auth: Delete code that is no longer used

2 files changed, 1 insertions, 114 deletions

diff --git a/gn3/auth/authorisation/groups/data.py b/gn3/auth/authorisation/groups/data.py
index 0c821d3..453cc71 100644
--- a/gn3/auth/authorisation/groups/data.py
+++ b/gn3/auth/authorisation/groups/data.py
@@ -9,105 +9,6 @@ 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]]:
-    """Retrieve ids for all data that are linked to groups in the auth db."""
-    with authdb.cursor(conn) as cursor:
-        cursor.execute(
-            "SELECT dataset_type, dataset_or_trait_id FROM linked_group_data "
-            "WHERE LOWER(dataset_type)=?",
-            (dataset_type,))
-        return tuple(dict(row) for row in cursor.fetchall())
-
-def __fetch_ungrouped_mrna_data__(
-        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, "
-             "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf "
-             "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName")
-    params: tuple[Any, ...] = tuple()
-    if bool(grouped_data):
-        clause = ", ".join(["%s"] * len(grouped_data))
-        query = f"{query} WHERE psf.Id NOT IN ({clause})"
-        params = tuple(item["dataset_or_trait_id"] for item in grouped_data)
-
-    query = f"{query} LIMIT 100 OFFSET %s"
-    with conn.cursor(DictCursor) as cursor:
-        cursor.execute(query, (params + (offset,)))
-        return tuple(dict(row) for row in cursor.fetchall())
-
-def __fetch_ungrouped_geno_data__(
-        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, "
-             "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf "
-             "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName")
-    params: tuple[Any, ...] = tuple()
-    if bool(grouped_data):
-        clause = ", ".join(["%s"] * len(grouped_data))
-        query = f"{query} WHERE gf.Id NOT IN ({clause})"
-        params = tuple(item["dataset_or_trait_id"] for item in grouped_data)
-
-    query = f"{query} LIMIT 100 OFFSET %s"
-    with conn.cursor(DictCursor) as cursor:
-        cursor.execute(query, (params + (offset,)))
-        return tuple(dict(row) for row in cursor.fetchall())
-
-def __fetch_ungrouped_pheno_data__(
-        conn: gn3db.Connection, grouped_data, offset: int) -> Sequence[dict]:
-    """Fetch ungrouped Phenotype data."""
-    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 pxf.Id NOT IN ({clause})"
-        params = tuple(item["dataset_or_trait_id"] for item in grouped_data)
-
-    query = f"{query} LIMIT 100 OFFSET %s"
-    with conn.cursor(DictCursor) as cursor:
-        cursor.execute(query, (params + (offset,)))
-        return tuple(dict(row) for row in cursor.fetchall())
-
-def __fetch_ungrouped_data__(
-        conn: gn3db.Connection, dataset_type: str,
-        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, offset)
-
-@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,
-        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, offset)
-
 def __fetch_mrna_data_by_ids__(
         conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
             dict, ...]:
diff --git a/gn3/auth/authorisation/groups/views.py b/gn3/auth/authorisation/groups/views.py
index e933bcd..0ff2903 100644
--- a/gn3/auth/authorisation/groups/views.py
+++ b/gn3/auth/authorisation/groups/views.py
@@ -12,7 +12,7 @@ from gn3 import db_utils as gn3dbutils
 from gn3.auth.dictify import dictify
 from gn3.auth.db_utils import with_db_connection
 
-from .data import link_data_to_group, retrieve_ungrouped_data
+from .data import link_data_to_group
 from .models import (
     Group, user_group, all_groups, DUMMY_GROUP, GroupRole, group_by_id,
     join_requests, group_role_by_id, GroupCreationError,
@@ -199,20 +199,6 @@ def unlinked_data(resource_type: str) -> Response:
 
     return jsonify(tuple())
 
-@groups.route("/<string:dataset_type>/ungrouped-data", methods=["GET"])
-@require_oauth("profile group resource")
-def ungrouped_data(dataset_type: str) -> Response:
-    """View data not linked to any group."""
-    if dataset_type not in ("all", "mrna", "genotype", "phenotype"):
-        raise AuthorisationError(f"Invalid dataset type {dataset_type}")
-
-    with require_oauth.acquire("profile group resource") as _the_token:
-        with gn3dbutils.database_connection(current_app.config["SQL_URI"]) as gn3conn:
-            return jsonify(with_db_connection(partial(
-                retrieve_ungrouped_data, gn3conn=gn3conn,
-                dataset_type=dataset_type,
-                offset = int(request.args.get("offset", 0)))))
-
 @groups.route("/data/link", methods=["POST"])
 @require_oauth("profile group resource")
 def link_data() -> Response: