Move `groups` package under `resources` package

With user groups being resources that users can act on (with the
recent changes), this commit moves the `groups` module to under the
`resources` module.

It also renames the `*_resources.py` modules by dropping the
`_resources` part since the code is under the `resources` module
anyway.

4 files changed, 0 insertions, 974 deletions

diff --git a/gn_auth/auth/authorisation/groups/__init__.py b/gn_auth/auth/authorisation/groups/__init__.py
deleted file mode 100644
index 1cb0bba..0000000
--- a/gn_auth/auth/authorisation/groups/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Initialise the `gn3.auth.authorisation.groups` package"""
-
-from .models import Group, GroupRole
diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py
deleted file mode 100644
index 1650405..0000000
--- a/gn_auth/auth/authorisation/groups/data.py
+++ /dev/null
@@ -1,107 +0,0 @@
-"""Handles the resource objects' data."""
-from MySQLdb.cursors import DictCursor
-
-from ..groups import Group
-from ..checks import authorised_p
-from ..errors import NotFoundError
-
-from ...db import mariadb as gn3db
-from ...db import sqlite3 as authdb
-
-def __fetch_mrna_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
-            dict, ...]:
-    """Fetch mRNA Assay data by ID."""
-    with conn.cursor(DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(dataset_ids))
-        cursor.execute(
-            "SELECT psf.Id, psf.Name AS dataset_name, "
-            "psf.FullName AS dataset_fullname, "
-            "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf "
-            "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName "
-            f"WHERE psf.Id IN ({paramstr})",
-            dataset_ids)
-        res = cursor.fetchall()
-        if res:
-            return tuple(dict(row) for row in res)
-        raise NotFoundError("Could not find mRNA Assay data with the given ID.")
-
-def __fetch_geno_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
-            dict, ...]:
-    """Fetch genotype data by ID."""
-    with conn.cursor(DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(dataset_ids))
-        cursor.execute(
-            "SELECT gf.Id, gf.Name AS dataset_name, "
-            "gf.FullName AS dataset_fullname, "
-            "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf "
-            "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName "
-            f"WHERE gf.Id IN ({paramstr})",
-            dataset_ids)
-        res = cursor.fetchall()
-        if res:
-            return tuple(dict(row) for row in res)
-        raise NotFoundError("Could not find Genotype data with the given ID.")
-
-def __fetch_pheno_data_by_ids__(
-        conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
-            dict, ...]:
-    """Fetch phenotype data by ID."""
-    with conn.cursor(DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(dataset_ids))
-        cursor.execute(
-            "SELECT pxf.Id, iset.InbredSetName, pf.Id AS dataset_id, "
-            "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, "
-            "ifiles.GN_AccesionId AS accession_id "
-            "FROM PublishXRef AS pxf "
-            "INNER JOIN InbredSet AS iset ON pxf.InbredSetId=iset.InbredSetId "
-            "INNER JOIN PublishFreeze AS pf ON iset.InbredSetId=pf.InbredSetId "
-            "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName "
-            f"WHERE pxf.Id IN ({paramstr})",
-            dataset_ids)
-        res = cursor.fetchall()
-        if res:
-            return tuple(dict(row) for row in res)
-        raise NotFoundError(
-            "Could not find Phenotype/Publish data with the given IDs.")
-
-def __fetch_data_by_id(
-        conn: gn3db.DbConnection, dataset_type: str,
-        dataset_ids: tuple[str, ...]) -> tuple[dict, ...]:
-    """Fetch data from MySQL by IDs."""
-    fetch_fns = {
-        "mrna": __fetch_mrna_data_by_ids__,
-        "genotype": __fetch_geno_data_by_ids__,
-        "phenotype": __fetch_pheno_data_by_ids__
-    }
-    return fetch_fns[dataset_type](conn, dataset_ids)
-
-@authorised_p(("system:data:link-to-group",),
-              error_description=(
-                  "You do not have sufficient privileges to link data to (a) "
-                  "group(s)."),
-              oauth2_scope="profile group resource")
-def link_data_to_group(
-        authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
-        dataset_type: str, dataset_ids: tuple[str, ...], group: Group) -> tuple[
-            dict, ...]:
-    """Link the given data to the specified group."""
-    the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_ids)
-    with authdb.cursor(authconn) as cursor:
-        params = tuple({
-            "group_id": str(group.group_id), "dataset_type": {
-                "mrna": "mRNA", "genotype": "Genotype",
-                "phenotype": "Phenotype"
-            }[dataset_type],
-            "dataset_or_trait_id": item["Id"],
-            "dataset_name": item["dataset_name"],
-            "dataset_fullname": item["dataset_fullname"],
-            "accession_id": item["accession_id"]
-        } for item in the_data)
-        cursor.executemany(
-            "INSERT INTO linked_group_data VALUES"
-            "(:group_id, :dataset_type, :dataset_or_trait_id, :dataset_name, "
-            ":dataset_fullname, :accession_id)",
-            params)
-        return params
diff --git a/gn_auth/auth/authorisation/groups/models.py b/gn_auth/auth/authorisation/groups/models.py
deleted file mode 100644
index c40adbd..0000000
--- a/gn_auth/auth/authorisation/groups/models.py
+++ /dev/null
@@ -1,433 +0,0 @@
-"""Handle the management of resource/user groups."""
-import json
-from uuid import UUID, uuid4
-from functools import reduce
-from typing import Any, Sequence, Iterable, Optional, NamedTuple
-
-from flask import g
-from pymonad.maybe import Just, Maybe, Nothing
-
-from ...db import sqlite3 as db
-from ...dictify import dictify
-from ...authentication.users import User, user_by_id
-
-from ..checks import authorised_p
-from ..privileges import Privilege
-from ..errors import NotFoundError, AuthorisationError, InconsistencyError
-from ..roles.models import (
-    Role, create_role, check_user_editable, revoke_user_role_by_name,
-    assign_user_role_by_name)
-
-class Group(NamedTuple):
-    """Class representing a group."""
-    group_id: UUID
-    group_name: str
-    group_metadata: dict[str, Any]
-
-    def dictify(self):
-        """Return a dict representation of `Group` objects."""
-        return {
-            "group_id": self.group_id, "group_name": self.group_name,
-            "group_metadata": self.group_metadata
-        }
-
-DUMMY_GROUP = Group(
-    group_id=UUID("77cee65b-fe29-4383-ae41-3cb3b480cc70"),
-    group_name="GN3_DUMMY_GROUP",
-    group_metadata={
-        "group-description": "This is a dummy group to use as a placeholder"
-    })
-
-class GroupRole(NamedTuple):
-    """Class representing a role tied/belonging to a group."""
-    group_role_id: UUID
-    group: Group
-    role: Role
-
-    def dictify(self) -> dict[str, Any]:
-        """Return a dict representation of `GroupRole` objects."""
-        return {
-            "group_role_id": self.group_role_id, "group": dictify(self.group),
-            "role": dictify(self.role)
-        }
-
-class GroupCreationError(AuthorisationError):
-    """Raised whenever a group creation fails"""
-
-class MembershipError(AuthorisationError):
-    """Raised when there is an error with a user's membership to a group."""
-
-    def __init__(self, user: User, groups: Sequence[Group]):
-        """Initialise the `MembershipError` exception object."""
-        groups_str = ", ".join(group.group_name for group in groups)
-        error_description = (
-            f"User '{user.name} ({user.email})' is a member of {len(groups)} "
-            f"groups ({groups_str})")
-        super().__init__(f"{type(self).__name__}: {error_description}.")
-
-def user_membership(conn: db.DbConnection, user: User) -> Sequence[Group]:
-    """Returns all the groups that a member belongs to"""
-    query = (
-        "SELECT groups.group_id, group_name, groups.group_metadata "
-        "FROM group_users INNER JOIN groups "
-        "ON group_users.group_id=groups.group_id "
-        "WHERE group_users.user_id=?")
-    with db.cursor(conn) as cursor:
-        cursor.execute(query, (str(user.user_id),))
-        groups = tuple(Group(row[0], row[1], json.loads(row[2]))
-                       for row in cursor.fetchall())
-
-    return groups
-
-@authorised_p(
-    privileges = ("system:group:create-group",),
-    error_description = (
-        "You do not have the appropriate privileges to enable you to "
-        "create a new group."),
-    oauth2_scope = "profile group")
-def create_group(
-        conn: db.DbConnection, group_name: str, group_leader: User,
-        group_description: Optional[str] = None) -> Group:
-    """Create a new group."""
-    def resource_category_by_key(
-        cursor: db.DbCursor, category_key: str):
-        """Retrieve a resource category by its key."""
-        cursor.execute(
-            "SELECT * FROM resource_categories WHERE "
-            "resource_category_key=?",
-            (category_key,))
-        results = cursor.fetchone()
-        if results:
-            return dict(results)
-        raise NotFoundError(
-            f"Could not find a ResourceCategory with key '{category_key}'")
-
-    user_groups = user_membership(conn, group_leader)
-    if len(user_groups) > 0:
-        raise MembershipError(group_leader, user_groups)
-
-    with db.cursor(conn) as cursor:
-        new_group = save_group(
-            cursor, group_name,(
-                {"group_description": group_description}
-                if group_description else {}))
-        group_resource = {
-            "group_id": str(new_group.group_id),
-            "resource_id": str(uuid4()),
-            "resource_name": group_name,
-            "resource_category_id": str(
-                resource_category_by_key(cursor, "group")["resource_category_id"]),
-            "public": 0
-        }
-        cursor.execute(
-            "INSERT INTO resources VALUES "
-            "(:resource_id, :resource_name, :resource_category_id, :public)",
-            group_resource)
-        cursor.execute(
-            "INSERT INTO group_resources(resource_id, group_id) "
-            "VALUES(:resource_id, :group_id)",
-            group_resource)
-        add_user_to_group(cursor, new_group, group_leader)
-        revoke_user_role_by_name(cursor, group_leader, "group-creator")
-        assign_user_role_by_name(
-            cursor,
-            group_leader,
-            UUID(str(group_resource["resource_id"])),
-            "group-leader")
-        return new_group
-
-@authorised_p(("group:role:create-role",),
-              error_description="Could not create the group role")
-def create_group_role(
-        conn: db.DbConnection, group: Group, role_name: str,
-        privileges: Iterable[Privilege]) -> GroupRole:
-    """Create a role attached to a group."""
-    with db.cursor(conn) as cursor:
-        group_role_id = uuid4()
-        role = create_role(cursor, role_name, privileges)
-        cursor.execute(
-            ("INSERT INTO group_roles(group_role_id, group_id, role_id) "
-             "VALUES(?, ?, ?)"),
-            (str(group_role_id), str(group.group_id), str(role.role_id)))
-
-    return GroupRole(group_role_id, group, role)
-
-def authenticated_user_group(conn) -> Maybe:
-    """
-    Returns the currently authenticated user's group.
-
-    Look into returning a Maybe object.
-    """
-    user = g.user
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            ("SELECT groups.* FROM group_users "
-             "INNER JOIN groups ON group_users.group_id=groups.group_id "
-             "WHERE group_users.user_id = ?"),
-            (str(user.user_id),))
-        groups = tuple(Group(UUID(row[0]), row[1], json.loads(row[2] or "{}"))
-                       for row in cursor.fetchall())
-
-    if len(groups) > 1:
-        raise MembershipError(user, groups)
-
-    if len(groups) == 1:
-        return Just(groups[0])
-
-    return Nothing
-
-def user_group(conn: db.DbConnection, user: User) -> Maybe[Group]:
-    """Returns the given user's group"""
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            ("SELECT groups.group_id, groups.group_name, groups.group_metadata "
-             "FROM group_users "
-             "INNER JOIN groups ON group_users.group_id=groups.group_id "
-             "WHERE group_users.user_id = ?"),
-            (str(user.user_id),))
-        groups = tuple(
-            Group(UUID(row[0]), row[1], json.loads(row[2] or "{}"))
-            for row in cursor.fetchall())
-
-        if len(groups) > 1:
-            raise MembershipError(user, groups)
-
-        if len(groups) == 1:
-            return Just(groups[0])
-
-    return Nothing
-
-def is_group_leader(conn: db.DbConnection, user: User, group: Group) -> bool:
-    """Check whether the given `user` is the leader of `group`."""
-
-    ugroup = user_group(conn, user).maybe(
-        False, lambda val: val) # type: ignore[arg-type, misc]
-    if not group:
-        # User cannot be a group leader if not a member of ANY group
-        return False
-
-    if not ugroup == group:
-        # User cannot be a group leader if not a member of THIS group
-        return False
-
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            ("SELECT roles.role_name FROM user_roles LEFT JOIN roles "
-             "ON user_roles.role_id = roles.role_id WHERE user_id = ?"),
-            (str(user.user_id),))
-        role_names = tuple(row[0] for row in cursor.fetchall())
-
-        return "group-leader" in role_names
-
-def all_groups(conn: db.DbConnection) -> Maybe[Sequence[Group]]:
-    """Retrieve all existing groups"""
-    with db.cursor(conn) as cursor:
-        cursor.execute("SELECT * FROM groups")
-        res = cursor.fetchall()
-        if res:
-            return Just(tuple(
-                Group(row["group_id"], row["group_name"],
-                      json.loads(row["group_metadata"])) for row in res))
-
-    return Nothing
-
-def save_group(
-        cursor: db.DbCursor, group_name: str,
-        group_metadata: dict[str, Any]) -> Group:
-    """Save a group to db"""
-    the_group = Group(uuid4(), group_name, group_metadata)
-    cursor.execute(
-        ("INSERT INTO groups "
-         "VALUES(:group_id, :group_name, :group_metadata) "
-         "ON CONFLICT (group_id) DO UPDATE SET "
-         "group_name=:group_name, group_metadata=:group_metadata"),
-        {"group_id": str(the_group.group_id), "group_name": the_group.group_name,
-         "group_metadata": json.dumps(the_group.group_metadata)})
-    return the_group
-
-def add_user_to_group(cursor: db.DbCursor, the_group: Group, user: User):
-    """Add `user` to `the_group` as a member."""
-    cursor.execute(
-        ("INSERT INTO group_users VALUES (:group_id, :user_id) "
-         "ON CONFLICT (group_id, user_id) DO NOTHING"),
-        {"group_id": str(the_group.group_id), "user_id": str(user.user_id)})
-
-@authorised_p(
-    privileges = ("system:group:view-group",),
-    error_description = (
-        "You do not have the appropriate privileges to access the list of users"
-        " in the group."))
-def group_users(conn: db.DbConnection, group_id: UUID) -> Iterable[User]:
-    """Retrieve all users that are members of group with id `group_id`."""
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            "SELECT u.* FROM group_users AS gu INNER JOIN users AS u "
-            "ON gu.user_id = u.user_id WHERE gu.group_id=:group_id",
-            {"group_id": str(group_id)})
-        results = cursor.fetchall()
-
-    return (User(UUID(row["user_id"]), row["email"], row["name"])
-            for row in results)
-
-@authorised_p(
-    privileges = ("system:group:view-group",),
-    error_description = (
-        "You do not have the appropriate privileges to access the group."))
-def group_by_id(conn: db.DbConnection, group_id: UUID) -> Group:
-    """Retrieve a group by its ID"""
-    with db.cursor(conn) as cursor:
-        cursor.execute("SELECT * FROM groups WHERE group_id=:group_id",
-                       {"group_id": str(group_id)})
-        row = cursor.fetchone()
-        if row:
-            return Group(
-                UUID(row["group_id"]),
-                row["group_name"],
-                json.loads(row["group_metadata"]))
-
-    raise NotFoundError(f"Could not find group with ID '{group_id}'.")
-
-@authorised_p(("system:group:view-group", "system:group:edit-group"),
-              error_description=("You do not have the appropriate authorisation"
-                                 " to act upon the join requests."),
-              oauth2_scope="profile group")
-def join_requests(conn: db.DbConnection, user: User):
-    """List all the join requests for the user's group."""
-    with db.cursor(conn) as cursor:
-        group = user_group(conn, user).maybe(DUMMY_GROUP, lambda grp: grp)# type: ignore[misc]
-        if group != DUMMY_GROUP and is_group_leader(conn, user, group):
-            cursor.execute(
-                "SELECT gjr.*, u.email, u.name FROM group_join_requests AS gjr "
-                "INNER JOIN users AS u ON gjr.requester_id=u.user_id "
-                "WHERE gjr.group_id=? AND gjr.status='PENDING'",
-                (str(group.group_id),))
-            return tuple(dict(row)for row in cursor.fetchall())
-
-    raise AuthorisationError(
-        "You do not have the appropriate authorisation to access the "
-        "group's join requests.")
-
-@authorised_p(("system:group:view-group", "system:group:edit-group"),
-              error_description=("You do not have the appropriate authorisation"
-                                 " to act upon the join requests."),
-              oauth2_scope="profile group")
-def accept_reject_join_request(
-        conn: db.DbConnection, request_id: UUID, user: User, status: str) -> dict:
-    """Accept/Reject a join request."""
-    assert status in ("ACCEPTED", "REJECTED"), f"Invalid status '{status}'."
-    with db.cursor(conn) as cursor:
-        group = user_group(conn, user).maybe(DUMMY_GROUP, lambda grp: grp) # type: ignore[misc]
-        cursor.execute("SELECT * FROM group_join_requests WHERE request_id=?",
-                       (str(request_id),))
-        row = cursor.fetchone()
-        if row:
-            if group.group_id == UUID(row["group_id"]):
-                try:
-                    the_user = user_by_id(conn, UUID(row["requester_id"]))
-                    if status == "ACCEPTED":
-                        add_user_to_group(cursor, group, the_user)
-                        revoke_user_role_by_name(cursor, the_user, "group-creator")
-                    cursor.execute(
-                        "UPDATE group_join_requests SET status=? "
-                        "WHERE request_id=?",
-                        (status, str(request_id)))
-                    return {"request_id": request_id, "status": status}
-                except NotFoundError as nfe:
-                    raise InconsistencyError(
-                        "Could not find user associated with join request."
-                    ) from nfe
-            raise AuthorisationError(
-                "You cannot act on other groups join requests")
-        raise NotFoundError(f"Could not find request with ID '{request_id}'")
-
-def __organise_privileges__(acc, row):
-    role_id = UUID(row["role_id"])
-    role = acc.get(role_id, False)
-    if role:
-        return {
-            **acc,
-            role_id: Role(
-                role.role_id, role.role_name,
-                bool(int(row["user_editable"])),
-                role.privileges + (
-                    Privilege(row["privilege_id"],
-                              row["privilege_description"]),))
-        }
-    return {
-        **acc,
-        role_id: Role(
-            UUID(row["role_id"]), row["role_name"],
-            bool(int(row["user_editable"])),
-            (Privilege(row["privilege_id"], row["privilege_description"]),))
-    }
-
-# @authorised_p(("group:role:view",),
-#               "Insufficient privileges to view role",
-#               oauth2_scope="profile group role")
-def group_role_by_id(
-        conn: db.DbConnection, group: Group, group_role_id: UUID) -> GroupRole:
-    """Retrieve GroupRole from id by its `group_role_id`."""
-    ## TODO: do privileges check before running actual query
-    ##       the check commented out above doesn't work correctly
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            "SELECT gr.group_role_id, r.*, p.* "
-            "FROM group_roles AS gr "
-            "INNER JOIN roles AS r ON gr.role_id=r.role_id "
-            "INNER JOIN role_privileges AS rp ON rp.role_id=r.role_id "
-            "INNER JOIN privileges AS p ON p.privilege_id=rp.privilege_id "
-            "WHERE gr.group_role_id=? AND gr.group_id=?",
-            (str(group_role_id), str(group.group_id)))
-        rows = cursor.fetchall()
-        if rows:
-            roles: tuple[Role,...] = tuple(reduce(
-                __organise_privileges__, rows, {}).values())
-            assert len(roles) == 1
-            return GroupRole(group_role_id, group, roles[0])
-        raise NotFoundError(
-            f"Group role with ID '{group_role_id}' does not exist.")
-
-@authorised_p(("group:role:edit-role",),
-              "You do not have the privilege to edit a role.",
-              oauth2_scope="profile group role")
-def add_privilege_to_group_role(conn: db.DbConnection, group_role: GroupRole,
-                                privilege: Privilege) -> GroupRole:
-    """Add `privilege` to `group_role`."""
-    ## TODO: do privileges check.
-    check_user_editable(group_role.role)
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            "INSERT INTO role_privileges(role_id,privilege_id) "
-            "VALUES (?, ?) ON CONFLICT (role_id, privilege_id) "
-            "DO NOTHING",
-            (str(group_role.role.role_id), str(privilege.privilege_id)))
-        return GroupRole(
-            group_role.group_role_id,
-            group_role.group,
-            Role(group_role.role.role_id,
-                 group_role.role.role_name,
-                 group_role.role.user_editable,
-                 group_role.role.privileges + (privilege,)))
-
-@authorised_p(("group:role:edit-role",),
-              "You do not have the privilege to edit a role.",
-              oauth2_scope="profile group role")
-def delete_privilege_from_group_role(
-        conn: db.DbConnection, group_role: GroupRole,
-        privilege: Privilege) -> GroupRole:
-    """Delete `privilege` to `group_role`."""
-    ## TODO: do privileges check.
-    check_user_editable(group_role.role)
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            "DELETE FROM role_privileges WHERE "
-            "role_id=? AND privilege_id=?",
-            (str(group_role.role.role_id), str(privilege.privilege_id)))
-        return GroupRole(
-            group_role.group_role_id,
-            group_role.group,
-            Role(group_role.role.role_id,
-                 group_role.role.role_name,
-                 group_role.role.user_editable,
-                 tuple(priv for priv in group_role.role.privileges
-                       if priv != privilege)))
diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/groups/views.py
deleted file mode 100644
index 4dc17e0..0000000
--- a/gn_auth/auth/authorisation/groups/views.py
+++ /dev/null
@@ -1,431 +0,0 @@
-"""The views/routes for the `gn3.auth.authorisation.groups` package."""
-import uuid
-import datetime
-from typing import Iterable
-from functools import partial
-
-from MySQLdb.cursors import DictCursor
-from flask import request, jsonify, Response, Blueprint, current_app
-
-from ...db import sqlite3 as db
-from ...db import mariadb as gn3db
-
-from ...dictify import dictify
-from ...db.sqlite3 import with_db_connection
-
-from .data import link_data_to_group
-from .models import (
-    Group, user_group, all_groups, DUMMY_GROUP, GroupRole, group_by_id,
-    join_requests, group_role_by_id, GroupCreationError,
-    accept_reject_join_request, group_users as _group_users,
-    create_group as _create_group, add_privilege_to_group_role,
-    delete_privilege_from_group_role, create_group_role as _create_group_role)
-
-from ..roles.models import Role
-from ..roles.models import user_roles
-
-from ..checks import authorised_p
-from ..privileges import Privilege, privileges_by_ids
-from ..errors import InvalidData, NotFoundError, AuthorisationError
-
-from ...authentication.users import User
-from ...authentication.oauth2.resource_server import require_oauth
-
-groups = Blueprint("groups", __name__)
-
-@groups.route("/list", methods=["GET"])
-@require_oauth("profile group")
-def list_groups():
-    """Return the list of groups that exist."""
-    with db.connection(current_app.config["AUTH_DB"]) as conn:
-        the_groups = all_groups(conn)
-
-    return jsonify(the_groups.maybe(
-        [], lambda grps: [dictify(grp) for grp in grps]))
-
-@groups.route("/create", methods=["POST"])
-@require_oauth("profile group")
-def create_group():
-    """Create a new group."""
-    with require_oauth.acquire("profile group") as the_token:
-        group_name=request.form.get("group_name", "").strip()
-        if not bool(group_name):
-            raise GroupCreationError("Could not create the group.")
-
-        db_uri = current_app.config["AUTH_DB"]
-        with db.connection(db_uri) as conn:
-            user = the_token.user
-            new_group = _create_group(
-                conn, group_name, user, request.form.get("group_description"))
-            return jsonify({
-                **dictify(new_group), "group_leader": dictify(user)
-            })
-
-@groups.route("/members/<uuid:group_id>", methods=["GET"])
-@require_oauth("profile group")
-def group_members(group_id: uuid.UUID) -> Response:
-    """Retrieve all the members of a group."""
-    with require_oauth.acquire("profile group") as the_token:# pylint: disable=[unused-variable]
-        db_uri = current_app.config["AUTH_DB"]
-        ## Check that user has appropriate privileges and remove the pylint disable above
-        with db.connection(db_uri) as conn:
-            return jsonify(tuple(
-                dictify(user) for user in _group_users(conn, group_id)))
-
-@groups.route("/requests/join/<uuid:group_id>", methods=["POST"])
-@require_oauth("profile group")
-def request_to_join(group_id: uuid.UUID) -> Response:
-    """Request to join a group."""
-    def __request__(conn: db.DbConnection, user: User, group_id: uuid.UUID,
-                    message: str):
-        with db.cursor(conn) as cursor:
-            group = user_group(conn, user).maybe(# type: ignore[misc]
-                False, lambda grp: grp)# type: ignore[arg-type]
-            if group:
-                error = AuthorisationError(
-                    "You cannot request to join a new group while being a "
-                    "member of an existing group.")
-                error.error_code = 400
-                raise error
-            request_id = uuid.uuid4()
-            cursor.execute(
-                "INSERT INTO group_join_requests VALUES "
-                "(:request_id, :group_id, :user_id, :ts, :status, :msg)",
-                {
-                    "request_id": str(request_id),
-                    "group_id": str(group_id),
-                    "user_id": str(user.user_id),
-                    "ts": datetime.datetime.now().timestamp(),
-                    "status": "PENDING",
-                    "msg": message
-                })
-            return {
-                "request_id":  request_id,
-                "message": "Successfully sent the join request."
-            }
-
-    with require_oauth.acquire("profile group") as the_token:
-        form = request.form
-        results = with_db_connection(partial(
-            __request__, user=the_token.user, group_id=group_id, message=form.get(
-                "message", "I hereby request that you add me to your group.")))
-        return jsonify(results)
-
-@groups.route("/requests/join/list", methods=["GET"])
-@require_oauth("profile group")
-def list_join_requests() -> Response:
-    """List the pending join requests."""
-    with require_oauth.acquire("profile group") as the_token:
-        return jsonify(with_db_connection(partial(
-            join_requests, user=the_token.user)))
-
-@groups.route("/requests/join/accept", methods=["POST"])
-@require_oauth("profile group")
-def accept_join_requests() -> Response:
-    """Accept a join request."""
-    with require_oauth.acquire("profile group") as the_token:
-        form = request.form
-        request_id = uuid.UUID(form.get("request_id"))
-        return jsonify(with_db_connection(partial(
-            accept_reject_join_request, request_id=request_id,
-            user=the_token.user, status="ACCEPTED")))
-
-@groups.route("/requests/join/reject", methods=["POST"])
-@require_oauth("profile group")
-def reject_join_requests() -> Response:
-    """Reject a join request."""
-    with require_oauth.acquire("profile group") as the_token:
-        form = request.form
-        request_id = uuid.UUID(form.get("request_id"))
-        return jsonify(with_db_connection(partial(
-            accept_reject_join_request, request_id=request_id,
-            user=the_token.user, status="REJECTED")))
-
-def unlinked_mrna_data(
-        conn: db.DbConnection, group: Group) -> tuple[dict, ...]:
-    """
-    Retrieve all mRNA Assay data linked to a group but not linked to any
-    resource.
-    """
-    query = (
-        "SELECT lmd.* FROM linked_mrna_data lmd "
-        "LEFT JOIN mrna_resources mr ON lmd.data_link_id=mr.data_link_id "
-        "WHERE lmd.group_id=? AND mr.data_link_id IS NULL")
-    with db.cursor(conn) as cursor:
-        cursor.execute(query, (str(group.group_id),))
-        return tuple(dict(row) for row in cursor.fetchall())
-
-def unlinked_genotype_data(
-        conn: db.DbConnection, group: Group) -> tuple[dict, ...]:
-    """
-    Retrieve all genotype data linked to a group but not linked to any resource.
-    """
-    query = (
-        "SELECT lgd.* FROM linked_genotype_data lgd "
-        "LEFT JOIN genotype_resources gr ON lgd.data_link_id=gr.data_link_id "
-        "WHERE lgd.group_id=? AND gr.data_link_id IS NULL")
-    with db.cursor(conn) as cursor:
-        cursor.execute(query, (str(group.group_id),))
-        return tuple(dict(row) for row in cursor.fetchall())
-
-def unlinked_phenotype_data(
-        authconn: db.DbConnection, gn3conn: gn3db.DbConnection,
-        group: Group) -> tuple[dict, ...]:
-    """
-    Retrieve all phenotype data linked to a group but not linked to any
-    resource.
-    """
-    with db.cursor(authconn) as authcur, gn3conn.cursor(DictCursor) as gn3cur:
-        authcur.execute(
-            "SELECT lpd.* FROM linked_phenotype_data AS lpd "
-            "LEFT JOIN phenotype_resources AS pr "
-            "ON lpd.data_link_id=pr.data_link_id "
-            "WHERE lpd.group_id=? AND pr.data_link_id IS NULL",
-            (str(group.group_id),))
-        results = authcur.fetchall()
-        ids: dict[tuple[str, ...], str] = {
-            (
-                row["SpeciesId"], row["InbredSetId"], row["PublishFreezeId"],
-                row["PublishXRefId"]): row["data_link_id"]
-            for row in results
-        }
-        if len(ids.keys()) < 1:
-            return tuple()
-        paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(ids.keys()))
-        gn3cur.execute(
-            "SELECT spc.SpeciesId, spc.SpeciesName, iset.InbredSetId, "
-            "iset.InbredSetName, pf.Id AS PublishFreezeId, "
-            "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, "
-            "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId, "
-            "pub.PubMed_ID, pub.Title, pub.Year, "
-            "phen.Pre_publication_description, "
-            "phen.Post_publication_description, phen.Original_description "
-            "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 "
-            "INNER JOIN Publication AS pub "
-            "ON pxr.PublicationId=pub.Id "
-            "INNER JOIN Phenotype AS phen "
-            "ON pxr.PhenotypeId=phen.Id "
-            "WHERE (spc.SpeciesId, iset.InbredSetId, pf.Id, pxr.Id) "
-            f"IN ({paramstr})",
-            tuple(item for sublist in ids.keys() for item in sublist))
-        return tuple({
-            **{key: value for key, value in row.items() if key not in
-               ("Post_publication_description", "Pre_publication_description",
-                "Original_description")},
-            "description": (
-                row["Post_publication_description"] or
-                row["Pre_publication_description"] or
-                row["Original_description"]),
-            "data_link_id": ids[tuple(str(row[key]) for key in (
-                "SpeciesId", "InbredSetId", "PublishFreezeId",
-                "PublishXRefId"))]
-        } for row in gn3cur.fetchall())
-
-@groups.route("/<string:resource_type>/unlinked-data")
-@require_oauth("profile group resource")
-def unlinked_data(resource_type: str) -> Response:
-    """View data linked to the group but not linked to any resource."""
-    if resource_type not in ("all", "mrna", "genotype", "phenotype"):
-        raise AuthorisationError(f"Invalid resource type {resource_type}")
-
-    with require_oauth.acquire("profile group resource") as the_token:
-        db_uri = current_app.config["AUTH_DB"]
-        gn3db_uri = current_app.config["SQL_URI"]
-        with (db.connection(db_uri) as authconn,
-              gn3db.database_connection(gn3db_uri) as gn3conn):
-            ugroup = user_group(authconn, the_token.user).maybe(# type: ignore[misc]
-                DUMMY_GROUP, lambda grp: grp)
-            if ugroup == DUMMY_GROUP:
-                return jsonify(tuple())
-
-            unlinked_fns = {
-                "mrna": unlinked_mrna_data,
-                "genotype": unlinked_genotype_data,
-                "phenotype": lambda conn, grp: partial(
-                    unlinked_phenotype_data, gn3conn=gn3conn)(
-                        authconn=conn, group=grp)
-            }
-            return jsonify(tuple(
-                dict(row) for row in unlinked_fns[resource_type](
-                    authconn, ugroup)))
-
-    return jsonify(tuple())
-
-@groups.route("/data/link", methods=["POST"])
-@require_oauth("profile group resource")
-def link_data() -> Response:
-    """Link selected data to specified group."""
-    with require_oauth.acquire("profile group resource") as _the_token:
-        form = request.form
-        group_id = uuid.UUID(form["group_id"])
-        dataset_ids = form.getlist("dataset_ids")
-        dataset_type = form.get("dataset_type")
-        if dataset_type not in ("mrna", "genotype", "phenotype"):
-            raise InvalidData("Unexpected dataset type requested!")
-        def __link__(conn: db.DbConnection):
-            group = group_by_id(conn, group_id)
-            with gn3db.database_connection(current_app.config["SQL_URI"]) as gn3conn:
-                return link_data_to_group(
-                    conn, gn3conn, dataset_type, dataset_ids, group)
-
-        return jsonify(with_db_connection(__link__))
-
-@groups.route("/roles", methods=["GET"])
-@require_oauth("profile group")
-def group_roles():
-    """Return a list of all available group roles."""
-    with require_oauth.acquire("profile group role") as the_token:
-        def __list_roles__(conn: db.DbConnection):
-            ## TODO: Check that user has appropriate privileges
-            with db.cursor(conn) as cursor:
-                group = user_group(conn, the_token.user).maybe(# type: ignore[misc]
-                    DUMMY_GROUP, lambda grp: grp)
-                if group == DUMMY_GROUP:
-                    return tuple()
-                cursor.execute(
-                    "SELECT gr.group_role_id, r.* "
-                    "FROM group_roles AS gr INNER JOIN roles AS r "
-                    "ON gr.role_id=r.role_id "
-                    "WHERE group_id=?",
-                    (str(group.group_id),))
-                return tuple(
-                    GroupRole(uuid.UUID(row["group_role_id"]),
-                              group,
-                              Role(uuid.UUID(row["role_id"]),
-                                   row["role_name"],
-                                   bool(int(row["user_editable"])),
-                                   tuple()))
-                    for row in cursor.fetchall())
-        return jsonify(tuple(
-            dictify(role) for role in with_db_connection(__list_roles__)))
-
-@groups.route("/privileges", methods=["GET"])
-@require_oauth("profile group")
-def group_privileges():
-    """Return a list of all available group roles."""
-    with require_oauth.acquire("profile group role") as the_token:
-        def __list_privileges__(conn: db.DbConnection) -> Iterable[Privilege]:
-            ## TODO: Check that user has appropriate privileges
-            this_user_roles = user_roles(conn, the_token.user)
-            with db.cursor(conn) as cursor:
-                cursor.execute("SELECT * FROM privileges "
-                               "WHERE privilege_id LIKE 'group:%'")
-                group_level_roles = tuple(
-                    Privilege(row["privilege_id"], row["privilege_description"])
-                    for row in cursor.fetchall())
-            return tuple(privilege for arole in this_user_roles
-                         for privilege in arole.privileges) + group_level_roles
-        return jsonify(tuple(
-            dictify(priv) for priv in with_db_connection(__list_privileges__)))
-
-
-
-@groups.route("/role/create", methods=["POST"])
-@require_oauth("profile group")
-def create_group_role():
-    """Create a new group role."""
-    with require_oauth.acquire("profile group role") as the_token:
-        ## TODO: Check that user has appropriate privileges
-        @authorised_p(("group:role:create-role",),
-                      "You do not have the privilege to create new roles",
-                      oauth2_scope="profile group role")
-        def __create__(conn: db.DbConnection) -> GroupRole:
-            ## TODO: Check user cannot assign any privilege they don't have.
-            form = request.form
-            role_name = form.get("role_name", "").strip()
-            privileges_ids = form.getlist("privileges[]")
-            if len(role_name) == 0:
-                raise InvalidData("Role name not provided!")
-            if len(privileges_ids) == 0:
-                raise InvalidData(
-                    "At least one privilege needs to be provided.")
-
-            group = user_group(conn, the_token.user).maybe(# type: ignore[misc]
-                    DUMMY_GROUP, lambda grp: grp)
-
-            if group == DUMMY_GROUP:
-                raise AuthorisationError(
-                    "A user without a group cannot create a new role.")
-            privileges = privileges_by_ids(conn, tuple(privileges_ids))
-            if len(privileges_ids) != len(privileges):
-                raise InvalidData(
-                    f"{len(privileges_ids) - len(privileges)} of the selected "
-                    "privileges were not found in the database.")
-
-            return _create_group_role(conn, group, role_name, privileges)
-
-        return jsonify(with_db_connection(__create__))
-
-@groups.route("/role/<uuid:group_role_id>", methods=["GET"])
-@require_oauth("profile group")
-def view_group_role(group_role_id: uuid.UUID):
-    """Return the details of the given role."""
-    with require_oauth.acquire("profile group role") as the_token:
-        def __group_role__(conn: db.DbConnection) -> GroupRole:
-            group = user_group(conn, the_token.user).maybe(#type: ignore[misc]
-                DUMMY_GROUP, lambda grp: grp)
-
-            if group == DUMMY_GROUP:
-                raise AuthorisationError(
-                    "A user without a group cannot view group roles.")
-            return group_role_by_id(conn, group, group_role_id)
-        return jsonify(dictify(with_db_connection(__group_role__)))
-
-def __add_remove_priv_to_from_role__(conn: db.DbConnection,
-                                     group_role_id: uuid.UUID,
-                                     direction: str,
-                                     user: User) -> GroupRole:
-    assert direction in ("ADD", "DELETE")
-    group = user_group(conn, user).maybe(# type: ignore[misc]
-        DUMMY_GROUP, lambda grp: grp)
-
-    if group == DUMMY_GROUP:
-        raise AuthorisationError(
-            "You need to be a member of a group to edit roles.")
-    try:
-        privilege_id = request.form.get("privilege_id", "")
-        assert bool(privilege_id), "Privilege to add must be provided."
-        privileges = privileges_by_ids(conn, (privilege_id,))
-        if len(privileges) == 0:
-            raise NotFoundError("Privilege not found.")
-        dir_fns = {
-            "ADD": add_privilege_to_group_role,
-            "DELETE": delete_privilege_from_group_role
-        }
-        return dir_fns[direction](
-            conn,
-            group_role_by_id(conn, group, group_role_id),
-            privileges[0])
-    except AssertionError as aerr:
-        raise InvalidData(aerr.args[0]) from aerr
-
-@groups.route("/role/<uuid:group_role_id>/privilege/add", methods=["POST"])
-@require_oauth("profile group")
-def add_priv_to_role(group_role_id: uuid.UUID) -> Response:
-    """Add privilege to group role."""
-    with require_oauth.acquire("profile group role") as the_token:
-        return jsonify({
-            **dictify(with_db_connection(partial(
-                __add_remove_priv_to_from_role__, group_role_id=group_role_id,
-                direction="ADD", user=the_token.user))),
-            "description": "Privilege added successfully"
-        })
-
-@groups.route("/role/<uuid:group_role_id>/privilege/delete", methods=["POST"])
-@require_oauth("profile group")
-def delete_priv_from_role(group_role_id: uuid.UUID) -> Response:
-    """Delete privilege from group role."""
-    with require_oauth.acquire("profile group role") as the_token:
-        return jsonify({
-            **dictify(with_db_connection(partial(
-                __add_remove_priv_to_from_role__, group_role_id=group_role_id,
-                direction="DELETE", user=the_token.user))),
-            "description": "Privilege deleted successfully"
-        })