From 3b4aaddf5e01613966af5ecf106771bca3d2de38 Mon Sep 17 00:00:00 2001
From: Lawrence Babb <lbabb@broadinstitute.org>
Date: Tue, 19 Nov 2024 16:38:05 -0500
Subject: [PATCH] add first batch of v2 schema scripts

---
 scripts/general/all_schemas-func.sql          |  4 ++--
 scripts/general/all_schemas-v2-func.sql       | 23 +++++++++++++++++++
 scripts/general/schema-on-v2-func.sql         | 15 ++++++++++++
 .../general/schemas-on-or-after-v2-func.sql   | 17 ++++++++++++++
 .../general/schemas-on-or-before-v2-func.sql  | 16 +++++++++++++
 5 files changed, 73 insertions(+), 2 deletions(-)
 create mode 100644 scripts/general/all_schemas-v2-func.sql
 create mode 100644 scripts/general/schema-on-v2-func.sql
 create mode 100644 scripts/general/schemas-on-or-after-v2-func.sql
 create mode 100644 scripts/general/schemas-on-or-before-v2-func.sql

diff --git a/scripts/general/all_schemas-func.sql b/scripts/general/all_schemas-func.sql
index 83d6794..823b6f9 100644
--- a/scripts/general/all_schemas-func.sql
+++ b/scripts/general/all_schemas-func.sql
@@ -19,9 +19,9 @@ AS (
     FROM INFORMATION_SCHEMA.SCHEMATA iss
     WHERE 
       (
-        REGEXP_CONTAINS(iss.schema_name, r'^clinvar_\d{4}_\d{2}_\d{2}_v\d+_\d+_\d+$')
+        REGEXP_CONTAINS(iss.schema_name, r'^clinvar_\d{4}_\d{2}_\d{2}_v1_\d+_\d+$')
       OR
-        REGEXP_CONTAINS(iss.schema_name, r'^clinvar_\d{4}_\d{2}_\d{2}_v\d+_\d+_\d+_beta\d+$') 
+        REGEXP_CONTAINS(iss.schema_name, r'^clinvar_\d{4}_\d{2}_\d{2}_v1_\d+_\d+_beta\d+$') 
       )
       AND
       iss.schema_name <> "clinvar_2019_06_01_v0"
diff --git a/scripts/general/all_schemas-v2-func.sql b/scripts/general/all_schemas-v2-func.sql
new file mode 100644
index 0000000..bc6c119
--- /dev/null
+++ b/scripts/general/all_schemas-v2-func.sql
@@ -0,0 +1,23 @@
+CREATE OR REPLACE TABLE FUNCTION `clinvar_ingest.all_schemas_v2`()
+AS (
+  -- the state of al clinvar schemas available at the moment
+  SELECT 
+    r.schema_name,
+    r.release_date,
+    LAG(r.release_date, 1, DATE('0001-01-01')) OVER (ORDER BY r.release_date ASC) AS prev_release_date,
+    LEAD(r.release_date, 1, DATE('9999-12-31')) OVER (ORDER BY r.release_date ASC) AS next_release_date
+  FROM (
+
+    SELECT
+      iss.schema_name,
+      CAST(REGEXP_REPLACE(iss.schema_name, r'clinvar_(\d{4})_(\d{2})_(\d{2}).*', '\\1-\\2-\\3') as DATE) AS release_date
+    FROM INFORMATION_SCHEMA.SCHEMATA iss
+    WHERE 
+      (
+        REGEXP_CONTAINS(iss.schema_name, r'^clinvar_\d{4}_\d{2}_\d{2}_v2_\d+_\d+$')
+      OR
+        REGEXP_CONTAINS(iss.schema_name, r'^clinvar_\d{4}_\d{2}_\d{2}_v2_\d+_\d+_(alpha|beta)\d*$') 
+      )
+  ) r
+  ORDER BY 2
+);  
\ No newline at end of file
diff --git a/scripts/general/schema-on-v2-func.sql b/scripts/general/schema-on-v2-func.sql
new file mode 100644
index 0000000..71fce23
--- /dev/null
+++ b/scripts/general/schema-on-v2-func.sql
@@ -0,0 +1,15 @@
+CREATE OR REPLACE TABLE FUNCTION `clinvar_ingest.schema_on_v2`(on_date DATE)
+AS (
+  -- the state of schemas available on a certain date
+  -- if the date lands on a schema release date then that will be the schema
+  -- otherwise the schema with the release date just prior to that date will be the schema
+  SELECT
+    x.schema_name,
+    x.release_date,
+    x.prev_release_date,
+    x.next_release_date
+  FROM `clinvar_ingest.all_schemas_v2`() x
+  WHERE on_date >= x.release_date
+  ORDER BY 2 DESC
+  LIMIT 1
+);
\ No newline at end of file
diff --git a/scripts/general/schemas-on-or-after-v2-func.sql b/scripts/general/schemas-on-or-after-v2-func.sql
new file mode 100644
index 0000000..a73b1ba
--- /dev/null
+++ b/scripts/general/schemas-on-or-after-v2-func.sql
@@ -0,0 +1,17 @@
+CREATE OR REPLACE TABLE FUNCTION `clinvar_ingest.schemas_on_or_after_v2`(on_or_after_date DATE)
+AS (
+  -- the state of schemas available on or after a certain date
+  -- if the date lands on a schema release date then that will be the first schema
+  -- if the date is prior to the earliest release date then return all schemas
+  -- otherwise the schema with the release date just prior to that date will be the first schema
+  SELECT
+    x.schema_name,
+    x.release_date,
+    x.prev_release_date,
+    x.next_release_date
+  FROM `clinvar_ingest.all_schemas_v2`() x
+  WHERE (on_or_after_date > x.prev_release_date AND on_or_after_date < x.next_release_date) OR on_or_after_date <= x.release_date
+  ORDER BY 2
+);
+
+-- select * from `clinvar_ingest.schemas_on_or_after`(DATE('2020-06-01'));
\ No newline at end of file
diff --git a/scripts/general/schemas-on-or-before-v2-func.sql b/scripts/general/schemas-on-or-before-v2-func.sql
new file mode 100644
index 0000000..6b99614
--- /dev/null
+++ b/scripts/general/schemas-on-or-before-v2-func.sql
@@ -0,0 +1,16 @@
+CREATE OR REPLACE TABLE FUNCTION `clinvar_ingest.schemas_on_or_before_v2`(on_or_before_date DATE)
+AS (
+  -- the state of schemas available on or before a certain date
+  -- if the date lands on a schema release date then that will be the last schema
+  -- otherwise the schema with the release date just prior to that date will be the last schema
+  SELECT
+    x.schema_name,
+    x.release_date,
+    x.prev_release_date,
+    x.next_release_date
+  FROM `clinvar_ingest.all_schemas_v2`() x
+  WHERE on_or_before_date >= x.release_date
+  ORDER BY 2
+);
+
+-- select * from `clinvar_ingest.schemas_on_or_before`(DATE('2020-06-01'));
\ No newline at end of file