
+            'gender',
+            'race_display',
+            'enc_class_code',
+            'ed_note']
+    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
+    :param filename: path to output file, default 'count.sql' in PWD
+    """
+    seperator = '-- ###########################################################'
+    concat = list()
+
+    for create_view in create_view_list:
+        concat.append(seperator + 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
+    """
+    with open(filename, 'w') as fout:
+        fout.write(concat_view_sql(view_list_sql))
+
+
+if __name__ == '__main__':
+
+    write_view_sql([
+        count_dx('week'),
+        count_dx('month'),
+        count_pcr('week'),
+        count_pcr('month'),
+        count_study_period('week'),
+        count_study_period('month'),
+        count_study_period('year')])

cumulus_library_covid/covid_symptom/count.sql

@@ -0,0 +1,139 @@
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_dx_week AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , cond_week, enc_class_code, age_at_visit, ed_note, variant_era        
+        FROM covid_symptom__dx
+        group by CUBE
+        ( cond_week, enc_class_code, age_at_visit, ed_note, variant_era )
+    )
+    select
+          cnt_encounter  as cnt 
+        , cond_week, enc_class_code, age_at_visit, ed_note, variant_era
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_dx_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , cond_month, enc_class_code, age_at_visit, ed_note, variant_era        
+        FROM covid_symptom__dx
+        group by CUBE
+        ( cond_month, enc_class_code, age_at_visit, ed_note, variant_era )
+    )
+    select
+          cnt_encounter  as cnt 
+        , cond_month, enc_class_code, age_at_visit, ed_note, variant_era
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_pcr_week AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , covid_pcr_week, covid_pcr_result_display, variant_era, ed_note, age_at_visit, gender, race_display        
+        FROM covid_symptom__pcr
+        group by CUBE
+        ( covid_pcr_week, covid_pcr_result_display, variant_era, ed_note, age_at_visit, gender, race_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , covid_pcr_week, covid_pcr_result_display, variant_era, ed_note, age_at_visit, gender, race_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_pcr_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , covid_pcr_month, covid_pcr_result_display, variant_era, ed_note, age_at_visit, gender, race_display        
+        FROM covid_symptom__pcr
+        group by CUBE
+        ( covid_pcr_month, covid_pcr_result_display, variant_era, ed_note, age_at_visit, gender, race_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , covid_pcr_month, covid_pcr_result_display, variant_era, ed_note, age_at_visit, gender, race_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_study_period_week AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , start_week, variant_era, start_month, ed_note, gender, age_group, race_display        
+        FROM covid_symptom__study_period
+        group by CUBE
+        ( start_week, variant_era, start_month, ed_note, gender, age_group, race_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , start_week, variant_era, start_month, ed_note, gender, age_group, race_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_study_period_month AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , start_month, variant_era, start_month, ed_note, gender, age_group, race_display        
+        FROM covid_symptom__study_period
+        group by CUBE
+        ( start_month, variant_era, start_month, ed_note, gender, age_group, race_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , start_month, variant_era, start_month, ed_note, gender, age_group, race_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+
+
+-- ####################################
+CREATE or replace VIEW covid_symptom__count_study_period_year AS 
+    with powerset as
+    (
+        select
+        count(distinct subject_ref)   as cnt_subject
+        , count(distinct encounter_ref)   as cnt_encounter
+        , start_year, variant_era, start_month, ed_note, gender, age_group, race_display        
+        FROM covid_symptom__study_period
+        group by CUBE
+        ( start_year, variant_era, start_month, ed_note, gender, age_group, race_display )
+    )
+    select
+          cnt_encounter  as cnt 
+        , start_year, variant_era, start_month, ed_note, gender, age_group, race_display
+    from powerset 
+    WHERE cnt_subject >= 10 
+    ORDER BY cnt desc;
+