Allow linking of data by passing the raw ids too.

2 files changed, 23 insertions, 10 deletions

diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py
index 08a0524..63b3f12 100644
--- a/gn_auth/auth/authorisation/data/phenotypes.py
+++ b/gn_auth/auth/authorisation/data/phenotypes.py
@@ -83,7 +83,7 @@ def ungrouped_phenotype_data(
 
     return tuple()
 
-def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]:
+def pheno_traits_from_db(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]:
     """An internal utility function. Don't use outside of this module."""
     if len(params) < 1:
         return tuple()
@@ -110,21 +110,24 @@ def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dic
                 for itm in sublist))
         return cursor.fetchall()
 
+
 @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_phenotype_data(
-        authconn:authdb.DbConnection, gn3conn: gn3db.Connection, group: Group,
-        traits: tuple[dict, ...]) -> dict:
+        authconn:authdb.DbConnection,
+        group: Group,
+        traits: tuple[dict, ...]
+) -> dict:
     """Link phenotype traits to a user group."""
     with authdb.cursor(authconn) as cursor:
         params = tuple({
             "data_link_id": str(uuid.uuid4()),
             "group_id": str(group.group_id),
             **item
-        } for item in __traits__(gn3conn, traits))
+        } for item in traits)
         cursor.executemany(
             "INSERT INTO linked_phenotype_data "
             "VALUES ("
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
index 6d66788..fc20e86 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -35,8 +35,8 @@ from ..resources.models import (
 from ...authentication.users import User
 from ...authentication.oauth2.resource_server import require_oauth
 
-from ..data.phenotypes import link_phenotype_data
 from ..data.mrna import link_mrna_data, ungrouped_mrna_data
+from ..data.phenotypes import link_phenotype_data, pheno_traits_from_db
 from ..data.genotypes import link_genotype_data, ungrouped_genotype_data
 
 data = Blueprint("data", __name__)
@@ -327,14 +327,24 @@ def link_phenotype() -> Response:
             raise InvalidData("Expected at least one dataset to be provided.")
         return {
             "group_id": uuid.UUID(form["group_id"]),
-            "traits": form["selected"]
+            "traits": form["selected"],
+            "using_raw_ids": bool(form.get("using-raw-ids") == "on")
         }
 
     with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn:
-        def __link__(conn: db.DbConnection, group_id: uuid.UUID,
-                     traits: tuple[dict, ...]) -> dict:
-            return link_phenotype_data(
-                conn, gn3conn, group_by_id(conn, group_id), traits)
+        def __link__(
+                conn: db.DbConnection,
+                group_id: uuid.UUID,
+                traits: tuple[dict, ...],
+                using_raw_ids: bool = False
+        ) -> dict:
+            if using_raw_ids:
+                return link_phenotype_data(conn,
+                                           group_by_id(conn, group_id),
+                                           traits)
+            return link_phenotype_data(conn,
+                                       group_by_id(conn, group_id),
+                                       pheno_traits_from_db(gn3conn, traits))
 
         return jsonify(with_db_connection(
             partial(__link__, **__values__(request_json()))))