Merge branch 'release_19.05' into dev

config/datatypes_conf.xml.sample

@@ -160,6 +160,7 @@
     <datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mcool" type="galaxy.datatypes.binary:MCool" mimetype="application/octet-stream" display_in_upload="true"/>

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -182,6 +182,8 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         has_duplicate_inputs = False
         for job_input_assoc in job.input_datasets:
             input_dataset_instance = job_input_assoc.dataset
+            if input_dataset_instance is None:
+                continue
             if input_dataset_instance.get_total_size() == 0:
                 has_empty_inputs = True
             input_instance_id = input_dataset_instance.id

tools/stats/gsummary.py

@@ -13,7 +13,7 @@ except ImportError:
 
 def stop_err(msg):
     sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(1)
 
 
 def S3_METHODS(all="key"):