diff options
| -rw-r--r-- | gn3/auth/authorisation/groups/data.py | 20 |
1 files changed, 14 insertions, 6 deletions
diff --git a/gn3/auth/authorisation/groups/data.py b/gn3/auth/authorisation/groups/data.py index 93b8e1d..073449c 100644 --- a/gn3/auth/authorisation/groups/data.py +++ b/gn3/auth/authorisation/groups/data.py @@ -23,7 +23,8 @@ 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, " + query = ("SELECT psf.Id, psf.Name AS dataset_name, " + "psf.FullName AS dataset_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() @@ -41,7 +42,8 @@ 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, " + query = ("SELECT gf.Id, gf.Name AS dataset_name, " + "gf.FullName AS dataset_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() @@ -59,13 +61,19 @@ 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") + query = ("SELECT " + "pxf.Id, iset.InbredSetName, pf.Name AS dataset_name, " + "pf.FullName AS dataset_fullname, " + "pf.ShortName AS dataset_shortname " + "FROM PublishXRef AS pxf " + "INNER JOIN InbredSet AS iset " + "ON pxf.InbredSetId=iset.InbredSetId " + "LEFT JOIN PublishFreeze AS pf " + "ON iset.InbredSetId=pf.InbredSetId") params: tuple[Any, ...] = tuple() if bool(grouped_data): clause = ", ".join(["%s"] * len(grouped_data)) - query = f"{query} WHERE pf.Id NOT IN ({clause})" + query = f"{query} WHERE pxf.Id NOT IN ({clause})" params = tuple(item["dataset_or_trait_id"] for item in grouped_data) query = f"{query} LIMIT 100 OFFSET %s" |