Merge pull request #12 from mvdbeek/fixes_for_deployment

Fixes for deployment
galaxyproject · Oct 10, 2023 · 6f5b4df · 6f5b4df
2 parents 7f54913 + b79637d
commit 6f5b4df
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Showing 4 changed files with 12 additions and 4 deletions.
diff --git a/gx_tool_db/config.py b/gx_tool_db/config.py
@@ -15,7 +15,7 @@
     TEST_URL: 'test',
     USEGALAXY_EU_URL: 'eu',
     USEGALAXY_AU_URL: 'au',
-    "https://clipseq.usegalaxy.eu/": "cliqseq_eu",
+    "https://clipseq.usegalaxy.eu/": "clipseq_eu",
     "https://humancellatlas.usegalaxy.eu/": "humancellatlas_eu",
     "https://metabolomics.usegalaxy.eu/": "metabolomics_eu",
     "https://ml.usegalaxy.eu/": "ml_eu",
@@ -74,6 +74,7 @@ def label(self):
 
 class ViewDefintion(FilterArguments):
     id: str
+    name: Optional[str] = None
     output: Optional[str] = None
     view_type: str = DEFAULT_PANEL_VIEW_TYPE
     description: Optional[str] = None

diff --git a/gx_tool_db/db.py b/gx_tool_db/db.py
@@ -195,7 +195,11 @@ def panel_view_dict(self, server_label: str, view_def: ViewDefintion):
         filter_criteria.require_labels = view_def.require_labels
         filter_criteria.exclude_labels = view_def.exclude_labels
 
-        rval: Dict[str, Any] = {"id": view_def.id, "type": view_def.view_type}
+        rval: Dict[str, Any] = {
+            "id": view_def.id,
+            "type": view_def.view_type,
+            "name": view_def.name or view_def.id,
+        }
         if view_def.description:
             rval["description"] = view_def.description
 
@@ -229,6 +233,7 @@ def panel_view_dict(self, server_label: str, view_def: ViewDefintion):
                 section = {
                     "id": panel_skeleton_item_id,
                     "name": name,
+                    "type": "section",
                 }
                 # If we're requiring a label need to specify the elements, otherwise we can just
                 # count on a global exclude of the tools in the map.

diff --git a/gx_tool_db/main.py b/gx_tool_db/main.py
@@ -586,6 +586,7 @@ def arg_parser():
     parser_export_view.add_argument('--output', type=str, help="Output YAML (defaults to <id>.yml", default=None)
     HELP_ARG_VIEW_TYPE = "Panel view type (generic, activity, publication, training, ...)"
     parser_export_view.add_argument('--view-type', type=str, help=HELP_ARG_VIEW_TYPE, default=DEFAULT_PANEL_VIEW_TYPE)
+    parser_export_view.add_argument('--name', type=str, help="Name of panel view.")
     parser_export_view.add_argument('--description', type=str, help="End user description of panel view.")
     add_common_filters(parser_export_view)
 
@@ -666,6 +667,7 @@ def main(argv=None):
         view_def.output = args.output
         view_def.view_type = args.view_type
         view_def.description = args.description
+        view_def.name = args.name
         view_def.require_labels = args.require_labels
         view_def.exclude_labels = args.exclude_labels
         export_panel_view(config, args.server, view_def)

diff --git a/requirements.txt b/requirements.txt
@@ -4,8 +4,8 @@ google-auth-oauthlib
 gspread
 gxformat2
 packaging
-pydantic
+pydantic<2
 requests
 pyyaml
 typing-extensions
-urllib3
+urllib3