diff options
Diffstat (limited to 'migrations')
57 files changed, 0 insertions, 2460 deletions
diff --git a/migrations/__init__.py b/migrations/__init__.py deleted file mode 100644 index cedf48d..0000000 --- a/migrations/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"""Migrations package""" diff --git a/migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py b/migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py deleted file mode 100644 index d511f5d..0000000 --- a/migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py +++ /dev/null @@ -1,19 +0,0 @@ -""" -Initialise the auth(entic|oris)ation database. -""" - -from yoyo import step - -__depends__ = {} # type: ignore[var-annotated] - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS users( - user_id TEXT PRIMARY KEY NOT NULL, - email TEXT UNIQUE NOT NULL, - name TEXT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS users") -] diff --git a/migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py b/migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py deleted file mode 100644 index 48bd663..0000000 --- a/migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py +++ /dev/null @@ -1,20 +0,0 @@ -""" -create user_credentials table -""" - -from yoyo import step - -__depends__ = {'20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS user_credentials( - user_id TEXT PRIMARY KEY, - password TEXT NOT NULL, - FOREIGN KEY(user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS user_credentials") -] diff --git a/migrations/auth/20221108_01_CoxYh-create-the-groups-table.py b/migrations/auth/20221108_01_CoxYh-create-the-groups-table.py deleted file mode 100644 index 29f92d4..0000000 --- a/migrations/auth/20221108_01_CoxYh-create-the-groups-table.py +++ /dev/null @@ -1,19 +0,0 @@ -""" -Create the groups table -""" - -from yoyo import step - -__depends__ = {'20221103_02_sGrIs-create-user-credentials-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS groups( - group_id TEXT PRIMARY KEY NOT NULL, - group_name TEXT NOT NULL, - group_metadata TEXT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS groups") -] diff --git a/migrations/auth/20221108_02_wxTr9-create-privileges-table.py b/migrations/auth/20221108_02_wxTr9-create-privileges-table.py deleted file mode 100644 index 67720b2..0000000 --- a/migrations/auth/20221108_02_wxTr9-create-privileges-table.py +++ /dev/null @@ -1,18 +0,0 @@ -""" -Create privileges table -""" - -from yoyo import step - -__depends__ = {'20221108_01_CoxYh-create-the-groups-table'} - -steps = [ - step( - """ - CREATE TABLE privileges( - privilege_id TEXT PRIMARY KEY, - privilege_name TEXT NOT NULL - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS privileges") -] diff --git a/migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py b/migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py deleted file mode 100644 index ce752ef..0000000 --- a/migrations/auth/20221108_03_Pbhb1-create-resource-categories-table.py +++ /dev/null @@ -1,19 +0,0 @@ -""" -Create resource_categories table -""" - -from yoyo import step - -__depends__ = {'20221108_02_wxTr9-create-privileges-table'} - -steps = [ - step( - """ - CREATE TABLE resource_categories( - resource_category_id TEXT PRIMARY KEY, - resource_category_key TEXT NOT NULL, - resource_category_description TEXT NOT NULL - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS resource_categories") -] diff --git a/migrations/auth/20221108_04_CKcSL-init-data-in-resource-categories-table.py b/migrations/auth/20221108_04_CKcSL-init-data-in-resource-categories-table.py deleted file mode 100644 index 76ffbef..0000000 --- a/migrations/auth/20221108_04_CKcSL-init-data-in-resource-categories-table.py +++ /dev/null @@ -1,25 +0,0 @@ -""" -Init data in resource_categories table -""" - -from yoyo import step - -__depends__ = {'20221108_03_Pbhb1-create-resource-categories-table'} - -steps = [ - step( - """ - INSERT INTO resource_categories VALUES - ('fad071a3-2fc8-40b8-992b-cdefe7dcac79', 'mrna', 'mRNA Dataset'), - ('548d684b-d4d1-46fb-a6d3-51a56b7da1b3', 'phenotype', 'Phenotype (Publish) Dataset'), - ('48056f84-a2a6-41ac-8319-0e1e212cba2a', 'genotype', 'Genotype Dataset') - """, - """ - DELETE FROM resource_categories WHERE resource_category_id IN - ( - 'fad071a3-2fc8-40b8-992b-cdefe7dcac79', - '548d684b-d4d1-46fb-a6d3-51a56b7da1b3', - '48056f84-a2a6-41ac-8319-0e1e212cba2a' - ) - """) -] diff --git a/migrations/auth/20221109_01_HbD5F-add-resource-meta-field-to-resource-categories-field.py b/migrations/auth/20221109_01_HbD5F-add-resource-meta-field-to-resource-categories-field.py deleted file mode 100644 index 6c829b1..0000000 --- a/migrations/auth/20221109_01_HbD5F-add-resource-meta-field-to-resource-categories-field.py +++ /dev/null @@ -1,17 +0,0 @@ -""" -Add 'resource_meta' field to 'resource_categories' field. -""" - -from yoyo import step - -__depends__ = {'20221108_04_CKcSL-init-data-in-resource-categories-table'} - -steps = [ - step( - """ - ALTER TABLE resource_categories - ADD COLUMN - resource_meta TEXT NOT NULL DEFAULT '[]' - """, - "ALTER TABLE resource_categories DROP COLUMN resource_meta") -] diff --git a/migrations/auth/20221110_01_WtZ1I-create-resources-table.py b/migrations/auth/20221110_01_WtZ1I-create-resources-table.py deleted file mode 100644 index abc8895..0000000 --- a/migrations/auth/20221110_01_WtZ1I-create-resources-table.py +++ /dev/null @@ -1,26 +0,0 @@ -""" -Create 'resources' table -""" - -from yoyo import step - -__depends__ = {'20221109_01_HbD5F-add-resource-meta-field-to-resource-categories-field'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS resources( - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - resource_name TEXT NOT NULL UNIQUE, - resource_category_id TEXT NOT NULL, - PRIMARY KEY(group_id, resource_id), - FOREIGN KEY(group_id) REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(resource_category_id) - REFERENCES resource_categories(resource_category_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS resources") -] diff --git a/migrations/auth/20221110_05_BaNtL-create-roles-table.py b/migrations/auth/20221110_05_BaNtL-create-roles-table.py deleted file mode 100644 index 51e19e8..0000000 --- a/migrations/auth/20221110_05_BaNtL-create-roles-table.py +++ /dev/null @@ -1,19 +0,0 @@ -""" -Create 'roles' table -""" - -from yoyo import step - -__depends__ = {'20221110_01_WtZ1I-create-resources-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS roles( - role_id TEXT NOT NULL PRIMARY KEY, - role_name TEXT NOT NULL, - user_editable INTEGER NOT NULL DEFAULT 1 CHECK (user_editable=0 or user_editable=1) - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS roles") -] diff --git a/migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py b/migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py deleted file mode 100644 index 2b55c2b..0000000 --- a/migrations/auth/20221110_06_Pq2kT-create-generic-roles-table.py +++ /dev/null @@ -1,24 +0,0 @@ -""" -Create 'generic_roles' table - -The roles in this table will be template roles, defining some common roles that -can be used within the groups. - -They could also be used to define system-level roles, though those will not be -provided to the "common" users. -""" - -from yoyo import step - -__depends__ = {'20221110_05_BaNtL-create-roles-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS generic_roles( - role_id TEXT PRIMARY KEY, - role_name TEXT NOT NULL - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS generic_roles") -] diff --git a/migrations/auth/20221110_07_7WGa1-create-role-privileges-table.py b/migrations/auth/20221110_07_7WGa1-create-role-privileges-table.py deleted file mode 100644 index 0d0eeb9..0000000 --- a/migrations/auth/20221110_07_7WGa1-create-role-privileges-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -Create 'role_privileges' table -""" - -from yoyo import step - -__depends__ = {'20221110_06_Pq2kT-create-generic-roles-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS role_privileges( - role_id TEXT NOT NULL, - privilege_id TEXT NOT NULL, - PRIMARY KEY(role_id, privilege_id), - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(privilege_id) REFERENCES privileges(privilege_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS role_privileges"), - step( - """ - CREATE INDEX IF NOT EXISTS idx_tbl_role_privileges_cols_role_id - ON role_privileges(role_id) - """, - "DROP INDEX IF EXISTS idx_tbl_role_privileges_cols_role_id") -] diff --git a/migrations/auth/20221110_08_23psB-add-privilege-category-and-privilege-description-columns-to-privileges-table.py b/migrations/auth/20221110_08_23psB-add-privilege-category-and-privilege-description-columns-to-privileges-table.py deleted file mode 100644 index 077182b..0000000 --- a/migrations/auth/20221110_08_23psB-add-privilege-category-and-privilege-description-columns-to-privileges-table.py +++ /dev/null @@ -1,22 +0,0 @@ -""" -Add 'privilege_category' and 'privilege_description' columns to 'privileges' table -""" - -from yoyo import step - -__depends__ = {'20221110_07_7WGa1-create-role-privileges-table'} - -steps = [ - step( - """ - ALTER TABLE privileges ADD COLUMN - privilege_category TEXT NOT NULL DEFAULT 'common' - """, - "ALTER TABLE privileges DROP COLUMN privilege_category"), - step( - """ - ALTER TABLE privileges ADD COLUMN - privilege_description TEXT - """, - "ALTER TABLE privileges DROP COLUMN privilege_description") -] diff --git a/migrations/auth/20221113_01_7M0hv-enumerate-initial-privileges.py b/migrations/auth/20221113_01_7M0hv-enumerate-initial-privileges.py deleted file mode 100644 index 072f226..0000000 --- a/migrations/auth/20221113_01_7M0hv-enumerate-initial-privileges.py +++ /dev/null @@ -1,66 +0,0 @@ -""" -Enumerate initial privileges -""" - -from yoyo import step - -__depends__ = {'20221110_08_23psB-add-privilege-category-and-privilege-description-columns-to-privileges-table'} - -steps = [ - step( - """ - INSERT INTO - privileges(privilege_id, privilege_name, privilege_category, - privilege_description) - VALUES - -- group-management privileges - ('4842e2aa-38b9-4349-805e-0a99a9cf8bff', 'create-group', - 'group-management', 'Create a group'), - ('3ebfe79c-d159-4629-8b38-772cf4bc2261', 'view-group', - 'group-management', 'View the details of a group'), - ('52576370-b3c7-4e6a-9f7e-90e9dbe24d8f', 'edit-group', - 'group-management', 'Edit the details of a group'), - ('13ec2a94-4f1a-442d-aad2-936ad6dd5c57', 'delete-group', - 'group-management', 'Delete a group'), - ('ae4add8c-789a-4d11-a6e9-a306470d83d9', 'add-group-member', - 'group-management', 'Add a user to a group'), - ('f1bd3f42-567e-4965-9643-6d1a52ddee64', 'remove-group-member', - 'group-management', 'Remove a user from a group'), - ('80f11285-5079-4ec0-907c-06509f88a364', 'assign-group-leader', - 'group-management', 'Assign user group-leader privileges'), - ('d4afe2b3-4ca0-4edd-b37d-966535b5e5bd', - 'transfer-group-leadership', 'group-management', - 'Transfer leadership of the group to some other member'), - - -- resource-management privileges - ('aa25b32a-bff2-418d-b0a2-e26b4a8f089b', 'create-resource', - 'resource-management', 'Create a resource object'), - ('7f261757-3211-4f28-a43f-a09b800b164d', 'view-resource', - 'resource-management', 'view a resource and use it in computations'), - ('2f980855-959b-4339-b80e-25d1ec286e21', 'edit-resource', - 'resource-management', 'edit/update a resource'), - ('d2a070fd-e031-42fb-ba41-d60cf19e5d6d', 'delete-resource', - 'resource-management', 'Delete a resource'), - - -- role-management privileges - ('221660b1-df05-4be1-b639-f010269dbda9', 'create-role', - 'role-management', 'Create a new role'), - ('7bcca363-cba9-4169-9e31-26bdc6179b28', 'edit-role', - 'role-management', 'edit/update an existing role'), - ('5103cc68-96f8-4ebb-83a4-a31692402c9b', 'assign-role', - 'role-management', 'Assign a role to an existing user'), - ('1c59eff5-9336-4ed2-a166-8f70d4cb012e', 'delete-role', - 'role-management', 'Delete an existing role'), - - -- user-management privileges - ('e7252301-6ee0-43ba-93ef-73b607cf06f6', 'reset-any-password', - 'user-management', 'Reset the password for any user'), - ('1fe61370-cae9-4983-bd6c-ce61050c510f', 'delete-any-user', - 'user-management', 'Delete any user from the system'), - - -- sytem-admin privileges - ('519db546-d44e-4fdc-9e4e-25aa67548ab3', 'masquerade', - 'system-admin', 'Masquerade as some other user') - """, - "DELETE FROM privileges") -] diff --git a/migrations/auth/20221114_01_n8gsF-create-generic-role-privileges-table.py b/migrations/auth/20221114_01_n8gsF-create-generic-role-privileges-table.py deleted file mode 100644 index 2048f4a..0000000 --- a/migrations/auth/20221114_01_n8gsF-create-generic-role-privileges-table.py +++ /dev/null @@ -1,35 +0,0 @@ -""" -Create 'generic_role_privileges' table - -This table links the generic_roles to the privileges they provide -""" - -from yoyo import step - -__depends__ = {'20221113_01_7M0hv-enumerate-initial-privileges'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS generic_role_privileges( - generic_role_id TEXT NOT NULL, - privilege_id TEXT NOT NULL, - PRIMARY KEY(generic_role_id, privilege_id), - FOREIGN KEY(generic_role_id) REFERENCES generic_roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(privilege_id) REFERENCES privileges(privilege_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS generic_role_privileges"), - step( - """ - CREATE INDEX IF NOT EXISTS - idx_tbl_generic_role_privileges_cols_generic_role_id - ON generic_role_privileges(generic_role_id) - """, - """ - DROP INDEX IF EXISTS - idx_tbl_generic_role_privileges_cols_generic_role_id - """) -] diff --git a/migrations/auth/20221114_02_DKKjn-drop-generic-role-tables.py b/migrations/auth/20221114_02_DKKjn-drop-generic-role-tables.py deleted file mode 100644 index 6bd101b..0000000 --- a/migrations/auth/20221114_02_DKKjn-drop-generic-role-tables.py +++ /dev/null @@ -1,41 +0,0 @@ -""" -Drop 'generic_role*' tables -""" - -from yoyo import step - -__depends__ = {'20221114_01_n8gsF-create-generic-role-privileges-table'} - -steps = [ - step( - """ - DROP INDEX IF EXISTS - idx_tbl_generic_role_privileges_cols_generic_role_id - """, - """ - CREATE INDEX IF NOT EXISTS - idx_tbl_generic_role_privileges_cols_generic_role_id - ON generic_role_privileges(generic_role_id) - """), - step( - "DROP TABLE IF EXISTS generic_role_privileges", - """ - CREATE TABLE IF NOT EXISTS generic_role_privileges( - generic_role_id TEXT NOT NULL, - privilege_id TEXT NOT NULL, - PRIMARY KEY(generic_role_id, privilege_id), - FOREIGN KEY(generic_role_id) REFERENCES generic_roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(privilege_id) REFERENCES privileges(privilege_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """), - step( - "DROP TABLE IF EXISTS generic_roles", - """ - CREATE TABLE IF NOT EXISTS generic_roles( - role_id TEXT PRIMARY KEY, - role_name TEXT NOT NULL - ) WITHOUT ROWID - """) -] diff --git a/migrations/auth/20221114_03_PtWjc-create-group-roles-table.py b/migrations/auth/20221114_03_PtWjc-create-group-roles-table.py deleted file mode 100644 index a7e7b45..0000000 --- a/migrations/auth/20221114_03_PtWjc-create-group-roles-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -Create 'group_roles' table -""" - -from yoyo import step - -__depends__ = {'20221114_02_DKKjn-drop-generic-role-tables'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS group_roles( - group_id TEXT NOT NULL, - role_id TEXT NOT NULL, - PRIMARY KEY(group_id, role_id), - FOREIGN KEY(group_id) REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS group_roles"), - step( - """ - CREATE INDEX IF NOT EXISTS idx_tbl_group_roles_cols_group_id - ON group_roles(group_id) - """, - "DROP INDEX IF EXISTS idx_tbl_group_roles_cols_group_id") -] diff --git a/migrations/auth/20221114_04_tLUzB-initialise-basic-roles.py b/migrations/auth/20221114_04_tLUzB-initialise-basic-roles.py deleted file mode 100644 index 386f481..0000000 --- a/migrations/auth/20221114_04_tLUzB-initialise-basic-roles.py +++ /dev/null @@ -1,56 +0,0 @@ -""" -Initialise basic roles -""" - -from yoyo import step - -__depends__ = {'20221114_03_PtWjc-create-group-roles-table'} - -steps = [ - step( - """ - INSERT INTO roles(role_id, role_name, user_editable) VALUES - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', 'group-leader', '0'), - ('522e4d40-aefc-4a64-b7e0-768b8be517ee', 'resource-owner', '0') - """, - "DELETE FROM roles"), - step( - """ - INSERT INTO role_privileges(role_id, privilege_id) - VALUES - -- group-management - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '4842e2aa-38b9-4349-805e-0a99a9cf8bff'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '3ebfe79c-d159-4629-8b38-772cf4bc2261'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '52576370-b3c7-4e6a-9f7e-90e9dbe24d8f'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '13ec2a94-4f1a-442d-aad2-936ad6dd5c57'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - 'ae4add8c-789a-4d11-a6e9-a306470d83d9'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - 'f1bd3f42-567e-4965-9643-6d1a52ddee64'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - 'd4afe2b3-4ca0-4edd-b37d-966535b5e5bd'), - - -- resource-management - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - 'aa25b32a-bff2-418d-b0a2-e26b4a8f089b'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '7f261757-3211-4f28-a43f-a09b800b164d'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '2f980855-959b-4339-b80e-25d1ec286e21'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - 'd2a070fd-e031-42fb-ba41-d60cf19e5d6d'), - ('522e4d40-aefc-4a64-b7e0-768b8be517ee', - 'aa25b32a-bff2-418d-b0a2-e26b4a8f089b'), - ('522e4d40-aefc-4a64-b7e0-768b8be517ee', - '7f261757-3211-4f28-a43f-a09b800b164d'), - ('522e4d40-aefc-4a64-b7e0-768b8be517ee', - '2f980855-959b-4339-b80e-25d1ec286e21'), - ('522e4d40-aefc-4a64-b7e0-768b8be517ee', - 'd2a070fd-e031-42fb-ba41-d60cf19e5d6d') - """, - "DELETE FROM role_privileges") -] diff --git a/migrations/auth/20221114_05_hQun6-create-user-roles-table.py b/migrations/auth/20221114_05_hQun6-create-user-roles-table.py deleted file mode 100644 index e0de751..0000000 --- a/migrations/auth/20221114_05_hQun6-create-user-roles-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -Create 'user_roles' table. -""" - -from yoyo import step - -__depends__ = {'20221114_04_tLUzB-initialise-basic-roles'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS user_roles( - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - PRIMARY KEY(user_id, role_id), - FOREIGN KEY(user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS user_roles"), - step( - """ - CREATE INDEX IF NOT EXISTS idx_tbl_user_roles_cols_user_id - ON user_roles(user_id) - """, - "DROP INDEX IF EXISTS idx_tbl_user_roles_cols_user_id") -] diff --git a/migrations/auth/20221116_01_nKUmX-add-privileges-to-group-leader-role.py b/migrations/auth/20221116_01_nKUmX-add-privileges-to-group-leader-role.py deleted file mode 100644 index 2e4ae28..0000000 --- a/migrations/auth/20221116_01_nKUmX-add-privileges-to-group-leader-role.py +++ /dev/null @@ -1,35 +0,0 @@ -""" -Add privileges to 'group-leader' role. -""" - -from yoyo import step - -__depends__ = {'20221114_05_hQun6-create-user-roles-table'} - -steps = [ - step( - """ - INSERT INTO role_privileges(role_id, privilege_id) - VALUES - -- role management - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '221660b1-df05-4be1-b639-f010269dbda9'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '7bcca363-cba9-4169-9e31-26bdc6179b28'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '5103cc68-96f8-4ebb-83a4-a31692402c9b'), - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '1c59eff5-9336-4ed2-a166-8f70d4cb012e') - """, - """ - DELETE FROM role_privileges - WHERE - role_id='a0e67630-d502-4b9f-b23f-6805d0f30e30' - AND privilege_id IN ( - '221660b1-df05-4be1-b639-f010269dbda9', - '7bcca363-cba9-4169-9e31-26bdc6179b28', - '5103cc68-96f8-4ebb-83a4-a31692402c9b', - '1c59eff5-9336-4ed2-a166-8f70d4cb012e' - ) - """) -] diff --git a/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py b/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py deleted file mode 100644 index a4d7806..0000000 --- a/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py +++ /dev/null @@ -1,52 +0,0 @@ -""" -Modify 'group_roles': add 'group_role_id' - -At this point, there is no data in the `group_roles` table and therefore, it -should be safe to simply recreate it. -""" - -from yoyo import step - -__depends__ = {'20221116_01_nKUmX-add-privileges-to-group-leader-role'} - -steps = [ - step( - "DROP INDEX IF EXISTS idx_tbl_group_roles_cols_group_id", - """ - CREATE INDEX IF NOT EXISTS idx_tbl_group_roles_cols_group_id - ON group_roles(group_id) - """), - step( - "DROP TABLE IF EXISTS group_roles", - """ - CREATE TABLE IF NOT EXISTS group_roles( - group_id TEXT NOT NULL, - role_id TEXT NOT NULL, - PRIMARY KEY(group_id, role_id), - FOREIGN KEY(group_id) REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """), - step( - """ - CREATE TABLE IF NOT EXISTS group_roles( - group_role_id TEXT PRIMARY KEY, - group_id TEXT NOT NULL, - role_id TEXT NOT NULL, - UNIQUE (group_id, role_id), - FOREIGN KEY(group_id) REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS group_roles"), - step( - """ - CREATE INDEX IF NOT EXISTS idx_tbl_group_roles_cols_group_id - ON group_roles(group_id) - """, - "DROP INDEX IF EXISTS idx_tbl_group_roles_cols_group_id") -] diff --git a/migrations/auth/20221117_02_fmuZh-create-group-users-table.py b/migrations/auth/20221117_02_fmuZh-create-group-users-table.py deleted file mode 100644 index 92885ef..0000000 --- a/migrations/auth/20221117_02_fmuZh-create-group-users-table.py +++ /dev/null @@ -1,25 +0,0 @@ -""" -Create 'group_users' table. -""" - -from yoyo import step - -__depends__ = {'20221117_01_RDlfx-modify-group-roles-add-group-role-id'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS group_users( - group_id TEXT NOT NULL, - user_id TEXT NOT NULL UNIQUE, -- user can only be in one group - PRIMARY KEY(group_id, user_id) - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS group_users"), - step( - """ - CREATE INDEX IF NOT EXISTS tbl_group_users_cols_group_id - ON group_users(group_id) - """, - "DROP INDEX IF EXISTS tbl_group_users_cols_group_id") -] diff --git a/migrations/auth/20221206_01_BbeF9-create-group-user-roles-on-resources-table.py b/migrations/auth/20221206_01_BbeF9-create-group-user-roles-on-resources-table.py deleted file mode 100644 index 9aa3667..0000000 --- a/migrations/auth/20221206_01_BbeF9-create-group-user-roles-on-resources-table.py +++ /dev/null @@ -1,39 +0,0 @@ -""" -Create 'group_user_roles_on_resources' table -""" - -from yoyo import step - -__depends__ = {'20221117_02_fmuZh-create-group-users-table'} - -steps = [ - step( - """ - CREATE TABLE group_user_roles_on_resources ( - group_id TEXT NOT NULL, - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - PRIMARY KEY (group_id, user_id, role_id, resource_id), - FOREIGN KEY (user_id) - REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id, role_id) - REFERENCES group_roles(group_id, role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS group_user_roles_on_resources"), - step( - """ - CREATE INDEX IF NOT EXISTS - idx_tbl_group_user_roles_on_resources_group_user_resource - ON group_user_roles_on_resources(group_id, user_id, resource_id) - """, - """ - DROP INDEX IF EXISTS - idx_tbl_group_user_roles_on_resources_group_user_resource""") -] diff --git a/migrations/auth/20221208_01_sSdHz-add-public-column-to-resources-table.py b/migrations/auth/20221208_01_sSdHz-add-public-column-to-resources-table.py deleted file mode 100644 index 2238069..0000000 --- a/migrations/auth/20221208_01_sSdHz-add-public-column-to-resources-table.py +++ /dev/null @@ -1,16 +0,0 @@ -""" -Add 'public' column to 'resources' table -""" - -from yoyo import step - -__depends__ = {'20221206_01_BbeF9-create-group-user-roles-on-resources-table'} - -steps = [ - step( - """ - ALTER TABLE resources ADD COLUMN - public INTEGER NOT NULL DEFAULT 0 CHECK (public=0 or public=1) - """, - "ALTER TABLE resources DROP COLUMN public") -] diff --git a/migrations/auth/20221219_01_CI3tN-create-oauth2-clients-table.py b/migrations/auth/20221219_01_CI3tN-create-oauth2-clients-table.py deleted file mode 100644 index 475be01..0000000 --- a/migrations/auth/20221219_01_CI3tN-create-oauth2-clients-table.py +++ /dev/null @@ -1,25 +0,0 @@ -""" -create oauth2_clients table -""" - -from yoyo import step - -__depends__ = {'20221208_01_sSdHz-add-public-column-to-resources-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS oauth2_clients( - client_id TEXT NOT NULL, - client_secret TEXT NOT NULL, - client_id_issued_at INTEGER NOT NULL, - client_secret_expires_at INTEGER NOT NULL, - client_metadata TEXT, - user_id TEXT NOT NULL, - PRIMARY KEY(client_id), - FOREIGN KEY(user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS oauth2_clients") -] diff --git a/migrations/auth/20221219_02_buSEU-create-oauth2-tokens-table.py b/migrations/auth/20221219_02_buSEU-create-oauth2-tokens-table.py deleted file mode 100644 index 778282b..0000000 --- a/migrations/auth/20221219_02_buSEU-create-oauth2-tokens-table.py +++ /dev/null @@ -1,31 +0,0 @@ -""" -create oauth2_tokens table -""" - -from yoyo import step - -__depends__ = {'20221219_01_CI3tN-create-oauth2-clients-table'} - -steps = [ - step( - """ - CREATE TABLE oauth2_tokens( - token_id TEXT NOT NULL, - client_id TEXT NOT NULL, - token_type TEXT NOT NULL, - access_token TEXT UNIQUE NOT NULL, - refresh_token TEXT, - scope TEXT, - revoked INTEGER CHECK (revoked = 0 or revoked = 1), - issued_at INTEGER NOT NULL, - expires_in INTEGER NOT NULL, - user_id TEXT NOT NULL, - PRIMARY KEY(token_id), - FOREIGN KEY (client_id) REFERENCES oauth2_clients(client_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS oauth2_tokens") -] diff --git a/migrations/auth/20221219_03_PcTrb-create-authorisation-code-table.py b/migrations/auth/20221219_03_PcTrb-create-authorisation-code-table.py deleted file mode 100644 index 1683f87..0000000 --- a/migrations/auth/20221219_03_PcTrb-create-authorisation-code-table.py +++ /dev/null @@ -1,31 +0,0 @@ -""" -create authorisation_code table -""" - -from yoyo import step - -__depends__ = {'20221219_02_buSEU-create-oauth2-tokens-table'} - -steps = [ - step( - """ - CREATE TABLE authorisation_code ( - code_id TEXT NOT NULL, - code TEXT UNIQUE NOT NULL, - client_id NOT NULL, - redirect_uri TEXT, - scope TEXT, - nonce TEXT, - auth_time INTEGER NOT NULL, - code_challenge TEXT, - code_challenge_method TEXT, - user_id TEXT NOT NULL, - PRIMARY KEY (code_id), - FOREIGN KEY (client_id) REFERENCES oauth2_clients(client_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS authorisation_code") -] diff --git a/migrations/auth/20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader.py b/migrations/auth/20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader.py deleted file mode 100644 index 7e7fda2..0000000 --- a/migrations/auth/20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader.py +++ /dev/null @@ -1,40 +0,0 @@ -""" -remove 'create-group' privilege from group-leader. -""" - -from yoyo import step - -__depends__ = {'20221219_03_PcTrb-create-authorisation-code-table'} - -steps = [ - step( - """ - DELETE FROM role_privileges - WHERE role_id='a0e67630-d502-4b9f-b23f-6805d0f30e30' - AND privilege_id='4842e2aa-38b9-4349-805e-0a99a9cf8bff' - """, - """ - INSERT INTO role_privileges VALUES - ('a0e67630-d502-4b9f-b23f-6805d0f30e30', - '4842e2aa-38b9-4349-805e-0a99a9cf8bff') - """), - step( - """ - INSERT INTO roles(role_id, role_name, user_editable) VALUES - ('ade7e6b0-ba9c-4b51-87d0-2af7fe39a347', 'group-creator', '0') - """, - """ - DELETE FROM roles WHERE role_id='ade7e6b0-ba9c-4b51-87d0-2af7fe39a347' - """), - step( - """ - INSERT INTO role_privileges VALUES - ('ade7e6b0-ba9c-4b51-87d0-2af7fe39a347', - '4842e2aa-38b9-4349-805e-0a99a9cf8bff') - """, - """ - DELETE FROM role_privileges - WHERE role_id='ade7e6b0-ba9c-4b51-87d0-2af7fe39a347' - AND privilege_id='4842e2aa-38b9-4349-805e-0a99a9cf8bff' - """) -] diff --git a/migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py b/migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py deleted file mode 100644 index 1ef5ab0..0000000 --- a/migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py +++ /dev/null @@ -1,111 +0,0 @@ -""" -rework privileges schema -""" -import contextlib - -from yoyo import step - -__depends__ = {'20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader'} - -privileges = ( # format: (original_id, original_name, new_id, category) - ("13ec2a94-4f1a-442d-aad2-936ad6dd5c57", "delete-group", - "system:group:delete-group", "group-management"), - ("1c59eff5-9336-4ed2-a166-8f70d4cb012e", "delete-role", - "group:role:delete-role", "role-management"), - ("1fe61370-cae9-4983-bd6c-ce61050c510f", "delete-any-user", - "system:user:delete-user", "user-management"), - ("221660b1-df05-4be1-b639-f010269dbda9", "create-role", - "group:role:create-role", "role-management"), - ("2f980855-959b-4339-b80e-25d1ec286e21", "edit-resource", - "group:resource:edit-resource", "resource-management"), - ("3ebfe79c-d159-4629-8b38-772cf4bc2261", "view-group", - "system:group:view-group", "group-management"), - ("4842e2aa-38b9-4349-805e-0a99a9cf8bff", "create-group", - "system:group:create-group", "group-management"), - ("5103cc68-96f8-4ebb-83a4-a31692402c9b", "assign-role", - "group:user:assign-role", "role-management"), - ("519db546-d44e-4fdc-9e4e-25aa67548ab3", "masquerade", - "system:user:masquerade", "system-admin"), - ("52576370-b3c7-4e6a-9f7e-90e9dbe24d8f", "edit-group", - "system:group:edit-group", "group-management"), - ("7bcca363-cba9-4169-9e31-26bdc6179b28", "edit-role", - "group:role:edit-role", "role-management"), - ("7f261757-3211-4f28-a43f-a09b800b164d", "view-resource", - "group:resource:view-resource", "resource-management"), - ("80f11285-5079-4ec0-907c-06509f88a364", "assign-group-leader", - "system:user:assign-group-leader", "group-management"), - ("aa25b32a-bff2-418d-b0a2-e26b4a8f089b", "create-resource", - "group:resource:create-resource", "resource-management"), - ("ae4add8c-789a-4d11-a6e9-a306470d83d9", "add-group-member", - "group:user:add-group-member", "group-management"), - ("d2a070fd-e031-42fb-ba41-d60cf19e5d6d", "delete-resource", - "group:resource:delete-resource", "resource-management"), - ("d4afe2b3-4ca0-4edd-b37d-966535b5e5bd", "transfer-group-leadership", - "system:group:transfer-group-leader", "group-management"), - ("e7252301-6ee0-43ba-93ef-73b607cf06f6", "reset-any-password", - "system:user:reset-password", "user-management"), - ("f1bd3f42-567e-4965-9643-6d1a52ddee64", "remove-group-member", - "group:user:remove-group-member", "group-management")) - -def rework_privileges_table(cursor): - "rework the schema" - cursor.executemany( - ("UPDATE privileges SET privilege_id=:id " - "WHERE privilege_id=:old_id"), - ({"id": row[2], "old_id": row[0]} for row in privileges)) - cursor.execute("ALTER TABLE privileges DROP COLUMN privilege_category") - cursor.execute("ALTER TABLE privileges DROP COLUMN privilege_name") - -def restore_privileges_table(cursor): - "restore the schema" - cursor.execute(( - "CREATE TABLE privileges_restore (" - " privilege_id TEXT PRIMARY KEY," - " privilege_name TEXT NOT NULL," - " privilege_category TEXT NOT NULL DEFAULT 'common'," - " privilege_description TEXT" - ")")) - id_dict = {row[2]: {"id": row[0], "name": row[1], "cat": row[3]} - for row in privileges} - cursor.execute( - "SELECT privilege_id, privilege_description FROM privileges") - params = ({**id_dict[row[0]], "desc": row[1]} for row in cursor.fetchall()) - cursor.executemany( - "INSERT INTO privileges_restore VALUES (:id, :name, :cat, :desc)", - params) - cursor.execute("DROP TABLE privileges") - cursor.execute("ALTER TABLE privileges_restore RENAME TO privileges") - -def update_privilege_ids_in_role_privileges(cursor): - """Update the ids to new form.""" - cursor.executemany( - ("UPDATE role_privileges SET privilege_id=:new_id " - "WHERE privilege_id=:old_id"), - ({"new_id": row[2], "old_id": row[0]} for row in privileges)) - -def restore_privilege_ids_in_role_privileges(cursor): - """Restore original ids""" - cursor.executemany( - ("UPDATE role_privileges SET privilege_id=:old_id " - "WHERE privilege_id=:new_id"), - ({"new_id": row[2], "old_id": row[0]} for row in privileges)) - -def change_schema(conn): - """Change the privileges schema and IDs""" - with contextlib.closing(conn.cursor()) as cursor: - cursor.execute("PRAGMA foreign_keys=OFF") - rework_privileges_table(cursor) - update_privilege_ids_in_role_privileges(cursor) - cursor.execute("PRAGMA foreign_keys=ON") - -def restore_schema(conn): - """Change the privileges schema and IDs""" - with contextlib.closing(conn.cursor()) as cursor: - cursor.execute("PRAGMA foreign_keys=OFF") - restore_privilege_ids_in_role_privileges(cursor) - restore_privileges_table(cursor) - cursor.execute("PRAGMA foreign_keys=ON") - -steps = [ - step(change_schema, restore_schema) -] diff --git a/migrations/auth/20230207_01_r0bkZ-create-group-join-requests-table.py b/migrations/auth/20230207_01_r0bkZ-create-group-join-requests-table.py deleted file mode 100644 index ceae5ea..0000000 --- a/migrations/auth/20230207_01_r0bkZ-create-group-join-requests-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -Create group_requests table -""" - -from yoyo import step - -__depends__ = {'20230116_01_KwuJ3-rework-privileges-schema'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS group_join_requests( - request_id TEXT NOT NULL, - group_id TEXT NOT NULL, - requester_id TEXT NOT NULL, - timestamp REAL NOT NULL, - status TEXT NOT NULL DEFAULT 'PENDING', - message TEXT, - PRIMARY KEY(request_id, group_id), - FOREIGN KEY(group_id) REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE CASCADE, - FOREIGN KEY (requester_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE CASCADE, - UNIQUE(group_id, requester_id), - CHECK (status IN ('PENDING', 'ACCEPTED', 'REJECTED')) - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS group_join_requests") -] diff --git a/migrations/auth/20230210_01_8xMa1-system-admin-privileges-for-data-distribution.py b/migrations/auth/20230210_01_8xMa1-system-admin-privileges-for-data-distribution.py deleted file mode 100644 index 8b406a6..0000000 --- a/migrations/auth/20230210_01_8xMa1-system-admin-privileges-for-data-distribution.py +++ /dev/null @@ -1,22 +0,0 @@ -""" -System admin privileges for data distribution - -These privileges are focussed on allowing the system administrator to link the -datasets and traits in the main database to specific groups in the auth system. -""" - -from yoyo import step - -__depends__ = {'20230207_01_r0bkZ-create-group-join-requests-table'} - -steps = [ - step( - """ - INSERT INTO privileges VALUES - ('system:data:link-to-group', 'Link a dataset or trait to a group.') - """, - """ - DELETE FROM privileges WHERE privilege_id IN - ('system:data:link-to-group') - """) -] diff --git a/migrations/auth/20230210_02_lDK14-create-system-admin-role.py b/migrations/auth/20230210_02_lDK14-create-system-admin-role.py deleted file mode 100644 index 9b3fc2b..0000000 --- a/migrations/auth/20230210_02_lDK14-create-system-admin-role.py +++ /dev/null @@ -1,38 +0,0 @@ -""" -Create system-admin role -""" -import uuid -from contextlib import closing - -from yoyo import step - -__depends__ = {'20230210_01_8xMa1-system-admin-privileges-for-data-distribution'} - -def create_sys_admin_role(conn): - with closing(conn.cursor()) as cursor: - role_id = uuid.uuid4() - cursor.execute( - "INSERT INTO roles VALUES (?, 'system-administrator', '0')", - (str(role_id),)) - - cursor.executemany( - "INSERT INTO role_privileges VALUES (:role_id, :privilege_id)", - ({"role_id": f"{role_id}", "privilege_id": priv} - for priv in ( - "system:data:link-to-group", - "system:group:create-group", - "system:group:delete-group", - "system:group:edit-group", - "system:group:transfer-group-leader", - "system:group:view-group", - "system:user:assign-group-leader", - "system:user:delete-user", - "system:user:masquerade", - "system:user:reset-password"))) - -def drop_sys_admin_role(conn): - pass - -steps = [ - step(create_sys_admin_role, drop_sys_admin_role) -] diff --git a/migrations/auth/20230306_01_pRfxl-add-system-user-list-privilege.py b/migrations/auth/20230306_01_pRfxl-add-system-user-list-privilege.py deleted file mode 100644 index 84bbd49..0000000 --- a/migrations/auth/20230306_01_pRfxl-add-system-user-list-privilege.py +++ /dev/null @@ -1,26 +0,0 @@ -""" -Add system:user:list privilege -""" -import contextlib - -from yoyo import step - -__depends__ = {'20230210_02_lDK14-create-system-admin-role'} - -def insert_users_list_priv(conn): - """Create a new 'system:user:list' privilege.""" - with contextlib.closing(conn.cursor()) as cursor: - cursor.execute( - "INSERT INTO privileges(privilege_id, privilege_description) " - "VALUES('system:user:list', 'List users in the system') " - "ON CONFLICT (privilege_id) DO NOTHING") - -def delete_users_list_priv(conn): - """Delete the new 'system:user:list' privilege.""" - with contextlib.closing(conn.cursor()) as cursor: - cursor.execute( - "DELETE FROM privileges WHERE privilege_id='system:user:list'") - -steps = [ - step(insert_users_list_priv, delete_users_list_priv) -] diff --git a/migrations/auth/20230306_02_7GnRY-add-system-user-list-privilege-to-system-administrator-and-group-leader-roles.py b/migrations/auth/20230306_02_7GnRY-add-system-user-list-privilege-to-system-administrator-and-group-leader-roles.py deleted file mode 100644 index 3caad55..0000000 --- a/migrations/auth/20230306_02_7GnRY-add-system-user-list-privilege-to-system-administrator-and-group-leader-roles.py +++ /dev/null @@ -1,42 +0,0 @@ -""" -Add system:user:list privilege to system-administrator and group-leader roles. -""" -import uuid -import contextlib - -from yoyo import step - -__depends__ = {'20230306_01_pRfxl-add-system-user-list-privilege'} - -def role_ids(cursor): - """Get role ids from names""" - cursor.execute( - "SELECT * FROM roles WHERE role_name IN " - "('system-administrator', 'group-leader')") - return (uuid.UUID(row[0]) for row in cursor.fetchall()) - -def add_privilege_to_roles(conn): - """ - Add 'system:user:list' privilege to 'system-administrator' and - 'group-leader' roles.""" - with contextlib.closing(conn.cursor()) as cursor: - cursor.executemany( - "INSERT INTO role_privileges(role_id,privilege_id) " - "VALUES(?, ?)", - tuple((str(role_id), "system:user:list") - for role_id in role_ids(cursor))) - -def del_privilege_from_roles(conn): - """ - Delete 'system:user:list' privilege to 'system-administrator' and - 'group-leader' roles. - """ - with contextlib.closing(conn.cursor()) as cursor: - cursor.execute( - "DELETE FROM role_privileges WHERE " - "role_id IN (?, ?) AND privilege_id='system:user:list'", - tuple(str(role_id) for role_id in role_ids(cursor))) - -steps = [ - step(add_privilege_to_roles, del_privilege_from_roles) -] 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 deleted file mode 100644 index 647325f..0000000 --- a/migrations/auth/20230322_01_0dDZR-create-linked-phenotype-data-table.py +++ /dev/null @@ -1,30 +0,0 @@ -""" -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 deleted file mode 100644 index 7c9e986..0000000 --- a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -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 - ( - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, -- A resource can have multiple data items - data_link_id TEXT NOT NULL, - PRIMARY KEY(group_id, resource_id, data_link_id), - UNIQUE (data_link_id), -- ensure data is linked to only one resource - FOREIGN KEY (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - 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_01_VKxXg-create-linked-genotype-data-table.py b/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py deleted file mode 100644 index 02e8718..0000000 --- a/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -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 deleted file mode 100644 index 1a865e0..0000000 --- a/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -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 - ( - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, -- A resource can have multiple items - data_link_id TEXT NOT NULL, - PRIMARY KEY (group_id, resource_id, data_link_id), - UNIQUE (data_link_id) -- ensure data is linked to single resource - FOREIGN KEY (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - 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 deleted file mode 100644 index db9a6bf..0000000 --- a/migrations/auth/20230410_01_8mwaf-create-linked-mrna-data-table.py +++ /dev/null @@ -1,30 +0,0 @@ -""" -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 deleted file mode 100644 index 2ad1056..0000000 --- a/migrations/auth/20230410_02_WZqSf-create-mrna-resources-table.py +++ /dev/null @@ -1,28 +0,0 @@ -""" -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 - ( - group_id TEXT NOT NULL, - 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 (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - 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/migrations/auth/20230907_01_pjnxz-refactor-add-resource-ownership-table.py b/migrations/auth/20230907_01_pjnxz-refactor-add-resource-ownership-table.py deleted file mode 100644 index 37fcfe7..0000000 --- a/migrations/auth/20230907_01_pjnxz-refactor-add-resource-ownership-table.py +++ /dev/null @@ -1,32 +0,0 @@ -""" -refactor: add resource_ownership table -""" - -from yoyo import step - -__depends__ = {'20230410_02_WZqSf-create-mrna-resources-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS resource_ownership( - -- This table links resources to groups, where relevant - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - PRIMARY KEY(group_id, resource_id), - FOREIGN KEY(group_id) - REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS resource_ownership"), - step(# Copy over data - """ - INSERT INTO resource_ownership - SELECT group_id, resource_id FROM resources - """ - ) -] diff --git a/migrations/auth/20230907_02_Enicg-refactor-add-system-and-group-resource-categories.py b/migrations/auth/20230907_02_Enicg-refactor-add-system-and-group-resource-categories.py deleted file mode 100644 index c4397c9..0000000 --- a/migrations/auth/20230907_02_Enicg-refactor-add-system-and-group-resource-categories.py +++ /dev/null @@ -1,29 +0,0 @@ -""" -refactor: add 'system' and 'group' resource categories -""" - -from yoyo import step - -__depends__ = {'20230907_01_pjnxz-refactor-add-resource-ownership-table'} - -steps = [ - step( - """ - INSERT INTO resource_categories VALUES - ('aa3d787f-af6a-44fa-9b0b-c82d40e54ad2', - 'system', - 'The overall system.', - '{"default-access-level": "public-read"}'), - ('1e0f70ee-add5-4358-8c6c-43de77fa4cce', - 'group', - 'A group resource.', - '{}') - """, - """ - DELETE FROM resource_categories - WHERE resource_category_id IN ( - 'aa3d787f-af6a-44fa-9b0b-c82d40e54ad2', - '1e0f70ee-add5-4358-8c6c-43de77fa4cce' - ) - """) -] diff --git a/migrations/auth/20230907_03_BwAmf-refactor-drop-group-id-from-resources-table.py b/migrations/auth/20230907_03_BwAmf-refactor-drop-group-id-from-resources-table.py deleted file mode 100644 index 0f491c2..0000000 --- a/migrations/auth/20230907_03_BwAmf-refactor-drop-group-id-from-resources-table.py +++ /dev/null @@ -1,325 +0,0 @@ -""" -refactor: drop 'group_id' from 'resources' table. -""" - -import sqlite3 -from yoyo import step - -__depends__ = {'20230907_02_Enicg-refactor-add-system-and-group-resource-categories'} - -def drop_group_id_from_group_user_roles_on_resources(conn): - conn.execute( - "ALTER TABLE group_user_roles_on_resources " - "RENAME TO group_user_roles_on_resources_bkp") - conn.execute( - """ - CREATE TABLE group_user_roles_on_resources ( - group_id TEXT NOT NULL, - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - PRIMARY KEY (group_id, user_id, role_id, resource_id), - FOREIGN KEY (user_id) - REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id, role_id) - REFERENCES group_roles(group_id, role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO group_user_roles_on_resources " - "(group_id, user_id, role_id, resource_id)" - "SELECT group_id, user_id, role_id, resource_id " - "FROM group_user_roles_on_resources_bkp") - conn.execute("DROP TABLE IF EXISTS group_user_roles_on_resources_bkp") - -def drop_group_id_from_mrna_resources(conn): - conn.execute("ALTER TABLE mrna_resources RENAME TO mrna_resources_bkp") - conn.execute( - """ - 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 (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (data_link_id) REFERENCES linked_mrna_data(data_link_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO mrna_resources " - "SELECT resource_id, data_link_id FROM mrna_resources_bkp") - conn.execute("DROP TABLE IF EXISTS mrna_resources_bkp") - -def drop_group_id_from_genotype_resources(conn): - conn.execute( - "ALTER TABLE genotype_resources RENAME TO genotype_resources_bkp") - conn.execute( - """ - 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 - FOREIGN KEY (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (data_link_id) - REFERENCES linked_genotype_data(data_link_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO genotype_resources " - "SELECT resource_id, data_link_id FROM genotype_resources_bkp") - conn.execute("DROP TABLE IF EXISTS genotype_resources_bkp") - -def drop_group_id_from_phenotype_resources(conn): - conn.execute( - "ALTER TABLE phenotype_resources RENAME TO phenotype_resources_bkp") - conn.execute( - """ - 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 - FOREIGN KEY (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (data_link_id) - REFERENCES linked_phenotype_data(data_link_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO phenotype_resources " - "SELECT resource_id, data_link_id FROM phenotype_resources_bkp") - conn.execute("DROP TABLE IF EXISTS phenotype_resources_bkp") - -def drop_group_id_from_resources_table(conn): - conn.row_factory = sqlite3.Row - conn.execute("PRAGMA foreign_keys = OFF") - conn.execute( - """ - CREATE TABLE IF NOT EXISTS resources_new( - resource_id TEXT NOT NULL, - resource_name TEXT NOT NULL UNIQUE, - resource_category_id TEXT NOT NULL, - public INTEGER NOT NULL DEFAULT 0 CHECK (public=0 or public=1), - PRIMARY KEY(resource_id), - FOREIGN KEY(resource_category_id) - REFERENCES resource_categories(resource_category_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO resources_new " - "SELECT resource_id, resource_name, resource_category_id, public " - "FROM resources") - conn.execute("DROP TABLE IF EXISTS resources") - conn.execute("ALTER TABLE resources_new RENAME TO resources") - - drop_group_id_from_mrna_resources(conn) - drop_group_id_from_genotype_resources(conn) - drop_group_id_from_phenotype_resources(conn) - drop_group_id_from_group_user_roles_on_resources(conn) - - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -def restore_group_id_from_group_user_roles_on_resources(conn): - conn.execute( - "ALTER TABLE group_user_roles_on_resources " - "RENAME TO group_user_roles_on_resources_bkp") - conn.execute( - """ - CREATE TABLE group_user_roles_on_resources ( - group_id TEXT NOT NULL, - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - PRIMARY KEY (group_id, user_id, role_id, resource_id), - FOREIGN KEY (user_id) - REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id, role_id) - REFERENCES group_roles(group_id, role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO group_user_roles_on_resources " - "(group_id, user_id, role_id, resource_id)" - "SELECT group_id, user_id, role_id, resource_id " - "FROM group_user_roles_on_resources_bkp") - conn.execute("DROP TABLE IF EXISTS group_user_roles_on_resources_bkp") - -def restore_group_id_from_mrna_resources(conn, resource_group_map): - conn.execute("ALTER TABLE mrna_resources RENAME TO mrna_resources_bkp") - conn.execute( - """ - CREATE TABLE IF NOT EXISTS mrna_resources - -- Link mRNA data to specific resource - ( - group_id TEXT NOT NULL, - 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 (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (data_link_id) REFERENCES linked_mrna_data(data_link_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - - cursor = conn.cursor() - cursor.execute("SELECT * FROM mrna_resources_bkp") - resources = tuple({ - "group_id": resource_group_map[row["resource_id"]], - **dict(row) - } for row in cursor.fetchall()) - cursor.executemany( - "INSERT INTO mrna_resources(group_id, resource_id, data_link_id) " - "VALUES(:group_id, :resource_id, :data_link_id)", - resources) - conn.execute("DROP TABLE IF EXISTS mrna_resources_bkp") - -def restore_group_id_from_genotype_resources(conn, resource_group_map): - conn.execute( - "ALTER TABLE genotype_resources RENAME TO genotype_resources_bkp") - conn.execute( - """ - CREATE TABLE IF NOT EXISTS genotype_resources - -- Link genotype data to specific resource - ( - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, -- A resource can have multiple items - data_link_id TEXT NOT NULL, - PRIMARY KEY (group_id, resource_id, data_link_id), - UNIQUE (data_link_id) -- ensure data is linked to single resource - FOREIGN KEY (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (data_link_id) - REFERENCES linked_genotype_data(data_link_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - - cursor = conn.cursor() - cursor.execute("SELECT * FROM genotype_resources_bkp") - resources = tuple({ - "group_id": resource_group_map[row["resource_id"]], - **dict(row) - } for row in cursor.fetchall()) - cursor.executemany( - "INSERT INTO genotype_resources(group_id, resource_id, data_link_id) " - "VALUES(:group_id, :resource_id, :data_link_id)", - resources) - conn.execute("DROP TABLE IF EXISTS genotype_resources_bkp") - -def restore_group_id_from_phenotype_resources(conn, resource_group_map): - conn.execute( - "ALTER TABLE phenotype_resources RENAME TO phenotype_resources_bkp") - conn.execute( - """ - CREATE TABLE IF NOT EXISTS phenotype_resources - -- Link phenotype data to specific resources - ( - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, -- A resource can have multiple data items - data_link_id TEXT NOT NULL, - PRIMARY KEY(group_id, resource_id, data_link_id), - UNIQUE (data_link_id), -- ensure data is linked to only one resource - FOREIGN KEY (group_id, resource_id) - REFERENCES resources(group_id, resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (data_link_id) - REFERENCES linked_phenotype_data(data_link_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - - cursor = conn.cursor() - cursor.execute("SELECT * FROM phenotype_resources_bkp") - resources = tuple({ - "group_id": resource_group_map[row["resource_id"]], - **dict(row) - } for row in cursor.fetchall()) - cursor.executemany( - "INSERT INTO phenotype_resources(group_id, resource_id, data_link_id) " - "VALUES(:group_id, :resource_id, :data_link_id)", - resources) - conn.execute("DROP TABLE IF EXISTS phenotype_resources_bkp") - -def restore_group_id_to_resources_table(conn): - conn.row_factory = sqlite3.Row - conn.execute("PRAGMA foreign_keys = OFF") - - cursor = conn.cursor() - cursor.execute("ALTER TABLE resources RENAME TO resources_bkp") - cursor.execute( - "SELECT r.*, ro.group_id FROM resources_bkp AS r " - "INNER JOIN resource_ownership AS ro " - "ON r.resource_id=ro.resource_id") - group_resources = tuple(dict(row) for row in cursor.fetchall()) - cursor.execute( - """ - CREATE TABLE IF NOT EXISTS resources( - group_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - resource_name TEXT NOT NULL UNIQUE, - resource_category_id TEXT NOT NULL, - public INTEGER NOT NULL DEFAULT 0 CHECK (public=0 or public=1), - PRIMARY KEY(group_id, resource_id), - FOREIGN KEY(group_id) - REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(resource_category_id) - REFERENCES resource_categories(resource_category_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - cursor.executemany( - "INSERT INTO resources" - "(group_id, resource_id, resource_name, resource_category_id)" - "VALUES " - "(:group_id, :resource_id, :resource_name, :resource_category_id)", - group_resources) - cursor.execute("DROP TABLE IF EXISTS resources_bkp") - - resource_group_map = { - res["resource_id"]: res["group_id"] - for res in group_resources - } - restore_group_id_from_group_user_roles_on_resources(conn) - restore_group_id_from_mrna_resources(conn, resource_group_map) - restore_group_id_from_genotype_resources(conn, resource_group_map) - restore_group_id_from_phenotype_resources(conn, resource_group_map) - - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -steps = [ - step( - drop_group_id_from_resources_table, restore_group_id_to_resources_table) -] diff --git a/migrations/auth/20230907_04_3LnrG-refactor-create-group-resources-table.py b/migrations/auth/20230907_04_3LnrG-refactor-create-group-resources-table.py deleted file mode 100644 index a26834a..0000000 --- a/migrations/auth/20230907_04_3LnrG-refactor-create-group-resources-table.py +++ /dev/null @@ -1,58 +0,0 @@ -""" -refactor: create 'group_resources' table. -""" - -import uuid -import random -import string - -import sqlite3 -from yoyo import step - -__depends__ = {'20230907_03_BwAmf-refactor-drop-group-id-from-resources-table'} - -def randstr(length: int = 5): - """Generate random string.""" - return "".join(random.choices( - string.ascii_letters + string.digits, k=length)) - -def create_and_link_resources_for_existing_groups(conn): - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute("SELECT group_id, group_name FROM groups") - resources = tuple({ - "group_id": row["group_id"], - "resource_id": str(uuid.uuid4()), - "resource_name": f"{randstr(10)}: {row['group_name']}", - "resource_category_id": "1e0f70ee-add5-4358-8c6c-43de77fa4cce" - } for row in cursor.fetchall()) - cursor.executemany( - "INSERT INTO " - "resources(resource_id, resource_name, resource_category_id) " - "VALUES (:resource_id, :resource_name, :resource_category_id)", - resources) - cursor.executemany( - "INSERT INTO group_resources(resource_id, group_id) " - "VALUES (:resource_id, :group_id)", - resources) - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS group_resources( - -- Links groups to the resources of type 'group' that control access to - -- each group - resource_id TEXT NOT NULL, - group_id TEXT NOT NULL, - PRIMARY KEY(resource_id, group_id), - FOREIGN KEY (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id) - REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS group_resources"), - step(create_and_link_resources_for_existing_groups) -] diff --git a/migrations/auth/20230912_01_BxrhE-add-system-resource.py b/migrations/auth/20230912_01_BxrhE-add-system-resource.py deleted file mode 100644 index 66c6461..0000000 --- a/migrations/auth/20230912_01_BxrhE-add-system-resource.py +++ /dev/null @@ -1,39 +0,0 @@ -""" -Add 'system' resource. -""" - -import uuid - -import sqlite3 -from yoyo import step - -__depends__ = {'20230907_04_3LnrG-refactor-create-group-resources-table'} - -def add_system_resource(conn): - """Add a system resource.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "SELECT resource_category_id FROM resource_categories " - "WHERE resource_category_key='system'") - category_id = cursor.fetchone()["resource_category_id"] - cursor.execute( - "INSERT INTO " - "resources(resource_id, resource_name, resource_category_id, public) " - "VALUES(?, ?, ?, ?)", - (str(uuid.uuid4()), "GeneNetwork System", category_id, "1")) - -def delete_system_resource(conn): - """Add a system resource.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "SELECT resource_category_id FROM resource_categories " - "WHERE resource_category_key='system'") - category_id = cursor.fetchone()["resource_category_id"] - cursor.execute("DELETE FROM resources WHERE resource_category_id = ?", - (category_id,)) - -steps = [ - step(add_system_resource, delete_system_resource) -] diff --git a/migrations/auth/20230912_02_hFmSn-drop-group-id-and-fix-foreign-key-references-on-group-user-roles-on-resources-table.py b/migrations/auth/20230912_02_hFmSn-drop-group-id-and-fix-foreign-key-references-on-group-user-roles-on-resources-table.py deleted file mode 100644 index 1b3f0b1..0000000 --- a/migrations/auth/20230912_02_hFmSn-drop-group-id-and-fix-foreign-key-references-on-group-user-roles-on-resources-table.py +++ /dev/null @@ -1,227 +0,0 @@ -""" -Drop 'group_id' and fix foreign key references on 'group_user_roles_on_resources' table -""" - -import sqlite3 -from yoyo import step - -__depends__ = {'20230912_01_BxrhE-add-system-resource'} - -def drop_group_id(conn): - """Drop `group_id` from `group_user_roles_on_resources` table.""" - conn.execute("PRAGMA foreign_keys = OFF") - - conn.execute( - """ - ALTER TABLE group_user_roles_on_resources - RENAME TO group_user_roles_on_resources_bkp - """) - conn.execute( - """ - CREATE TABLE IF NOT EXISTS group_user_roles_on_resources ( - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - PRIMARY KEY (user_id, role_id, resource_id), - FOREIGN KEY (user_id) - REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (role_id) - REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - conn.execute( - "INSERT INTO group_user_roles_on_resources " - "SELECT user_id, role_id, resource_id " - "FROM group_user_roles_on_resources_bkp") - conn.execute("DROP TABLE IF EXISTS group_user_roles_on_resources_bkp") - - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -def restore_group_id(conn): - """Restore `group_id` to `group_user_roles_on_resources` table.""" - conn.execute("PRAGMA foreign_keys = OFF") - - conn.execute( - """ - ALTER TABLE group_user_roles_on_resources - RENAME TO group_user_roles_on_resources_bkp - """) - conn.execute( - """ - CREATE TABLE IF NOT EXISTS group_user_roles_on_resources ( - group_id TEXT NOT NULL, - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - resource_id TEXT NOT NULL, - PRIMARY KEY (group_id, user_id, role_id, resource_id), - FOREIGN KEY (user_id) - REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (group_id, role_id) - REFERENCES group_roles(group_id, role_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (resource_id) - REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - - cursor = conn.cursor() - cursor.execute( - """ - INSERT INTO group_user_roles_on_resources - SELECT - ro.group_id, gurorb.user_id, gurorb.role_id, gurorb.resource_id - FROM resource_ownership AS ro - INNER JOIN group_user_roles_on_resources_bkp AS gurorb - ON ro.resource_id=gurorb.resource_id - """) - - conn.execute("DROP TABLE IF EXISTS group_user_roles_on_resources_bkp") - - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -def link_sys_admin_user_roles(conn): - """Link system-admins to the system resource.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "SELECT ur.* FROM user_roles AS ur " - "INNER JOIN roles AS r ON ur.role_id=r.role_id " - "WHERE r.role_name='system-administrator'") - admins = cursor.fetchall() - cursor.execute( - "SELECT r.resource_id FROM resources AS r " - "INNER JOIN resource_categories AS rc " - "ON r.resource_category_id=rc.resource_category_id " - "WHERE rc.resource_category_key='system'") - system_resource_id = cursor.fetchone()["resource_id"] - cursor.executemany( - "INSERT INTO " - "group_user_roles_on_resources(user_id, role_id, resource_id) " - "VALUES (:user_id, :role_id, :resource_id)", - tuple({**admin, "resource_id": system_resource_id} for admin in admins)) - -def restore_sys_admin_user_roles(conn): - """Restore fields into older `user_roles` table.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "SELECT guror.user_id, guror.role_id " - "FROM group_user_roles_on_resources AS guror " - "INNER JOIN resources AS r " - "ON guror.resource_id=r.resource_id " - "INNER JOIN resource_categories AS rc " - "ON r.resource_category_id=rc.resource_category_id " - "WHERE rc.resource_category_key='system'") - user_roles = tuple(cursor.fetchall()) - cursor.executemany( - "INSERT INTO user_roles(user_id, role_id) " - "VALUES (:user_id, :role_id)", - user_roles) - -def link_group_leader_user_roles(conn): - """Link group leaders to their resources.""" - conn.execute( - """ - INSERT INTO group_user_roles_on_resources(user_id, role_id, resource_id) - SELECT gu.user_id, r.role_id, gr.resource_id - FROM group_resources AS gr INNER JOIN group_users AS gu - ON gr.group_id=gu.group_id INNER JOIN user_roles AS ur - ON gu.user_id=ur.user_id INNER JOIN roles AS r - ON ur.role_id=r.role_id - WHERE r.role_name='group-leader' - """) - -def restore_group_leader_user_roles(conn): - """Restore group admins to older `user_roles` table.""" - conn.execute( - """ - INSERT INTO user_roles(user_id, role_id) - SELECT guror.user_id, guror.role_id - FROM group_user_roles_on_resources AS guror - INNER JOIN resources AS r ON guror.resource_id=r.resource_id - INNER JOIN resource_categories AS rc - ON r.resource_category_id=rc.resource_category_id - WHERE rc.resource_category_key='group' - """) - -def link_group_creator_user_roles(conn): - """Link group-creators to system.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "SELECT ur.* FROM user_roles AS ur " - "INNER JOIN roles AS r ON ur.role_id=r.role_id " - "WHERE r.role_name='group_creator'") - creators = cursor.fetchall() - cursor.execute( - "SELECT r.resource_id FROM resources AS r " - "INNER JOIN resource_categories AS rc " - "ON r.resource_category_id=rc.resource_category_id " - "WHERE rc.resource_category_key='system'") - sys_res_id = cursor.fetchone()["resource_id"] - cursor.executemany( - "INSERT INTO " - "group_user_roles_on_resources(user_id, role_id, resource_id) " - "VALUES (:user_id, :role_id, :resource_id)", - tuple({**creator, "resource_id": sys_res_id} for creator in creators)) - -def restore_group_creator_user_roles(conn): - "Restore group-creator user roles." - conn.execute( - """ - INSERT INTO user_roles - SELECT guror.user_id, guror.role_id - FROM group_user_roles_on_resources AS guror - INNER JOIN roles AS r ON guror.role_id=r.role_id - WHERE r.role_name='group-creator'""") - -def rename_table(conn): - "rename `group_user_roles_on_resources`, drop `user_roles`." - conn.execute("PRAGMA foreign_keys = OFF") - - conn.execute("DROP TABLE IF EXISTS user_roles") - conn.execute( - "ALTER TABLE group_user_roles_on_resources RENAME TO user_roles") - - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -def restore_tables(conn): - "rename to `group_user_roles_on_resources`, recreate original `user_roles`." - conn.execute("PRAGMA foreign_keys = OFF") - - conn.execute( - "ALTER TABLE user_roles RENAME TO group_user_roles_on_resources") - conn.execute( - """ - CREATE TABLE user_roles( - user_id TEXT NOT NULL, - role_id TEXT NOT NULL, - PRIMARY KEY(user_id, role_id), - FOREIGN KEY(user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -steps = [ - step(drop_group_id, restore_group_id), - step(link_sys_admin_user_roles, restore_sys_admin_user_roles), - step(link_group_leader_user_roles, restore_group_leader_user_roles), - step(link_group_creator_user_roles, restore_group_creator_user_roles), - step(rename_table, restore_tables) -] - diff --git a/migrations/auth/20230925_01_TWJuR-add-new-public-view-role.py b/migrations/auth/20230925_01_TWJuR-add-new-public-view-role.py deleted file mode 100644 index 1172034..0000000 --- a/migrations/auth/20230925_01_TWJuR-add-new-public-view-role.py +++ /dev/null @@ -1,61 +0,0 @@ -""" -Add new "public-view" role -""" - -import sqlite3 - -from yoyo import step - -__depends__ = {'20230912_02_hFmSn-drop-group-id-and-fix-foreign-key-references-on-group-user-roles-on-resources-table'} - -def grant_to_all_users_public_view_role(conn): - """Grant the `public-view` role to all existing users.""" - conn.row_factory = sqlite3.Row - conn.execute("PRAGMA foreign_keys = ON") - cursor = conn.cursor() - cursor.execute("SELECT user_id FROM users") - user_ids = tuple(row["user_id"] for row in cursor.fetchall()) - - cursor.execute("SELECT resource_id FROM resources WHERE public=1") - resource_ids = tuple(row["resource_id"] for row in cursor.fetchall()) - - params = tuple({ - "user_id": user_id, - "resource_id": resource_id, - "role_id": "fd88bfed-d869-4969-87f2-67c4e8446ecb" - } for user_id in user_ids for resource_id in resource_ids) - cursor.executemany( - "INSERT INTO user_roles(user_id, role_id, resource_id) " - "VALUES (:user_id, :role_id, :resource_id) ", - params) - -def revoke_from_all_users_public_view_role(conn): - """Revoke the `public-view` role from all existing users.""" - conn.execute("PRAGMA foreign_keys = ON") - conn.execute( - "DELETE FROM user_roles " - "WHERE role_id='fd88bfed-d869-4969-87f2-67c4e8446ecb'") - -steps = [ - step( - """ - INSERT INTO roles(role_id, role_name, user_editable) - VALUES('fd88bfed-d869-4969-87f2-67c4e8446ecb', 'public-view', 0) - """, - """ - DELETE FROM roles WHERE role_id='fd88bfed-d869-4969-87f2-67c4e8446ecb' - """), - step( - """ - INSERT INTO role_privileges(role_id, privilege_id) - VALUES( - 'fd88bfed-d869-4969-87f2-67c4e8446ecb', - 'group:resource:view-resource') - """, - """ - DELETE FROM role_privileges - WHERE role_id='fd88bfed-d869-4969-87f2-67c4e8446ecb' - """), - step(grant_to_all_users_public_view_role, - revoke_from_all_users_public_view_role) -] 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 deleted file mode 100644 index 402e9a5..0000000 --- a/migrations/auth/20231002_01_tzxTf-link-inbredsets-to-auth-system.py +++ /dev/null @@ -1,84 +0,0 @@ -""" -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/migrations/auth/20231011_01_CS8NZ-create-new-inbredset-group-owner-role.py b/migrations/auth/20231011_01_CS8NZ-create-new-inbredset-group-owner-role.py deleted file mode 100644 index a4238ed..0000000 --- a/migrations/auth/20231011_01_CS8NZ-create-new-inbredset-group-owner-role.py +++ /dev/null @@ -1,40 +0,0 @@ -""" -Create new 'inbredset-group-owner' role -""" - -from yoyo import step - -__depends__ = {'20231002_01_tzxTf-link-inbredsets-to-auth-system'} - -steps = [ - step( - """ - INSERT INTO roles(role_id, role_name, user_editable) - VALUES('bde1c08b-b067-4d56-8353-462fc5928c32', 'inbredset-group-owner', 0) - """, - """ - DELETE FROM roles WHERE role_id='bde1c08b-b067-4d56-8353-462fc5928c32' - """), - step( - """ - INSERT INTO role_privileges(role_id, privilege_id) - VALUES - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:apply-case-attribute-edit'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:create-case-attribute'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:delete-case-attribute'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:edit-case-attribute'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:reject-case-attribute-edit'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:view-case-attribute') - """, - """ - DELETE FROM role_privileges - WHERE (role_id, privilege_id) - IN - (('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:apply-case-attribute-edit'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:create-case-attribute'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:delete-case-attribute'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:edit-case-attribute'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:reject-case-attribute-edit'), - ('bde1c08b-b067-4d56-8353-462fc5928c32', 'system:inbredset:view-case-attribute')) - """) -] diff --git a/migrations/auth/20240506_01_798tW-create-jwt-refresh-tokens-table.py b/migrations/auth/20240506_01_798tW-create-jwt-refresh-tokens-table.py deleted file mode 100644 index 049ac6b..0000000 --- a/migrations/auth/20240506_01_798tW-create-jwt-refresh-tokens-table.py +++ /dev/null @@ -1,34 +0,0 @@ -""" -Create jwt_refresh_tokens table -""" - -from yoyo import step - -__depends__ = {'20231011_01_CS8NZ-create-new-inbredset-group-owner-role'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS jwt_refresh_tokens - -- Store refresh tokens to verify refresh attempts - ( - token TEXT NOT NULL, - client_id TEXT NOT NULL, - user_id TEXT NOT NULL, - issued_with TEXT NOT NULL UNIQUE, -- JWT ID of JWT issued along with this refresh token - issued_at INTEGER NOT NULL, - expires INTEGER NOT NULL, - scope TEXT NOT NULL, - revoked INTEGER CHECK (revoked = 0 or revoked = 1), - parent_of TEXT UNIQUE, - PRIMARY KEY(token), - FOREIGN KEY (client_id) REFERENCES oauth2_clients(client_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY (parent_of) REFERENCES jwt_refresh_tokens(token) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS jwt_refresh_tokens") -] diff --git a/migrations/auth/20240529_01_ALNWj-update-schema-for-user-verification.py b/migrations/auth/20240529_01_ALNWj-update-schema-for-user-verification.py deleted file mode 100644 index 0cab1c3..0000000 --- a/migrations/auth/20240529_01_ALNWj-update-schema-for-user-verification.py +++ /dev/null @@ -1,64 +0,0 @@ -""" -update schema for user-verification -""" - -from yoyo import step - -__depends__ = {'20240506_01_798tW-create-jwt-refresh-tokens-table'} - -def add_verification_cols_to_users_table(conn): - "add verification columns to users table"; - conn.execute("PRAGMA foreign_keys = OFF") - - conn.execute( - """ - CREATE TABLE users_new( - user_id TEXT PRIMARY KEY NOT NULL, - email TEXT UNIQUE NOT NULL, - name TEXT, - created INTEGER NOT NULL DEFAULT (unixepoch()), - verified INTEGER NOT NULL DEFAULT 0 CHECK (verified=0 or verified=1) - ) WITHOUT ROWID - """) - conn.execute( - """ - INSERT INTO users_new(user_id, email, name) - SELECT user_id, email, name FROM users - """) - # the original table `users` has dependents, so we cannot simply do a - # `ALTER TABLE … RENAME TO …` since according to - # https://sqlite.org/lang_altertable.html#alter_table_rename - # from versions 3.26.0 onward, the foreign key references are **ALWAYS** - # changed. In this case, we create the new table first, do data transfers, - # drop the original and rename the new table to the same name as the - # original. - conn.execute("DROP TABLE IF EXISTS users") - conn.execute("ALTER TABLE users_new RENAME TO users") - - - print("turning foreign keys should back on.") - conn.execute("PRAGMA foreign_key_check") - conn.execute("PRAGMA foreign_keys = ON") - -def drop_verification_cols_from_users_table(conn): - "Drop verification columns from users table" - conn.execute("ALTER TABLE users DROP COLUMN created") - conn.execute("ALTER TABLE users DROP COLUMN verified") - -steps = [ - step(add_verification_cols_to_users_table, - drop_verification_cols_from_users_table), - step( - """ - CREATE TABLE IF NOT EXISTS user_verification_codes( - user_id TEXT NOT NULL, - code TEXT NOT NULL, - generated INTEGER NOT NULL, - expires INTEGER NOT NULL, - PRIMARY KEY(user_id), - FOREIGN KEY(user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE CASCADE - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS verification_codes") -] diff --git a/migrations/auth/20240606_01_xQDwL-move-role-manipulation-privileges-from-group-to-resources.py b/migrations/auth/20240606_01_xQDwL-move-role-manipulation-privileges-from-group-to-resources.py deleted file mode 100644 index a45fd30..0000000 --- a/migrations/auth/20240606_01_xQDwL-move-role-manipulation-privileges-from-group-to-resources.py +++ /dev/null @@ -1,94 +0,0 @@ -""" -Move role-manipulation privileges from group to resources -""" -import sqlite3 -from yoyo import step - -__depends__ = {'20240529_01_ALNWj-update-schema-for-user-verification'} - -def role_by_name(cursor, role_name): - """Fetch group-admin role""" - cursor.execute("SELECT * FROM roles WHERE role_name=?", - (role_name,)) - return dict(cursor.fetchone()) - - -def move_privileges_to_resources(conn): - """Move role-manipulation privileges from group to resource.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "DELETE FROM role_privileges WHERE privilege_id IN (" - " 'group:role:create-role'," - " 'group:role:delete-role'," - " 'group:role:edit-role'," - " 'group:user:assign-role'" - ")") - cursor.execute( - "DELETE FROM privileges WHERE privilege_id IN (" - " 'group:role:create-role'," - " 'group:role:delete-role'," - " 'group:role:edit-role'," - " 'group:user:assign-role'" - ")") - - resource_owner_role = role_by_name(cursor, "resource-owner") - privileges = ( - ("resource:role:create-role", - "Create a new role on a specific resource"), - ("resource:role:delete-role", - "Delete an existing role from a specific resource"), - ("resource:role:edit-role", - "Edit an existing role on a specific resource"), - ("resource:user:assign-role", - "Assign a user to a role on a specific resource")) - cursor.executemany( - ("INSERT INTO privileges(privilege_id, privilege_description) " - "VALUES (?, ?)"), - privileges) - cursor.executemany( - ("INSERT INTO role_privileges(role_id, privilege_id) " - "VALUES(?, ?)"), - tuple((resource_owner_role["role_id"], privilege[0]) - for privilege in privileges)) - cursor.close() - -def move_privileges_to_groups(conn): - """Move role-manipulation privileges from resource to group.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - "DELETE FROM role_privileges WHERE privilege_id IN (" - " 'resource:role:create-role'," - " 'resource:role:delete-role'," - " 'resource:role:edit-role'," - " 'resource:user:assign-role'" - ")") - cursor.execute( - "DELETE FROM privileges WHERE privilege_id IN (" - " 'resource:role:create-role'," - " 'resource:role:delete-role'," - " 'resource:role:edit-role'," - " 'resource:user:assign-role'" - ")") - - group_leader_role = role_by_name(cursor, "group-leader") - privileges = ( - ("group:role:create-role", "Create a new role"), - ("group:role:delete-role", "Delete an existing role"), - ("group:role:edit-role", "edit/update an existing role"), - ("group:user:assign-role", "Assign a role to an existing user")) - cursor.executemany( - ("INSERT INTO privileges(privilege_id, privilege_description) " - "VALUES (?, ?)"), - privileges) - cursor.executemany( - ("INSERT INTO role_privileges(role_id, privilege_id) " - "VALUES(?, ?)"), - tuple((group_leader_role["role_id"], privilege[0]) - for privilege in privileges)) - cursor.close() - -steps = [ - step(move_privileges_to_resources, move_privileges_to_groups) -] diff --git a/migrations/auth/20240606_02_ubZri-create-resource-roles-table.py b/migrations/auth/20240606_02_ubZri-create-resource-roles-table.py deleted file mode 100644 index 0695c0e..0000000 --- a/migrations/auth/20240606_02_ubZri-create-resource-roles-table.py +++ /dev/null @@ -1,36 +0,0 @@ -""" -Create 'resource_roles' table. -""" - -from yoyo import step - -__depends__ = {'20240606_01_xQDwL-move-role-manipulation-privileges-from-group-to-resources'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS resource_roles( - resource_id TEXT NOT NULL, - role_created_by TEXT NOT NULL, - role_id TEXT NOT NULL, - PRIMARY KEY (resource_id, role_created_by, role_id), - FOREIGN KEY(resource_id) REFERENCES resources(resource_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_created_by) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS resource_roles"), - step( - """ - CREATE INDEX IF NOT EXISTS - tbl_resource_roles_cols_resource_id_role_created_by - ON resource_roles(resource_id, role_created_by) - """, - """ - DROP INDEX IF EXISTS - tbl_resource_roles_cols_resource_id_role_created_by - """) -] diff --git a/migrations/auth/20240606_03_BY7Us-drop-group-roles-table.py b/migrations/auth/20240606_03_BY7Us-drop-group-roles-table.py deleted file mode 100644 index 45d689c..0000000 --- a/migrations/auth/20240606_03_BY7Us-drop-group-roles-table.py +++ /dev/null @@ -1,35 +0,0 @@ -""" -Drop 'group_roles' table. -""" -import sqlite3 -from yoyo import step - -__depends__ = {'20240606_02_ubZri-create-resource-roles-table'} - -def restore_group_roles(conn): - """Restore the `group_roles` table.""" - conn.row_factory = sqlite3.Row - cursor = conn.cursor() - cursor.execute( - """ - CREATE TABLE group_roles( - group_role_id TEXT PRIMARY KEY, - group_id TEXT NOT NULL, - role_id TEXT NOT NULL, - UNIQUE (group_id, role_id), - FOREIGN KEY(group_id) REFERENCES groups(group_id) - ON UPDATE CASCADE ON DELETE RESTRICT, - FOREIGN KEY(role_id) REFERENCES roles(role_id) - ON UPDATE CASCADE ON DELETE RESTRICT - ) WITHOUT ROWID - """) - cursor.execute( - """ - CREATE INDEX idx_tbl_group_roles_cols_group_id - ON group_roles(group_id) - """) - cursor.close() - -steps = [ - step("DROP TABLE IF EXISTS group_roles", restore_group_roles) -] diff --git a/migrations/auth/20240819_01_p2vXR-create-forgot-password-tokens-table.py b/migrations/auth/20240819_01_p2vXR-create-forgot-password-tokens-table.py deleted file mode 100644 index 44318bd..0000000 --- a/migrations/auth/20240819_01_p2vXR-create-forgot-password-tokens-table.py +++ /dev/null @@ -1,26 +0,0 @@ -""" -Create forgot_password_tokens table - -This will be used to enable users to validate/verify their password change -requests. -""" - -from yoyo import step - -__depends__ = {'20240606_03_BY7Us-drop-group-roles-table'} - -steps = [ - step( - """ - CREATE TABLE IF NOT EXISTS forgot_password_tokens( - user_id TEXT NOT NULL, - token TEXT NOT NULL, - generated INTEGER NOT NULL, - expires INTEGER NOT NULL, - PRIMARY KEY(user_id), - FOREIGN KEY(user_id) REFERENCES users(user_id) - ON UPDATE CASCADE ON DELETE CASCADE - ) WITHOUT ROWID - """, - "DROP TABLE IF EXISTS forgot_password_tokens") -] diff --git a/migrations/auth/20240924_01_thbvh-hooks-for-edu-domains.py b/migrations/auth/20240924_01_thbvh-hooks-for-edu-domains.py deleted file mode 100644 index 5c6e81d..0000000 --- a/migrations/auth/20240924_01_thbvh-hooks-for-edu-domains.py +++ /dev/null @@ -1,24 +0,0 @@ -""" -hooks_for_edu_domains -""" - -from yoyo import step - -__depends__ = {'20240819_01_p2vXR-create-forgot-password-tokens-table'} - -steps = [ - step( - """ - INSERT INTO roles(role_id, role_name, user_editable) VALUES - ('9bb203a2-7897-4fe3-ac4a-75e6a4f96f5d', 'hook-role-from-edu-domain', '0') - """, - "DELETE FROM roles WHERE role_name='hook-role-from-edu-domain'"), - step( - """ - INSERT INTO role_privileges(role_id, privilege_id) VALUES - ('9bb203a2-7897-4fe3-ac4a-75e6a4f96f5d', 'group:resource:view-resource'), - ('9bb203a2-7897-4fe3-ac4a-75e6a4f96f5d', 'group:resource:edit-resource') - """, - "DELETE FROM role_privileges WHERE role_id='9bb203a2-7897-4fe3-ac4a-75e6a4f96f5d'" - ) -] diff --git a/migrations/auth/__init__.py b/migrations/auth/__init__.py deleted file mode 100644 index 1358c9a..0000000 --- a/migrations/auth/__init__.py +++ /dev/null @@ -1 +0,0 @@ -"Auth(entic|oris)ation package." |