Switch _code_system to _system (#264)

* Switch _code_system to _system * rerun generate_md now while its relevant * revert ref sql
smart-on-fhir · Jul 11, 2024 · bd05325 · bd05325
1 parent d9e2207
commit bd05325
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Showing 15 changed files with 467 additions and 316 deletions.
diff --git a/cumulus_library/studies/core/core_templates/condition.sql.jinja b/cumulus_library/studies/core/core_templates/condition.sql.jinja
@@ -61,7 +61,7 @@ WITH temp_condition AS (
 SELECT
     tc.id,
     cdc.code AS category_code,
-    cdc.code_system AS category_code_system,
+    cdc.code_system AS category_system,
     cdc.display AS category_display,
     tc.code,
     tc.code_system,

diff --git a/cumulus_library/studies/core/core_templates/documentreference.sql.jinja b/cumulus_library/studies/core/core_templates/documentreference.sql.jinja
@@ -44,7 +44,7 @@ WITH temp_documentreference AS (
             ) 
         }},
         cdrt.code as type_code,
-        cdrt.code_system as type_code_system,
+        cdrt.code_system as type_system,
         cdrt.display as type_display,
         cdrc.code as category_code,
         cdrf.code as format_code
@@ -75,7 +75,7 @@ SELECT DISTINCT
     tdr.id,
     tdr.status,
     tdr.type_code,
-    tdr.type_code_system,
+    tdr.type_system,
     tdr.type_display,
     tdr.category_code,
     tdr.docStatus,

diff --git a/cumulus_library/studies/core/core_templates/encounter.sql.jinja b/cumulus_library/studies/core/core_templates/encounter.sql.jinja
@@ -27,7 +27,7 @@ temp_encounter_nullable AS (
                 [
                     'status',
                     ('class', 'code', 'class_code'),
-                    ('class', 'system', 'class_code_system'),
+                    ('class', 'system', 'class_system'),
                     ('subject', 'reference', 'subject_ref'),
                 ], 
                 schema
@@ -69,7 +69,7 @@ temp_encounter AS (
         e.id,
         e.status,
         e.class_code,
-        e.class_code_system,
+        e.class_system,
         e.subject_ref,
         e.period_start,
         e.period_start_day,
@@ -78,19 +78,19 @@ temp_encounter AS (
         e.period_start_month,
         e.period_start_year,
         edt.code AS type_code,
-        edt.code_system AS type_code_system,
+        edt.code_system AS type_system,
         edt.display AS type_display,
         eds.code AS serviceType_code,
-        eds.code_system AS serviceType_code_system,
+        eds.code_system AS serviceType_system,
         eds.display AS serviceType_display,
         edp.code AS priority_code,
-        edp.code_system AS priority_code_system,
+        edp.code_system AS priority_system,
         edp.display AS priority_display,
         edr.code AS reasonCode_code,
-        edr.code_system AS reasonCode_code_system,
+        edr.code_system AS reasonCode_system,
         edr.display AS reasonCode_display,
         edd.code AS dischargeDisposition_code,
-        edd.code_system AS dischargeDisposition_code_system,
+        edd.code_system AS dischargeDisposition_system,
         edd.display AS dischargeDisposition_display
 
     FROM temp_encounter_nullable AS e
@@ -107,19 +107,19 @@ SELECT DISTINCT
     ac.code AS class_code,
     ac.display AS class_display,
     e.type_code,
-    e.type_code_system,
+    e.type_system,
     e.type_display,
     e.serviceType_code,
-    e.serviceType_code_system,
+    e.serviceType_system,
     e.serviceType_display,
     e.priority_code,
-    e.priority_code_system,
+    e.priority_system,
     e.priority_display,
     e.reasonCode_code,
-    e.reasonCode_code_system,
+    e.reasonCode_system,
     e.reasonCode_display,
     e.dischargeDisposition_code,
-    e.dischargeDisposition_code_system,
+    e.dischargeDisposition_system,
     e.dischargeDisposition_display,
     date_diff('year', date(p.birthdate), e.period_start_day) AS age_at_visit,
     p.gender,

diff --git a/cumulus_library/studies/core/core_templates/medicationrequest.sql.jinja b/cumulus_library/studies/core/core_templates/medicationrequest.sql.jinja
@@ -59,9 +59,9 @@ temp_mr AS (
                 schema
         ) -}},
         mrc.code AS category_code,
-        mrc.code_system AS category_code_system,
+        mrc.code_system AS category_system,
         mrm.code AS medication_code,
-        mrm.code_system AS medication_code_system,
+        mrm.code_system AS medication_system,
         mrm.display AS medication_display,
         mrdt.dosageInstruction_text
     FROM medicationrequest AS mr
@@ -76,9 +76,9 @@ SELECT
     mr.status,
     mr.intent,
     mr.category_code,
-    mr.category_code_system,
+    mr.category_system,
     mr.reportedBoolean,
-    mr.medication_code_system,
+    mr.medication_system,
     mr.medication_code,
     mr.medication_display,
     mr.authoredOn,

diff --git a/cumulus_library/studies/core/core_templates/observation.sql.jinja b/cumulus_library/studies/core/core_templates/observation.sql.jinja
@@ -22,7 +22,7 @@ WITH temp_observation AS (
                     ('valueQuantity', 'value', 'valueQuantity_value'),
                     ('valueQuantity', 'comparator', 'valueQuantity_comparator'),
                     ('valueQuantity', 'unit', 'valueQuantity_unit'),
-                    ('valueQuantity', 'system', 'valueQuantity_code_system'),
+                    ('valueQuantity', 'system', 'valueQuantity_system'),
                     ('valueQuantity', 'code', 'valueQuantity_code'),
                 ],
                 schema
@@ -41,17 +41,17 @@ WITH temp_observation AS (
             ) 
         }},
         odc.code AS observation_code,
-        odc.code_system AS observation_code_system,
+        odc.code_system AS observation_system,
         odcat.code AS category_code,
-        odcat.code_system AS category_code_system,
+        odcat.code_system AS category_system,
         odi.code AS interpretation_code,
-        odi.code_system AS interpretation_code_system,
+        odi.code_system AS interpretation_system,
         odi.display AS interpretation_display,
         odvcc.code AS valueCodeableConcept_code,
-        odvcc.code_system AS valueCodeableConcept_code_system,
+        odvcc.code_system AS valueCodeableConcept_system,
         odvcc.display AS valueCodeableConcept_display,
         odda.code AS dataAbsentReason_code,
-        odda.code_system AS dataAbsentReason_code_system,
+        odda.code_system AS dataAbsentReason_system,
         odda.display AS dataAbsentReason_display
     FROM observation AS o
     LEFT JOIN core__observation_dn_category AS odcat ON o.id = odcat.id
@@ -64,28 +64,28 @@ WITH temp_observation AS (
 SELECT
     id,
     category_code,
-    category_code_system,
+    category_system,
     status,
     observation_code,
-    observation_code_system,
+    observation_system,
     interpretation_code,
-    interpretation_code_system,
+    interpretation_system,
     interpretation_display,
     effectiveDateTime_day,
     effectiveDateTime_week,
     effectiveDateTime_month,
     effectiveDateTime_year,
     valueCodeableConcept_code,
-    valueCodeableConcept_code_system,
+    valueCodeableConcept_system,
     valueCodeableConcept_display,
     valueQuantity_value,
     valueQuantity_comparator,
     valueQuantity_unit,
-    valueQuantity_code_system,
+    valueQuantity_system,
     valueQuantity_code,
     valueString,
     dataAbsentReason_code,
-    dataAbsentReason_code_system,
+    dataAbsentReason_system,
     dataAbsentReason_display,
     subject_ref,
     encounter_ref,

diff --git a/cumulus_library/studies/core/observation_type.sql b/cumulus_library/studies/core/observation_type.sql
@@ -6,11 +6,11 @@ CREATE TABLE core__observation_lab AS
 SELECT
     co.id,
     co.observation_code,
-    co.observation_code_system,
+    co.observation_system,
     co.category_code,
-    co.category_code_system,
+    co.category_system,
     co.valueCodeableConcept_code,
-    co.valueCodeableConcept_code_system,
+    co.valueCodeableConcept_system,
     co.valueCodeableConcept_display,
     co.effectiveDateTime_day,
     co.effectiveDateTime_week,
@@ -24,27 +24,27 @@ FROM
     core__observation AS co
 WHERE
     co.category_code = 'laboratory'
-    AND co.category_code_system
+    AND co.category_system
     = 'http://terminology.hl7.org/CodeSystem/observation-category';
 
 CREATE TABLE core__observation_vital_signs AS
 SELECT
     co.id,
     co.observation_code,
-    co.observation_code_system,
+    co.observation_system,
     co.category_code,
-    co.category_code_system,
+    co.category_system,
     co.valueCodeableConcept_code,
-    co.valueCodeableConcept_code_system,
+    co.valueCodeableConcept_system,
     co.valueCodeableConcept_display,
     co.valueQuantity_value,
     co.valueQuantity_comparator,
     co.valueQuantity_unit,
-    co.valueQuantity_code_system,
+    co.valueQuantity_system,
     co.valueQuantity_code,
     co.status,
     co.interpretation_code,
-    co.interpretation_code_system,
+    co.interpretation_system,
     co.interpretation_display,
     co.effectiveDateTime_day,
     co.effectiveDateTime_week,
@@ -57,5 +57,5 @@ FROM
     core__observation AS co
 WHERE
     co.category_code = 'vital-signs'
-    AND co.category_code_system
+    AND co.category_system
     = 'http://terminology.hl7.org/CodeSystem/observation-category';
diff --git a/cumulus_library/studies/core/reference_sql/builder_condition.sql b/cumulus_library/studies/core/reference_sql/builder_condition.sql
@@ -471,7 +471,7 @@ WITH temp_condition AS (
 SELECT
     tc.id,
     cdc.code AS category_code,
-    cdc.code_system AS category_code_system,
+    cdc.code_system AS category_system,
     cdc.display AS category_display,
     tc.code,
     tc.code_system,

diff --git a/cumulus_library/studies/core/reference_sql/builder_documentreference.sql b/cumulus_library/studies/core/reference_sql/builder_documentreference.sql
@@ -175,7 +175,7 @@ WITH temp_documentreference AS (
         date_trunc('year', date(from_iso8601_timestamp(dr."context"."period"."start")))
             AS author_year,
         cdrt.code as type_code,
-        cdrt.code_system as type_code_system,
+        cdrt.code_system as type_system,
         cdrt.display as type_display,
         cdrc.code as category_code,
         cdrf.code as format_code
@@ -201,7 +201,7 @@ SELECT DISTINCT
     tdr.id,
     tdr.status,
     tdr.type_code,
-    tdr.type_code_system,
+    tdr.type_system,
     tdr.type_display,
     tdr.category_code,
     tdr.docStatus,

diff --git a/cumulus_library/studies/core/reference_sql/builder_encounter.sql b/cumulus_library/studies/core/reference_sql/builder_encounter.sql
@@ -611,7 +611,7 @@ temp_encounter_nullable AS (
         e.id,
         e.status,
         e.class.code AS class_code,
-        e.class.system AS class_code_system,
+        e.class.system AS class_system,
         e.subject.reference AS subject_ref,
         date(from_iso8601_timestamp(e.period.start)) AS period_start,
         date_trunc('day', date(from_iso8601_timestamp(e."period"."end")))
@@ -638,7 +638,7 @@ temp_encounter AS (
         e.id,
         e.status,
         e.class_code,
-        e.class_code_system,
+        e.class_system,
         e.subject_ref,
         e.period_start,
         e.period_start_day,
@@ -647,19 +647,19 @@ temp_encounter AS (
         e.period_start_month,
         e.period_start_year,
         edt.code AS type_code,
-        edt.code_system AS type_code_system,
+        edt.code_system AS type_system,
         edt.display AS type_display,
         eds.code AS serviceType_code,
-        eds.code_system AS serviceType_code_system,
+        eds.code_system AS serviceType_system,
         eds.display AS serviceType_display,
         edp.code AS priority_code,
-        edp.code_system AS priority_code_system,
+        edp.code_system AS priority_system,
         edp.display AS priority_display,
         edr.code AS reasonCode_code,
-        edr.code_system AS reasonCode_code_system,
+        edr.code_system AS reasonCode_system,
         edr.display AS reasonCode_display,
         edd.code AS dischargeDisposition_code,
-        edd.code_system AS dischargeDisposition_code_system,
+        edd.code_system AS dischargeDisposition_system,
         edd.display AS dischargeDisposition_display
 
     FROM temp_encounter_nullable AS e
@@ -676,19 +676,19 @@ SELECT DISTINCT
     ac.code AS class_code,
     ac.display AS class_display,
     e.type_code,
-    e.type_code_system,
+    e.type_system,
     e.type_display,
     e.serviceType_code,
-    e.serviceType_code_system,
+    e.serviceType_system,
     e.serviceType_display,
     e.priority_code,
-    e.priority_code_system,
+    e.priority_system,
     e.priority_display,
     e.reasonCode_code,
-    e.reasonCode_code_system,
+    e.reasonCode_system,
     e.reasonCode_display,
     e.dischargeDisposition_code,
-    e.dischargeDisposition_code_system,
+    e.dischargeDisposition_system,
     e.dischargeDisposition_display,
     date_diff('year', date(p.birthdate), e.period_start_day) AS age_at_visit,
     p.gender,

diff --git a/cumulus_library/studies/core/reference_sql/builder_medicationrequest.sql b/cumulus_library/studies/core/reference_sql/builder_medicationrequest.sql
@@ -82,9 +82,9 @@ temp_mr AS (
         mr.subject.reference AS subject_ref,
         mr.encounter.reference AS encounter_ref,
         mrc.code AS category_code,
-        mrc.code_system AS category_code_system,
+        mrc.code_system AS category_system,
         mrm.code AS medication_code,
-        mrm.code_system AS medication_code_system,
+        mrm.code_system AS medication_system,
         mrm.display AS medication_display,
         mrdt.dosageInstruction_text
     FROM medicationrequest AS mr
@@ -99,9 +99,9 @@ SELECT
     mr.status,
     mr.intent,
     mr.category_code,
-    mr.category_code_system,
+    mr.category_system,
     mr.reportedBoolean,
-    mr.medication_code_system,
+    mr.medication_system,
     mr.medication_code,
     mr.medication_display,
     mr.authoredOn,