From 02e5c81e5d1281b66aa14ce47563997e845cea95 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 4 Apr 2023 12:13:11 +0300
Subject: Add tables to link genotype data

---
 ...22_02_Ll854-create-phenotype-resources-table.py |  2 +-
 ...4_01_VKxXg-create-linked-genotype-data-table.py | 29 ++++++++++++++++++++++
 ...404_02_la33P-create-genotype-resources-table.py | 22 ++++++++++++++++
 tests/unit/auth/test_migrations_create_tables.py   | 10 +++++++-
 4 files changed, 61 insertions(+), 2 deletions(-)
 create mode 100644 migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py
 create mode 100644 migrations/auth/20230404_02_la33P-create-genotype-resources-table.py

diff --git a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
index 6bd8782..d0ff541 100644
--- a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
+++ b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
@@ -16,7 +16,7 @@ steps = [
           data_link_id TEXT NOT NULL,
           PRIMARY KEY(resource_id, data_link_id),
           UNIQUE (data_link_id) -- ensure data is linked to only one resource
-        )
+        ) WITHOUT ROWID
         """,
         "DROP TABLE IF EXISTS phenotype_resources")
 ]
diff --git a/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py b/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py
new file mode 100644
index 0000000..02e8718
--- /dev/null
+++ b/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py
@@ -0,0 +1,29 @@
+"""
+Create linked genotype data table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230322_02_Ll854-create-phenotype-resources-table'}
+
+steps = [
+    step(
+        """
+        CREATE TABLE IF NOT EXISTS linked_genotype_data
+        -- Link genotype data in MariaDB to user groups in auth system
+        (
+          data_link_id TEXT NOT NULL PRIMARY KEY, -- A new ID for the auth system
+          group_id TEXT NOT NULL, -- The user group the data is linked to
+          SpeciesId TEXT NOT NULL, -- The species in MariaDB
+          InbredSetId TEXT NOT NULL, -- The traits group in MariaDB
+          GenoFreezeId TEXT NOT NULL, -- The dataset Id in MariaDB
+          dataset_name TEXT, -- dataset Name in MariaDB
+          dataset_fullname, -- dataset FullName in MariaDB
+          dataset_shortname, -- dataset ShortName in MariaDB
+          FOREIGN KEY (group_id)
+            REFERENCES groups(group_id) ON UPDATE CASCADE ON DELETE RESTRICT
+          UNIQUE (SpeciesId, InbredSetId, GenoFreezeId)
+        ) WITHOUT ROWID
+        """,
+        "DROP TABLE IF EXISTS linked_genotype_data")
+]
diff --git a/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py b/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
new file mode 100644
index 0000000..2d3a3bc
--- /dev/null
+++ b/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
@@ -0,0 +1,22 @@
+"""
+Create genotype resources table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230404_01_VKxXg-create-linked-genotype-data-table'}
+
+steps = [
+    step(
+        """
+        CREATE TABLE IF NOT EXISTS genotype_resources
+        -- Link genotype data to specific resource
+        (
+          resource_id TEXT NOT NULL, -- A resource can have multiple items
+          data_link_id TEXT NOT NULL,
+          PRIMARY KEY (resource_id, data_link_id),
+          UNIQUE (data_link_id) -- ensure data is linked to single resource
+        ) WITHOUT ROWID
+        """,
+        "DROP TABLE IF EXISTS genotype_resources")
+]
diff --git a/tests/unit/auth/test_migrations_create_tables.py b/tests/unit/auth/test_migrations_create_tables.py
index 65f3896..1664b5c 100644
--- a/tests/unit/auth/test_migrations_create_tables.py
+++ b/tests/unit/auth/test_migrations_create_tables.py
@@ -29,7 +29,15 @@ migrations_and_tables = (
     ("20221219_03_PcTrb-create-authorisation-code-table.py",
      "authorisation_code"),
     ("20230207_01_r0bkZ-create-group-join-requests-table.py",
-     "group_join_requests"))
+     "group_join_requests"),
+    ("20230322_01_0dDZR-create-linked-phenotype-data-table.py",
+     "linked_phenotype_data"),
+    ("20230322_02_Ll854-create-phenotype-resources-table.py",
+     "phenotype_resources"),
+    ("20230404_01_VKxXg-create-linked-genotype-data-table.py",
+     "linked_genotype_data"),
+    ("20230404_02_la33P-create-genotype-resources-table.py",
+     "genotype_resources"))
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize("migration_file,the_table", migrations_and_tables)
-- 
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