Fix job files API for case when nginx upload not being used.

Fixes regressions introduced with PR #110.

lib/galaxy/jobs/runners/pulsar.py

@@ -342,7 +342,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
 
         encoded_job_id = self.app.security.encode_id(job_id)
         job_key = self.app.security.encode_id( job_id, kind="jobs_files" )
-        endpoint_base = "%s/api/jobs/%s?job_key=%s"
+        endpoint_base = "%s/api/jobs/%s/files?job_key=%s"
         if self.app.config.nginx_upload_job_files_path:
             endpoint_base = "%s" + \
                             self.app.config.nginx_upload_job_files_path + \

lib/galaxy/webapps/galaxy/api/job_files.py

@@ -99,7 +99,12 @@ class JobFilesAPIController( BaseAPIController ):
         try:
             shutil.move( input_file.name, path )
         finally:
-            input_file.close()
+            try:
+                input_file.close()
+            except OSError:
+                # Fails to close file if not using nginx upload because the
+                # tempfile has moved and Python wants to delete it.
+                pass
         return {"message": "ok"}
 
     def __authorize_job_access(self, trans, encoded_job_id, **kwargs):