Add tools description

bin/jflow_admin.py

@@ -79,6 +79,11 @@ if __name__ == '__main__':
     sub_parser.add_argument("--errors", action="store_true", help="Display failed commands",
                             default=False, dest="display_errors")
     sub_parser.set_defaults(cmd_object="status")
+
+    # Add tools workflow availability
+    sub_parser = subparsers.add_parser("tools", help="Show tools used in a workflow")
+    sub_parser.add_argument("workflow_name", help="Name of the workflow")
+    sub_parser.set_defaults(cmd_object="tools")
     
     
     args = vars(parser.parse_args())
@@ -86,16 +91,6 @@ if __name__ == '__main__':
     if not "cmd_object" in args:
         print(parser.format_help())
         parser.exit(0, "")
-    
-    if args["cmd_object"] in wf_classes:
-        try:
-            workflow = wfmanager.get_workflow_by_class(args["cmd_object"])
-            workflow.check_parameters_rules(args)
-        except RuleException as e:
-            sub_parser.error(e)
-        except RuleIgnore:
-            pass
-        wfmanager.run_workflow(args["cmd_object"], args)
 
     elif args["cmd_object"] == "rerun":
         wfmanager.rerun_workflow(args["workflow_id"])
@@ -141,4 +136,13 @@ if __name__ == '__main__':
                     if i<len(workflows)-1: status += "\n"
             else: status = "no workflow available"
             print(status)
-            
\ No newline at end of file
+    elif args["cmd_object"] == "tools":
+        workflow = wfmanager.get_workflow_by_name(args["workflow_name"])
+        if workflow is not None:
+            nodes = workflow.tools.get_printable_tree()
+            i = 0
+            for node in nodes:
+                i += 1
+                print("{0}. {1}".format(i, node))
+        else:
+            print("Workflow not found: " + args["workflow_name"])

src/jflow/workflow.py

@@ -46,6 +46,7 @@ from jflow.utils import get_octet_string_representation, get_nb_octet
 from jflow.parameter import *
 from jflow.exceptions import RuleException
 import jflow.rules as j_rules
+from jflow.tooltree import ToolTree
 
 from cctools.util import time_format
 
@@ -153,6 +154,8 @@ class Workflow(threading.Thread):
         self.id = id
         self.name = self.get_name()
         self.description = self.get_description()
+        self.tools = ToolTree()
+        self.get_tools(self.tools)
         self.__group = self.jflow_config_reader.get_workflow_group(self.__class__.__name__) or Workflow.DEFAULT_GROUP
         
         # define the parameters 
@@ -913,6 +916,12 @@ class Workflow(threading.Thread):
         """
         raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
 
+    def get_tools(self, toolstree: ToolTree):
+        """
+        Return the workflow description, has to be implemented by subclasses
+        """
+        raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
+
     def get_summary(self):
         """
         Return a workflow summary, if implemented by subclasses

src/jflow/workflows_manager.py

@@ -194,6 +194,20 @@ class WorkflowsManager(object):
                 if class_name == workflow_class:
                     return obj()
         return None
+
+    def get_workflow_by_name(self, workflow_name):
+        """
+        Get workflow by name, case insensitive
+        :param workflow_name: workflow name
+        :return: workflow object
+        """
+        for importer, modname, ispkg in pkgutil.iter_modules(workflows.__path__, workflows.__name__ + "."):
+            __import__(modname)
+            # Search for Workflow classes
+            for class_name, obj in inspect.getmembers(sys.modules[modname], inspect.isclass):
+                if class_name.lower() == workflow_name.lower():
+                    return obj()
+        return None
     
     def get_workflow(self, workflow_id):
         rworkflow_id = utils.get_nb_string(workflow_id)