auth: migrations for linking phenotype data

2 files changed, 52 insertions, 0 deletions

diff --git a/migrations/auth/20230322_01_0dDZR-create-linked-phenotype-data-table.py b/migrations/auth/20230322_01_0dDZR-create-linked-phenotype-data-table.py
new file mode 100644
index 0000000..647325f
--- /dev/null
+++ b/migrations/auth/20230322_01_0dDZR-create-linked-phenotype-data-table.py
@@ -0,0 +1,30 @@
+"""
+Create linked-phenotype-data table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230306_02_7GnRY-add-system-user-list-privilege-to-system-administrator-and-group-leader-roles'}
+
+steps = [
+    step(
+        """
+        CREATE TABLE IF NOT EXISTS linked_phenotype_data
+        -- Link the data in MariaDB to user groups in the 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
+          PublishFreezeId 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
+          PublishXRefId TEXT NOT NULL, -- The trait's ID in MariaDB
+          FOREIGN KEY (group_id)
+            REFERENCES groups(group_id) ON UPDATE CASCADE ON DELETE RESTRICT
+          UNIQUE (SpeciesId, InbredSetId, PublishFreezeId, PublishXRefId)
+        ) WITHOUT ROWID
+        """,
+        "DROP TABLE IF EXISTS linked_phenotype_data")
+]
diff --git a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
new file mode 100644
index 0000000..6bd8782
--- /dev/null
+++ b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
@@ -0,0 +1,22 @@
+"""
+Create phenotype_resources table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230322_01_0dDZR-create-linked-phenotype-data-table'}
+
+steps = [
+    step(
+        """
+        CREATE TABLE IF NOT EXISTS phenotype_resources
+        -- Link phenotype data to specific resources
+        (
+          resource_id TEXT NOT NULL, -- A resource can have multiple data items
+          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
+        )
+        """,
+        "DROP TABLE IF EXISTS phenotype_resources")
+]