diff options
Diffstat (limited to 'migrations')
| -rw-r--r-- | migrations/auth/20230907_03_BwAmf-refactor-drop-group-id-from-resources-table.py | 325 |
1 files changed, 325 insertions, 0 deletions
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 new file mode 100644 index 0000000..0f491c2 --- /dev/null +++ b/migrations/auth/20230907_03_BwAmf-refactor-drop-group-id-from-resources-table.py @@ -0,0 +1,325 @@ +""" +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) +] |