New config option to prevent Galaxy from retrying set_meta internally if it fails externally, and accompanying code to allow users to retry set_meta upon failure.

lib/galaxy/config.py

@@ -53,6 +53,7 @@ class Configuration( object ):
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
         self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )
+        self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) )
         self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
         self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
         self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )

lib/galaxy/jobs/__init__.py

@@ -492,9 +492,12 @@ class JobWrapper( object ):
                     #either use the metadata from originating output dataset, or call set_meta on the copies
                     #it would be quicker to just copy the metadata from the originating output dataset, 
                     #but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
-                    if not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ):
-                        # Only set metadata values if they are missing...
+                    if not self.app.config.set_metadata_externally or \
+                     ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) \
+                       and self.app.config.retry_metadata_internally ):
                         dataset.set_meta( overwrite = False )
+                    elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and not context['stderr']:
+                        dataset._state = model.Dataset.states.FAILED_METADATA
                     else:
                         #load metadata from file
                         #we need to no longer allow metadata to be edited while the job is still running,

lib/galaxy/model/__init__.py

@@ -402,7 +402,8 @@ class Dataset( object ):
                     EMPTY = 'empty',
                     ERROR = 'error',
                     DISCARDED = 'discarded',
-                    SETTING_METADATA = 'setting_metadata' )
+                    SETTING_METADATA = 'setting_metadata',
+                    FAILED_METADATA = 'failed_metadata' )
     permitted_actions = get_permitted_actions( filter='DATASET' )
     file_path = "/tmp/"
     engine = None

lib/galaxy/tools/__init__.py

@@ -1708,6 +1708,11 @@ class SetMetadataTool( Tool ):
             external_metadata = galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper( job )
             if external_metadata.external_metadata_set_successfully( dataset, app.model.context ):
                 dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset, app.model.context ).filename_out )    
+            else:
+                dataset._state = model.Dataset.states.FAILED_METADATA
+                self.sa_session.add( dataset )
+                self.sa_session.flush()
+                return
             # If setting external metadata has failed, how can we inform the user?
             # For now, we'll leave the default metadata and set the state back to its original.
             dataset.datatype.after_setting_metadata( dataset )

lib/galaxy/web/controllers/root.py

@@ -335,6 +335,9 @@ class RootController( BaseController, UsesHistory, UsesAnnotations ):
                     if params.annotation:
                         annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' )
                         self.add_item_annotation( trans, data, annotation )
+                    # If setting metadata previously failed and all required elements have now been set, clear the failed state.
+                    if data._state == trans.model.Dataset.states.FAILED_METADATA and not data.missing_meta():
+                        data._state = None
                     trans.sa_session.flush()
                     return trans.show_ok_message( "Attributes updated%s" % message, refresh_frames=['history'] )
                 else:

static/june_2007_style/blue/history.css

@@ -7,6 +7,8 @@ div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;}
 div.historyItem div.historyItem{margin-right:-11px;}
 div.historyItem-ok{border-color:#66AA66;background:#CCFFCC;}
 div.historyItem-ok .state-icon{display:none;}
+div.historyItem-failed_metadata{border-color:#66AA66;background:#CCFFCC;}
+div.historyItem-failed_metadata .state-icon{display:none;}
 div.historyItem-error{border-color:#AA6666;background:#FFCCCC;}
 div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px -0px;}
 div.historyItem-empty{border-color:#AA6666;background:#FFCCCC;}

static/june_2007_style/history.css.tmpl

@@ -46,13 +46,15 @@ div.historyItem div.historyItem {
 }
 
 ## Change background/border color depending on state
-div.historyItem-ok {
+div.historyItem-ok,
+div.historyItem-failed_metadata {
     border-color: $history_ok_border;
     background: $history_ok_bg;
     .state-icon {
         display: none;
     }
 }
+
 div.historyItem-error {
     border-color: $history_error_border;
     background: $history_error_bg;

templates/dataset/edit_attributes.mako

@@ -92,7 +92,9 @@
             </div>
         </form>
         %if data.missing_meta():
-            <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div>
+            <div class="form-row">
+                <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div>
+            </div>
         %endif
     </div>
 </div>

templates/mobile/history/detail.mako

@@ -55,8 +55,11 @@
                 <div>Metadata is being Auto-Detected.</div>
             %elif data_state == "empty":
                 <div>No data: <i>${data.display_info()}</i></div>
-            %elif data_state == "ok":
+            %elif data_state in [ "ok", "failed_metadata" ]:
                 <div>
+                    %if data_state == "failed_metadata":
+                        Warning: setting metadata failed,
+                    %endif
                     ${data.blurb},
                     format: <span class="${data.ext}">${data.ext}</span>, 
                     database: <span class="${data.dbkey}">${data.dbkey}</span>

templates/root/history.mako

@@ -19,7 +19,7 @@ ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "class", "jquery.jstor
 
 <script type="text/javascript">
 
-<% TERMINAL_STATES = ["ok", "error", "empty", "deleted", "discarded"] %>
+<% TERMINAL_STATES = ["ok", "error", "empty", "deleted", "discarded", "failed_metadata"] %>
 TERMINAL_STATES = ${ h.to_json_string(TERMINAL_STATES) };
 
 $(function() {

templates/root/history_common.mako

@@ -100,7 +100,12 @@
             <div>${_('Metadata is being Auto-Detected.')}</div>
         %elif data_state == "empty":
             <div>${_('No data: ')}<i>${data.display_info()}</i></div>
-        %elif data_state == "ok":
+        %elif data_state in [ "ok", "failed_metadata" ]:
+            %if data_state == "failed_metadata":
+                <div class="warningmessagesmall" style="margin: 4px 0 4px 0">
+                    An error occurred setting the metadata for this dataset.  You may be able to <a href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main">set it manually or retry auto-detection</a>.
+                </div>
+            %endif
             <div>
                 ${data.blurb},
                 format: <span class="${data.ext}">${data.ext}</span>, 

universe_wsgi.ini.sample

@@ -346,6 +346,13 @@ use_interactive = True
 # unresponsive when this operation occurs internally.
 #set_metadata_externally = False
 
+# Although it is fairly reliable, setting metadata can occasionally fail.  In
+# these instances, you can choose to retry setting it internally or leave it in
+# a failed state (since retrying internally may cause the Galaxy process to be
+# unresponsive).  If this option is set to False, the user will be given the
+# option to retry externally, or set metadata manually (when possible).
+#retry_metadata_internally = True
+
 # Number of concurrent jobs to run (local job runner)
 #local_job_queue_workers = 5