Merge remote-tracking branch 'upstream/dev' into webpack_4_minimal_flat

config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako

@@ -9,8 +9,8 @@ ie_request.load_deploy_config()
 ie_request.attr.docker_port = 80
 ie_request.attr.import_volume = False
 
-bam = ie_request.volume(hda.file_name, '/input/bamfile.bam', how='ro')
-bam_index = ie_request.volume(hda.metadata.bam_index.file_name, '/input/bamfile.bam.bai', how='ro')
+bam = ie_request.volume(hda.file_name, '/input/bamfile.bam', mode='ro')
+bam_index = ie_request.volume(hda.metadata.bam_index.file_name, '/input/bamfile.bam.bai', mode='ro')
 
 ie_request.launch(volumes=[bam, bam_index], env_override={
     'PUB_HTTP_PORT': ie_request.attr.galaxy_config.dynamic_proxy_bind_port,

config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako

@@ -9,7 +9,7 @@
 
     import os
     mount_path = hda.file_name
-    data_vol = ie_request.volume(mount_path, '/data/data_pack.tar.gz', how='rw')
+    data_vol = ie_request.volume(mount_path, '/data/data_pack.tar.gz', mode='rw')
 
     # Add all environment variables collected from Galaxy's IE infrastructure
     # Launch the IE.

config/plugins/interactive_environments/neo/templates/neo.mako

@@ -7,7 +7,7 @@
     # if the user knows ahead of time that they will need it.
     import os
     mount_path = str(os.path.dirname(hda.file_name)) + '/dataset_{}_files'.format( hda.dataset.id )
-    data_vol = ie_request.volume(mount_path, '/data', how='rw')
+    data_vol = ie_request.volume(mount_path, '/data', mode='rw')
     # data_vol = ie_request.volume('${HOME}/neo4j/data', '/data/', how='rw')
     # Add all environment variables collected from Galaxy's IE infrastructure
     # Launch the IE.

config/plugins/tours/core.galaxy_ui.yaml

@@ -89,19 +89,19 @@ steps:
         - 'a[href$="tool_runner?tool_id=Filter1"]'
 
     - title: "Filter Tool"
-      element: '#center-panel'
+      element: '.center-panel'
       intro: "Your tool is loaded into the main Galaxy page and ready for use."
       position: "right"
       #backdropContainer: 'background'
       #backdrop: true
 
     - title: "Tool parameters"
-      element: '#center-panel .ui-portlet-limited'
+      element: '.center-panel .ui-portlet'
       intro: "Here you can choose your tool parameters. Select your input dataset from your history and specify parameters for your analysis."
       position: "right"
 
     - title: "Tool help"
-      element: 'div.ui-form-help'
+      element: 'div.form-help'
       intro: "Every Galaxy tool has a help section with detailed information about the tool and its parameters.
               Have a look and study your tool in depth by reading it."
       position: "top"

config/plugins/visualizations/graphviz/config/graphviz.xml

@@ -13,6 +13,11 @@
             <test test_attr="ext" result_type="datatype">txt</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext" result_type="datatype">graph_dot</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
             <test type="has_dataprovider" test_attr="datatype">node-edge</test>
@@ -23,4 +28,4 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <template>graphviz.mako</template>
-</visualization>
+</visualization>

config/plugins/webhooks/demo/tour_generator/__init__.py

@@ -76,7 +76,7 @@ class TourGenerator(object):
                 upload_tool = self._trans.app.toolbox.get_tool('upload1')
                 filename = os.path.basename(input_path)
 
-                with open(input_path, 'r') as f:
+                with open(input_path, 'rb') as f:
                     content = f.read()
                     headers = {
                         'content-disposition':