Check for sample job_conf files if the standard one doesn't exist, ot…

…her miscellaneous fixes

Updated __main__ code and get_destination_list_from_job_config  to
check for the sample job config files if the default one doesn't
exist, and if in verbose mode, notify the user to which one will
be used.

Also changed the version number to 1.1

Also removed references to waffles in the test files

lib/galaxy/jobs/dynamic_tool_destination.py

@@ -14,7 +14,7 @@
 
 from yaml import load
 
-__version__ = '1.0.0'
+__version__ = '1.1.0'
 
 # log to galaxy's logger
 log = logging.getLogger(__name__)
@@ -1591,14 +1591,17 @@ def map_tool_to_destination(
     return destination
 
 
-def get_destination_list_from_job_config(job_config_location='/config/job_conf.xml'):
+def get_destination_list_from_job_config(job_config_location):
     """
     returns A list of all destination IDs declared in the job configuration
 
     @type job_config_location: str
     @param job_config_location: The location of the job config file relative
-                to the galaxy root directory. Defaults to
-                galaxy/config/job_conf.xml
+                to the galaxy root directory. If NoneType, defaults to
+                galaxy/config/job_conf.xml,
+                galaxy/config/job_conf.xml.sample_advanced, or
+                galaxy/config/job_conf.xml.sample_basic
+                (first one that exists)
 
     @rtype: list
     @return: A list of all of the destination IDs declared in the job
@@ -1609,10 +1612,36 @@ def get_destination_list_from_job_config(job_config_location='/config/job_conf.x
     # os.path.realpath gets the path of DynamicToolDestination.py
     # and then os.path.join is used to go back four directories
 
-    if job_config_location == "/config/job_conf.xml":
-        config_location = os.path.join(
-            os.path.dirname(os.path.realpath(__file__)), '../../..')
-        job_config_location = config_location + job_config_location
+    config_location = os.path.join(
+              os.path.dirname(os.path.realpath(__file__)), '../../..')
+
+    if job_config_location:
+      local_path = re.compile('^/config/.+$')
+      if  local_path.match(job_config_location):
+          job_config_location = config_location + job_config_location
+    else: # Pick one of the default ones
+      message = "* No job config specified, "
+      if os.path.isfile(config_location + "/config/job_conf.xml"):
+        job_config_location = config_location + "/config/job_conf.xml"
+        message += "using 'config/job_conf.xml'. *"
+
+      elif os.path.isfile(config_location +
+          "/config/job_conf.xml.sample_advanced"):
+        job_config_location = (config_location
+          + "/config/job_conf.xml.sample_advanced")
+        message += "using 'config/job_conf.xml.sample_advanced'. *"
+
+      elif os.path.isfile(config_location +
+          "/config/job_conf.xml.sample_basic"):
+        job_config_location = (config_location
+          + "/config/job_conf.xml.sample_basic")
+        message += "using 'config/job_conf.xml.sample_basic'. *"
+      else:
+        message += "and no default job configs in 'config/'. Failing... *"
+
+      if verbose:
+        log.debug(message)
+
 
     job_conf = ET.parse(job_config_location)
 
@@ -1765,21 +1794,17 @@ def get_typo_correction(typo_str, word_set, max_dist):
         parser.print_help()
         sys.exit(1)
 
-    if args.check_config and args.job_config:
-        valid_config = parse_yaml(path=args.check_config,
-                                  job_conf_path=args.job_config, return_bool=True)
+    if args.job_config:
+      job_conf = args.job_config
+    else:
+      job_conf = None
 
-    elif args.check_config:
+    if args.check_config:
         valid_config = parse_yaml(path=args.check_config,
-                                  job_conf_path="/config/job_conf.xml", return_bool=True)
-
-    elif args.job_config:
-        valid_config = parse_yaml(path="/config/tool_destinations.yml",
-                                  job_conf_path=args.job_config, return_bool=True)
-
+                                  job_conf_path=job_conf, return_bool=True)
     else:
         valid_config = parse_yaml(path="/config/tool_destinations.yml",
-                                  job_conf_path="/config/job_conf.xml", return_bool=True)
+                                  job_conf_path=job_conf, return_bool=True)
 
     if valid_config:
         print("Configuration is valid!")

test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml

@@ -116,9 +116,9 @@ tools:
 
 default_destination:
   priority:
-    low: waffles_default_low
-    med: waffles_default_med
-    high: waffles_default_high
+    low: cluster_default_low
+    med: cluster_default_med
+    high: cluster_default_high
 users:
   user@email.com:
     priority: high

test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml

@@ -6,6 +6,6 @@ tools:
         lower_bound: 1 KB
         upper_bound: Infinity
         destination: Destination1
-    default_destination: waffles_default
-default_destination: waffles_default
+    default_destination: cluster_default
+default_destination: cluster_default
 verbose: False

test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml

@@ -1,6 +1,6 @@
 tools:
   spades:
-    default_destination: waffles_default
+    default_destination: cluster_default
   smalt:
     rules:
       - rule_type: num_input_datasets
@@ -13,5 +13,5 @@ tools:
         lower_bound: 200
         upper_bound: Infinity
         destination: cluster_high_32
-default_destination: waffles_low
+default_destination: cluster_low
 verbose: True

test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml

@@ -22,7 +22,7 @@ tools:
         lower_bound: 5
         upper_bound: Infinity
         destination: Destination3
-    default_destination: waffles_default
+    default_destination: cluster_default
 
   test_overlap:
     rules:
@@ -46,7 +46,7 @@ tools:
         lower_bound: 5
         upper_bound: Infinity
         destination: Destination5
-    default_destination: waffles_default
+    default_destination: cluster_default
 
   test_db:
     rules:
@@ -61,7 +61,7 @@ tools:
         lower_bound: 0
         upper_bound: 1 KB
         destination: Destination4
-    default_destination: waffles_default
+    default_destination: cluster_default
 
   test_db_high:
     rules:
@@ -70,7 +70,7 @@ tools:
         lower_bound: 0
         upper_bound: Infinity
         destination: Destination5
-    default_destination: waffles_default
+    default_destination: cluster_default
 
   test_arguments:
     rules:
@@ -79,7 +79,7 @@ tools:
         arguments:
           careful: true
         destination: Destination6
-    default_destination: waffles_default
+    default_destination: cluster_default
 
-default_destination: waffles_default
+default_destination: cluster_default
 verbose: True