diff options
Diffstat (limited to 'gn3/auth')
| -rw-r--r-- | gn3/auth/authorisation/groups/data.py | 19 | ||||
| -rw-r--r-- | gn3/auth/authorisation/groups/views.py | 4 |
2 files changed, 11 insertions, 12 deletions
diff --git a/gn3/auth/authorisation/groups/data.py b/gn3/auth/authorisation/groups/data.py index 073449c..fd76648 100644 --- a/gn3/auth/authorisation/groups/data.py +++ b/gn3/auth/authorisation/groups/data.py @@ -20,8 +20,7 @@ def __fetch_grouped_data__( return tuple(dict(row) for row in cursor.fetchall()) def __fetch_ungrouped_mrna_data__( - conn: gn3db.Connection, grouped_data, - offset: int = 0) -> Sequence[dict]: + conn: gn3db.Connection, grouped_data, offset: int) -> Sequence[dict]: """Fetch ungrouped mRNA Assay data.""" query = ("SELECT psf.Id, psf.Name AS dataset_name, " "psf.FullName AS dataset_fullname, " @@ -39,8 +38,7 @@ def __fetch_ungrouped_mrna_data__( return tuple(dict(row) for row in cursor.fetchall()) def __fetch_ungrouped_geno_data__( - conn: gn3db.Connection, grouped_data, - offset: int = 0) -> Sequence[dict]: + conn: gn3db.Connection, grouped_data, offset: int) -> Sequence[dict]: """Fetch ungrouped Genotype data.""" query = ("SELECT gf.Id, gf.Name AS dataset_name, " "gf.FullName AS dataset_fullname, " @@ -58,8 +56,7 @@ def __fetch_ungrouped_geno_data__( return tuple(dict(row) for row in cursor.fetchall()) def __fetch_ungrouped_pheno_data__( - conn: gn3db.Connection, grouped_data, - offset: int = 0) -> Sequence[dict]: + conn: gn3db.Connection, grouped_data, offset: int) -> Sequence[dict]: """Fetch ungrouped Phenotype data.""" query = ("SELECT " "pxf.Id, iset.InbredSetName, pf.Name AS dataset_name, " @@ -83,14 +80,15 @@ def __fetch_ungrouped_pheno_data__( def __fetch_ungrouped_data__( conn: gn3db.Connection, dataset_type: str, - ungrouped: Sequence[dict[str, Any]]) -> Sequence[dict[str, Any]]: + ungrouped: Sequence[dict[str, Any]], + offset) -> 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) + return fetch_fns[dataset_type](conn, ungrouped, offset) @authorised_p(("system:data:link-to-group",), error_description=( @@ -100,14 +98,15 @@ def __fetch_ungrouped_data__( def retrieve_ungrouped_data( authconn: authdb.DbConnection, gn3conn: gn3db.Connection, - dataset_type: str) -> Sequence[dict]: + dataset_type: str, + offset: int = 0) -> 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) + return __fetch_ungrouped_data__(gn3conn, dataset_type, grouped_data, offset) def __fetch_mrna_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict: """Fetch mRNA Assay data by ID.""" diff --git a/gn3/auth/authorisation/groups/views.py b/gn3/auth/authorisation/groups/views.py index 7b967d7..0b21800 100644 --- a/gn3/auth/authorisation/groups/views.py +++ b/gn3/auth/authorisation/groups/views.py @@ -177,7 +177,6 @@ def unlinked_data(resource_type: str) -> Response: f") {type_filter}") cursor.execute(ids_query) ids = cursor.fetchall() - print(f"THE IDS: {ids} ==> {type_filter}") if ids: clause = ", ".join(["(?, ?, ?)"] * len(ids)) @@ -204,7 +203,8 @@ def ungrouped_data(dataset_type: str) -> Response: with gn3dbutils.database_connection() as gn3conn: return jsonify(with_db_connection(partial( retrieve_ungrouped_data, gn3conn=gn3conn, - dataset_type=dataset_type))) + dataset_type=dataset_type, + offset = int(request.args.get("offset", 0))))) @groups.route("/data/link", methods=["POST"]) @require_oauth("profile group resource") |