Write out registry.xml file in case jobs are missing this file

lib/galaxy/jobs/handler.py

@@ -93,6 +93,16 @@ def job_pair_for_id( self, id ):
         job = self.sa_session.query( model.Job ).get( id )
         return job, self.job_wrapper( job, use_persisted_destination=True )
 
+    def __write_registry_file_if_absent(self, job):
+        job_wrapper =  self.job_wrapper(job)
+        cwd = job_wrapper.working_directory
+        datatypes_config = os.path.join(cwd, "registry.xml")
+        if not os.path.exists(datatypes_config):
+            try:
+                self.app.datatypes_registry.to_xml_file(path=datatypes_config)
+            except OSError:
+                pass
+
     def __check_jobs_at_startup( self ):
         """
         Checks all jobs that are in the 'new', 'queued' or 'running' state in
@@ -120,6 +130,7 @@ def __check_jobs_at_startup( self ):
                          ( model.Job.handler == self.app.config.server_name ) ).all()
 
         for job in jobs_at_startup:
+            self.__write_registry_file_if_absent(job)
             if not self.app.toolbox.has_tool( job.tool_id, job.tool_version, exact=True ):
                 log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) )
                 self.job_wrapper( job ).fail( 'This tool was disabled before the job completed.  Please contact your Galaxy administrator.' )

lib/galaxy_ext/metadata/set_metadata.py

@@ -81,6 +81,16 @@ def set_metadata():
 
     # Set up datatypes registry
     datatypes_config = sys.argv.pop( 1 )
+    if not os.path.exists(datatypes_config):
+        # This path should exist, except for jobs that started running on release 17.05, where a global
+        # datatypes_config (instead of a datatypes_config per job) was used. For a while release 17.05
+        # would remove the global datatypes config on shutdown and toolbox reload, which would lead to
+        # failed metadata jobs. To remedy this we scan jobs at startup for missing registry.xml files,
+        # and if we detect such a job we write out the current registry.xml file.
+        datatypes_config = os.path.join(tool_job_working_directory, "registry.xml")
+        if not os.path.exists(datatypes_config):
+            print("Metadata setting failed because registry.xml could not be found. You may retry setting metadata.")
+            sys.exit(1)
     datatypes_registry = galaxy.datatypes.registry.Registry()
     datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config )
     galaxy.model.set_datatypes_registry( datatypes_registry )