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Diffstat (limited to 'scripts/assign_data_to_default_admin.py')
| -rw-r--r-- | scripts/assign_data_to_default_admin.py | 434 |
1 files changed, 434 insertions, 0 deletions
diff --git a/scripts/assign_data_to_default_admin.py b/scripts/assign_data_to_default_admin.py new file mode 100644 index 0000000..69fc50c --- /dev/null +++ b/scripts/assign_data_to_default_admin.py @@ -0,0 +1,434 @@ +""" +Assign any existing data (that is not currently assigned to any group) to the +default sys-admin group for accessibility purposes. +""" +import sys +import json +import time +import random +import logging +from pathlib import Path +from uuid import UUID, uuid4 + +import click +from gn_libs import mysqldb as biodb +from MySQLdb.cursors import DictCursor + +import gn_auth.auth.db.sqlite3 as authdb +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, add_resources_to_group) +from gn_auth.auth.authorisation.resources.common import assign_resource_owner_role +from gn_auth.auth.authorisation.resources.models import Resource, ResourceCategory + + +class DataNotFound(Exception): + """Raise if no admin user exists.""" + + +def sys_admins(conn: authdb.DbConnection) -> tuple[User, ...]: + """Retrieve all the existing system admins.""" + with authdb.cursor(conn) as cursor: + cursor.execute( + "SELECT u.* FROM users AS u " + "INNER JOIN user_roles AS ur ON u.user_id=ur.user_id " + "INNER JOIN roles AS r ON ur.role_id=r.role_id " + "WHERE r.role_name='system-administrator'") + return tuple(User.from_sqlite3_row(row) for row in cursor.fetchall()) + return tuple() + + +def choose_admin(enum_admins: dict[int, User]) -> int: + """Prompt and read user choice.""" + while True: + try: + print("\n===========================\n") + print("We found the following system administrators:") + for idx, admin in enum_admins.items(): + print(f"\t{idx}: {admin.name} ({admin.email})") + choice = input(f"Choose [1 .. {len(enum_admins)}]: ") + return int(choice) + except ValueError as _verr: + if choice.lower() == "quit": + print("Goodbye!") + sys.exit(0) + print(f"\nERROR: Invalid choice '{choice}'!") + + +def select_sys_admin(admins: tuple[User, ...]) -> User: + """Pick one admin out of list.""" + if len(admins) > 0: + if len(admins) == 1: + print(f"-> Found Admin: {admins[0].name} ({admins[0].email})") + return admins[0] + enum_admins = dict(enumerate(admins, start=1)) + chosen = enum_admins[choose_admin(enum_admins)] + print(f"-> Chosen Admin: {chosen.name} ({chosen.email})") + return chosen + raise DataNotFound( + "No administrator user found. Create an administrator user first.") + + +def admin_group(conn: authdb.DbConnection, admin: User) -> Group: + """Retrieve the admin's user group. If none exist, create one.""" + with authdb.cursor(conn) as cursor: + cursor.execute( + "SELECT g.* FROM users AS u " + "INNER JOIN group_users AS gu ON u.user_id=gu.user_id " + "INNER JOIN groups AS g on gu.group_id=g.group_id " + "WHERE u.user_id = ?", + (str(admin.user_id),)) + row = cursor.fetchone() + if row: + return Group(UUID(row["group_id"]), + row["group_name"], + json.loads(row["group_metadata"])) + new_group = save_group(cursor, "AutoAdminGroup", { + "group_description": ( + "Created by script for existing data visibility. " + "Existing data was migrated into this group and assigned " + "to publicly visible resources according to type.") + }) + + cursor.execute( + "SELECT * FROM resource_categories WHERE " + "resource_category_key='group'") + res_cat_id = cursor.fetchone()["resource_category_id"] + grp_res = { + "group_id": str(new_group.group_id), + "resource_id": str(uuid4()), + "resource_name": new_group.group_name, + "resource_category_id": res_cat_id, + "public": 0 + } + cursor.execute( + "INSERT INTO resources VALUES " + "(:resource_id, :resource_name, :resource_category_id, :public)", + grp_res) + cursor.execute( + "INSERT INTO group_resources(resource_id, group_id) " + "VALUES(:resource_id, :group_id)", + grp_res) + cursor.execute("INSERT INTO group_users VALUES (?, ?)", + (str(new_group.group_id), str(admin.user_id))) + revoke_user_role_by_name(cursor, admin, "group-creator") + assign_user_role_by_name( + cursor, admin, UUID(grp_res["resource_id"]), "group-leader") + return new_group + + +def __resource_category_by_key__( + cursor: authdb.DbCursor, category_key: str) -> ResourceCategory: + """Retrieve a resource category by its ID.""" + cursor.execute( + "SELECT * FROM resource_categories WHERE resource_category_key = ?", + (category_key,)) + row = cursor.fetchone() + if not bool(row): + raise DataNotFound( + f"Could not find resource category with key {category_key}") + return ResourceCategory(UUID(row["resource_category_id"]), + row["resource_category_key"], + row["resource_category_description"]) + + +def __create_resources__(cursor: authdb.DbCursor) -> tuple[Resource, ...]: + """Create default resources.""" + resources = tuple(Resource( + uuid4(), name, __resource_category_by_key__(cursor, catkey), + True, tuple() + ) for name, catkey in ( + ("mRNA-euhrin", "mrna"), + ("pheno-xboecp", "phenotype"), + ("geno-welphd", "genotype"))) + cursor.executemany( + "INSERT INTO resources VALUES (:rid, :rname, :rcid, :pub)", + tuple({ + "rid": str(res.resource_id), + "rname": res.resource_name, + "rcid": str(res.resource_category.resource_category_id), + "pub": 1 + } for res in resources)) + return resources + + +def default_resources(conn: authdb.DbConnection, group: Group) -> tuple[ + Resource, ...]: + """Create default resources, or return them if they exist.""" + with authdb.cursor(conn) as cursor: + cursor.execute( + "SELECT r.resource_id, r.resource_name, r.public, 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 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) + + return tuple(Resource( + UUID(row["resource_id"]), + row["resource_name"], + ResourceCategory( + UUID(row["resource_category_id"]), + row["resource_category_key"], + row["resource_category_description"]), + bool(row["public"]), + tuple() + ) for row in rows) + + +def delay(): + """Delay a while: anything from 2 seconds to 15 seconds.""" + time.sleep(random.choice(range(2,16))) + + +def __assigned_mrna__(authconn): + """Retrieve assigned mRNA items.""" + with authdb.cursor(authconn) as cursor: + cursor.execute( + "SELECT SpeciesId, InbredSetId, ProbeFreezeId, ProbeSetFreezeId " + "FROM linked_mrna_data") + return tuple( + (row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"], + row["ProbeSetFreezeId"]) for row in cursor.fetchall()) + + +def __unassigned_mrna__(bioconn, assigned): + """Retrieve unassigned mRNA data items.""" + query = ( + "SELECT s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, " + "psf.Id AS ProbeSetFreezeId, psf.Name AS dataset_name, " + "psf.FullName AS dataset_fullname, psf.ShortName AS dataset_shortname " + "FROM Species AS s INNER JOIN InbredSet AS iset " + "ON s.SpeciesId=iset.SpeciesId INNER JOIN ProbeFreeze AS pf " + "ON iset.InbredSetId=pf.InbredSetId INNER JOIN ProbeSetFreeze AS psf " + "ON pf.ProbeFreezeId=psf.ProbeFreezeId " + "WHERE s.Name != 'human' ") + if len(assigned) > 0: + paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(assigned)) + query = query + ( + "AND (s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, psf.Id) " + f"NOT IN ({paramstr}) ") + + query = query + "LIMIT 100000" + with bioconn.cursor(DictCursor) as cursor: + 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, group): + "Assign any unassigned mRNA data to resource." + while True: + unassigned = tuple({ + "data_link_id": str(uuid4()), + "group_id": str(group.group_id), + "resource_id": str(resource.resource_id), + **row + } for row in __unassigned_mrna__( + bioconn, __assigned_mrna__(authconn))) + + if len(unassigned) <= 0: + print("-> mRNA: Completed!") + break + with authdb.cursor(authconn) as cursor: + cursor.executemany( + "INSERT INTO linked_mrna_data VALUES " + "(:data_link_id, :group_id, :SpeciesId, :InbredSetId, " + ":ProbeFreezeId, :ProbeSetFreezeId, :dataset_name, " + ":dataset_fullname, :dataset_shortname)", + unassigned) + cursor.executemany( + "INSERT INTO mrna_resources VALUES " + "(:resource_id, :data_link_id)", + unassigned) + print(f"-> mRNA: Linked {len(unassigned)}") + delay() + + +def __assigned_geno__(authconn): + """Retrieve assigned genotype data.""" + with authdb.cursor(authconn) as cursor: + cursor.execute( + "SELECT SpeciesId, InbredSetId, GenoFreezeId " + "FROM linked_genotype_data") + return tuple((row["SpeciesId"], row["InbredSetId"], row["GenoFreezeId"]) + for row in cursor.fetchall()) + +def __unassigned_geno__(bioconn, assigned): + """Fetch unassigned genotype data.""" + query = ( + "SELECT s.SpeciesId, iset.InbredSetId, iset.InbredSetName, " + "gf.Id AS GenoFreezeId, gf.Name AS dataset_name, " + "gf.FullName AS dataset_fullname, " + "gf.ShortName AS dataset_shortname " + "FROM Species AS s INNER JOIN InbredSet AS iset " + "ON s.SpeciesId=iset.SpeciesId INNER JOIN GenoFreeze AS gf " + "ON iset.InbredSetId=gf.InbredSetId " + "WHERE s.Name != 'human' ") + if len(assigned) > 0: + paramstr = ", ".join(["(%s, %s, %s)"] * len(assigned)) + query = query + ( + "AND (s.SpeciesId, iset.InbredSetId, gf.Id) " + f"NOT IN ({paramstr}) ") + + query = query + "LIMIT 100000" + with bioconn.cursor(DictCursor) as cursor: + 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, group): + "Assign any unassigned Genotype data to resource." + while True: + unassigned = tuple({ + "data_link_id": str(uuid4()), + "group_id": str(group.group_id), + "resource_id": str(resource.resource_id), + **row + } for row in __unassigned_geno__( + bioconn, __assigned_geno__(authconn))) + + if len(unassigned) <= 0: + print("-> Genotype: Completed!") + break + with authdb.cursor(authconn) as cursor: + cursor.executemany( + "INSERT INTO linked_genotype_data VALUES " + "(:data_link_id, :group_id, :SpeciesId, :InbredSetId, " + ":GenoFreezeId, :dataset_name, :dataset_fullname, " + ":dataset_shortname)", + unassigned) + cursor.executemany( + "INSERT INTO genotype_resources VALUES " + "(:resource_id, :data_link_id)", + unassigned) + print(f"-> Genotype: Linked {len(unassigned)}") + delay() + + +def __assigned_pheno__(authconn): + """Retrieve assigned phenotype data.""" + with authdb.cursor(authconn) as cursor: + cursor.execute( + "SELECT SpeciesId, InbredSetId, PublishFreezeId, PublishXRefId " + "FROM linked_phenotype_data") + return tuple(( + row["SpeciesId"], row["InbredSetId"], row["PublishFreezeId"], + row["PublishXRefId"]) for row in cursor.fetchall()) + + +def __unassigned_pheno__(bioconn, assigned): + """Retrieve all unassigned Phenotype data.""" + query = ( + "SELECT spc.SpeciesId, iset.InbredSetId, " + "pf.Id AS PublishFreezeId, pf.Name AS dataset_name, " + "pf.FullName AS dataset_fullname, " + "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId " + "FROM " + "Species AS spc " + "INNER JOIN InbredSet AS iset " + "ON spc.SpeciesId=iset.SpeciesId " + "INNER JOIN PublishFreeze AS pf " + "ON iset.InbredSetId=pf.InbredSetId " + "INNER JOIN PublishXRef AS pxr " + "ON pf.InbredSetId=pxr.InbredSetId " + "WHERE spc.Name != 'human' ") + if len(assigned) > 0: + paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(assigned)) + query = query + ( + "AND (spc.SpeciesId, iset.InbredSetId, pf.Id, pxr.Id) " + f"NOT IN ({paramstr}) ") + + query = query + "LIMIT 100000" + with bioconn.cursor(DictCursor) as cursor: + 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, group): + """Assign any unassigned Phenotype data to resource.""" + while True: + unassigned = tuple({ + "data_link_id": str(uuid4()), + "group_id": str(group.group_id), + "resource_id": str(resource.resource_id), + **row + } for row in __unassigned_pheno__( + bioconn, __assigned_pheno__(authconn))) + + if len(unassigned) <= 0: + print("-> Phenotype: Completed!") + break + with authdb.cursor(authconn) as cursor: + cursor.executemany( + "INSERT INTO linked_phenotype_data VALUES " + "(:data_link_id, :group_id, :SpeciesId, :InbredSetId, " + ":PublishFreezeId, :dataset_name, :dataset_fullname, " + ":dataset_shortname, :PublishXRefId)", + unassigned) + cursor.executemany( + "INSERT INTO phenotype_resources VALUES " + "(:resource_id, :data_link_id)", + unassigned) + print(f"-> Phenotype: Linked {len(unassigned)}") + delay() + + +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__, + "genotype": __assign_geno__, + "phenotype": __assign_pheno__ + } + return assigner_fns[resource.resource_category.resource_category_key]( + authconn, bioconn, resource, group) + + +def entry(authdbpath, mysqldburi): + """Entry-point for data migration.""" + if not Path(authdbpath).exists(): + print( + f"ERROR: Auth db file `{authdbpath}` does not exist.", + file=sys.stderr) + sys.exit(2) + try: + with (authdb.connection(authdbpath) as authconn, + biodb.database_connection(mysqldburi) as bioconn): + admin = select_sys_admin(sys_admins(authconn)) + 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, the_admin_group) + with authdb.cursor(authconn) as cursor: + assign_resource_owner_role( + cursor, resource.resource_id, admin.user_id) + except DataNotFound as dnf: + print(dnf.args[0], file=sys.stderr) + sys.exit(1) + + +@click.command() +@click.argument("authdbpath") # "Path to the Auth(entic|oris)ation database" +@click.argument("mysqldburi") # "URI to the MySQL database with the biology data" +@click.option("--loglevel", default="WARNING", show_default=True, + type=click.Choice(["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"])) +def run(authdbpath, mysqldburi, loglevel): + """Setup command-line arguments.""" + globallogger = logging.getLogger() + globallogger.setLevel(loglevel) + entry(authdbpath, mysqldburi) + + +if __name__ == "__main__": + run() # pylint: disable=[no-value-for-parameter] |