[DC-3645] Update Union QC notebook with fixes for column name and moving notes check

data_steward/analytics/cdr_ops/combined.py

@@ -274,6 +274,30 @@
 execute(client, query)
 # -
 
+# ## Verify Note text data
+
+# +
+query = f'''
+SELECT 'note_text' AS field, note_text AS field_value, COUNT(note_text) AS row_count,
+FROM `{PROJECT_ID}.{DATASET_ID}.note`
+GROUP BY note_text
+
+UNION ALL
+
+SELECT 'note_title' AS field, note_title AS field_value, COUNT(note_title) AS row_count,
+FROM `{PROJECT_ID}.{DATASET_ID}.note`
+GROUP BY note_title
+
+UNION ALL
+
+SELECT 'note_source_value' AS field, note_source_value AS field_value, COUNT(note_source_value) AS row_count,
+FROM `{PROJECT_ID}.{DATASET_ID}.note`
+GROUP BY note_source_value
+'''
+
+execute(client, query)
+# -
+
 # ## Date and datetime fields should have the same date
 # The date represented by associated `_date` and `_datetime` fields of the same
 # row should be the same. If there any discrepancies, there may be a bug in the

data_steward/analytics/cdr_ops/ehr_union_qc.py

@@ -157,7 +157,7 @@
   GROUP BY
     src_hpo_id)
 SELECT
-  cc.src_hpo_id,
+  src_hpo_id,
   coalesce(previous_unioned_ct, 0) as previous_unioned_ct,
   coalesce(current_unioned_ct, 0)  AS current_unioned_ct,
   coalesce(cast((current_unioned_ct - previous_unioned_ct)/ current_unioned_ct * 100 as INT64), 100) as percentage_change 
@@ -172,77 +172,53 @@
 execute(client, query)
 # -
 
-# ## Verify Note text data
-
-# +
-query = f'''
-SELECT 'note_text' AS field, note_text AS field_value, COUNT(note_text) AS row_count,
-FROM `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.note`
-GROUP BY note_text
-
-UNION ALL
-
-SELECT 'note_title' AS field, note_title AS field_value, COUNT(note_title) AS row_count,
-FROM `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.note`
-GROUP BY note_title
-
-UNION ALL
-
-SELECT 'note_source_value' AS field, note_source_value AS field_value, COUNT(note_source_value) AS row_count,
-FROM `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.note`
-GROUP BY note_source_value
-'''
-
-execute(client, query)
-# -
-
 # ## Verifying no data past cut-off date
 
 # +
 query = f'''
 SELECT
   'observation' AS TABLE,
-  COUNT(*) AS non_clompling_rows
+  COUNT(*) AS non_complying_rows
 FROM
   `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.observation`
 WHERE
   observation_date > DATE('{EHR_CUTOFF_DATE}')
 UNION ALL
 SELECT
   'measurement' AS TABLE,
-  COUNT(*) AS non_clompling_rows
+  COUNT(*) AS non_complying_rows
 FROM
   `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.measurement`
 WHERE
   measurement_date > DATE('{EHR_CUTOFF_DATE}')
 UNION ALL
 SELECT
   'visit_occurrence' AS TABLE,
-  COUNT(*) AS non_clompling_rows
+  COUNT(*) AS non_complying_rows
 FROM
   `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.visit_occurrence`
 WHERE
   visit_end_date > DATE('{EHR_CUTOFF_DATE}')
 UNION ALL
 SELECT
   'drug_exposure' AS TABLE,
-  COUNT(*) AS non_clompling_rows
+  COUNT(*) AS non_complying_rows
 FROM
   `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.drug_exposure`
 WHERE
   drug_exposure_end_date > DATE('{EHR_CUTOFF_DATE}')
 UNION ALL
 SELECT
   'procedure' AS TABLE,
-  COUNT(*) AS non_clompling_rows
+  COUNT(*) AS non_complying_rows
 FROM
   `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.procedure_occurrence`
 WHERE
   procedure_date > DATE('{EHR_CUTOFF_DATE}')
   UNION ALL
 SELECT
   'visit_detail' AS TABLE,
-  COUNT(*) AS non_clompling_rows
+  COUNT(*) AS non_complying_rows
 FROM
   `{PROJECT_ID}.{CURRENT_UNIONED_EHR_DATASET_ID}.visit_detail`
 WHERE
@@ -353,7 +329,7 @@
     SELECT 
         aou_death_id, 
         CASE WHEN aou_death_id IN (
-            SELECT aou_death_id FROM `{{project_id}}.{{dataset_id}}.aou_death`
+            SELECT aou_death_id FROM `{{project_id}}.{{dataset}}.aou_death`
             WHERE death_date IS NOT NULL -- NULL death_date records must not become primary --
             QUALIFY RANK() OVER (
                 PARTITION BY person_id