FHIR field naming conformance (#201)

* FHIR field naming conformance * Light docs tweaks, styling nits * regression
smart-on-fhir · Apr 1, 2024 · bf37eec · bf37eec
1 parent df6be1d
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diff --git a/cumulus_library/.sqlfluff b/cumulus_library/.sqlfluff
@@ -2,8 +2,13 @@
 templater = jinja
 dialect = athena
 sql_file_exts = .sql,.sql.jinja
-# this rule overfires on athena nested arrays
-exclude_rules=references.from,structure.column_order,aliasing.unused
+exclude_rules=
+    # these rule overfires on athena nested arrays
+    references.from,
+    structure.column_order,
+    aliasing.unused,
+    # this rule interferes with FHIR naming conventions
+    capitalisation.identifiers
 max_line_length = 90
 
 [sqlfluff:indentation]
@@ -100,12 +105,12 @@ schema =
             'category': {
                 'coding': True, 'code': True, 'display': True, 'system': True, 'userSelected': True, 'version': True, 'text': True
             },
-            'clinicalstatus': {
+            'clinicalStatus': {
                 'coding': True, 'code': True, 'display': True, 'system': True, 'userSelected': True, 'version': True, 'text': True
             },
             'id': True, 
-            'recordeddate': True, 
-            'verificationstatus': {
+            'recordedDate': True, 
+            'verificationStatus': {
                 'coding': True, 'code': True, 'display': True, 'system': True, 'userSelected': True, 'version': True, 'text': True},
             'subject': {
                 'reference': True, 'display': False, 'type': True
@@ -118,7 +123,7 @@ schema =
             'id': True, 
             'type': True, 
             'status': True, 
-            'docstatus': True, 
+            'docStatus': True, 
             'context': {
                 'period': True, 'start': True
             }, 
@@ -143,7 +148,7 @@ schema =
             'id': True, 
             'status': True, 
             'intent': True, 
-            'authoredon': True, 
+            'authoredOn': True, 
             'category': {
                 'code': True, 'system': True, 'display': False
             }, 
@@ -166,14 +171,14 @@ schema =
             'interpretation': {
                 'coding': True, 'code': True, 'display': True, 'system': True, 'text': True
             }, 
-            'referencerange': {
+            'referenceRange': {
                 'low': False, 'high': False, 'normalvalue': False, 'type': False, 'appliesto': False, 'age': False, 'text': True
             }, 
             'effectivedatetime': True, 
-            'valuequantity': {
+            'valueQuantity': {
                 'value': True, 'comparator': False, 'unit': False, 'system': False, 'code': False
             }, 
-            'valuecodeableconcept': {
+            'valueCodeableConcept': {
                 'coding': True, 'code': True, 'display': True, 'system': True
             }, 
             'subject': {

diff --git a/cumulus_library/statistics/statistics_templates/count.sql.jinja b/cumulus_library/statistics/statistics_templates/count.sql.jinja
@@ -5,7 +5,7 @@ statistics/counts.py level -#}
 {%- if fhir_resource in ('encounter', 'condition') -%}
 encounter_ref
 {%- elif fhir_resource == 'documentreference' -%}
-doc_ref
+documentreference_ref
 {%- elif fhir_resource == 'observation'-%}
 observation_ref
 {%- else -%}
@@ -28,7 +28,7 @@ logic at the statistics/counts.py level -#}
             {{- syntax.comma_delineate(loop) }}
             {%- endfor %}
             {%- if fhir_resource in ('documentreference', 'observation' ) -%},
-            enc_class_display
+            class_display
             {% endif %}
 {%- endmacro -%}
 
@@ -40,7 +40,7 @@ which will drop nulls, resulting in potentially non-unique keys -#}
                 {{- syntax.comma_delineate(loop) }}
                 {%- endfor %}
                 {%- if fhir_resource in ('documentreference', 'observation' ) -%},
-                COALESCE(enc_class_display,'')
+                COALESCE(class_display,'')
                 {% endif %}
 {%- endmacro -%}
 
@@ -73,7 +73,7 @@ CREATE TABLE {{ table_name }} AS (
             s.{{ tertiary }},
             {%- endif -%}
             {%- if fhir_resource in ('documentreference', 'observation') %}
-            e.enc_class_display,
+            e.class_display,
             {%- endif %}
             {#- these exceptions deal with table aliasing related to
             single table queries, where this may be a multitable query
@@ -123,9 +123,9 @@ CREATE TABLE {{ table_name }} AS (
             {%- endif -%}
             {%- if fhir_resource in ('documentreference', 'observation' )%}
             coalesce(
-                cast(enc_class_display AS varchar), 
+                cast(class_display AS varchar), 
                 '{{ missing_null }}'
-            ) AS enc_class_display,
+            ) AS class_display,
             {%- endif -%}
             {%- for col in table_cols %}
             coalesce(
@@ -203,7 +203,7 @@ CREATE TABLE {{ table_name }} AS (
         {{- syntax.comma_delineate(loop) }}
         {%- endfor %}
         {%- if fhir_resource in ('documentreference', 'observation' ) -%},
-        p.enc_class_display
+        p.class_display
         {%- endif %}
     FROM powerset AS p
     {%- if secondary %}

diff --git a/cumulus_library/studies/core/builder_condition.py b/cumulus_library/studies/core/builder_condition.py
@@ -23,7 +23,7 @@
             "text",
         ],
         "id": [],
-        "recordeddate": [],
+        "recordedDate": [],
         "verificationstatus": [
             "coding",
             "code",

diff --git a/cumulus_library/studies/core/builder_documentreference.py b/cumulus_library/studies/core/builder_documentreference.py
@@ -7,7 +7,7 @@
         "id": [],
         "type": [],
         "status": [],
-        "docstatus": [],
+        "docStatus": [],
         "subject": ["reference"],
         "context": ["encounter", "period", "start"],
         "category": [],

diff --git a/cumulus_library/studies/core/builder_medicationrequest.py b/cumulus_library/studies/core/builder_medicationrequest.py
@@ -12,13 +12,13 @@
         "id": [],
         "status": [],
         "intent": [],
-        "authoredon": [],
-        "reportedboolean": [],
+        "authoredOn": [],
+        "reportedBoolean": [],
         "category": ["code", "system", "display"],
-        "medicationcodeableconcept": ["code", "system", "display"],
+        "medicationCodeableConcept": ["code", "system", "display"],
         "subject": ["reference"],
         "encounter": ["reference"],
-        "dosageinstruction": ["text"],
+        "dosageInstruction": ["text"],
     }
 }
 

diff --git a/cumulus_library/studies/core/builder_observation.py b/cumulus_library/studies/core/builder_observation.py
@@ -13,19 +13,19 @@
         "status": [],
         "code": ["coding", "code", "display", "system", "text"],
         "interpretation": ["coding", "code", "display", "system", "text"],
-        "referencerange": [
+        "referenceRange": [
             "low",
             "high",
-            "normalvalue",
+            "normalValue",
             "type",
-            "appliesto",
+            "appliesTo",
             "age",
             "text",
         ],
-        "effectivedatetime": [],
-        "valuequantity": ["value", "comparator", "unit", "system", "code"],
-        "valuecodeableconcept": ["coding", "code", "display", "system"],
-        "valuestring": [],
+        "effectiveDateTime": [],
+        "valueQuantity": ["value", "comparator", "unit", "system", "code"],
+        "valueCodeableConcept": ["coding", "code", "display", "system"],
+        "valueString": [],
         "subject": ["reference"],
         "encounter": ["reference"],
     }

diff --git a/cumulus_library/studies/core/builder_patient.py b/cumulus_library/studies/core/builder_patient.py
@@ -10,7 +10,7 @@
         "id": [],
         "gender": [],
         "address": [],
-        "birthdate": [],
+        "birthDate": [],
     }
 }
 

diff --git a/cumulus_library/studies/core/core_templates/condition.sql.jinja b/cumulus_library/studies/core/core_templates/condition.sql.jinja
@@ -39,7 +39,7 @@ WITH temp_condition AS (
             utils.date_cols_from_str(
                 'condition',
                 'c',
-                ['recordeddate'],
+                ['recordedDate'],
                 schema
             ) 
         }},
@@ -48,15 +48,15 @@ WITH temp_condition AS (
                 'condition',
                 'c',
                 [
-                    ('recordeddate', 'week'),
-                    ('recordeddate', 'month'),
-                    ('recordeddate', 'year'),
+                    ('recordedDate', 'week'),
+                    ('recordedDate', 'month'),
+                    ('recordedDate', 'year'),
                 ],
                 schema
             ) 
         }},
-        c.verificationstatus,
-        c.clinicalstatus
+        c.verificationStatus,
+        c.clinicalStatus
     FROM condition AS c
     LEFT JOIN core__condition_codable_concepts_all AS cca ON c.id = cca.id
 )
@@ -71,17 +71,17 @@ SELECT
     tc.subject_ref,
     tc.encounter_ref,
     concat('Condition/', tc.id) AS condition_ref,
-    tc.recordeddate,
-    tc.recordeddate_week AS recorded_week,
-    tc.recordeddate_month AS recorded_month,
-    tc.recordeddate_year AS recorded_year,
-    t_clinicalstatus_coding.clinicalstatus_row.code AS clinicalstatus_code,
-    t_verificationstatus_coding.verificationstatus_row.code AS verificationstatus_code
+    tc.recordedDate,
+    tc.recordedDate_week,
+    tc.recordedDate_month,
+    tc.recordedDate_year,
+    t_clinicalStatus_coding.clinicalStatus_row.code AS clinicalStatus_code,
+    t_verificationStatus_coding.verificationStatus_row.code AS verificationStatus_code
 FROM temp_condition AS tc,
     unnest(category) AS t_category (category_coding),
     unnest(category_coding.coding) AS t_category_coding (category_row),
-    unnest(clinicalstatus.coding) AS t_clinicalstatus_coding (clinicalstatus_row),
-    unnest(verificationstatus.coding)
-        AS t_verificationstatus_coding (verificationstatus_row)
+    unnest(clinicalStatus.coding) AS t_clinicalStatus_coding (clinicalStatus_row),
+    unnest(verificationStatus.coding)
+        AS t_verificationStatus_coding (verificationStatus_row)
 
-WHERE tc.recordeddate BETWEEN date('2016-01-01') AND current_date;
+WHERE tc.recordedDate BETWEEN date('2016-01-01') AND current_date;
diff --git a/cumulus_library/studies/core/core_templates/core_utils.jinja b/cumulus_library/studies/core/core_templates/core_utils.jinja
@@ -71,7 +71,7 @@ targets is an array expecting a data type of the following:
         {#- depth two nested column -#}
         {%- elif col is not string and col|length ==4%}
         {%- if schema[table][col[0]][col[2]] %}
-        date(from_iso8601_timestamp({{ alias }}.{{ col[0] }}.{{ col[1] }}.{{ col[2].lower() }})) AS {{col[3]}}
+        date(from_iso8601_timestamp({{ alias }}.{{ col[0] }}.{{ col[1] }}.{{ col[2] }})) AS {{col[3]}}
         {%- else %}
         cast(NULL AS date) AS {{ col[3].lower() }}
         {%- endif %}

diff --git a/cumulus_library/studies/core/core_templates/documentreference.sql.jinja b/cumulus_library/studies/core/core_templates/documentreference.sql.jinja
@@ -19,7 +19,7 @@ WITH temp_documentreference AS (
                     'type',
                     'status',
                     'date',
-                    'docstatus',
+                    'docStatus',
                     'context',                
                     ('subject', 'reference', 'subject_ref'),
                     ('context', 'period', 'start', 'author_date')
@@ -39,11 +39,11 @@ WITH temp_documentreference AS (
                 schema
             ) 
         }},
-        cdrt.code as doc_type_code,
-        cdrt.code_system as doc_type_code_system,
-        cdrt.display as doc_type_display,
-        cdrc.code as doc_category_code,
-        cdrf.code as doc_format_code
+        cdrt.code as type_code,
+        cdrt.code_system as type_code_system,
+        cdrt.display as type_display,
+        cdrc.code as category_code,
+        cdrf.code as format_code
     FROM documentreference AS dr
     LEFT JOIN core__documentreference_dn_type AS cdrt ON dr.id = cdrt.id
     LEFT JOIN core__documentreference_dn_category AS cdrc ON dr.id = cdrc.id
@@ -70,20 +70,20 @@ temp_encounters AS (
 SELECT DISTINCT
     tdr.id,
     tdr.status,
-    tdr.doc_type_code,
-    tdr.doc_type_code_system,
-    tdr.doc_type_display,
-    tdr.doc_category_code,
-    tdr.docstatus,
+    tdr.type_code,
+    tdr.type_code_system,
+    tdr.type_display,
+    tdr.category_code,
+    tdr.docStatus,
     tdr."date",
-    tdr.author_day AS author_date,
+    tdr.author_day,
     tdr.author_week,
     tdr.author_month,
     tdr.author_year,
-    tdr.doc_format_code,
+    tdr.format_code,
     tdr.subject_ref,
     te.encounter_ref,
-    concat('DocumentReference/', tdr.id) AS doc_ref
+    concat('DocumentReference/', tdr.id) AS documentreference_ref
 FROM temp_documentreference AS tdr
 LEFT JOIN temp_encounters AS te ON tdr.id = te.id
 WHERE date(tdr.author_day) BETWEEN date('2016-06-01') AND current_date;