wire e2e gene set loading prototype

server/cli/launch.py

@@ -36,12 +36,12 @@ def annotation_args(func):
     )
     @click.option(
         "--annotations-dir",
+        "--data-dir",
         default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__directory,
         show_default=False,
         multiple=False,
         metavar="<directory path>",
-        help="Directory of where to save output annotations; filename will be specified in the application. "
-        "Incompatible with --annotations-file.",
+        help="Directory of where to save annotations and gene sets; filename will be specified in the application. Incompatible with --annotations-file and --genesets-file.",
     )
     @click.option(
         "--experimental-annotations-ontology",
@@ -57,6 +57,21 @@ def annotation_args(func):
         metavar="<path or url>",
         help="Location of OBO file defining cell annotation autosuggest terms.",
     )
+    @click.option(
+        "--disable-genesets-save",
+        is_flag=True,
+        default=not DEFAULT_CONFIG.default_dataset_config.user_annotations__genesets__readonly,
+        show_default=False,
+        help="Disable saving gene sets. If disabled, users will be able to make changes to gene sets but all changes will be lost on browser refresh.",
+    )
+    @click.option(
+        "--genesets-file",
+        default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__genesets_file,
+        show_default=True,
+        multiple=False,
+        metavar="<path>",
+        help="CSV file to initialize editing of gene sets; will be altered in-place. Incompatible with --data-dir.",
+    )
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
         return func(*args, **kwargs)
@@ -325,6 +340,8 @@ def launch(
     disable_annotations,
     annotations_file,
     annotations_dir,
+    genesets_file,
+    disable_genesets_save,
     backed,
     disable_diffexp,
     experimental_annotations_ontology,
@@ -389,6 +406,8 @@ def launch(
             user_annotations__enable=not disable_annotations,
             user_annotations__local_file_csv__file=annotations_file,
             user_annotations__local_file_csv__directory=annotations_dir,
+            user_annotations__local_file_csv__genesets_file=genesets_file,
+            user_annotations__genesets__readonly=disable_genesets_save,
             user_annotations__ontology__enable=experimental_annotations_ontology,
             user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
             presentation__max_categories=max_category_items,