diff options
Diffstat (limited to 'gn3/auth/authorisation/resources/data.py')
| -rw-r--r-- | gn3/auth/authorisation/resources/data.py | 96 |
1 files changed, 91 insertions, 5 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 |