diff options
4 files changed, 61 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 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) |