Migrations for linking genotype files.

5 files changed, 64 insertions, 2 deletions

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 d0ff541..19ee885 100644
--- a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
+++ b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
@@ -15,7 +15,10 @@ steps = [
           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
+          UNIQUE (data_link_id), -- ensure data is linked to only one resource
+          FOREIGN KEY (data_link_id)
+            REFERENCES linked_phenotype_data(data_link_id)
+            ON UPDATE CASCADE ON DELETE RESTRICT
         ) WITHOUT ROWID
         """,
         "DROP TABLE IF EXISTS phenotype_resources")
diff --git a/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py b/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
index 2d3a3bc..e967ce6 100644
--- a/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
+++ b/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
@@ -16,6 +16,9 @@ steps = [
           data_link_id TEXT NOT NULL,
           PRIMARY KEY (resource_id, data_link_id),
           UNIQUE (data_link_id) -- ensure data is linked to single resource
+          FOREIGN KEY (data_link_id)
+            REFERENCES linked_genotype_data(data_link_id)
+            ON UPDATE CASCADE ON DELETE RESTRICT
         ) WITHOUT ROWID
         """,
         "DROP TABLE IF EXISTS genotype_resources")
diff --git a/migrations/auth/20230410_01_8mwaf-create-linked-mrna-data-table.py b/migrations/auth/20230410_01_8mwaf-create-linked-mrna-data-table.py
new file mode 100644
index 0000000..db9a6bf
--- /dev/null
+++ b/migrations/auth/20230410_01_8mwaf-create-linked-mrna-data-table.py
@@ -0,0 +1,30 @@
+"""
+Create linked mrna data table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230404_02_la33P-create-genotype-resources-table'}
+
+steps = [
+    step(
+        """
+        CREATE TABLE IF NOT EXISTS linked_mrna_data
+        -- Link mRNA Assay 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
+          ProbeFreezeId TEXT NOT NULL, -- The study ID in MariaDB
+          ProbeSetFreezeId 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, ProbeFreezeId, ProbeSetFreezeId)
+        ) WITHOUT ROWID
+        """,
+        "DROP TABLE IF EXISTS linked_mrna_data")
+]
diff --git a/migrations/auth/20230410_02_WZqSf-create-mrna-resources-table.py b/migrations/auth/20230410_02_WZqSf-create-mrna-resources-table.py
new file mode 100644
index 0000000..de348c0
--- /dev/null
+++ b/migrations/auth/20230410_02_WZqSf-create-mrna-resources-table.py
@@ -0,0 +1,24 @@
+"""
+Create mRNA resources table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230410_01_8mwaf-create-linked-mrna-data-table'}
+
+steps = [
+    step(
+        """
+        CREATE TABLE IF NOT EXISTS mrna_resources
+        -- Link mRNA 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
+          FOREIGN KEY (data_link_id) REFERENCES linked_mrna_data(data_link_id)
+            ON UPDATE CASCADE ON DELETE RESTRICT
+        ) WITHOUT ROWID
+        """,
+        "DROP TABLE IF EXISTS mrna_resources")
+]
diff --git a/tests/unit/auth/test_migrations_create_tables.py b/tests/unit/auth/test_migrations_create_tables.py
index 1664b5c..2b8140b 100644
--- a/tests/unit/auth/test_migrations_create_tables.py
+++ b/tests/unit/auth/test_migrations_create_tables.py
@@ -37,7 +37,9 @@ migrations_and_tables = (
     ("20230404_01_VKxXg-create-linked-genotype-data-table.py",
      "linked_genotype_data"),
     ("20230404_02_la33P-create-genotype-resources-table.py",
-     "genotype_resources"))
+     "genotype_resources"),
+    ("20230410_01_8mwaf-create-linked-mrna-data-table.py", "linked_mrna_data"),
+    ("20230410_02_WZqSf-create-mrna-resources-table.py", "mrna_resources"))
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize("migration_file,the_table", migrations_and_tables)