added parseTraitSet BQ func

clingen-data-model · Oct 23, 2024 · 2b86e7d · 2b86e7d
1 parent e3b298e
commit 2b86e7d
Showing 1 changed file with 115 additions and 0 deletions.
diff --git a/scripts/parsing-funcs/parse-parseTraitSet-func.sql b/scripts/parsing-funcs/parse-parseTraitSet-func.sql
@@ -0,0 +1,115 @@
+CREATE OR REPLACE FUNCTION `clinvar_ingest.parseTraitSet`(json STRING)
+RETURNS STRUCT<
+  trait ARRAY<STRUCT<
+    name ARRAY<STRUCT<
+      element_value STRING,
+      type STRING,
+      citation ARRAY<STRUCT<id ARRAY<STRUCT<id STRING,source STRING, curie STRING>>,url STRING,type STRING,abbrev STRING, text STRING>>,
+      xref ARRAY<STRUCT<db STRING, id STRING, url STRING, type STRING, status STRING>>,
+      comment ARRAY<STRUCT<text STRING, type STRING, source STRING>>
+    >>,
+    symbol ARRAY<STRUCT<
+      element_value STRING,
+      type STRING,
+      citation ARRAY<STRUCT<id ARRAY<STRUCT<id STRING,source STRING, curie STRING>>,url STRING,type STRING,abbrev STRING, text STRING>>,
+      xref ARRAY<STRUCT<db STRING, id STRING, url STRING, type STRING, status STRING>>,
+      comment ARRAY<STRUCT<text STRING, type STRING, source STRING>>
+    >>,
+    attribute_set ARRAY<STRUCT<
+      attribute STRUCT<
+        type STRING,
+        value STRING,
+        integer_value INT64,
+        date_value DATE
+      >,
+      citation ARRAY<STRUCT<id ARRAY<STRUCT<id STRING,source STRING, curie STRING>>,url STRING,type STRING,abbrev STRING, text STRING>>,
+      xref ARRAY<STRUCT<db STRING, id STRING, url STRING, type STRING, status STRING>>,
+      comment ARRAY<STRUCT<text STRING, type STRING, source STRING>>
+    >>,
+    trait_relationship STRUCT<type STRING,id STRING>,
+    citation ARRAY<STRUCT<id ARRAY<STRUCT<id STRING,source STRING, curie STRING>>,url STRING,type STRING,abbrev STRING, text STRING>>,
+    xref ARRAY<STRUCT<db STRING, id STRING, url STRING, type STRING, status STRING>>,
+    comment ARRAY<STRUCT<text STRING, type STRING, source STRING>>,
+    type STRING,
+    id STRING
+  >>,
+  type STRING,
+  id STRING
+>
+LANGUAGE js  
+  OPTIONS (
+    library=['gs://clinvar-ingest/bq-tools/parse-utils.js'])
+AS r"""
+  return parseTraitSet(json);
+""";
+
+-- test
+WITH x as (
+  SELECT
+  """
+  {
+    "@Type":"Disease",
+    "@ID":"8827",
+    "Trait":[
+      {
+      "@ID":"1053",
+      "@Type":"Disease",
+      "Name":{
+        "ElementValue":{
+          "@Type":"Preferred",
+          "$":"Brachydactyly type B1"
+        },
+        "XRef":[{
+          "@ID":"Brachydactyly+type+B1/7857","@DB":"Genetic Alliance"
+        },{
+          "@ID":"MONDO:0007220","@DB":"MONDO"
+        }]
+      },
+      "Symbol":[{
+        "ElementValue":{
+          "@Type":"Preferred","$":"BDB1"
+        },
+        "XRef":{
+          "@Type":"MIM","@ID":"113000","@DB":"OMIM"
+        }
+      },{
+        "ElementValue":{
+          "@Type":"Alternate","$":"BDB"
+        },
+        "XRef":{
+          "@Type":"MIM","@ID":"113000","@DB":"OMIM"
+        }
+      }],
+      "AttributeSet":[{
+        "Attribute":{
+          "@Type":"keyword","$":"ROR2-Related Disorders"
+        }
+      },{
+        "Attribute":{
+          "@Type":"GARD id","@integerValue":"18009"
+        },
+        "XRef":{"@ID":"18009","@DB":"Office of Rare Diseases"
+
+        }
+      }],
+      "TraitRelationship":{
+        "@Type":"co-occurring condition","@ID":"70"
+      },
+      "XRef":[{
+        "@ID":"MONDO:0007220","@DB":"MONDO"
+      },{
+        "@ID":"C1862112","@DB":"MedGen"
+      },{
+        "@ID":"93383","@DB":"Orphanet"
+      },{
+        "@Type":"MIM","@ID":"113000","@DB":"OMIM"
+      }]
+    }]
+  }
+  """ as content  
+),
+traitSets as (
+  select `clinvar_ingest.parseTraitSet`(FORMAT('{"TraitSet": %s}', x.content)) as traitSet from x
+)
+select ts.* from traitSets as ts
+;