corrected code style, corrected load_input.sql algorhythm.

OHDSI · Sep 25, 2024 · f952ae2 · f952ae2
1 parent edede7c
commit f952ae2
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diff --git a/ATC/load_stage.sql b/ATC/load_stage.sql
diff --git a/ATC/manual work/class_to_drug.sql b/ATC/manual work/class_to_drug.sql
diff --git a/ATC/manual work/load_input.sql b/ATC/manual work/load_input.sql
diff --git a/ATC/manual work/new_class_to_drug.sql b/ATC/manual work/new_class_to_drug.sql
diff --git a/ATC/manual work/tests/ancestor_checks.sql b/ATC/manual work/tests/ancestor_checks.sql
diff --git a/ATC/manual work/tests/custom_tests.sql b/ATC/manual work/tests/custom_tests.sql
@@ -137,8 +137,8 @@ WHERE r.concept_id NOT IN (
  JOIN dev_atc.concept c ON c.concept_id = ca.descendant_concept_id
  WHERE ancestor_concept_id IN (21602745, 21602723));
 
-select *
-from atc_checks;
+SELECT *
+FROM atc_checks;
 
 /*****
 Checks that require examination
@@ -546,9 +546,8 @@ ORDER BY t1.dev_atc_cr, t1.dev_atc_cid;
 
 --- Home many combo drugs come to ATC mono codes
 
-SELECT
- concept_code,
- count (concept_id)
+SELECT concept_code,
+ COUNT(concept_id)
 FROM (SELECT c1.concept_code,
  c1.concept_name,
  c2.concept_id,
@@ -573,103 +572,91 @@ FROM (SELECT c1.concept_code,
  GROUP BY c1.concept_code, c1.concept_name, c2.concept_id, c2.concept_name
  HAVING COUNT(cr2.concept_id_2) > 1) t1
 GROUP BY concept_code
-ORDER BY count desc;
+ORDER BY count DESC;
 
 
 -- How manu GCS in clinical drug forms, that bineded to 'D07AB30', 'D07XB30'
-WITH CTE_1 AS (
- SELECT
- c1.concept_id AS concept_id_atc,
- c1.concept_code AS concept_code_atc,
- c1.concept_name AS concept_name_atc,
- cr.relationship_id AS relationship_id,
- c2.concept_id AS concept_id_rx,
- c2.concept_name AS concept_name_rx,
- c2.concept_class_id AS concept_class_rx,
- string_agg(c3.concept_name, ',') AS ings
- FROM
- concept_relationship cr
- JOIN
- concept c1 ON cr.concept_id_1 = c1.concept_id
- AND c1.vocabulary_id = 'ATC'
- AND c1.invalid_reason IS NULL
- AND cr.invalid_reason IS NULL
- AND cr.relationship_id = 'ATC - RxNorm'
- AND c1.concept_code IN ('D07AB30', 'D07XB30')
- JOIN
- concept c2 ON cr.concept_id_2 = c2.concept_id
- AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension')
- AND c2.invalid_reason IS NULL
- JOIN
- concept_relationship cr2 ON cr2.concept_id_1 = c2.concept_id
- AND cr2.invalid_reason IS NULL
- AND c2.invalid_reason IS NULL
- AND cr2.relationship_id = 'RxNorm has ing'
- JOIN
- concept c3 ON cr2.concept_id_2 = c3.concept_id
- GROUP BY
- c1.concept_id, c1.concept_code, c1.concept_name, cr.relationship_id, c2.concept_id, c2.concept_name, c2.concept_class_id
-),
-gcs_list AS (
- SELECT UNNEST(ARRAY[
- 'betamethasone',
- 'cortisone',
- 'dexamethasone',
- 'fludrocortisone',
- 'fluocortolone',
- 'hydrocortisone',
- 'methylprednisolone',
- 'prednisolone',
- 'prednisone',
- 'prednylidene',
- 'triamcinolone',
- 'beclomethasone',
- 'budesonide',
- 'deflazacort',
- 'desonide',
- 'diflucortolone',
- 'fluocinonide',
- 'fluorometholone',
- 'fluticasone',
- 'halcinonide',
- 'mometasone',
- 'paramethasone',
- 'rimexolone',
- 'clobetasone',
- 'fluocinolone',
- 'flumethasone',
- 'alclometasone',
- 'diflorasone',
- 'desoximetasone',
- 'fluprednisolone',
- 'medrysone',
- 'tixocortol',
- 'ciclesonide',
- 'loteprednol'
- ]) AS gcs_name
-)
-SELECT
- t.concept_id_atc,
- t.concept_code_atc,
- t.concept_name_atc,
- t.concept_id_rx,
- t.concept_name_rx,
- t.ings,
- COUNT(DISTINCT gcs_name) AS gcs_count
-FROM
- CTE_1 t
-CROSS JOIN
- gcs_list
-WHERE
- EXISTS (
- SELECT 1
- FROM unnest(string_to_array(t.ings, ',')) AS ingredient
- WHERE ingredient = gcs_name
- )
-GROUP BY
- t.concept_id_atc,
- t.concept_code_atc,
- t.concept_name_atc,
- t.concept_id_rx,
- t.concept_name_rx,
- t.ings;
+WITH CTE_1 AS (SELECT c1.concept_id AS concept_id_atc,
+ c1.concept_code AS concept_code_atc,
+ c1.concept_name AS concept_name_atc,
+ cr.relationship_id AS relationship_id,
+ c2.concept_id AS concept_id_rx,
+ c2.concept_name AS concept_name_rx,
+ c2.concept_class_id AS concept_class_rx,
+ STRING_AGG(c3.concept_name, ',') AS ings
+ FROM concept_relationship cr
+ JOIN
+ concept c1 ON cr.concept_id_1 = c1.concept_id
+ AND c1.vocabulary_id = 'ATC'
+ AND c1.invalid_reason IS NULL
+ AND cr.invalid_reason IS NULL
+ AND cr.relationship_id = 'ATC - RxNorm'
+ AND c1.concept_code IN ('D07AB30', 'D07XB30')
+ JOIN
+ concept c2 ON cr.concept_id_2 = c2.concept_id
+ AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension')
+ AND c2.invalid_reason IS NULL
+ JOIN
+ concept_relationship cr2 ON cr2.concept_id_1 = c2.concept_id
+ AND cr2.invalid_reason IS NULL
+ AND c2.invalid_reason IS NULL
+ AND cr2.relationship_id = 'RxNorm has ing'
+ JOIN
+ concept c3 ON cr2.concept_id_2 = c3.concept_id
+ GROUP BY c1.concept_id, c1.concept_code, c1.concept_name, cr.relationship_id, c2.concept_id,
+ c2.concept_name, c2.concept_class_id),
+ gcs_list AS (SELECT UNNEST(ARRAY [
+ 'betamethasone',
+ 'cortisone',
+ 'dexamethasone',
+ 'fludrocortisone',
+ 'fluocortolone',
+ 'hydrocortisone',
+ 'methylprednisolone',
+ 'prednisolone',
+ 'prednisone',
+ 'prednylidene',
+ 'triamcinolone',
+ 'beclomethasone',
+ 'budesonide',
+ 'deflazacort',
+ 'desonide',
+ 'diflucortolone',
+ 'fluocinonide',
+ 'fluorometholone',
+ 'fluticasone',
+ 'halcinonide',
+ 'mometasone',
+ 'paramethasone',
+ 'rimexolone',
+ 'clobetasone',
+ 'fluocinolone',
+ 'flumethasone',
+ 'alclometasone',
+ 'diflorasone',
+ 'desoximetasone',
+ 'fluprednisolone',
+ 'medrysone',
+ 'tixocortol',
+ 'ciclesonide',
+ 'loteprednol'
+ ]) AS gcs_name)
+SELECT t.concept_id_atc,
+ t.concept_code_atc,
+ t.concept_name_atc,
+ t.concept_id_rx,
+ t.concept_name_rx,
+ t.ings,
+ COUNT(DISTINCT gcs_name) AS gcs_count
+FROM CTE_1 t
+ CROSS JOIN
+ gcs_list
+WHERE EXISTS (SELECT 1
+ FROM UNNEST(STRING_TO_ARRAY(t.ings, ',')) AS ingredient
+ WHERE ingredient = gcs_name)
+GROUP BY t.concept_id_atc,
+ t.concept_code_atc,
+ t.concept_name_atc,
+ t.concept_id_rx,
+ t.concept_name_rx,
+ t.ings;