Add missing modules

Copy over missing modules and functions to completely disconnect
gn-auth from GN3.

3 files changed, 462 insertions, 0 deletions

diff --git a/scripts/__init__.py b/scripts/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/scripts/__init__.py
diff --git a/scripts/migrate_existing_data.py b/scripts/migrate_existing_data.py
new file mode 100644
index 0000000..4452f41
--- /dev/null
+++ b/scripts/migrate_existing_data.py
@@ -0,0 +1,381 @@
+"""
+Migrate existing data that is not assigned to any group to the default sys-admin
+group for accessibility purposes.
+"""
+import sys
+import json
+import time
+import random
+from pathlib import Path
+from uuid import UUID, uuid4
+
+import click
+from MySQLdb.cursors import DictCursor
+
+from gn_auth.auth.db import mariadb as biodb
+
+from gn_auth.auth.db import sqlite3 as authdb
+from gn_auth.auth.authentication.users import User
+from gn_auth.auth.authorisation.groups.models import Group, save_group
+from gn_auth.auth.authorisation.roles.models import (
+    revoke_user_role_by_name, assign_user_role_by_name)
+from gn_auth.auth.authorisation.resources.models import (
+    Resource, ResourceCategory, __assign_resource_owner_role__)
+
+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(UUID(row["user_id"]), row["email"], row["name"])
+                     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("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, "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, group: Group) -> tuple[
+        Resource, ...]:
+    """Create default resources."""
+    resources = tuple(Resource(
+        group, 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 (:gid, :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))
+    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 resources AS r INNER JOIN resource_categories AS rc "
+            "ON r.resource_category_id=rc.resource_category_id "
+            "WHERE r.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 tuple(Resource(
+            group,
+            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 ")
+    if len(assigned) > 0:
+        paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(assigned))
+        query = query + (
+            "WHERE (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):
+    "Assign any unassigned mRNA data to resource."
+    while True:
+        unassigned = tuple({
+            "data_link_id": str(uuid4()),
+            "group_id": str(resource.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 "
+                "(:group_id, :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 ")
+    if len(assigned) > 0:
+        paramstr = ", ".join(["(%s, %s, %s)"] * len(assigned))
+        query = query + (
+            "WHERE (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):
+    "Assign any unassigned Genotype data to resource."
+    while True:
+        unassigned = tuple({
+            "data_link_id": str(uuid4()),
+            "group_id": str(resource.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 "
+                "(:group_id, :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 ")
+    if len(assigned) > 0:
+        paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(assigned))
+        query = query + (
+            "WHERE (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):
+    """Assign any unassigned Phenotype data to resource."""
+    while True:
+        unassigned = tuple({
+            "data_link_id": str(uuid4()),
+            "group_id": str(resource.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 "
+                "(:group_id, :resource_id, :data_link_id)",
+                unassigned)
+            print(f"-> Phenotype: Linked {len(unassigned)}")
+            delay()
+
+def assign_data_to_resource(authconn, bioconn, resource: Resource):
+    """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)
+
+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))
+            resources = default_resources(
+                authconn, admin_group(authconn, admin))
+            for resource in resources:
+                assign_data_to_resource(authconn, bioconn, resource)
+                with authdb.cursor(authconn) as cursor:
+                    __assign_resource_owner_role__(cursor, resource, admin)
+    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"
+def run(authdbpath, mysqldburi):
+    """Setup command-line arguments."""
+    entry(authdbpath, mysqldburi)
+
+if __name__ == "__main__":
+    run() # pylint: disable=[no-value-for-parameter]
diff --git a/scripts/register_sys_admin.py b/scripts/register_sys_admin.py
new file mode 100644
index 0000000..7d4d667
--- /dev/null
+++ b/scripts/register_sys_admin.py
@@ -0,0 +1,81 @@
+"""Script to register and mark a user account as sysadmin."""
+import sys
+import uuid
+import getpass
+from pathlib import Path
+
+import click
+from email_validator import validate_email, EmailNotValidError
+
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.authentication.users import hash_password
+
+def fetch_email() -> str:
+    """Prompt user for email."""
+    while True:
+        try:
+            user_input = input("Enter the administrator's email: ")
+            email = validate_email(user_input.strip(), check_deliverability=True)
+            return email["email"]
+        except EmailNotValidError as _enve:
+            print("You did not provide a valid email address. Try again...",
+                  file=sys.stderr)
+
+def fetch_password() -> str:
+    """Prompt user for password."""
+    while True:
+        passwd = getpass.getpass(prompt="Enter password: ").strip()
+        passwd2 = getpass.getpass(prompt="Confirm password: ").strip()
+        if passwd != "" and passwd == passwd2:
+            return passwd
+        if passwd == "":
+            print("Empty password not accepted", file=sys.stderr)
+            continue
+        if passwd != passwd2:
+            print("Passwords *MUST* match", file=sys.stderr)
+            continue
+
+def fetch_name() -> str:
+    """Prompt user for name"""
+    while True:
+        name = input("Enter the user's name: ").strip()
+        if name == "":
+            print("Invalid name.")
+            continue
+        return name
+
+def save_admin(conn: db.DbConnection, name: str, email: str, passwd: str):
+    """Save the details to the database and assign the new user as admin."""
+    admin_id = uuid.uuid4()
+    admin = {
+        "user_id": str(admin_id),
+        "email": email,
+        "name": name,
+        "hash": hash_password(passwd)
+    }
+    with db.cursor(conn) as cursor:
+        cursor.execute("INSERT INTO users VALUES (:user_id, :email, :name)",
+                       admin)
+        cursor.execute("INSERT INTO user_credentials VALUES (:user_id, :hash)",
+                       admin)
+        cursor.execute(
+            "SELECT * FROM roles WHERE role_name='system-administrator'")
+        admin_role = cursor.fetchone()
+        cursor.execute("INSERT INTO user_roles VALUES (:user_id, :role_id)",
+                       {**admin, "role_id": admin_role["role_id"]})
+        return 0
+
+def register_admin(authdbpath: Path):
+    """Register a user as a system admin."""
+    assert authdbpath.exists(), "Could not find database file."
+    with db.connection(str(authdbpath)) as conn:
+        return save_admin(conn, fetch_name(), fetch_email(), fetch_password())
+
+if __name__ == "__main__":
+    @click.command()
+    @click.argument("authdbpath")
+    def run(authdbpath):
+        """Entry-point for when script is run directly"""
+        return register_admin(Path(authdbpath).absolute())
+
+    run()# pylint: disable=[no-value-for-parameter]