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, 995 insertions, 0 deletions

diff --git a/gn_auth/auth/authorisation/resources/groups/__init__.py b/gn_auth/auth/authorisation/resources/groups/__init__.py
new file mode 100644
index 0000000..1cb0bba
--- /dev/null
+++ b/gn_auth/auth/authorisation/resources/groups/__init__.py
@@ -0,0 +1,3 @@
+"""Initialise the `gn3.auth.authorisation.groups` package"""
+
+from .models import Group, GroupRole
diff --git a/gn_auth/auth/authorisation/resources/groups/data.py b/gn_auth/auth/authorisation/resources/groups/data.py
new file mode 100644
index 0000000..9fcdc6e
--- /dev/null
+++ b/gn_auth/auth/authorisation/resources/groups/data.py
@@ -0,0 +1,107 @@
+"""Handles the resource objects' data."""
+from MySQLdb.cursors import DictCursor
+
+from gn_auth.auth.db import mariadb as gn3db
+from gn_auth.auth.db import sqlite3 as authdb
+
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.errors import NotFoundError
+from gn_auth.auth.authorisation.resources.groups import Group
+
+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/resources/groups/models.py b/gn_auth/auth/authorisation/resources/groups/models.py
new file mode 100644
index 0000000..5ec26c5
--- /dev/null
+++ b/gn_auth/auth/authorisation/resources/groups/models.py
@@ -0,0 +1,453 @@
+"""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 gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.authentication.users import User, user_by_id
+
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.privileges import Privilege
+from gn_auth.auth.authorisation.resources.base import Resource
+from gn_auth.auth.authorisation.resources.errors import MissingGroupError
+from gn_auth.auth.authorisation.errors import (
+    NotFoundError, AuthorisationError, InconsistencyError)
+from gn_auth.auth.authorisation.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)))
+
+def resource_owner(conn: db.DbConnection, resource: Resource) -> Group:
+    """Return the user group that owns the resource."""
+    with db.cursor(conn) as cursor:
+        cursor.execute(
+            "SELECT g.* FROM resource_ownership AS ro "
+            "INNER JOIN groups AS g ON ro.group_id=g.group_id "
+            "WHERE ro.resource_id=?",
+            (str(resource.resource_id),))
+        row = cursor.fetchone()
+        if row:
+            return Group(
+                UUID(row["group_id"]),
+                row["group_name"],
+                json.loads(row["group_metadata"]))
+
+    raise MissingGroupError("Resource has no 'owning' group.")
diff --git a/gn_auth/auth/authorisation/resources/groups/views.py b/gn_auth/auth/authorisation/resources/groups/views.py
new file mode 100644
index 0000000..f146ffd
--- /dev/null
+++ b/gn_auth/auth/authorisation/resources/groups/views.py
@@ -0,0 +1,432 @@
+"""
+The views/routes for the `gn3.auth.authorisation.resources.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 gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.db import mariadb as gn3db
+from gn_auth.auth.db.sqlite3 import with_db_connection
+from gn_auth.auth.dictify import dictify
+
+from gn_auth.auth.authorisation.roles.models import Role
+from gn_auth.auth.authorisation.roles.models import user_roles
+
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.privileges import Privilege, privileges_by_ids
+from gn_auth.auth.authorisation.errors import InvalidData, NotFoundError, AuthorisationError
+
+from gn_auth.auth.authentication.users import User
+from gn_auth.auth.authentication.oauth2.resource_server import require_oauth
+
+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)
+
+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"
+        })