back from master submission option

application.properties

@@ -20,8 +20,6 @@ makeflow = /usr/bin/makeflow
 batch_system_type = local
 # add these options to all batch submit files
 batch_options = 
-# should the master job be submitted on the cluster (False|True)
-submit_master_job = False
 # on which socket host should run the web server
 server_socket_host = 127.0.0.1
 # on which socket port should run the web server

src/jflow/config_reader.py

@@ -80,9 +80,4 @@ class JFlowConfigReader(object):
             return self.reader.get("components", component_class+".batch_options")
         except:
             return ""
-        
-    def submit_master_job(self):
-        try:
-            return self.reader.get("global", "submit_master_job") == "True"
-        except:
-            return False
\ No newline at end of file
+        
\ No newline at end of file

src/jflow/workflows_manager.py

@@ -24,25 +24,10 @@ import imp
 import os
 import pickle
 import threading
-import tempfile
 
 import jflow.utils as utils
 from jflow.config_reader import JFlowConfigReader
 
-from weaver.function import PythonFunction
-from weaver.nest import Nest
-from weaver.options import Options
-
-
-def run_workflow_wrapper(workflow_serial_path):
-    import pickle
-    # load the workflow object
-    workflow_dump = open(workflow_serial_path, "rb")
-    workflow = pickle.load(workflow_dump)
-    workflow_dump.close()
-    # and start it
-    workflow.start()
-
 class WorkflowsManager(object):
     """
     """
@@ -56,13 +41,6 @@ class WorkflowsManager(object):
         """ 
         """
         self.config_reader = JFlowConfigReader()
-        self.options = Options()
-        # try to parse engine arguments
-        try:
-            type, options = self.jflow_config_reader.get_batch()
-            if type: self.engine_arguments += ' -T ' + type
-            if options : self.engine_arguments += ' -B "' + options + '"'
-        except: self.engine_arguments = None
         if not os.path.isdir(self.get_output_directory()):
             os.makedirs(self.get_output_directory(), 0751)
         self.ids_file = os.path.join(self.get_output_directory(), self.IDS_FILE_NAME)
@@ -82,49 +60,16 @@ class WorkflowsManager(object):
     
     def rerun_workflow(self, workflow_id):
         workflow = self.get_workflow(workflow_id)
-        if self.config_reader.submit_master_job():
-            workflow_dump_path = self.get_temporary_file(".dump")
-            workflow_dump = open(workflow_dump_path, "wb")
-            pickle.dump(workflow, workflow_dump)
-            workflow_dump.close()
-            # Execute nest
-            with Nest(self.get_temporary_directory(), path=self.config_reader.get_makeflow_path()) as nest:
-                with self.options:
-                    rw = PythonFunction(run_workflow_wrapper, cmd_format="{EXE} {IN} > {OUT}")
-                    rw(inputs=workflow_dump_path, outputs=self.get_temporary_file(".stdout"))
-                    try:
-                        nest.compile()
-                        nest.execute(self.engine_arguments, exit_on_failure=True)
-                    except:
-                        raise
-        else:
-            workflow.start()
-        return workflow
-
-    def run_workflow(self, workflow_class, args):   
+        workflow.start()
+    
+    def run_workflow(self, workflow_class, args):
         # Load all modules within the workflow module
         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 == workflow_class: workflow = obj(args, id=self.get_next_id())
-        if self.config_reader.submit_master_job():
-            workflow_dump_path = self.get_temporary_file(".dump")
-            workflow_dump = open(workflow_dump_path, "wb")
-            pickle.dump(workflow, workflow_dump)
-            workflow_dump.close()
-            # Execute nest
-            with Nest(self.get_temporary_directory(), path=self.config_reader.get_makeflow_path()) as nest:
-                with self.options:
-                    rw = PythonFunction(run_workflow_wrapper, cmd_format="{EXE} {IN} > {OUT}")
-                    rw(inputs=workflow_dump_path, outputs=self.get_temporary_file(".stdout"))
-                    try:
-                        nest.compile()
-                        nest.execute(self.engine_arguments, exit_on_failure=True)
-                    except:
-                        raise
-        else:
-            workflow.start()
+        workflow.start()
         return workflow
         
     def get_output_directory(self):
@@ -202,20 +147,4 @@ class WorkflowsManager(object):
         finally:
             WorkflowsManager.lock_ids_file.release()
         return cid
-    
-    def get_temporary_file(self, suffix=".txt"):
-        # first check if tmp directory exists
-        if not os.path.isdir(self.config_reader.get_tmp_directory()):
-            os.makedirs(self.config_reader.get_tmp_directory(), 0751)
-        tempfile_name = os.path.basename(tempfile.NamedTemporaryFile(suffix=suffix).name)
-        return os.path.join(self.config_reader.get_tmp_directory(), tempfile_name)
-    
-    def get_temporary_directory(self):
-        # first check if tmp directory exists
-        if not os.path.isdir(self.config_reader.get_tmp_directory()):
-            os.makedirs(self.config_reader.get_tmp_directory(), 0751)
-        tempdir_name = os.path.basename(tempfile.NamedTemporaryFile().name)
-        tempdir = os.path.join(self.config_reader.get_tmp_directory(), tempdir_name)
-        os.makedirs(tempdir, 0751)
-        return tempdir
     
\ No newline at end of file