Adds status to study tables (#31)

cumulus_library_covid/covid_symptom/counts.py

@@ -85,7 +85,7 @@ def count_symptom(self, duration="week"):
         covid_symptom__count_symptom_month
         """
         view_name = self.get_table_name("count_symptom", duration)
-        from_table = self.get_table_name("symptom_nlp")
+        from_table = self.get_table_name("symptom_ctakes_negation")
         cols = [
             f"author_{duration}",
             "symptom_display",
@@ -115,4 +115,4 @@ def prepare_queries(self, cursor=None, schema=None):
 
 if __name__ == "__main__":
     builder = CovidCountsBuilder()
-    builder.write_counts(f"{Path(__file__).resolve().parent}/count.sql")
+    builder.write_counts(f"{Path(__file__).resolve().parent}/counts.sql")

cumulus_library_covid/covid_symptom/count.sql → cumulus_library_covid/covid_symptom/counts.sql

@@ -29,8 +29,9 @@ CREATE TABLE covid_symptom__count_dx_month AS (
         "ed_note",
         "variant_era"
     FROM powerset
-    WHERE 
+    WHERE
         cnt_subject >= 10
+
 );
 
 -- ###########################################################
@@ -64,8 +65,9 @@ CREATE TABLE covid_symptom__count_dx_week AS (
         "ed_note",
         "variant_era"
     FROM powerset
-    WHERE 
+    WHERE
         cnt_subject >= 10
+
 );
 
 -- ###########################################################
@@ -105,8 +107,9 @@ CREATE TABLE covid_symptom__count_pcr_month AS (
         "gender",
         "race_display"
     FROM powerset
-    WHERE 
+    WHERE
         cnt_subject >= 10
+
 );
 
 -- ###########################################################
@@ -146,8 +149,9 @@ CREATE TABLE covid_symptom__count_pcr_week AS (
         "gender",
         "race_display"
     FROM powerset
-    WHERE 
+    WHERE
         cnt_subject >= 10
+
 );
 
 -- ###########################################################
@@ -184,8 +188,9 @@ CREATE TABLE covid_symptom__count_study_period_month AS (
         "age_group",
         "race_display"
     FROM powerset
-    WHERE 
+    WHERE
         cnt_subject >= 10
+
 );
 
 -- ###########################################################
@@ -222,8 +227,9 @@ CREATE TABLE covid_symptom__count_study_period_week AS (
         "age_group",
         "race_display"
     FROM powerset
-    WHERE 
+    WHERE
         cnt_subject >= 10
+
 );
 
 -- ###########################################################
@@ -241,7 +247,7 @@ CREATE TABLE covid_symptom__count_symptom_week AS (
             "race_display",
             "enc_class_code",
             "ed_note"
-        FROM covid_symptom__symptom_nlp
+        FROM covid_symptom__symptom_ctakes_negation
         GROUP BY
             cube(
                 "author_week",
@@ -285,7 +291,7 @@ CREATE TABLE covid_symptom__count_symptom_month AS (
             "race_display",
             "enc_class_code",
             "ed_note"
-        FROM covid_symptom__symptom_nlp
+        FROM covid_symptom__symptom_ctakes_negation
         GROUP BY
             cube(
                 "author_month",

cumulus_library_covid/covid_symptom/table_dx.sql

@@ -19,6 +19,7 @@ WITH define_dx AS (
 SELECT DISTINCT
     c.subject_ref,
     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,

cumulus_library_covid/covid_symptom/table_pcr.sql

@@ -28,6 +28,7 @@ SELECT DISTINCT
     o.lab_date AS covid_pcr_date,
     o.lab_week AS covid_pcr_week,
     o.lab_month AS covid_pcr_month,
+    s.status,
     s.variant_era,
     s.author_date,
     s.author_week,

cumulus_library_covid/covid_symptom/table_prevalence_ed.sql

@@ -1,5 +1,5 @@
 CREATE TABLE covid_symptom__prevalence_ed AS
-WITH from_period AS (
+WITH study_period AS (
     SELECT DISTINCT
         encounter_ref,
         subject_ref,
@@ -10,13 +10,15 @@ WITH from_period AS (
         age_at_visit,
         age_group,
         variant_era,
-        enc_class_display
+        enc_class_display,
+        status
     FROM covid_symptom__study_period
     WHERE ed_note
 ),
 
 join_2020 AS (
     SELECT DISTINCT
+        p.status,
         p.author_week,
         p.author_month,
         p.gender,
@@ -31,12 +33,13 @@ join_2020 AS (
         COALESCE(dx.cond_code, 'None') AS covid_icd10,
         (dx.cond_code IS NOT NULL OR pcr.covid_pcr_result_display = 'POSITIVE')
         AS covid_dx,
-        COALESCE(nlp.symptom_display, 'None') AS covid_symptom,
+        COALESCE(cn.symptom_display, 'None') AS covid_symptom,
         COALESCE(icd10.icd10_display, 'None') AS symptom_icd10_display
-    FROM from_period AS p
+    FROM study_period AS p
     LEFT JOIN covid_symptom__dx AS dx ON p.encounter_ref = dx.encounter_ref
     LEFT JOIN covid_symptom__pcr AS pcr ON p.encounter_ref = pcr.encounter_ref
-    LEFT JOIN covid_symptom__symptom_nlp AS nlp ON p.encounter_ref = nlp.encounter_ref
+    LEFT JOIN covid_symptom__symptom_ctakes_negation AS cn
+        ON p.encounter_ref = cn.encounter_ref
     LEFT JOIN covid_symptom__symptom_icd10 AS icd10
         ON p.encounter_ref = icd10.encounter_ref
 )

cumulus_library_covid/covid_symptom/table_study_period.sql

@@ -16,11 +16,13 @@ SELECT DISTINCT
     s.encounter_ref,
     s.doc_ref,
     s.diff_enc_note_days,
+    s.enc_class_code,
     s.enc_class_display,
     s.doc_type_code,
     s.doc_type_display,
     s.ed_note, -- TODO https://github.com/smart-on-fhir/cumulus-library-covid/issues/10
-    a.age_group
+    a.age_group,
+    s.status
 FROM core__study_period AS s,
     covid_symptom__define_period AS v,
     covid_symptom__define_age AS a

cumulus_library_covid/covid_symptom/table_symptom.sql

@@ -17,7 +17,7 @@
 
 -- ############################################################################
 
-CREATE TABLE covid_symptom__symptom_nlp AS
+CREATE TABLE covid_symptom__symptom_ctakes_negation AS
 WITH mention AS (
     SELECT
         t.concept,
@@ -51,7 +51,8 @@ SELECT DISTINCT
     s.gender,
     s.race_display,
     s.enc_class_display,
-    s.ed_note
+    s.ed_note,
+    s.status
 FROM mention AS m,
     covid_symptom__define_symptom_cui AS def,
     covid_symptom__study_period AS s