Merge remote-tracking branch 'upstream/release_17.09' into dev

lib/galaxy/tools/data_manager/manager.py

@@ -317,10 +317,10 @@ class DataManager(object):
                         self.process_move(data_table_name, name, output_ref_values[name].extra_files_path, **data_table_value)
                         data_table_value[name] = self.process_value_translation(data_table_name, name, **data_table_value)
                 data_table.add_entry(data_table_value, persist=True, entry_source=self)
-                send_control_task(self.data_managers.app,
-                                  'reload_tool_data_tables',
-                                  noop_self=True,
-                                  kwargs={'table_name': data_table_name})
+            send_control_task(self.data_managers.app,
+                              'reload_tool_data_tables',
+                              noop_self=True,
+                              kwargs={'table_name': data_table_name})
         if self.undeclared_tables and data_tables_dict:
             # We handle the data move, by just moving all the data out of the extra files path
             # moving a directory and the target already exists, we move the contents instead
@@ -338,9 +338,9 @@ class DataManager(object):
                         if name in path_column_names:
                             data_table_value[name] = os.path.abspath(os.path.join(self.data_managers.app.config.galaxy_data_manager_data_path, value))
                     data_table.add_entry(data_table_value, persist=True, entry_source=self)
-                    send_control_task(self.data_managers.app, 'reload_tool_data_tables',
-                                      noop_self=True,
-                                      kwargs={'table_name': data_table_name})
+                send_control_task(self.data_managers.app, 'reload_tool_data_tables',
+                                  noop_self=True,
+                                  kwargs={'table_name': data_table_name})
         else:
             for data_table_name, data_table_values in data_tables_dict.items():
                 # tool returned extra data table entries, but data table was not declared in data manager

lib/galaxy/tools/error_reports/plugins/sentry.py

@@ -73,6 +73,17 @@ class SentryPlugin(ErrorPlugin):
             error_message = ERROR_TEMPLATE.format(**extra)
 
             # Update context with user information in a sentry-specific manner
+
+            # Getting the url allows us to link to the dataset info page in case
+            # anything is missing from this report.
+            try:
+                url = web.url_for(controller="dataset",
+                                  action="show_params",
+                                  dataset_id=self.app.security.encode_id(dataset.id),
+                                  qualified=True)
+            except AttributeError:
+                # The above does not work when handlers are separate from the web handlers
+                url = None
             self.sentry_client.context.merge({
                 # User information here also places email links + allows seeing
                 # a list of affected users in the tags/filtering.
@@ -80,14 +91,8 @@ class SentryPlugin(ErrorPlugin):
                     'name': user.username,
                     'email': user.email,
                 },
-                # This allows us to link to the dataset info page in case
-                # anything is missing from this report.
                 'request': {
-                    'url': web.url_for(
-                        controller="dataset", action="show_params",
-                        dataset_id=self.app.security.encode_id(dataset.id),
-                        qualified=True
-                    )
+                    'url': url
                 }
             })
 

lib/galaxy/tools/toolbox/watcher.py

@@ -252,6 +252,10 @@ class LocFileEventHandler(FileSystemEventHandler):
                 if self.loc_watcher.path_hash.get(path) == cur_hash:
                     return
                 else:
+                    time.sleep(0.5)
+                    if cur_hash != md5_hash_file(path):
+                        # We're still modifying the file, it'll be picked up later
+                        return
                     self.loc_watcher.path_hash[path] = cur_hash
                     self.loc_watcher.tool_data_tables.reload_tables(path=path)
 

templates/webapps/galaxy/history/display_structured.mako

@@ -231,7 +231,7 @@ elif entity_name == "WorkflowInvocation":
     <% id = trans.security.encode_id( hda.id ) %>
     <%
         folder = hda.copied_from_library_dataset_dataset_association.library_dataset.folder
-        folder_id = 'F' + trans.security.encode_id( folder.id )
+        folder_id = trans.security.encode_id( folder.id )
     %>
     <div class="copied-from copied-from-library">
         <div class="header">