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-rw-r--r--gn3/auth/authorisation/groups/data.py86
-rw-r--r--gn3/auth/authorisation/groups/views.py4
2 files changed, 54 insertions, 36 deletions
diff --git a/gn3/auth/authorisation/groups/data.py b/gn3/auth/authorisation/groups/data.py
index fd76648..0c821d3 100644
--- a/gn3/auth/authorisation/groups/data.py
+++ b/gn3/auth/authorisation/groups/data.py
@@ -108,58 +108,74 @@ def retrieve_ungrouped_data(
grouped_data = __fetch_grouped_data__(authconn, dataset_type)
return __fetch_ungrouped_data__(gn3conn, dataset_type, grouped_data, offset)
-def __fetch_mrna_data_by_id__(conn: gn3db.Connection, dataset_id: str) -> dict:
+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, psf.FullName, "
+ "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 "
- "WHERE psf.Id=%s",
- (dataset_id,))
- res = cursor.fetchone()
+ f"WHERE psf.Id IN ({paramstr})",
+ dataset_ids)
+ res = cursor.fetchall()
if res:
- return dict(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_id__(conn: gn3db.Connection, dataset_id: str) -> dict:
+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, gf.FullName, "
+ "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 "
- "WHERE gf.Id=%s",
- (dataset_id,))
- res = cursor.fetchone()
+ f"WHERE gf.Id IN ({paramstr})",
+ dataset_ids)
+ res = cursor.fetchall()
if res:
- return dict(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_id__(conn: gn3db.Connection, dataset_id: str) -> dict:
+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 pf.Id, pf.Name, pf.FullName, "
- "ifiles.GN_AccesionId AS accession_id FROM PublishFreeze AS pf "
+ "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 "
- "WHERE pf.Id=%s",
- (dataset_id,))
- res = cursor.fetchone()
+ f"WHERE pxf.Id IN ({paramstr})",
+ dataset_ids)
+ res = cursor.fetchall()
if res:
- return dict(res)
+ return tuple(dict(row) for row in res)
raise NotFoundError(
- "Could not find Phenotype/Publish data with the given ID.")
+ "Could not find Phenotype/Publish data with the given IDs.")
def __fetch_data_by_id(
- conn: gn3db.Connection, dataset_type: str, dataset_id: str) -> dict:
- """Fetch data from MySQL 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_id__,
- "genotype": __fetch_geno_data_by_id__,
- "phenotype": __fetch_pheno_data_by_id__
+ "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_id)
+ return fetch_fns[dataset_type](conn, dataset_ids)
@authorised_p(("system:data:link-to-group",),
error_description=(
@@ -168,20 +184,22 @@ def __fetch_data_by_id(
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:
+ 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_id)
+ the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_ids)
with authdb.cursor(authconn) as cursor:
- params = {
+ params = tuple({
"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(
+ "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)",
diff --git a/gn3/auth/authorisation/groups/views.py b/gn3/auth/authorisation/groups/views.py
index 0b21800..6f1a6df 100644
--- a/gn3/auth/authorisation/groups/views.py
+++ b/gn3/auth/authorisation/groups/views.py
@@ -213,7 +213,7 @@ def link_data() -> Response:
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_ids = form.getlist("dataset_ids")
dataset_type = form.get("dataset_type")
if dataset_type not in ("mrna", "genotype", "phenotype"):
raise InvalidData("Unexpected dataset type requested!")
@@ -221,7 +221,7 @@ def link_data() -> Response:
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)
+ conn, gn3conn, dataset_type, dataset_ids, group)
return jsonify(with_db_connection(__link__))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 08:31:29 +0000