Copy over files from GN3 repository.

1 files changed, 431 insertions, 0 deletions

diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/groups/views.py
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+++ b/gn_auth/auth/authorisation/groups/views.py
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+"""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 gn3.auth import db
+from gn3 import db_utils as gn3db
+
+from gn3.auth.dictify import dictify
+from gn3.auth.db_utils 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.Connection,
+        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"
+        })