Update for cumulus_library 2.0

cumulus_library_hypertension/htn/counts.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from cumulus_library.schema.counts import CountsBuilder
+from cumulus_library.statistics.counts import CountsBuilder
 
 class HtnCountsBuilder(CountsBuilder):
     display_text = "Creating htn counts..."
@@ -137,7 +137,7 @@ def count_procedure(self, duration=None):
 
         return self.count_encounter(view_name, from_table, cols)
 
-    def prepare_queries(self, cursor=None, schema=None):
+    def prepare_queries(self, *args, **kwargs):
         self.queries =[
             self.count_study_period(),
             self.count_study_period('month'),

cumulus_library_hypertension/htn/study_period.sql

@@ -1,32 +1,32 @@
 CREATE table htn__study_period AS
 SELECT DISTINCT
-    e.start_date,
-    e.start_week,
-    e.start_month,
-    e.end_date,
+    e.period_start_day as start_date,
+    e.period_start_week as start_week,
+    e.period_start_month as start_month,
+    e.period_end_day as end_date,
     e.age_at_visit,
     e.status,
     p.gender,
     p.race_display,
     p.ethnicity_display,
-    e.enc_class_code,
-    e.enc_class_display,
-    COALESCE(e.enc_type_system, 'None') as enc_type_system,
-    COALESCE(e.enc_type_code, 'None')   as enc_type_code,
-    COALESCE(e.enc_type_display, 'None')    as enc_type_display,
-    COALESCE(e.enc_service_system, 'None')  as enc_service_system,
-    COALESCE(e.enc_service_code, 'None')    as enc_service_code,
-    COALESCE(e.enc_service_display, 'None') as enc_service_display,
-    COALESCE(e.enc_priority_system, 'None') as enc_priority_system,
-    COALESCE(e.enc_priority_code, 'None')   as enc_priority_code,
-    COALESCE(e.enc_priority_display, 'None') as enc_priority_display,
+    e.class_code AS enc_class_code,
+    e.class_display AS enc_class_display,
+    COALESCE(e.type_code_system, 'None') as enc_type_system,
+    COALESCE(e.type_code, 'None')        as enc_type_code,
+    COALESCE(e.type_display, 'None')     as enc_type_display,
+    COALESCE(e.serviceType_code_system, 'None') as enc_service_system,
+    COALESCE(e.serviceType_code, 'None')        as enc_service_code,
+    COALESCE(e.serviceType_display, 'None')     as enc_service_display,
+    COALESCE(e.priority_code_system, 'None') as enc_priority_system,
+    COALESCE(e.priority_code, 'None')        as enc_priority_code,
+    COALESCE(e.priority_display, 'None')     as enc_priority_display,
     p.subject_ref,
     e.encounter_ref
 FROM
     core__patient AS p,
-    core__encounter_type AS e
+    core__encounter AS e
 WHERE
     (p.subject_ref = e.subject_ref)
-    AND (e.start_date BETWEEN date('2016-01-01') AND current_date)
-    AND (e.end_date BETWEEN date('2016-01-01') AND current_date)
+    AND (e.period_start_day BETWEEN date('2016-01-01') AND current_date)
+    AND (e.period_end_day BETWEEN date('2016-01-01') AND current_date)
 ;

cumulus_library_hypertension/htn/table_bp.sql

@@ -24,24 +24,28 @@ define_component as
     (select * from htn__define_bp where component!='panel')
 select distinct
     define_component.*,
-    component_code,
-    component_part.valueQuantity,
-    component_part.valueQuantity.value as mmHg,
-    O.obs_date,
-    O.obs_week,
-    O.obs_month,
-    O.obs_year,
+    OCC.code as component_code,
+    OCVQ.value as mmHg,
+    O.effectiveDateTime_day as obs_date,
+    O.effectiveDateTime_week as obs_week,
+    O.effectiveDateTime_month as obs_month,
+    O.effectiveDateTime_year as obs_year,
     status,
     O.observation_ref,
     O.encounter_ref,
     O.subject_ref
 from    define_panel,
         define_component,
         core__observation_vital_signs as O,
-        UNNEST(O.component) t (component_part),
-        UNNEST(component_part.code.coding) u (component_code)
-where   define_panel.code = O.obs_code.code
-and     define_component.code = component_code.code
+        core__observation_component_code as OCC,
+        core__observation_component_valuequantity as OCVQ,
+where   define_panel.code = O.observation_code
+and     define_panel.system = O.observation_code_system
+and     define_component.code = OCC.code
+and     define_component.system = OCC.code_system
+and     O.id = OCC.id
+and     O.id = OCVQ.id
+and     OCC.row = OCVQ.row
 ;
 
 -- #########################################################################

cumulus_library_hypertension/htn/table_comorbidity.sql

@@ -13,9 +13,9 @@ WITH condition_row AS
         c.code AS comorbidity_code,
         c.code_display as comorbidity_display,
         fhirspec.code_system as comorbidity_system_display,
-        c.recorded_month AS comorbidity_month,
-        c.recorded_week AS comorbidity_week,
-        c.recordeddate as comorbidity_date
+        c.recordedDate_month AS comorbidity_month,
+        c.recordedDate_week AS comorbidity_week,
+        c.recordedDate as comorbidity_date
     FROM
         core__condition AS c,
         core__fhir_mapping_code_system_uri as fhirspec

cumulus_library_hypertension/htn/table_dx.sql

@@ -15,9 +15,9 @@ SELECT DISTINCT
     dx.display as cond_display,
     fhirspec.uri as cond_system,
     fhirspec.code_system as cond_system_display,
-    c.recorded_month AS cond_month,
-    c.recorded_week AS cond_week,
-    c.recordeddate as cond_date
+    c.recordedDate_month AS cond_month,
+    c.recordedDate_week AS cond_week,
+    c.recordedDate as cond_date
 FROM
     htn__define_dx AS dx,
     core__fhir_mapping_code_system_uri as fhirspec,
@@ -37,9 +37,9 @@ SELECT DISTINCT
     dx.display as cond_display,
     fhirspec.uri as cond_system,
     fhirspec.code_system as cond_system_display,
-    c.recordeddate as cond_date,
-    c.recorded_month AS cond_month,
-    c.recorded_week AS cond_week,
+    c.recordedDate as cond_date,
+    c.recordedDate_month AS cond_month,
+    c.recordedDate_week AS cond_week,
     s.enc_class_code,
     s.enc_class_display,
     s.enc_type_display,

pyproject.toml

@@ -1,10 +1,10 @@
 [project]
 name = "cumulus-library-hypertension"
-version = "0.1.3"
-requires-python = ">= 3.9"
+version = "1.0.0"
+requires-python = ">= 3.10"
 dependencies = [
-    "cumulus-library >= 1.4, < 2",
-    "sqlfluff == 2.0.2"
+    "cumulus-library >= 2.1, < 3",
+    "sqlfluff >= 3",
 ]
 description = "SQL generation for Cumulus hypertension analysis"
 readme = "README.md"