v2 cutover

cumulus_library_covid/covid_symptom/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 CovidCountsBuilder(CountsBuilder):
@@ -98,7 +98,7 @@ def count_symptom(self, duration="week"):
         ]
         return self.count_encounter(view_name, from_table, cols)
 
-    def prepare_queries(self, cursor=None, schema=None):
+    def prepare_queries(self, cursor=None, schema=None, **kwargs):
         self.queries = [
             self.count_dx("month"),
             self.count_dx("week"),
@@ -112,7 +112,6 @@ def prepare_queries(self, cursor=None, schema=None):
             self.count_prevalence_ed("week"),
         ]
 
-
 if __name__ == "__main__":
     builder = CovidCountsBuilder()
-    builder.write_counts(f"{Path(__file__).resolve().parent}/counts.sql")
+    builder.write_counts(f"{Path(__file__).resolve().parent}/counts.sql")

cumulus_library_covid/covid_symptom/table_dx.sql

@@ -21,9 +21,9 @@ SELECT DISTINCT
     c.encounter_ref,
     s.status,
     c.code AS cond_code, -- noqa: LT01,RF02
-    c.recorded_week AS cond_week,
-    c.recorded_month AS cond_month,
-    c.recorded_year AS cond_year,
+    c.recordeddate_week AS cond_week,
+    c.recordeddate_month AS cond_month,
+    c.recordeddate_year AS cond_year,
     s.enc_class_display,
     s.age_at_visit,
     s.ed_note,

cumulus_library_covid/covid_symptom/table_pcr.sql

@@ -24,10 +24,10 @@ WITH obs_interpret AS (
 
 SELECT DISTINCT
     obs_interpret.display AS covid_pcr_result_display,
-    o.lab_code AS covid_pcr_code,
-    o.lab_date AS covid_pcr_date,
-    o.lab_week AS covid_pcr_week,
-    o.lab_month AS covid_pcr_month,
+    o.observation_code AS covid_pcr_code,
+    o.effectivedatetime_day AS covid_pcr_date,
+    o.effectivedatetime_week AS covid_pcr_week,
+    o.effectivedatetime_month AS covid_pcr_month,
     s.status,
     s.variant_era,
     s.author_date,
@@ -51,9 +51,9 @@ FROM core__observation_lab AS o,
 WHERE
     (s.encounter_ref = o.encounter_ref)
     AND (s.variant_era = p.variant_era)
-    AND (o.lab_week BETWEEN p.variant_start AND p.variant_end)
-    AND (o.lab_code.code = pcr.code)
-    AND (o.lab_result.code = obs_interpret.code);
+    AND (o.effectivedatetime_week BETWEEN p.variant_start AND p.variant_end)
+    AND (o.observation_code = pcr.code)
+    AND (o.valuecodeableconcept_code = obs_interpret.code);
 
 -- TODO Cerner specific handling of lab RESULT
 -- https://github.com/smart-on-fhir/cumulus-library-covid/issues/13

cumulus_library_covid/covid_symptom/table_study_period.sql

@@ -1,20 +1,20 @@
 CREATE TABLE covid_symptom__study_period AS
 SELECT DISTINCT
     v.variant_era,
-    s.start_date,
-    s.start_week,
-    s.start_month,
-    s.end_date,
+    s.period_start_day as start_date,
+    s.period_start_week as start_week,
+    s.period_start_month as start_month,
+    s.period_end_day as end_date,
     s.age_at_visit,
-    s.author_date,
+    s.author_day as author_date,
     s.author_week,
     s.author_month,
     s.author_year,
     s.gender,
     s.race_display,
     s.subject_ref,
     s.encounter_ref,
-    s.doc_ref,
+    s.documentreference_ref,
     s.diff_enc_note_days,
     s.enc_class_code,
     s.enc_class_display,
@@ -29,8 +29,8 @@ FROM core__study_period AS s,
 WHERE
     s.age_at_visit = a.age
     AND s.gender IN ('female', 'male')
-    AND s.author_date BETWEEN v.variant_start AND v.variant_end
-    AND s.start_date BETWEEN v.variant_start AND v.variant_end
+    AND s.author_day BETWEEN v.variant_start AND v.variant_end
+    AND s.period_start_day BETWEEN v.variant_start AND v.variant_end
     AND s.diff_enc_note_days BETWEEN -30 AND 30;
 
 CREATE TABLE covid_symptom__meta_date AS

cumulus_library_covid/covid_symptom/table_symptom.sql

@@ -43,8 +43,8 @@ SELECT DISTINCT
     s.encounter_ref,
     m.docref_id,
     def.pref AS symptom_display,
-    s.start_date AS start_date,
-    s.end_date AS end_date,
+    s.start_date,
+    s.end_date,
     s.author_week,
     s.author_month,
     s.age_group,

pyproject.toml

@@ -1,10 +1,10 @@
 [project]
 name = "cumulus-library-covid"
 requires-python = ">= 3.9"
-version = "0.2.2"
+version = "1.0.0"
 dependencies = [
-    "cumulus-library >= 1.4.0, <2",
-    "sqlfluff == 2.0.2"
+    "cumulus-library >= 2.0, <3",
+    "sqlfluff >= 3"
 ]
 description = "SQL generation for cumulus covid symptom analysis"
 readme = "README.md"