From: Diane Trout <diane@caltech.edu>
Date: Mon, 1 Jul 2013 23:02:46 +0000 (-0700)
Subject: Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=6f05ae54b482745afbacc8da7d9cc31f9b067d23;hp=d9697c7e4a93736e5bb17bcc771c86ce377713c1

Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
---

diff --git a/encode_submission/trackhub.py b/encode_submission/trackhub.py
index c5c2543..fb0cea8 100644
--- a/encode_submission/trackhub.py
+++ b/encode_submission/trackhub.py
@@ -27,7 +27,6 @@ import RDF
 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
 
-
 from htsworkflow.util import api
 from htsworkflow.util.rdfhelp import \
      dafTermOntology, \
@@ -78,10 +77,10 @@ def main(cmdline=None):
             logger.warn("File %s doesn't exist.", a)
 
     if opts.make_link_tree_from is not None:
-        results.make_tree_from(opts.make_tree_from, link=True)
+        results.make_tree_from(opts.make_link_tree_from, link=True)
 
     if opts.copy_tree_from is not None:
-        results.make_tree_from(opts.make_tree_from, link=False)
+        results.make_tree_from(opts.copy_tree_from, link=False)
 
     if opts.fastq:
         logger.info("Building fastq extraction scripts")
diff --git a/htsworkflow/submission/results.py b/htsworkflow/submission/results.py
index 5007752..5633745 100644
--- a/htsworkflow/submission/results.py
+++ b/htsworkflow/submission/results.py
@@ -2,6 +2,7 @@
 """
 from collections import MutableMapping
 import os
+import shutil
 import logging
 
 from collections import namedtuple
@@ -75,11 +76,11 @@ class ResultMap(MutableMapping):
                 if not os.path.exists(source_pathname):
                     raise IOError(
                         "{0} does not exist".format(source_pathname))
-                if not os.path.exists(target_pathname):
+                if not (os.path.exists(target_pathname) or os.path.isdir(source_pathname)):
                     if link:
                         os.symlink(source_pathname, target_pathname)
                     else:
-                        os.copy(source_pathname, target_pathname)
+                        shutil.copy(source_pathname, target_pathname)
                     LOGGER.info(
                         'LINK {0} to {1}'.format(source_pathname,
                                                  target_pathname))