Add more columns to lab-realted output, refs #284

outcomesinsights · Nov 16, 2023 · e0bc7cd · e0bc7cd
1 parent 5bea15e
commit e0bc7cd
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Showing 4 changed files with 75 additions and 3 deletions.
diff --git a/lib/conceptql/behaviors/labish.rb b/lib/conceptql/behaviors/labish.rb
@@ -5,7 +5,9 @@ def self.included(base)
         base.require_column :value_as_number
         base.require_column :value_as_string
         base.require_column :value_as_concept_id
-        base.require_column :unit_source_value
+        base.require_column :value_as_concept
+        base.require_column :unit_concept_id
+        base.require_column :unit_concept
         base.require_column :range_low
         base.require_column :range_high
       end

diff --git a/lib/conceptql/query_modifiers/gdm/lab_query_modifier.rb b/lib/conceptql/query_modifiers/gdm/lab_query_modifier.rb
@@ -10,7 +10,9 @@ def self.provided_columns
             :value_as_number,
             :value_as_string,
             :value_as_concept_id,
-            :unit_source_value,
+            :value_as_concept,
+            :unit_concept_id,
+            :unit_concept,
             :range_low,
             :range_high
           ]
@@ -28,11 +30,14 @@ def modified_query
           query.from_self(alias: :cc)
             .left_join(Sequel[:measurement_details].as(:md), Sequel[:cc][:measurement_detail_id] => Sequel[:md][:id])
             .left_join(dm.concepts_table(query.db).as(:unit_con), Sequel[:md][:unit_concept_id] => Sequel[:unit_con][:id])
+            .left_join(dm.concepts_table(query.db).as(:concept_con), Sequel[:md][:result_as_concept_id] => Sequel[:concept_con][:id])
             .select_all(:cc)
             .select_append(Sequel[:md][:result_as_number].as(:value_as_number))
             .select_append(Sequel[:md][:result_as_string].as(:value_as_string))
             .select_append(Sequel[:md][:result_as_concept_id].as(:value_as_concept_id))
-            .select_append(Sequel[:unit_con][:concept_text].as(:unit_source_value))
+            .select_append(Sequel[:concept_con][:concept_code].as(:value_as_concept))
+            .select_append(Sequel[:md][:unit_concept_id].as(:unit_concept_id))
+            .select_append(Sequel[:unit_con][:concept_code].as(:unit_concept))
             .select_append(Sequel[:md][:normal_range_low].as(:range_low))
             .select_append(Sequel[:md][:normal_range_high].as(:range_high))
             .from_self

diff --git a/test/results/gdm/loinc/results_2.json b/test/results/gdm/loinc/results_2.json
@@ -0,0 +1,59 @@
+[
+  {
+    "person_id": 200,
+    "criterion_id": 100001,
+    "criterion_table": "clinical_codes",
+    "criterion_domain": "observation",
+    "start_date": "2009-03-03",
+    "end_date": "2009-03-03",
+    "source_value": "4548-4",
+    "source_vocabulary_id": "LOINC",
+    "label": null,
+    "value_as_number": 5.1,
+    "value_as_string": null,
+    "value_as_concept_id": null,
+    "value_as_concept": null,
+    "unit_concept_id": 8554,
+    "unit_concept": "%",
+    "range_low": 4.0,
+    "range_high": 5.6
+  },
+  {
+    "person_id": 200,
+    "criterion_id": 100002,
+    "criterion_table": "clinical_codes",
+    "criterion_domain": "observation",
+    "start_date": "2009-03-03",
+    "end_date": "2009-03-03",
+    "source_value": "72166-2",
+    "source_vocabulary_id": "LOINC",
+    "label": null,
+    "value_as_number": null,
+    "value_as_string": null,
+    "value_as_concept_id": 45881517,
+    "value_as_concept": "LA18976-3",
+    "unit_concept_id": null,
+    "unit_concept": null,
+    "range_low": null,
+    "range_high": null
+  },
+  {
+    "person_id": 200,
+    "criterion_id": 100003,
+    "criterion_table": "clinical_codes",
+    "criterion_domain": "observation",
+    "start_date": "2009-03-03",
+    "end_date": "2009-03-03",
+    "source_value": "64558-0",
+    "source_vocabulary_id": "LOINC",
+    "label": null,
+    "value_as_number": null,
+    "value_as_string": "On a dare",
+    "value_as_concept_id": null,
+    "value_as_concept": null,
+    "unit_concept_id": null,
+    "unit_concept": null,
+    "range_low": null,
+    "range_high": null
+  }
+]
diff --git a/test/statements/loinc/results_2.json b/test/statements/loinc/results_2.json
@@ -0,0 +1,6 @@
+[
+  "loinc",
+  "4548-4",
+  "72166-2",
+  "64558-0"
+]