diff options
| -rw-r--r-- | gn3/auth/authorisation/resources/data.py | 96 | ||||
| -rw-r--r-- | gn3/auth/authorisation/resources/views.py | 34 | ||||
| -rw-r--r-- | gn3/db_utils.py | 2 |
3 files changed, 119 insertions, 13 deletions
diff --git a/gn3/auth/authorisation/resources/data.py b/gn3/auth/authorisation/resources/data.py index 7598f34..93b8e1d 100644 --- a/gn3/auth/authorisation/resources/data.py +++ b/gn3/auth/authorisation/resources/data.py @@ -5,7 +5,9 @@ from MySQLdb.cursors import DictCursor from gn3 import db_utils as gn3db from gn3.auth import db as authdb -from gn3.auth.authorisation.errors import InvalidData +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]]: @@ -31,7 +33,7 @@ def __fetch_ungrouped_mrna_data__( params = tuple(item["dataset_or_trait_id"] for item in grouped_data) query = f"{query} LIMIT 100 OFFSET %s" - with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg] + with conn.cursor(DictCursor) as cursor: cursor.execute(query, (params + (offset,))) return tuple(dict(row) for row in cursor.fetchall()) @@ -49,7 +51,7 @@ def __fetch_ungrouped_geno_data__( params = tuple(item["dataset_or_trait_id"] for item in grouped_data) query = f"{query} LIMIT 100 OFFSET %s" - with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg] + with conn.cursor(DictCursor) as cursor: cursor.execute(query, (params + (offset,))) return tuple(dict(row) for row in cursor.fetchall()) @@ -67,7 +69,7 @@ def __fetch_ungrouped_pheno_data__( params = tuple(item["dataset_or_trait_id"] for item in grouped_data) query = f"{query} LIMIT 100 OFFSET %s" - with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg] + with conn.cursor(DictCursor) as cursor: cursor.execute(query, (params + (offset,))) return tuple(dict(row) for row in cursor.fetchall()) @@ -82,6 +84,11 @@ def __fetch_ungrouped_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, @@ -92,5 +99,84 @@ def retrieve_ungrouped_data( "Requested dataset type is invalid. Expected one of " "'mrna', 'genotype' or 'phenotype'.") grouped_data = __fetch_grouped_data__(authconn, dataset_type) - print(f"GROUPED DATA: {grouped_data}") 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/resources/views.py b/gn3/auth/authorisation/resources/views.py index 44e2c4e..e373182 100644 --- a/gn3/auth/authorisation/resources/views.py +++ b/gn3/auth/authorisation/resources/views.py @@ -7,13 +7,13 @@ from flask import request, jsonify, Response, Blueprint, current_app as app from gn3 import db_utils as gn3dbutils from gn3.auth.db_utils import with_db_connection -from .data import retrieve_ungrouped_data +from .data import link_data_to_group, retrieve_ungrouped_data from .models import ( resource_by_id, resource_categories, resource_category_by_id, create_resource as _create_resource) -from ..errors import AuthorisationError -from ..groups.models import user_group, DUMMY_GROUP +from ..errors import InvalidData, AuthorisationError +from ..groups.models import user_group, DUMMY_GROUP, group_by_id from ... import db from ...dictify import dictify @@ -115,7 +115,27 @@ def ungrouped_data(dataset_type: str) -> Response: if dataset_type not in ("all", "mrna", "genotype", "phenotype"): raise AuthorisationError(f"Invalid dataset type {dataset_type}") - with gn3dbutils.database_connection() as gn3conn: - return jsonify(with_db_connection(partial( - retrieve_ungrouped_data, gn3conn=gn3conn, - 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))) + +@resources.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__)) diff --git a/gn3/db_utils.py b/gn3/db_utils.py index 23a570b..ad934d7 100644 --- a/gn3/db_utils.py +++ b/gn3/db_utils.py @@ -28,7 +28,7 @@ def database_connector() -> mdb.Connection: # pylint: disable=missing-class-docstring, missing-function-docstring, too-few-public-methods class Connection(Protocol): """Type Annotation for MySQLdb's connection object""" - def cursor(self) -> Any: + def cursor(self, *args) -> Any: """A cursor in which queries may be performed""" ... |