diff options
Diffstat (limited to 'gn3/auth/authorisation/groups')
| -rw-r--r-- | gn3/auth/authorisation/groups/data.py | 182 | ||||
| -rw-r--r-- | gn3/auth/authorisation/groups/views.py | 93 |
2 files changed, 272 insertions, 3 deletions
diff --git a/gn3/auth/authorisation/groups/data.py b/gn3/auth/authorisation/groups/data.py new file mode 100644 index 0000000..93b8e1d --- /dev/null +++ b/gn3/auth/authorisation/groups/data.py @@ -0,0 +1,182 @@ +"""Handles the resource objects' data.""" +from typing import Any, Sequence + +from MySQLdb.cursors import DictCursor + +from gn3 import db_utils as gn3db +from gn3.auth import db as authdb +from gn3.auth.authorisation.groups import Group +from gn3.auth.authorisation.checks import authorised_p +from gn3.auth.authorisation.errors import InvalidData, NotFoundError + +def __fetch_grouped_data__( + conn: authdb.DbConnection, dataset_type: str) -> Sequence[dict[str, Any]]: + """Retrieve ids for all data that are linked to groups in the auth db.""" + with authdb.cursor(conn) as cursor: + cursor.execute( + "SELECT dataset_type, dataset_or_trait_id FROM linked_group_data " + "WHERE LOWER(dataset_type)=?", + (dataset_type,)) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_mrna_data__( + conn: gn3db.Connection, grouped_data, + offset: int = 0) -> Sequence[dict]: + """Fetch ungrouped mRNA Assay data.""" + query = ("SELECT psf.Id, psf.Name, psf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf " + "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName") + params: tuple[Any, ...] = tuple() + if bool(grouped_data): + clause = ", ".join(["%s"] * len(grouped_data)) + query = f"{query} WHERE psf.Id NOT IN ({clause})" + params = tuple(item["dataset_or_trait_id"] for item in grouped_data) + + query = f"{query} LIMIT 100 OFFSET %s" + with conn.cursor(DictCursor) as cursor: + cursor.execute(query, (params + (offset,))) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_geno_data__( + conn: gn3db.Connection, grouped_data, + offset: int = 0) -> Sequence[dict]: + """Fetch ungrouped Genotype data.""" + query = ("SELECT gf.Id, gf.Name, gf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf " + "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName") + params: tuple[Any, ...] = tuple() + if bool(grouped_data): + clause = ", ".join(["%s"] * len(grouped_data)) + query = f"{query} WHERE gf.Id NOT IN ({clause})" + params = tuple(item["dataset_or_trait_id"] for item in grouped_data) + + query = f"{query} LIMIT 100 OFFSET %s" + with conn.cursor(DictCursor) as cursor: + cursor.execute(query, (params + (offset,))) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_pheno_data__( + conn: gn3db.Connection, grouped_data, + offset: int = 0) -> Sequence[dict]: + """Fetch ungrouped Phenotype data.""" + query = ("SELECT pf.Id, pf.Name, pf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM PublishFreeze AS pf " + "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName") + params: tuple[Any, ...] = tuple() + if bool(grouped_data): + clause = ", ".join(["%s"] * len(grouped_data)) + query = f"{query} WHERE pf.Id NOT IN ({clause})" + params = tuple(item["dataset_or_trait_id"] for item in grouped_data) + + query = f"{query} LIMIT 100 OFFSET %s" + with conn.cursor(DictCursor) as cursor: + cursor.execute(query, (params + (offset,))) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_data__( + conn: gn3db.Connection, dataset_type: str, + ungrouped: Sequence[dict[str, Any]]) -> Sequence[dict[str, Any]]: + """Fetch any ungrouped data.""" + fetch_fns = { + "mrna": __fetch_ungrouped_mrna_data__, + "genotype": __fetch_ungrouped_geno_data__, + "phenotype": __fetch_ungrouped_pheno_data__ + } + return fetch_fns[dataset_type](conn, ungrouped) + +@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 retrieve_ungrouped_data( + authconn: authdb.DbConnection, + gn3conn: gn3db.Connection, + dataset_type: str) -> Sequence[dict]: + """Retrieve any data not linked to any group.""" + if dataset_type not in ("mrna", "genotype", "phenotype"): + raise InvalidData( + "Requested dataset type is invalid. Expected one of " + "'mrna', 'genotype' or 'phenotype'.") + grouped_data = __fetch_grouped_data__(authconn, dataset_type) + return __fetch_ungrouped_data__(gn3conn, dataset_type, grouped_data) + +def __fetch_mrna_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict: + """Fetch mRNA Assay data by ID.""" + with conn.cursor(DictCursor) as cursor: + cursor.execute( + "SELECT psf.Id, psf.Name, psf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf " + "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName " + "WHERE psf.Id=%s", + (dataset_id,)) + res = cursor.fetchone() + if res: + return dict(res) + raise NotFoundError("Could not find mRNA Assay data with the given ID.") + +def __fetch_geno_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict: + """Fetch genotype data by ID.""" + with conn.cursor(DictCursor) as cursor: + cursor.execute( + "SELECT gf.Id, gf.Name, gf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf " + "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName " + "WHERE gf.Id=%s", + (dataset_id,)) + res = cursor.fetchone() + if res: + return dict(res) + raise NotFoundError("Could not find Genotype data with the given ID.") + +def __fetch_pheno_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict: + """Fetch phenotype data by ID.""" + with conn.cursor(DictCursor) as cursor: + cursor.execute( + "SELECT pf.Id, pf.Name, pf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM PublishFreeze AS pf " + "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName " + "WHERE pf.Id=%s", + (dataset_id,)) + res = cursor.fetchone() + if res: + return dict(res) + raise NotFoundError( + "Could not find Phenotype/Publish data with the given ID.") + +def __fetch_data_by_id( + conn: gn3db.Connection, dataset_type: str, dataset_id: str) -> dict: + """Fetch data from MySQL by ID.""" + fetch_fns = { + "mrna": __fetch_mrna_data_by_id__, + "genotype": __fetch_geno_data_by_id__, + "phenotype": __fetch_pheno_data_by_id__ + } + return fetch_fns[dataset_type](conn, dataset_id) + +@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.Connection, + dataset_type: str, dataset_id: str, group: Group) -> dict: + """Link the given data to the specified group.""" + the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_id) + with authdb.cursor(authconn) as cursor: + params = { + "group_id": str(group.group_id), "dataset_type": { + "mrna": "mRNA", "genotype": "Genotype", + "phenotype": "Phenotype" + }[dataset_type], + "dataset_or_trait_id": dataset_id, "dataset_name": the_data["Name"], + "dataset_fullname": the_data["FullName"], + "accession_id": the_data["accession_id"] + } + cursor.execute( + "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/gn3/auth/authorisation/groups/views.py b/gn3/auth/authorisation/groups/views.py index d3710f6..d21466c 100644 --- a/gn3/auth/authorisation/groups/views.py +++ b/gn3/auth/authorisation/groups/views.py @@ -6,15 +6,18 @@ from functools import partial from flask import request, jsonify, Response, Blueprint, current_app from gn3.auth import db +from gn3 import db_utils as gn3dbutils + from gn3.auth.dictify import dictify from gn3.auth.db_utils import with_db_connection +from .data import link_data_to_group, retrieve_ungrouped_data from .models import ( - user_group, all_groups, join_requests, GroupCreationError, - accept_reject_join_request, group_users as _group_users, + user_group, all_groups, DUMMY_GROUP, group_by_id, join_requests, + GroupCreationError, accept_reject_join_request, group_users as _group_users, create_group as _create_group) -from ..errors import AuthorisationError +from ..errors import InvalidData, AuthorisationError from ...authentication.users import User from ...authentication.oauth2.resource_server import require_oauth @@ -128,3 +131,87 @@ def reject_join_requests() -> Response: return jsonify(with_db_connection(partial( accept_reject_join_request, request_id=request_id, user=the_token.user, status="REJECTED"))) + +@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"] + with db.connection(db_uri) as conn, db.cursor(conn) as cursor: + ugroup = user_group(cursor, the_token.user).maybe(# type: ignore[misc] + DUMMY_GROUP, lambda grp: grp) + if ugroup == DUMMY_GROUP: + return jsonify(tuple()) + type_filter = { + "all": "", + "mrna": 'WHERE dataset_type="mRNA"', + "genotype": 'WHERE dataset_type="Genotype"', + "phenotype": 'WHERE dataset_type="Phenotype"' + }[resource_type] + + except_filter = ( + "SELECT group_id, dataset_type, " + "dataset_id AS dataset_or_trait_id FROM mrna_resources " + "UNION " + "SELECT group_id, dataset_type, " + "trait_id AS dataset_or_trait_id FROM genotype_resources " + "UNION " + "SELECT group_id, dataset_type, " + "trait_id AS dataset_or_trait_id FROM phenotype_resources") + + ids_query = ("SELECT group_id, dataset_type, dataset_or_trait_id " + "FROM linked_group_data " + f"{type_filter} " + f"EXCEPT {except_filter} ") + cursor.execute(ids_query) + ids = cursor.fetchall() + + if ids: + clause = ", ".join(["(?, ?, ?)"] * len(ids)) + data_query = ( + "SELECT * FROM linked_group_data " + "WHERE (group_id, dataset_type, dataset_or_trait_id) " + f"IN (VALUES {clause})") + params = tuple(item for sublist in + ((row[0], row[1], row[2]) for row in ids) + for item in sublist) + cursor.execute(data_query, params) + return jsonify(tuple(dict(row) for row in cursor.fetchall())) + + return jsonify(tuple()) + +@groups.route("/<string:dataset_type>/ungrouped-data", methods=["GET"]) +@require_oauth("profile group resource") +def ungrouped_data(dataset_type: str) -> Response: + """View data not linked to any group.""" + if dataset_type not in ("all", "mrna", "genotype", "phenotype"): + raise AuthorisationError(f"Invalid dataset type {dataset_type}") + + with require_oauth.acquire("profile group resource") as _the_token: + with gn3dbutils.database_connection() as gn3conn: + return jsonify(with_db_connection(partial( + retrieve_ungrouped_data, gn3conn=gn3conn, + dataset_type=dataset_type))) + +@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_id = form["dataset_id"] + 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 gn3dbutils.database_connection() as gn3conn: + return link_data_to_group( + conn, gn3conn, dataset_type, dataset_id, group) + + return jsonify(with_db_connection(__link__)) |