2 files changed, 36 insertions, 9 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 3946a0f..3d656d2 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -96,20 +96,34 @@ def dataset_phenotypes(# pylint: disable=[too-many-arguments, too-many-positiona
         xref_ids: tuple[int, ...] = tuple()
 ) -> tuple[dict, ...]:
     """Fetch the actual phenotypes."""
-    _query = (
-        "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode "
+    _narrow_by_ids = (
+            f" AND pxr.Id IN ({', '.join(['%s'] * len(xref_ids))})"
+            if len(xref_ids) > 0 else "")
+    _narrow_by_limit = (
+        f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
+    _pub_query = (
+        "SELECT pub.* "
+        "FROM PublishXRef AS pxr "
+        "INNER JOIN  Publication AS pub ON pxr.PublicationId=pub.Id "
+        "WHERE pxr.InbredSetId=%s") + _narrow_by_ids
+    _pheno_query = ((
+        "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, pxr.PublicationId, "
+        "ist.InbredSetCode "
         "FROM Phenotype AS pheno "
         "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
         "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
         "INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id "
-        "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + (
-            f" AND pxr.Id IN ({', '.join(['%s'] * len(xref_ids))})"
-            if len(xref_ids) > 0 else "") + (
-            f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
+        "WHERE pxr.InbredSetId=%s AND pf.Id=%s") +
+                    _narrow_by_ids +
+                    _narrow_by_limit)
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute(_query, (population_id, dataset_id) + xref_ids)
+        cursor.execute(_pub_query, (population_id,) + xref_ids)
         debug_query(cursor, logger)
-        return tuple(dict(row) for row in cursor.fetchall())
+        _pubs = {row["Id"]: dict(row) for row in cursor.fetchall()}
+        cursor.execute(_pheno_query, (population_id, dataset_id) + xref_ids)
+        debug_query(cursor, logger)
+        return tuple({**dict(row), "publication": _pubs[row["PublicationId"]]}
+                     for row in cursor.fetchall())
 
 
 def __phenotype_se__(cursor: BaseCursor, xref_id, dataids_and_strainids):
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 23bc682..c03f3f5 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -317,6 +317,11 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
         dataset_shortname = (
             form["dataset-shortname"] or form["dataset-name"]).strip()
         _pheno_dataset = save_new_dataset(
+            # It's not necessary to update the authorisation server to register
+            # new phenotype resource here, since each phenotype trait can, in
+            # theory, have its own access control allowing/disallowing access to
+            # it. In practice, however, we tend to gather multiple traits into a
+            # single resource for access control.
             cursor,
             population["Id"],
             form["dataset-name"].strip(),
@@ -662,6 +667,8 @@ def review_job_data(
                                        conn, int(_job_metadata["publicationid"]))
                                    if _job_metadata.get("publicationid")
                                    else None),
+                               user=session.user_details(),
+                               timestamp=datetime.datetime.now().isoformat(),
                                activelink="add-phenotypes")
 
 
@@ -741,9 +748,15 @@ def load_data_to_database(
                     "publication_id": _meta["publicationid"],
                     "authserver": oauth2client.authserver_uri(),
                     "token": token["access_token"],
+                    "dataname": request.form["data_name"].strip(),
                     "success_handler": (
                         "uploader.phenotypes.views"
-                        ".load_phenotypes_success_handler")
+                        ".load_phenotypes_success_handler"),
+                    **{
+                        key: request.form[key]
+                        for key in ("data_description",)
+                        if key in request.form.keys()
+                    }
                 },
                 external_id=session.logged_in_user_id())
         ).then(