diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/migrate_existing_data.py | 50 |
1 files changed, 24 insertions, 26 deletions
diff --git a/scripts/migrate_existing_data.py b/scripts/migrate_existing_data.py index c9ac343..ab3e739 100644 --- a/scripts/migrate_existing_data.py +++ b/scripts/migrate_existing_data.py @@ -19,7 +19,8 @@ from gn_auth.auth.authentication.users import User from gn_auth.auth.authorisation.roles.models import ( revoke_user_role_by_name, assign_user_role_by_name) -from gn_auth.auth.authorisation.resources.groups.models import Group, save_group +from gn_auth.auth.authorisation.resources.groups.models import ( + Group, save_group, add_resources_to_group) from gn_auth.auth.authorisation.resources.models import ( Resource, ResourceCategory, __assign_resource_owner_role__) @@ -128,8 +129,7 @@ def __resource_category_by_key__( row["resource_category_key"], row["resource_category_description"]) -def __create_resources__(cursor: authdb.DbCursor, group: Group) -> tuple[ - Resource, ...]: +def __create_resources__(cursor: authdb.DbCursor) -> tuple[Resource, ...]: """Create default resources.""" resources = tuple(Resource( uuid4(), name, __resource_category_by_key__(cursor, catkey), @@ -139,20 +139,13 @@ def __create_resources__(cursor: authdb.DbCursor, group: Group) -> tuple[ ("pheno-xboecp", "phenotype"), ("geno-welphd", "genotype"))) cursor.executemany( - "INSERT INTO resources VALUES (:gid, :rid, :rname, :rcid, :pub)", + "INSERT INTO resources VALUES (:rid, :rname, :rcid, :pub)", tuple({ - "gid": str(group.group_id), "rid": str(res.resource_id), "rname": res.resource_name, "rcid": str(res.resource_category.resource_category_id), "pub": 1 } for res in resources)) - cursor.executemany("INSERT INTO resource_ownership(group_id, resource_id) " - "VALUES (:group_id, :resource_id)", - tuple({ - "group_id": str(group.group_id), - "resource_id": str(resource.resource_id) - } for resource in resources)) return resources def default_resources(conn: authdb.DbConnection, group: Group) -> tuple[ @@ -161,14 +154,16 @@ def default_resources(conn: authdb.DbConnection, group: Group) -> tuple[ with authdb.cursor(conn) as cursor: cursor.execute( "SELECT r.resource_id, r.resource_name, r.public, rc.* " - "FROM resources AS r INNER JOIN resource_categories AS rc " + "FROM resource_ownership AS ro INNER JOIN resources AS r " + "ON ro.resource_id=r.resource_id " + "INNER JOIN resource_categories AS rc " "ON r.resource_category_id=rc.resource_category_id " - "WHERE r.group_id=? AND r.resource_name IN " + "WHERE ro.group_id=? AND r.resource_name IN " "('mRNA-euhrin', 'pheno-xboecp', 'geno-welphd')", (str(group.group_id),)) rows = cursor.fetchall() if len(rows) == 0: - return __create_resources__(cursor, group) + return __create_resources__(cursor) return tuple(Resource( UUID(row["resource_id"]), @@ -216,12 +211,12 @@ def __unassigned_mrna__(bioconn, assigned): cursor.execute(query, tuple(item for row in assigned for item in row)) return (row for row in cursor.fetchall()) -def __assign_mrna__(authconn, bioconn, resource): +def __assign_mrna__(authconn, bioconn, resource, group): "Assign any unassigned mRNA data to resource." while True: unassigned = tuple({ "data_link_id": str(uuid4()), - "group_id": str(resource.group.group_id), + "group_id": str(group.group_id), "resource_id": str(resource.resource_id), **row } for row in __unassigned_mrna__( @@ -239,7 +234,7 @@ def __assign_mrna__(authconn, bioconn, resource): unassigned) cursor.executemany( "INSERT INTO mrna_resources VALUES " - "(:group_id, :resource_id, :data_link_id)", + "(:resource_id, :data_link_id)", unassigned) print(f"-> mRNA: Linked {len(unassigned)}") delay() @@ -274,12 +269,12 @@ def __unassigned_geno__(bioconn, assigned): cursor.execute(query, tuple(item for row in assigned for item in row)) return (row for row in cursor.fetchall()) -def __assign_geno__(authconn, bioconn, resource): +def __assign_geno__(authconn, bioconn, resource, group): "Assign any unassigned Genotype data to resource." while True: unassigned = tuple({ "data_link_id": str(uuid4()), - "group_id": str(resource.group.group_id), + "group_id": str(group.group_id), "resource_id": str(resource.resource_id), **row } for row in __unassigned_geno__( @@ -297,7 +292,7 @@ def __assign_geno__(authconn, bioconn, resource): unassigned) cursor.executemany( "INSERT INTO genotype_resources VALUES " - "(:group_id, :resource_id, :data_link_id)", + "(:resource_id, :data_link_id)", unassigned) print(f"-> Genotype: Linked {len(unassigned)}") delay() @@ -338,12 +333,12 @@ def __unassigned_pheno__(bioconn, assigned): cursor.execute(query, tuple(item for row in assigned for item in row)) return (row for row in cursor.fetchall()) -def __assign_pheno__(authconn, bioconn, resource): +def __assign_pheno__(authconn, bioconn, resource, group): """Assign any unassigned Phenotype data to resource.""" while True: unassigned = tuple({ "data_link_id": str(uuid4()), - "group_id": str(resource.group.group_id), + "group_id": str(group.group_id), "resource_id": str(resource.resource_id), **row } for row in __unassigned_pheno__( @@ -361,12 +356,13 @@ def __assign_pheno__(authconn, bioconn, resource): unassigned) cursor.executemany( "INSERT INTO phenotype_resources VALUES " - "(:group_id, :resource_id, :data_link_id)", + "(:resource_id, :data_link_id)", unassigned) print(f"-> Phenotype: Linked {len(unassigned)}") delay() -def assign_data_to_resource(authconn, bioconn, resource: Resource): +def assign_data_to_resource( + authconn, bioconn, resource: Resource, group: Group): """Assign existing data, not linked to any group to the resource.""" assigner_fns = { "mrna": __assign_mrna__, @@ -374,7 +370,7 @@ def assign_data_to_resource(authconn, bioconn, resource: Resource): "phenotype": __assign_pheno__ } return assigner_fns[resource.resource_category.resource_category_key]( - authconn, bioconn, resource) + authconn, bioconn, resource, group) def entry(authdbpath, mysqldburi): """Entry-point for data migration.""" @@ -390,8 +386,10 @@ def entry(authdbpath, mysqldburi): the_admin_group = admin_group(authconn, admin) resources = default_resources( authconn, the_admin_group) + add_resources_to_group(authconn, resources, the_admin_group) for resource in resources: - assign_data_to_resource(authconn, bioconn, resource) + assign_data_to_resource( + authconn, bioconn, resource, the_admin_group) with authdb.cursor(authconn) as cursor: __assign_resource_owner_role__( cursor, resource, admin, the_admin_group) |