Merge pull request #70 from OHDSI/ladams-fix-postgres-failing-tests

fix: use explicit seed types or null type casts where necessary for postgres
OHDSI · Oct 3, 2024 · 81a21d9 · 81a21d9
2 parents 952fee4 + 16fb0a9
commit 81a21d9
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Showing 4 changed files with 44 additions and 10 deletions.
diff --git a/models/intermediate/int__person.sql b/models/intermediate/int__person.sql
@@ -19,9 +19,9 @@ SELECT
         WHEN upper(p.ethnicity) = 'NONHISPANIC' THEN 38003564
         ELSE 0
     END AS ethnicity_concept_id
-    , NULL AS location_id
-    , NULL AS provider_id
-    , NULL AS care_site_id
+    , {{ dbt.cast("NULL", api.Column.translate_type("integer")) }}  AS location_id
+    , {{ dbt.cast("NULL", api.Column.translate_type("integer")) }}  AS provider_id
+    , {{ dbt.cast("NULL", api.Column.translate_type("integer")) }}  AS care_site_id
     , p.patient_id AS person_source_value
     , p.patient_gender AS gender_source_value
     , 0 AS gender_source_concept_id

diff --git a/models/omop/visit_detail.sql b/models/omop/visit_detail.sql
@@ -21,7 +21,7 @@ SELECT
     , av.visit_end_date AS visit_detail_end_datetime
     , 32827 AS visit_detail_type_concept_id
     , pr.provider_id
-    , null AS care_site_id
+    , {{ dbt.cast("NULL", api.Column.translate_type("integer")) }}  AS care_site_id
     , 0 AS admitted_from_concept_id
     , 0 AS discharged_to_concept_id
     , lag(av.visit_occurrence_id)
@@ -32,9 +32,9 @@ SELECT
     + 1000000 AS preceding_visit_detail_id
     , av.encounter_id AS visit_detail_source_value
     , 0 AS visit_detail_source_concept_id
-    , null AS admitted_from_source_value
-    , null AS discharged_to_source_value
-    , null AS parent_visit_detail_id
+    , NULL AS admitted_from_source_value
+    , NULL AS discharged_to_source_value
+    , {{ dbt.cast("NULL", api.Column.translate_type("integer")) }}  AS parent_visit_detail_id
     , av.visit_occurrence_id
 FROM {{ ref( 'int__all_visits') }} AS av
 INNER JOIN {{ ref( 'person') }} AS p

diff --git a/models/omop/visit_occurrence.sql b/models/omop/visit_occurrence.sql
@@ -16,13 +16,13 @@ SELECT
     , av.visit_end_date AS visit_end_datetime
     , 32827 AS visit_type_concept_id
     , pr.provider_id
-    , null AS care_site_id
+    , {{ dbt.cast("NULL", api.Column.translate_type("integer")) }}  AS care_site_id
     , av.encounter_id AS visit_source_value
     , 0 AS visit_source_concept_id
     , 0 AS admitted_from_concept_id
-    , null AS admitted_from_source_value
+    , NULL AS admitted_from_source_value
     , 0 AS discharged_to_concept_id
-    , null AS discharged_to_source_value
+    , NULL AS discharged_to_source_value
     , lag(av.visit_occurrence_id)
         OVER (
             PARTITION BY p.person_id

diff --git a/seeds/vocabulary/_sources.yml b/seeds/vocabulary/_sources.yml
@@ -0,0 +1,34 @@
+seeds:
+  - name: concept_synonym_seed
+    config:
+      column_types:
+        concept_id: integer
+        concept_synonym_name: varchar(1000)
+        language_concept_id: integer
+  - name: source_to_concept_map_seed
+    config:
+      column_types:
+        source_code: varchar(50)
+        source_concept_id: integer
+        source_vocabulary_id: varchar(20)
+        source_code_description: varchar(255)
+        target_concept_id: integer
+        target_vocabulary_id: varchar(20)
+        valid_start_date: date
+        valid_end_date: date
+        invalid_reason: varchar(1)
+  - name: drug_strength_seed
+    config:
+      column_types:
+        drug_concept_id: integer
+        ingredient_concept_id: integer
+        amount_value: numeric
+        amount_unit_concept_id: integer
+        numerator_value: numeric
+        numerator_unit_concept_id: integer
+        denominator_value: numeric
+        denominator_unit_concept_id: integer
+        box_size: integer
+        valid_start_date: date
+        valid_end_date: date
+        invalid_reason: varchar