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src/jflow/workflow.py

@@ -21,7 +21,6 @@ import re
 import sys
 import uuid
 import pkgutil
-import urllib2 
 import tempfile
 import pickle
 import time
@@ -30,7 +29,6 @@ from ConfigParser import ConfigParser, NoOptionError
 import types
 import logging
 from inspect import getcallargs
-from urlparse import urlparse
 
 import jflow
 import jflow.utils as utils
@@ -224,43 +222,8 @@ class Workflow(threading.Thread):
     def get_components_nameid(self):
         return self.component_nameids.keys()
     
-    def _download_url(self, url):
-        print "Downloading " + url + " ..."
-        uri_object = urlparse(url)
-        opener = urllib2.urlopen(url)
-        block_size = 8000
-        jflowconf = JFlowConfigReader()
-        tmp_directory = os.path.join(jflowconf.get_tmp_directory(), os.path.basename(tempfile.NamedTemporaryFile().name))
-        os.mkdir(tmp_directory) 
-        downloaded_file_path = os.path.join(tmp_directory, os.path.basename(uri_object.path))
-        downloaded_file = open(downloaded_file_path, 'wb')
-        metadata = opener.info()
-        while True:
-            buffer = opener.read(block_size)
-            # End of download
-            if not buffer: break
-            # Parts of download
-            downloaded_file.write(buffer)
-        downloaded_file.close()
-        logging.getLogger("types.ifile").debug("URL file '{0}' successfully downloaded as: {1}".format(url, downloaded_file_path))
-        return downloaded_file_path
-    
-    def _is_url(self, file):
-        uri_object = urlparse(file)
-        return uri_object.scheme != ''
-    
-    def _download_input_files(self):
-        for param in self.parameters:
-            if param.type.__name__ == "inputfile":
-                if param.action == "append":
-                    for i, file in enumerate(self.args[param.name]):
-                        if self._is_url(file):
-                            # download file
-                            self.args[param.name][i] = self._download_url(file)
-                else:
-                    if self._is_url(file):
-                        # download file
-                        self.args[param.name] = self._download_url(file)
+    def wf_execution_wrapper(self):
+        getattr(self, self.function)()
     
     def run(self):
         """
@@ -272,7 +235,6 @@ class Workflow(threading.Thread):
             self.step = 0
             self.status = self.STATUS_STARTED
             self.end_time = None
-            self._download_input_files()
             self._serialize()
         # if pre_processing has not been done yet    
         if self.step == 0:
@@ -282,7 +244,7 @@ class Workflow(threading.Thread):
         # if collecting components and running workflow has not been done yet
         if self.step == 1:
             try: 
-                getattr(self, self.function)()
+                self.wf_execution_wrapper()
             except SystemExit, e: 
                 self.status = self.STATUS_FAILED
                 self.end_time = time.time()
@@ -298,7 +260,7 @@ class Workflow(threading.Thread):
         # if the workflow was a dynamic one
         if self.step == 2:
             try: 
-                getattr(self, self.function)()
+                self.wf_execution_wrapper()
             except SystemExit, e: 
                 self.status = self.STATUS_FAILED
                 self.end_time = time.time()