add graph info

bin/jflow_cli.py

@@ -132,6 +132,12 @@ if __name__ == '__main__':
                             required=True, dest="workflow_id")
     sub_parser.set_defaults(cmd_object="rerun")
 
+    # Add rerun workflow availability
+    sub_parser = subparsers.add_parser("execution-graph", help="Display the workflow execution graph")
+    sub_parser.add_argument("--workflow-id", type=str, help="Which workflow should be considered",
+                            required=True, dest="workflow_id")
+    sub_parser.set_defaults(cmd_object="execution_graph")
+
     # Add status workflow availability
     sub_parser = subparsers.add_parser("status", help="monitor a specific workflow")
     sub_parser.add_argument("--workflow-id", type=str, help="Which workflow status should be displayed",
@@ -176,6 +182,8 @@ if __name__ == '__main__':
         wfmanager.run_workflow(args["cmd_object"], args)
     elif args["cmd_object"] == "rerun":
         wfmanager.rerun_workflow(args["workflow_id"])
+    elif args["cmd_object"] == "execution_graph":
+        wfmanager.get_workflow_execution_graph(args["workflow_id"])
     elif args["cmd_object"] == "status":
         if args["workflow_id"]:
             workflow = wfmanager.get_workflow(args["workflow_id"])

src/jflow/graph.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+class Graph(object):
+
+    def __init__(self, graph_dict={}):
+        """ initializes a graph object """
+        self.__graph_dict = graph_dict
+
+    def vertices(self):
+        """ returns the vertices of a graph """
+        return list(self.__graph_dict.keys())
+
+    def edges(self):
+        """ returns the edges of a graph """
+        return self.__generate_edges()
+
+    def add_vertex(self, vertex):
+        """ If the vertex "vertex" is not in 
+            self.__graph_dict, a key "vertex" with an empty
+            list as a value is added to the dictionary. 
+            Otherwise nothing has to be done. 
+        """
+        if vertex not in self.__graph_dict:
+            self.__graph_dict[vertex] = []
+
+    def add_edge(self, edge):
+        """ assumes that edge is of type set, tuple or list; 
+            between two vertices can be multiple edges! 
+        """
+        edge = set(edge)
+        (vertex1, vertex2) = tuple(edge)
+        if vertex1 in self.__graph_dict:
+            self.__graph_dict[vertex1].append(vertex2)
+        else:
+            self.__graph_dict[vertex1] = [vertex2]
+
+    def __generate_edges(self):
+        """ A static method generating the edges of the 
+            graph "graph". Edges are represented as sets 
+            with one (a loop back to the vertex) or two 
+            vertices 
+        """
+        edges = []
+        for vertex in self.__graph_dict:
+            for neighbour in self.__graph_dict[vertex]:
+                if {neighbour, vertex} not in edges:
+                    edges.append({vertex, neighbour})
+        return edges
+
+    def __str__(self):
+        res = "vertices: "
+        for k in self.__graph_dict:
+            res += str(k) + " "
+        res += "\nedges: "
+        for edge in self.__generate_edges():
+            res += str(edge) + " "
+        return res

src/jflow/workflow.py

@@ -34,6 +34,7 @@ from inspect import getcallargs
 
 import jflow
 import jflow.utils as utils
+from jflow.graph import Graph
 from jflow.workflows_manager import WorkflowsManager, JFlowConfigReader
 from jflow.parameter import *
 
@@ -283,6 +284,17 @@ class Workflow(threading.Thread):
                                 final_sub_args[sub_param.name] = sub_param.default
                         self.__getattribute__(param.name).append(sub_args)
     
+    def get_execution_graph(self):
+        graph = Graph()
+        for cpt in self.components:
+            graph.add_vertex(cpt.get_nameid())
+            for ioparameter in cpt.__dict__.values():
+                if ( issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, OutputFile) 
+                     or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, OutputFileList) ):
+                    print ioparameter.name, ioparameter.component_nameid, ioparameter.parent_component_nameid
+                    graph.add_edge({ioparameter.component_nameid, ioparameter.parent_component_nameid})
+        print graph
+    
     def set_stderr(self):
         if hasattr(self, "stderr") and self.stderr is not None:
             os.rename( self.stderr, os.path.join(self.directory, str(time.time()) + "wf_stderr.old") )

src/jflow/workflows_manager.py

@@ -104,6 +104,10 @@ class WorkflowsManager(object):
     def get_output_directory(self):
         return self.config_reader.get_work_directory()
     
+    def get_workflow_execution_graph(self, workflow_id):
+        workflow = self.get_workflow(workflow_id)
+        workflow.get_execution_graph()
+        
     def get_workflows(self):
         workflows = []
         try: