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-rw-r--r--migrations/auth/20231002_01_tzxTf-link-inbredsets-to-auth-system.py84
-rw-r--r--tests/unit/auth/test_migrations_add_data_to_table.py16
-rw-r--r--tests/unit/auth/test_migrations_create_tables.py7
3 files changed, 105 insertions, 2 deletions
diff --git a/migrations/auth/20231002_01_tzxTf-link-inbredsets-to-auth-system.py b/migrations/auth/20231002_01_tzxTf-link-inbredsets-to-auth-system.py
new file mode 100644
index 0000000..402e9a5
--- /dev/null
+++ b/migrations/auth/20231002_01_tzxTf-link-inbredsets-to-auth-system.py
@@ -0,0 +1,84 @@
+"""
+link InbredSets to auth system
+"""
+
+from yoyo import step
+
+__depends__ = {'20230925_01_TWJuR-add-new-public-view-role', '__init__'}
+
+steps = [
+ step(
+ """
+ INSERT INTO resource_categories
+ (
+ resource_category_id,
+ resource_category_key,
+ resource_category_description,
+ resource_meta
+ )
+ VALUES
+ (
+ 'b3654600-4ab0-4745-8292-5849b34173a7',
+ 'inbredset-group',
+ 'A resource that controls access to a particular InbredSet group',
+ '{"default-access-level":"public-read"}'
+ )
+ """,
+ """
+ DELETE FROM resource_categories WHERE
+ resource_category_id = 'b3654600-4ab0-4745-8292-5849b34173a7'
+ """
+ ),
+ step(
+ """
+ CREATE TABLE IF NOT EXISTS linked_inbredset_groups
+ -- Link InbredSet groups in MariaDB to auth system
+ (
+ data_link_id TEXT NOT NULL PRIMARY KEY, -- A new ID for the auth system
+ SpeciesId TEXT NOT NULL, -- Species ID in MariaDB
+ InbredSetId TEXT NOT NULL, -- The InbredSet ID in MariaDB
+ InbredSetName TEXT NOT NULL, -- The InbredSet group's name in MariaDB
+ InbredSetFullName TEXT NOT NULL, -- The InbredSet group's full name in MariaDB
+ UNIQUE(SpeciesId, InbredSetId)
+ ) WITHOUT ROWID
+ """,
+ "DROP TABLE IF EXISTS linked_inbredset_groups"),
+ step(
+ """
+ CREATE TABLE IF NOT EXISTS inbredset_group_resources
+ -- Link the InbredSet data to a specific resource
+ (
+ resource_id TEXT NOT NULL, -- Linked resource: one-to-one
+ data_link_id TEXT NOT NULL,
+ PRIMARY KEY(resource_id, data_link_id),
+ UNIQUE(resource_id), -- resource is linked to only one InbredSet
+ UNIQUE(data_link_id), -- InbredSet is linked to only one resource
+ FOREIGN KEY(resource_id)
+ REFERENCES resources(resource_id)
+ ON UPDATE CASCADE ON DELETE RESTRICT,
+ FOREIGN KEY(data_link_id)
+ REFERENCES linked_inbredset_groups(data_link_id)
+ ON UPDATE CASCADE ON DELETE RESTRICT
+ ) WITHOUT ROWID
+ """,
+ "DROP TABLE IF EXISTS inbredset_group_resources"),
+ step(
+ """
+ INSERT INTO privileges(privilege_id, privilege_description) VALUES
+ ('system:inbredset:create-case-attribute', 'Create a new case attribute for an InbredSet group.'),
+ ('system:inbredset:delete-case-attribute', 'Delete an existing case-attribute from an InbredSet group'),
+ ('system:inbredset:edit-case-attribute', 'Edit the values of case-attributes of an InbredSet group'),
+ ('system:inbredset:view-case-attribute', 'View the case-attributes of an InbredSet group'),
+ ('system:inbredset:apply-case-attribute-edit', 'Apply an edit to case-attributes performed by another user for an InbredSet group'),
+ ('system:inbredset:reject-case-attribute-edit', 'Reject an edit to case-attributes performed by another user for an InbredSet group')
+ """,
+ """
+ DELETE FROM privileges WHERE privilege_id IN (
+ 'system:inbredset:create-case-attribute',
+ 'system:inbredset:delete-case-attribute',
+ 'system:inbredset:edit-case-attribute',
+ 'system:inbredset:view-case-attribute',
+ 'system:inbredset:apply-case-attribute-edit',
+ 'system:inbredset:reject-case-attribute-edit')
+ """)
+]
diff --git a/tests/unit/auth/test_migrations_add_data_to_table.py b/tests/unit/auth/test_migrations_add_data_to_table.py
index b686f25..d9e2ca4 100644
--- a/tests/unit/auth/test_migrations_add_data_to_table.py
+++ b/tests/unit/auth/test_migrations_add_data_to_table.py
@@ -22,7 +22,21 @@ test_params = (
("a0e67630-d502-4b9f-b23f-6805d0f30e30",
"5103cc68-96f8-4ebb-83a4-a31692402c9b"),
("a0e67630-d502-4b9f-b23f-6805d0f30e30",
- "1c59eff5-9336-4ed2-a166-8f70d4cb012e"))),)
+ "1c59eff5-9336-4ed2-a166-8f70d4cb012e"))),
+ ("20231002_01_tzxTf-link-inbredsets-to-auth-system.py",
+ "SELECT privilege_id FROM privileges WHERE privilege_id IN (?, ?, ?, ?, ?, ?)",
+ ("system:inbredset:create-case-attribute",
+ "system:inbredset:delete-case-attribute",
+ "system:inbredset:edit-case-attribute",
+ "system:inbredset:view-case-attribute",
+ "system:inbredset:apply-case-attribute-edit",
+ "system:inbredset:reject-case-attribute-edit"),
+ (("system:inbredset:create-case-attribute",),
+ ("system:inbredset:delete-case-attribute",),
+ ("system:inbredset:edit-case-attribute",),
+ ("system:inbredset:view-case-attribute",),
+ ("system:inbredset:apply-case-attribute-edit",),
+ ("system:inbredset:reject-case-attribute-edit",))))
@pytest.mark.unit_test
@pytest.mark.parametrize("migration_file,query,query_params,data", test_params)
diff --git a/tests/unit/auth/test_migrations_create_tables.py b/tests/unit/auth/test_migrations_create_tables.py
index 8b0f36e..90c3fb8 100644
--- a/tests/unit/auth/test_migrations_create_tables.py
+++ b/tests/unit/auth/test_migrations_create_tables.py
@@ -43,7 +43,11 @@ migrations_and_tables = (
("20230907_01_pjnxz-refactor-add-resource-ownership-table.py",
"resource_ownership"),
("20230907_04_3LnrG-refactor-create-group-resources-table.py",
- "group_resources"))
+ "group_resources"),
+ ("20231002_01_tzxTf-link-inbredsets-to-auth-system.py",
+ "linked_inbredset_groups"),
+ ("20231002_01_tzxTf-link-inbredsets-to-auth-system.py",
+ "inbredset_group_resources"))
@pytest.mark.unit_test
@pytest.mark.parametrize("migration_file,the_table", migrations_and_tables)
@@ -64,6 +68,7 @@ def test_create_table(
apply_single_migration(backend, get_migration(migration_path))
cursor.execute("SELECT name FROM sqlite_schema WHERE type='table'")
result_after_migration = cursor.fetchall()
+ rollback_single_migration(backend, get_migration(migration_path))
rollback_migrations(backend, older_migrations)
assert the_table not in [row[0] for row in result_before_migration]