Merge branch 'release_19.05' into dev

client/galaxy/scripts/mvc/workflow/workflow-node.js

@@ -65,7 +65,15 @@ var Node = Backbone.Model.extend({
         const output = this.nodeView.outputViews[outputName].output;
         output_terminal.force_datatype = datatype;
         output.force_datatype = datatype;
-        this.nodeView.updateDataOutputView(output);
+        if (datatype) {
+            this.post_job_actions['ChangeDatatypeAction' + outputName] = {
+                action_arguments: {newtype: datatype},
+                action_type: "ChangeDatatypeAction",
+                output_name: outputName,
+            };
+        } else {
+            delete this.post_job_actions['ChangeDatatypeAction' + outputName];
+        }
         this.markChanged();
         output_terminal.destroyInvalidConnections();
     },

client/galaxy/scripts/mvc/workflow/workflow-view-node.js

@@ -115,14 +115,6 @@ export default Backbone.View.extend({
         this.tool_body.append(outputView.$el.append(terminalView.terminalElements()));
     },
 
-    updateDataOutputView: function(output) {
-        const terminalView = this.terminalViewForOutput(output);
-        const outputView = this.outputViews[output.name];
-        const newOutputView = this.outputViewforOutput(output, terminalView);
-        newOutputView.$el.append(terminalView.terminalElements());
-        outputView.$el.html(newOutputView.$el);
-    },
-
     redrawWorkflowOutputs: function() {
         _.each(this.outputViews, outputView => {
             outputView.redrawWorkflowOutput();

lib/galaxy/jobs/__init__.py

@@ -272,7 +272,7 @@ class JobConfiguration(ConfiguresHandlers):
         self.default_handler_id = None
         self.handler_assignment_methods = None
         self.handler_assignment_methods_configured = False
-        self.handler_max_grab = 1
+        self.handler_max_grab = None
         self.destinations = {}
         self.destination_tags = {}
         self.default_destination_id = None

lib/galaxy/jobs/handler.py

@@ -107,8 +107,9 @@ class JobHandlerQueue(Monitors):
             .where(and_(
                 model.Job.table.c.handler.in_(self.app.job_config.self_handler_tags),
                 model.Job.table.c.state == model.Job.states.NEW)) \
-            .order_by(model.Job.table.c.id) \
-            .limit(self.app.job_config.handler_max_grab)
+            .order_by(model.Job.table.c.id)
+        if self.app.job_config.handler_max_grab:
+            subq = subq.limit(self.app.job_config.handler_max_grab)
         if method == HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED:
             subq = subq.with_for_update(skip_locked=True)
         self.__grab_query = model.Job.table.update() \

lib/galaxy/tool_util/deps/conda_util.py

@@ -35,19 +35,19 @@ CONDA_LICENSE = "http://docs.continuum.io/anaconda/eula"
 VERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@(.*)")
 UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
 USE_PATH_EXEC_DEFAULT = False
-CONDA_VERSION = "4.3.33"
-CONDA_BUILD_VERSION = "2.1.18"
+CONDA_VERSION = "4.6.14"
+CONDA_BUILD_VERSION = "3.17.8"
 USE_LOCAL_DEFAULT = False
 
 
 def conda_link():
     if IS_OS_X:
-        url = "https://repo.continuum.io/miniconda/Miniconda3-4.3.31-MacOSX-x86_64.sh"
+        url = "https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-MacOSX-x86_64.sh"
     else:
         if sys.maxsize > 2**32:
-            url = "https://repo.continuum.io/miniconda/Miniconda3-4.3.31-Linux-x86_64.sh"
+            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh"
         else:
-            url = "https://repo.continuum.io/miniconda/Miniconda3-4.3.31-Linux-x86.sh"
+            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.5.12-Linux-x86.sh"
     return url
 
 

lib/galaxy/web/stack/handlers.py

@@ -125,6 +125,8 @@ class ConfiguresHandlers(object):
             if self.handler_assignment_methods == [HANDLER_ASSIGNMENT_METHODS.MEM_SELF]:
                 self.app.config.track_jobs_in_database = False
             self.handler_max_grab = handling_config_dict.get('max_grab', self.handler_max_grab)
+            if self.handler_max_grab is not None:
+                self.handler_max_grab = int(self.handler_max_grab)
 
     def _set_default_handler_assignment_methods(self):
         if not self.handler_assignment_methods_configured:

lib/galaxy/workflow/scheduling_manager.py

@@ -47,7 +47,7 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
         self.handlers = {}
         self.handler_assignment_methods_configured = False
         self.handler_assignment_methods = None
-        self.handler_max_grab = 1
+        self.handler_max_grab = None
         self.default_handler_id = None
 
         self.__plugin_classes = self.__plugins_dict()