From 51c35ffa629b8c6013602a2ffbb8b2f970d35537 Mon Sep 17 00:00:00 2001
From: Lawrence Babb <lbabb@broadinstitute.org>
Date: Mon, 30 Sep 2024 21:51:43 -0400
Subject: [PATCH] * convert createSigTypes to typescript bq-utils.js

---
 scripts/general/bq-createSigTypes-func.sql    |  8 ++++
 .../createSigType-func.sql                    | 27 -------------
 .../initialize-tables.sql                     |  9 +++++
 src/bq-utils.ts                               | 40 +++++++++++++++++++
 test/bq-utils.test.js                         | 39 ++++++++++++++++++
 5 files changed, 96 insertions(+), 27 deletions(-)
 create mode 100644 scripts/general/bq-createSigTypes-func.sql
 delete mode 100644 scripts/temporal-table-procs/createSigType-func.sql

diff --git a/scripts/general/bq-createSigTypes-func.sql b/scripts/general/bq-createSigTypes-func.sql
new file mode 100644
index 0000000..57bad18
--- /dev/null
+++ b/scripts/general/bq-createSigTypes-func.sql
@@ -0,0 +1,8 @@
+CREATE OR REPLACE FUNCTION `clinvar_ingest.createSigTypes`(nosig_count INTEGER, unc_count INTEGER, sig_count INTEGER)
+RETURNS ARRAY<STRUCT<count INTEGER, percent NUMERIC>>
+LANGUAGE js  
+  OPTIONS (
+    library=['gs://clinvar-ingest/bq-tools/bq-utils.js'])
+AS r"""
+  return createSigTypes(nosig_count, unc_count, sig_count);
+""";
\ No newline at end of file
diff --git a/scripts/temporal-table-procs/createSigType-func.sql b/scripts/temporal-table-procs/createSigType-func.sql
deleted file mode 100644
index ad8124a..0000000
--- a/scripts/temporal-table-procs/createSigType-func.sql
+++ /dev/null
@@ -1,27 +0,0 @@
-
--- agg_sig_type sig|unc|nosig as 2|1|0 so
----  7 = 111  or yes to all 3. (sig conflict)
----  6 = 110  or yes to sig and unc only (sig conflict)
----  5 = 101  or yes to sig and nosig only (sig conflict)
----  4 = 100  or yes to sig only. (no conflict - sig)
----  3 = 011  or yes to unc and no sig (nosig conflict*)
----  2 = 010. or yes to unc only (no conflict - nosig)
----  1 = 001. or yes to nosig only (no conflict - nosig)
-
-
-
-
-CREATE OR REPLACE FUNCTION `clinvar_ingest.createSigType`(nosig_count INTEGER, unc_count INTEGER, sig_count INTEGER)
-RETURNS ARRAY<STRUCT<count INTEGER, percent NUMERIC>>
-AS (
-  IF(
-    (nosig_count + unc_count + sig_count ) = 0,
-    ARRAY[STRUCT<count INTEGER, percent NUMERIC>(0,0),STRUCT<count INTEGER, percent NUMERIC>(0,0),STRUCT<count INTEGER, percent NUMERIC>(0,0)],
-    -- order is significant, OFFSET 0=no-sig, 1=uncertain, 2=sig
-    ARRAY[ 
-      STRUCT<count INTEGER, percent NUMERIC>( nosig_count, CAST(ROUND(nosig_count/(sig_count + unc_count + nosig_count ),3) as NUMERIC)),
-      STRUCT<count INTEGER, percent NUMERIC>( unc_count, CAST(ROUND(unc_count/(sig_count + unc_count + nosig_count ),3) as NUMERIC)),
-      STRUCT<count INTEGER, percent NUMERIC>( sig_count, CAST(ROUND(sig_count/(sig_count + unc_count + nosig_count ),3) as NUMERIC))
-      ]
-  )
-);
\ No newline at end of file
diff --git a/scripts/temporal-table-procs/initialize-tables.sql b/scripts/temporal-table-procs/initialize-tables.sql
index 7de1871..169cefb 100644
--- a/scripts/temporal-table-procs/initialize-tables.sql
+++ b/scripts/temporal-table-procs/initialize-tables.sql
@@ -415,4 +415,13 @@ CREATE OR REPLACE TABLE `clinvar_ingest.clinvar_gc_scvs`
   end_release_date DATE,
   deleted_release_date DATE,
   deleted_count INT DEFAULT 0
+);
+
+
+-- *****************  clinvar_var_scv_change *****************
+CREATE OR REPLACE TABLE `clinvar_ingest.clinvar_var_scv_change`
+(
+  variation_id STRING NOT NULL,
+  start_release_date DATE,
+  end_release_date DATE
 );
\ No newline at end of file
diff --git a/src/bq-utils.ts b/src/bq-utils.ts
index 40477ce..d084700 100644
--- a/src/bq-utils.ts
+++ b/src/bq-utils.ts
@@ -210,3 +210,43 @@ function normalizeAndKeyById(inputObject: JsonObjectWithId): Record<string, Json
 if (typeof global !== 'undefined') {
   (global as any).formatNearestMonth = formatNearestMonth;
 }
+
+
+type SigType = {
+  count: number;
+  percent: number;
+};
+
+/**
+ * Creates an array of SigType objects representing the count and percentage of each significance type.
+ *
+ * @param nosig_count - The count of non-significant items.
+ * @param unc_count - The count of uncertain items.
+ * @param sig_count - The count of significant items.
+ * @returns An array of SigType objects, each containing the count and percentage of the respective significance type.
+ *
+ * @remarks
+ * - If the total count of all types is zero, the function returns an array with zero counts and percentages.
+ * - Percentages are rounded to three decimal places.
+ */
+function createSigType(nosig_count: number, unc_count: number, sig_count: number): SigType[] {
+  // Check if the total count is zero to avoid division by zero
+  if ((nosig_count + unc_count + sig_count) === 0) {
+    return [
+      { count: 0, percent: 0 },
+      { count: 0, percent: 0 },
+      { count: 0, percent: 0 }
+    ];
+  }
+
+  // Calculate the total count
+  const total = nosig_count + unc_count + sig_count;
+
+  // Calculate percentages and return an array of SigType objects
+  // The returned array ORDINAL positions must be: 0 = nosig, 1 = unc, 2 = sig
+  return [
+    { count: nosig_count, percent: Math.round((nosig_count / total) * 1000) / 1000 },
+    { count: unc_count, percent: Math.round((unc_count / total) * 1000) / 1000 },
+    { count: sig_count, percent: Math.round((sig_count / total) * 1000) / 1000 }
+  ];
+}
diff --git a/test/bq-utils.test.js b/test/bq-utils.test.js
index 1fa80a9..124f4ab 100644
--- a/test/bq-utils.test.js
+++ b/test/bq-utils.test.js
@@ -50,3 +50,42 @@ test('normalizeAndKeyById should normalize and key input object correctly', () =
     }
   });
 });
+const createSigType = bqUtils.__get__('createSigType');
+
+test('createSigType should return correct counts and percentages', () => {
+    expect(createSigType(0, 0, 0)).toEqual([
+        { count: 0, percent: 0 },
+        { count: 0, percent: 0 },
+        { count: 0, percent: 0 }
+    ]);
+
+    expect(createSigType(10, 0, 0)).toEqual([
+        { count: 10, percent: 1 },
+        { count: 0, percent: 0 },
+        { count: 0, percent: 0 }
+    ]);
+
+    expect(createSigType(0, 10, 0)).toEqual([
+        { count: 0, percent: 0 },
+        { count: 10, percent: 1 },
+        { count: 0, percent: 0 }
+    ]);
+
+    expect(createSigType(0, 0, 10)).toEqual([
+        { count: 0, percent: 0 },
+        { count: 0, percent: 0 },
+        { count: 10, percent: 1 }
+    ]);
+
+    expect(createSigType(10, 10, 10)).toEqual([
+        { count: 10, percent: 0.333 },
+        { count: 10, percent: 0.333 },
+        { count: 10, percent: 0.333 }
+    ]);
+
+    expect(createSigType(5, 10, 15)).toEqual([
+        { count: 5, percent: 0.167 },
+        { count: 10, percent: 0.333 },
+        { count: 15, percent: 0.5 }
+    ]);
+});
\ No newline at end of file