Bug fixes for recent commits.

Outputs weren't getting rewritten when using remote_copy and remote_transfer, this made a bunch of tests pass that should have been failing and things seem more correct than they actually were.

lwr/lwr_client/action_mapper.py

 from json import load
+from os import makedirs
+from os.path import exists
 from os.path import abspath
 from os.path import dirname
 from os.path import join
@@ -265,8 +267,12 @@ class RemoteCopyAction(BaseAction):
         galaxy.util.copy_to_path(open(self.path, "rb"), path)
 
     def write_from_path(self, lwr_path):
+        destination = self.path
+        parent_directory = dirname(destination)
+        if not exists(parent_directory):
+            makedirs(parent_directory)
         with open(lwr_path, "rb") as f:
-            galaxy.util.copy_to_path(f, self.path)
+            galaxy.util.copy_to_path(f, destination)
 
 
 class RemoteTransferAction(BaseAction):

lwr/lwr_client/staging/up.py

@@ -381,7 +381,7 @@ class TransferTracker(object):
 
     def register_rewrite(self, local_path, remote_path, type, force=False):
         action = self.__action(local_path, type)
-        if action.action_type in ['transfer', 'copy'] or force:
+        if action.staging_needed or force:
             self.file_renames[local_path] = remote_path
 
     def rewrite_input_paths(self):

lwr/lwr_client/transport/curl.py

@@ -41,7 +41,7 @@ class PycurlTransport(object):
 def post_file(url, path):
     c = _new_curl_object()
     c.setopt(c.URL, url.encode('ascii'))
-    c.setopt(c.HTTPPOST, [("file", (c.FORM_FILE, path))])
+    c.setopt(c.HTTPPOST, [("file", (c.FORM_FILE, path.encode('ascii')))])
     c.perform()
 
 

lwr/managers/staging/postprocess.py

+import os
+
 from lwr.lwr_client import action_mapper
 from lwr.lwr_client import staging
 from lwr.lwr_client.staging import LwrOutputs
@@ -44,6 +46,11 @@ class LwrServerOutputCollector(object):
         if action.staging_action_local:
             return  # Galaxy (client) will collect output.
 
+        if not name:
+            # TODO: Would not work on Windows. Any use in allowing
+            # remote_transfer action for Windows?
+            name = os.path.basename(action.path)
+
         lwr_path = self.job_directory.calculate_path(name, output_type)
         action.write_from_path(lwr_path)
 

lwr/managers/stateful.py

@@ -45,20 +45,21 @@ class StatefulManagerProxy(ManagerProxy):
 
     def handle_remote_staging(self, job_id, staging_config):
         job_directory = self._proxied_manager.job_directory(job_id)
-
-        def do_preprocess():
-            preprocess(job_directory, staging_config.get("setup", []))
-        new_thread_for_manager(self, "preprocess", do_preprocess, daemon=False)
-
         job_directory.store_metadata("staging_config", staging_config)
 
     def launch(self, job_id, *args, **kwargs):
         job_directory = self._proxied_manager.job_directory(job_id)
-        result = self._proxied_manager.launch(job_id, *args, **kwargs)
-        with job_directory.lock("status"):
-            job_directory.store_metadata(JOB_FILE_PREPROCESSED, True)
-        self.active_jobs.activate_job(job_id)
-        return result
+
+        def do_preprocess():
+            # TODO: Handle preprocess or launch failures!
+            staging_config = job_directory.load_metadata("staging_config", {})
+            preprocess(job_directory, staging_config.get("setup", []))
+            self._proxied_manager.launch(job_id, *args, **kwargs)
+            with job_directory.lock("status"):
+                job_directory.store_metadata(JOB_FILE_PREPROCESSED, True)
+            self.active_jobs.activate_job(job_id)
+
+        new_thread_for_manager(self, "preprocess", do_preprocess, daemon=False)
 
     def get_status(self, job_id):
         """ Compute status used proxied manager and handle state transitions

test/test_utils.py

@@ -2,7 +2,9 @@ from contextlib import contextmanager
 from stat import S_IXOTH
 import json
 from os import pardir, stat, chmod, access, X_OK, pathsep, environ
+from os import makedirs
 from os.path import join, dirname, isfile, split
+from os.path import exists
 from tempfile import mkdtemp
 from shutil import rmtree
 
@@ -244,6 +246,9 @@ class JobFilesApp(object):
         path = params['path']
         if not galaxy.util.in_directory(path, self.root_directory):
             assert False, "%s not in %s" % (path, self.root_directory)
+        parent_directory = dirname(path)
+        if not exists(parent_directory):
+            makedirs(parent_directory)
         galaxy.util.copy_to_path(params["file"].file, path)
         return webob.Response(body='')