Start of get access to output files

src/jflow/component.py

@@ -24,7 +24,7 @@ from jflow.workflows_manager import WorkflowsManager
 from jflow.config_reader import JFlowConfigReader
 from jflow.dataset import ArrayList
 from jflow.utils import which
-from jflow.iotypes import DynamicOutput
+from jflow.iotypes import DynamicOutput, OutputFile, OutputFileList
 
 from weaver.util import parse_string_list
 
@@ -52,6 +52,16 @@ class Component(object):
             if issubclass( attribute_value.__class__, DynamicOutput ):
                 dynamic_outputs.append( attribute_value )
         return dynamic_outputs
+    
+    def get_component_outputs(self):
+        outputs = list()
+        for attribute_value in self.__dict__.values():
+            if ( issubclass( attribute_value.__class__, DynamicOutput ) or
+                 issubclass( attribute_value.__class__, OutputFileList) ): 
+                outputs.extend( attribute_value )
+            elif issubclass( attribute_value.__class__, OutputFile):
+                outputs.append( attribute_value )
+        return outputs
         
     def _longestCommonSubstr(self, data, clean_end=True):
         substr = ''

src/jflow/workflow.py

@@ -71,6 +71,7 @@ class Workflow(threading.Thread):
         self.jflow_config_reader = JFlowConfigReader()
         self.manager = WorkflowsManager()
         self.components_to_exec = []
+        self.components = []
         self.makes = {}
         self.globals = {}
         self.options = Options()
@@ -113,6 +114,12 @@ class Workflow(threading.Thread):
         for arg in arg_lines:
             yield arg
     
+    def get_outputs_per_components(self):
+        outputs_files = {}
+        for current_components in self.components:
+            outputs_files[current_components.get_nameid()] = current_components.get_component_outputs()
+        return outputs_files
+    
     def __setstate__(self, state):
         self.__dict__ = state.copy()
         threading.Thread.__init__(self, name=self.name)
@@ -172,6 +179,7 @@ class Workflow(threading.Thread):
                 if self.component_nameids_is_init:
                     # add the component
                     self.components_to_exec.append(cmpt_object)
+                    self.components.append(cmpt_object)
                     self._execute_weaver()
                     # update outputs
                     for output in cmpt_object.get_dynamic_outputs():
@@ -182,15 +190,18 @@ class Workflow(threading.Thread):
                                             cmpt_object.prefix + " already exist in this pipeline!")
                     self.component_nameids[cmpt_object.get_nameid()] = None
                     self.components_to_exec = []
+                    self.components = []
             else:
                 if self.component_nameids_is_init:
                     # add the component
                     self.components_to_exec.append(cmpt_object)
+                    self.components.append(cmpt_object)
                 elif not self.component_nameids_is_init and not self.dynamic_component_present:
                     if self._component_is_duplicated(cmpt_object):
                         raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                             cmpt_object.prefix + " already exist in this pipeline!")
                     self.components_to_exec.append(cmpt_object)
+                    self.components.append(cmpt_object)
                 else:
                     if self._component_is_duplicated(cmpt_object):
                         raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
@@ -569,7 +580,7 @@ class Workflow(threading.Thread):
                         self.end_time = time.time()
                         self._serialize()
                         raise
-                self.components_to_exec = []
+                self.components_to_exec = []  
                 # Once a weaver script is compiled, serialize the workflow
                 self._serialize()
                 try:

src/jflow/workflows_manager.py

@@ -89,7 +89,11 @@ class WorkflowsManager(object):
         # Add the workflow dump path to the workflows dump
         self._add_workflow(workflow)
         return workflow
-        
+    
+    def get_workflow_ouputs(self, workflow_id):
+        workflow = self.get_workflow(workflow_id)
+        return workflow.get_outputs_per_components()
+    
     def get_output_directory(self):
         return self.config_reader.get_work_directory()