some code cleanup and changing default priority on tools

The default priority for tools if not specified in the tool destination config is now whatever the middle priority is in the list of global default destinations

lib/galaxy/jobs/dynamic_tool_destination.py

@@ -787,6 +787,12 @@ def infinite_defaultdict():
                             if verbose:
                                 log.debug(error)
                             valid_config = False
+
+                    if len(priority_list) < 1:
+                        error = ("No valid default priorities found!")
+                        if verbose:
+                            log.debug(error)
+                        valid_config = False
 
                 else:
                     error = "No default priority destinations specified in config!"
@@ -820,9 +826,8 @@ def infinite_defaultdict():
                             if curr['priority'] in ['low', 'med', 'high']: ### DO THINGS HERE (maybe)
                                 new_config['users'][user]['priority'] = curr['priority']
                             else:
-                                error = ("User '" + user + "', priority classification "
-                                    + "is not valid: Must be one of the values "
-                                    + "specified in the config.")
+                                error = ("User '" + user + "', priority '"
+                                    + str(curr['priority']) + "' is not valid")
                                 if verbose:
                                     log.debug(error)
                                 valid_config = False
@@ -863,16 +868,14 @@ def infinite_defaultdict():
 
                                 if ('priority' in curr['default_destination'] and isinstance(curr['default_destination']['priority'], dict)):
                                     ####new code
-                                    ####May not be necessary check
-                                    all_mandatory_classes_defined = True
+                                    ###May not be necessary check if something has all priorities specified as default
                                     for priority in priority_list:
                                         if priority not in curr['default_destination']['priority']:
                                             error = ("No default for priority classification "
                                                 + str(priority) + " in tool " + str(tool))
                                             if verbose:
                                                 log.debug(error)
                                             valid_config = False
-                                            all_mandatory_classes_defined = False
 
                                    ## if all_mandatory_classes_defined == True:
                                     for priority in curr['default_destination']['priority']:
@@ -1246,9 +1249,17 @@ def map_tool_to_destination(
     # For each different rule for the tool that's running
     fail_message = None
 
-    # set default priority to med
-    default_priority = 'med' ###May need to find a better default
-    priority = default_priority
+    # set default priority to whatever the middle one is in the list
+    # The priorities won't necessarily be in order, but it can't be
+    # worse than choosing a random value (probably)
+    if len(priority_list) > 0:
+        default_priority = priority_list[len(priority_list) / 2]
+        priority = default_priority
+    else:
+        error = "No priorities found so no default priorty set!"
+        if verbose:
+            log.debug(error)
+        valid_config = False
 
     if config is not None:
         # get the users priority
@@ -1406,7 +1417,7 @@ def map_tool_to_destination(
 
     return destination
 
-### new method
+#### new method
 def get_valid_destinations_from_config(config_location='/config/job_conf.xml'):
     """
     returns A list of all destination IDs declared in the job configuration
@@ -1435,12 +1446,9 @@ def get_valid_destinations_from_config(config_location='/config/job_conf.xml'):
             valid_destinations.append(destination.get("id"))
 
         else:
-            ###Not sure what to do here, because we're technically
-            ###only validating the tool destination config, not
-            ###the job configuration
-            error = "ID for destination " + str(destination)
-            error += " cannot be parsed."
-            error += " Ignoring..."
+            error = "Destination ID '" + str(destination)
+            error += "' in job configuration file cannot be"
+            error += " parsed. Things may not work as expected!"
             log.debug(error)
 
     return valid_destinations