Merge pull request #78 from OHDSI/76-inconsistent-keyword-quoting-in-…

…staging-models
OHDSI · Oct 7, 2024 · b9010cd · b9010cd
2 parents 415130d + 2df584a
commit b9010cd
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Showing 16 changed files with 46 additions and 38 deletions.
diff --git a/macros/create_synthea_tables.sql b/macros/create_synthea_tables.sql
@@ -11,7 +11,7 @@
                 encounter    VARCHAR(1000),
                 code         VARCHAR(100),
                 "system"       VARCHAR(255),
-                "description"  VARCHAR(255),
+                description  VARCHAR(255),
                 "type"       VARCHAR(255),
                 category     VARCHAR(255),
                 reaction1    VARCHAR(255),
@@ -30,7 +30,7 @@
                 patient       VARCHAR(1000),
                 encounter     VARCHAR(1000),
                 code          VARCHAR(100),
-                "description"   VARCHAR(255),
+                description   VARCHAR(255),
                 reasoncode    VARCHAR(255),
                 reasondescription   VARCHAR(255)
             );
@@ -56,7 +56,7 @@
                 payer           VARCHAR(1000),
                 encounterclass  VARCHAR(1000),
                 code            VARCHAR(100),
-                "description"     VARCHAR(255),
+                description     VARCHAR(255),
                 base_encounter_cost NUMERIC,
                 total_claim_cost    NUMERIC,
                 payer_coverage  NUMERIC,
@@ -70,7 +70,7 @@
                 patient       VARCHAR(1000),
                 encounter     VARCHAR(1000),
                 code          VARCHAR(100),
-                "description"   VARCHAR(255),
+                description   VARCHAR(255),
                 base_cost     NUMERIC
             );
         {% endif %}
@@ -99,7 +99,7 @@
                 payer         VARCHAR(1000),
                 encounter     VARCHAR(1000),
                 code          VARCHAR(100),
-                "description"   VARCHAR(1000),
+                description   VARCHAR(1000),
                 base_cost     NUMERIC,
                 payer_coverage    NUMERIC,
                 dispenses     INT,
@@ -115,7 +115,7 @@
                 encounter     VARCHAR(1000),
                 category      VARCHAR(1000),
                 code          VARCHAR(100),
-                "description"   VARCHAR(255),
+                description   VARCHAR(255),
                 "value"         VARCHAR(1000),
                 units         VARCHAR(100),
                 "type"        VARCHAR(100)
@@ -125,9 +125,9 @@
             CREATE TABLE {{schema}}.organizations (
                 id              VARCHAR(1000),
                 "name"          VARCHAR(1000),
-                "address"         VARCHAR(1000),
+                address         VARCHAR(1000),
                 city            VARCHAR(100),
-                "state"           VARCHAR(100),
+                state           VARCHAR(100),
                 zip             VARCHAR(100),
                 lat             NUMERIC,
                 lon             NUMERIC,
@@ -154,9 +154,9 @@
                 ethnicity       VARCHAR(100),
                 gender          VARCHAR(100),
                 birthplace      VARCHAR(100),
-                "address"         VARCHAR(100),
+                address         VARCHAR(100),
                 city            VARCHAR(100),
-                "state"           VARCHAR(100),
+                state           VARCHAR(100),
                 county          VARCHAR(100),
                 zip             VARCHAR(100),
                 lat             NUMERIC,
@@ -172,7 +172,7 @@
                 patient       VARCHAR(1000),
                 encounter     VARCHAR(1000),
                 code          VARCHAR(100),
-                "description"   VARCHAR(255),
+                description   VARCHAR(255),
                 base_cost     NUMERIC,
                 reasoncode    VARCHAR(1000),
                 reasondescription VARCHAR(1000)
@@ -182,12 +182,12 @@
             CREATE TABLE {{schema}}.providers (
                 id VARCHAR(1000),
                 organization VARCHAR(1000),
-                "name" VARCHAR(100),
+                name VARCHAR(100),
                 gender VARCHAR(100),
                 speciality VARCHAR(100),
-                "address" VARCHAR(255),
+                address VARCHAR(255),
                 city VARCHAR(100),
-                "state" VARCHAR(100),
+                state VARCHAR(100),
                 zip VARCHAR(100),
                 lat NUMERIC,
                 lon NUMERIC,
@@ -201,7 +201,7 @@
                 patient       VARCHAR(1000),
                 encounter     VARCHAR(1000),
                 code          VARCHAR(100),
-                "description"   VARCHAR(255),
+                description   VARCHAR(255),
                 udi           VARCHAR(255)
             );
         {% endif %}
@@ -285,15 +285,15 @@
                 end_year         TIMESTAMP,
                 payer            VARCHAR(1000),
                 secondary_payer  VARCHAR(1000),
-                "ownership"        VARCHAR(1000),
+                ownership        VARCHAR(1000),
                 ownername       VARCHAR(1000)
             );
         {% endif %}
         {% if not check_if_exists(database, schema, "payers") %}
             CREATE TABLE {{schema}}.payers (
                 id                       VARCHAR(1000),
-                "name"                     VARCHAR(1000),
-                "address"                  VARCHAR(1000),
+                name                     VARCHAR(1000),
+                address                  VARCHAR(1000),
                 city                     VARCHAR(1000),
                 state_headquartered      VARCHAR(1000),
                 zip                      VARCHAR(1000),
@@ -320,7 +320,7 @@
                 patient      VARCHAR(1000),
                 encounter    VARCHAR(1000),
                 code         VARCHAR(1000),
-                "description"  VARCHAR(1000),
+                description  VARCHAR(1000),
                 quantity     NUMERIC
             );
         {% endif %}

diff --git a/macros/lowercase_columns.sql b/macros/lowercase_columns.sql
@@ -1,6 +1,14 @@
 {% macro lowercase_columns(column_names) %}
+    {# List of SQL Keywords in use by dbt-synthea #}
+    {% set sql_keywords = ["start", "stop", "type", "system", "date", "first", "last", "value", "name"] %}
     {% for column_name in column_names %} 
-        "{{ column_name }}" AS {{ column_name | lower }} 
+        {% set lowercase_column = column_name | lower %}
+        {# If a keyword - quote the output column name so it can be safely used in models #}
+        {% if column_name | lower in sql_keywords %}
+            "{{ column_name }}" AS "{{ lowercase_column }}"
+        {% else %}
+        "{{ column_name }}" AS {{ lowercase_column }}
+        {% endif %}
         {% if not loop.last %},{% endif %} 
     {% endfor %}
 {% endmacro %}
diff --git a/models/staging/synthea/stg_synthea__allergies.sql b/models/staging/synthea/stg_synthea__allergies.sql
@@ -19,7 +19,7 @@ WITH cte_allergies_lower AS (
         , encounter AS encounter_id
         , code AS allergy_code
         , "system" AS allergy_code_system
-        , "description" AS allergy_description
+        , description AS allergy_description
         , "type" AS allergy_type
         , category AS allergy_category
         , reaction1 AS reaction_1_code

diff --git a/models/staging/synthea/stg_synthea__careplans.sql b/models/staging/synthea/stg_synthea__careplans.sql
@@ -19,7 +19,7 @@ WITH cte_careplans_lower AS (
         , patient AS patient_id
         , encounter AS encounter_id
         , code AS careplan_code
-        , "description" AS careplan_description
+        , description AS careplan_description
         , reasoncode AS careplan_reason_code
         , reasondescription AS careplan_reason_description
     FROM cte_careplans_lower

diff --git a/models/staging/synthea/stg_synthea__conditions.sql b/models/staging/synthea/stg_synthea__conditions.sql
@@ -18,7 +18,7 @@ WITH cte_conditions_lower AS (
         , patient AS patient_id
         , encounter AS encounter_id
         , code AS condition_code
-        , "description" AS condition_description
+        , description AS condition_description
     FROM cte_conditions_lower
 
 )

diff --git a/models/staging/synthea/stg_synthea__devices.sql b/models/staging/synthea/stg_synthea__devices.sql
@@ -20,7 +20,7 @@ WITH cte_devices_lower AS (
         , patient AS patient_id
         , encounter AS encounter_id
         , code AS device_code
-        , "description" AS device_description
+        , description AS device_description
         , udi
     FROM cte_devices_lower
 

diff --git a/models/staging/synthea/stg_synthea__imaging_studies.sql b/models/staging/synthea/stg_synthea__imaging_studies.sql
@@ -13,7 +13,7 @@ WITH cte_imaging_studies_lower AS (
 , cte_imaging_studies_rename AS (
 
     SELECT
-        "id" AS imaging_id
+        id AS imaging_id
         , "date" AS imaging_datetime
         , patient AS patient_id
         , encounter AS encounter_id

diff --git a/models/staging/synthea/stg_synthea__immunizations.sql b/models/staging/synthea/stg_synthea__immunizations.sql
@@ -17,7 +17,7 @@ WITH cte_immunizations_lower AS (
         , patient AS patient_id
         , encounter AS encounter_id
         , code AS immunization_code
-        , "description" AS immunization_description
+        , description AS immunization_description
         , {{ dbt.cast("base_cost", api.Column.translate_type("decimal")) }} AS immunization_base_cost
     FROM cte_immunizations_lower
 

diff --git a/models/staging/synthea/stg_synthea__medications.sql b/models/staging/synthea/stg_synthea__medications.sql
@@ -21,7 +21,7 @@ WITH cte_medications_lower AS (
         , payer AS payer_id
         , encounter AS encounter_id
         , code AS medication_code
-        , "description" AS medication_description
+        , description AS medication_description
         , {{ dbt.cast("base_cost", api.Column.translate_type("decimal")) }} AS medication_base_cost
         , payer_coverage AS medication_payer_coverage
         , dispenses

diff --git a/models/staging/synthea/stg_synthea__observations.sql b/models/staging/synthea/stg_synthea__observations.sql
@@ -19,7 +19,7 @@ WITH cte_observations_lower AS (
         , encounter AS encounter_id
         , category AS observation_category
         , code AS observation_code
-        , "description" AS observation_description
+        , description AS observation_description
         , "value" AS observation_value
         , units AS observation_units
         , "type" AS observation_value_type

diff --git a/models/staging/synthea/stg_synthea__organizations.sql b/models/staging/synthea/stg_synthea__organizations.sql
@@ -14,7 +14,7 @@ WITH cte_organizations_lower AS (
 
     SELECT
         id AS organization_id
-        , name AS organization_name
+        , "name" AS organization_name
         , address AS organization_address
         , city AS organization_city
         , state AS organization_state

diff --git a/models/staging/synthea/stg_synthea__patients.sql b/models/staging/synthea/stg_synthea__patients.sql
@@ -29,9 +29,9 @@ WITH cte_patients_lower AS (
         , ethnicity
         , gender AS patient_gender
         , birthplace
-        , "address" AS patient_address
+        , address AS patient_address
         , city AS patient_city
-        , "state" AS patient_state
+        , state AS patient_state
         , county AS patient_county
         , zip AS patient_zip
         , lat AS patient_latitude

diff --git a/models/staging/synthea/stg_synthea__payer_transitions.sql b/models/staging/synthea/stg_synthea__payer_transitions.sql
@@ -21,7 +21,7 @@ WITH cte_payer_transitions_lower AS (
         , {{ dbt.cast("end_year", api.Column.translate_type("date")) }} AS coverage_end_date
         , payer AS payer_id
         , secondary_payer AS secondary_payer_id
-        , "ownership" AS plan_owner_relationship
+        , ownership AS plan_owner_relationship
         , ownername AS plan_owner_name
     FROM cte_payer_transitions_lower
 

diff --git a/models/staging/synthea/stg_synthea__procedures.sql b/models/staging/synthea/stg_synthea__procedures.sql
@@ -14,13 +14,13 @@ WITH cte_procedures_lower AS (
 
     SELECT
         "start" AS procedure_start_datetime
-        , {{ dbt.cast("start", api.Column.translate_type("date")) }} AS procedure_start_date
+        , {{ dbt.cast("\"start\"", api.Column.translate_type("date")) }} AS procedure_start_date
         , "stop" AS procedure_stop_datetime
-        , {{ dbt.cast("stop", api.Column.translate_type("date")) }} AS procedure_stop_date
+        , {{ dbt.cast("\"stop\"", api.Column.translate_type("date")) }} AS procedure_stop_date
         , patient AS patient_id
         , encounter AS encounter_id
         , code AS procedure_code
-        , "description" AS procedure_description
+        , description AS procedure_description
         , {{ dbt.cast("base_cost", api.Column.translate_type("decimal")) }} AS procedure_base_cost
         , reasoncode AS procedure_reason_code
         , reasondescription AS procedure_reason_description

diff --git a/models/staging/synthea/stg_synthea__providers.sql b/models/staging/synthea/stg_synthea__providers.sql
@@ -18,9 +18,9 @@ WITH cte_providers_lower AS (
         , "name" AS provider_name
         , gender AS provider_gender
         , speciality AS provider_specialty
-        , "address" AS provider_address
+        , address AS provider_address
         , city AS provider_city
-        , "state" AS provider_state
+        , state AS provider_state
         , zip AS provider_zip
         , lat AS provider_latitude
         , lon AS provider_longitude

diff --git a/models/staging/synthea/stg_synthea__supplies.sql b/models/staging/synthea/stg_synthea__supplies.sql
@@ -17,7 +17,7 @@ WITH cte_supplies_lower AS (
         , patient AS patient_id
         , encounter AS encounter_id
         , code AS supply_code
-        , "description" AS supply_description
+        , description AS supply_description
         , quantity AS supply_quantity
     FROM cte_supplies_lower