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authorFrederick Muriuki Muriithi2023-08-04 10:10:28 +0300
committerFrederick Muriuki Muriithi2023-08-04 10:20:09 +0300
commit8b7c598407a5fea9a3d78473e72df87606998cd4 (patch)
tree8526433a17eca6b511feb082a0574f9b15cb9469 /gn_auth/auth/authorisation/groups/data.py
parentf7fcbbcc014686ac597b783a8dcb38b43024b9d6 (diff)
downloadgn-auth-8b7c598407a5fea9a3d78473e72df87606998cd4.tar.gz
Copy over files from GN3 repository.
Diffstat (limited to 'gn_auth/auth/authorisation/groups/data.py')
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diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py
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+"""Handles the resource objects' data."""
+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 NotFoundError
+
+def __fetch_mrna_data_by_ids__(
+ conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+ dict, ...]:
+ """Fetch mRNA Assay data by ID."""
+ with conn.cursor(DictCursor) as cursor:
+ paramstr = ", ".join(["%s"] * len(dataset_ids))
+ cursor.execute(
+ "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 "
+ f"WHERE psf.Id IN ({paramstr})",
+ dataset_ids)
+ res = cursor.fetchall()
+ if res:
+ return tuple(dict(row) for row in res)
+ raise NotFoundError("Could not find mRNA Assay data with the given ID.")
+
+def __fetch_geno_data_by_ids__(
+ conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+ dict, ...]:
+ """Fetch genotype data by ID."""
+ with conn.cursor(DictCursor) as cursor:
+ paramstr = ", ".join(["%s"] * len(dataset_ids))
+ cursor.execute(
+ "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 "
+ f"WHERE gf.Id IN ({paramstr})",
+ dataset_ids)
+ res = cursor.fetchall()
+ if res:
+ return tuple(dict(row) for row in res)
+ raise NotFoundError("Could not find Genotype data with the given ID.")
+
+def __fetch_pheno_data_by_ids__(
+ conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+ dict, ...]:
+ """Fetch phenotype data by ID."""
+ with conn.cursor(DictCursor) as cursor:
+ paramstr = ", ".join(["%s"] * len(dataset_ids))
+ cursor.execute(
+ "SELECT pxf.Id, iset.InbredSetName, pf.Id AS dataset_id, "
+ "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, "
+ "ifiles.GN_AccesionId AS accession_id "
+ "FROM PublishXRef AS pxf "
+ "INNER JOIN InbredSet AS iset ON pxf.InbredSetId=iset.InbredSetId "
+ "INNER JOIN PublishFreeze AS pf ON iset.InbredSetId=pf.InbredSetId "
+ "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName "
+ f"WHERE pxf.Id IN ({paramstr})",
+ dataset_ids)
+ res = cursor.fetchall()
+ if res:
+ return tuple(dict(row) for row in res)
+ raise NotFoundError(
+ "Could not find Phenotype/Publish data with the given IDs.")
+
+def __fetch_data_by_id(
+ conn: gn3db.Connection, dataset_type: str,
+ dataset_ids: tuple[str, ...]) -> tuple[dict, ...]:
+ """Fetch data from MySQL by IDs."""
+ fetch_fns = {
+ "mrna": __fetch_mrna_data_by_ids__,
+ "genotype": __fetch_geno_data_by_ids__,
+ "phenotype": __fetch_pheno_data_by_ids__
+ }
+ return fetch_fns[dataset_type](conn, dataset_ids)
+
+@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_ids: tuple[str, ...], group: Group) -> tuple[
+ dict, ...]:
+ """Link the given data to the specified group."""
+ the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_ids)
+ with authdb.cursor(authconn) as cursor:
+ params = tuple({
+ "group_id": str(group.group_id), "dataset_type": {
+ "mrna": "mRNA", "genotype": "Genotype",
+ "phenotype": "Phenotype"
+ }[dataset_type],
+ "dataset_or_trait_id": item["Id"],
+ "dataset_name": item["dataset_name"],
+ "dataset_fullname": item["dataset_fullname"],
+ "accession_id": item["accession_id"]
+ } for item in the_data)
+ cursor.executemany(
+ "INSERT INTO linked_group_data VALUES"
+ "(:group_id, :dataset_type, :dataset_or_trait_id, :dataset_name, "
+ ":dataset_fullname, :accession_id)",
+ params)
+ return params