From: Diane Trout <diane@caltech.edu>
Date: Sat, 8 May 2010 00:32:32 +0000 (+0000)
Subject: Always return a count from carefully_make_hardlinks
X-Git-Tag: 0.4.0~2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=646783204499645dfdaacaf8db28fc39de98fd90

Always return a count from carefully_make_hardlinks
Be more flexible about which json parser to use
---

diff --git a/scripts/make-library-tree b/scripts/make-library-tree
index f4e854a..822af48 100644
--- a/scripts/make-library-tree
+++ b/scripts/make-library-tree
@@ -1,7 +1,12 @@
 #!/usr/bin/env python
 
 from ConfigParser import SafeConfigParser
-import json
+# try to deal with python <2.6
+try:
+  import json
+except ImportError:
+  import simplejson as json
+
 import logging
 import os
 from optparse import OptionParser
@@ -193,8 +198,9 @@ def carefully_make_hardlink(source, destination, dry_run=False):
             logging.debug('SAME: %s -> %s' % (source, destination))
             return 0
         else:
-            raise IOError('%s and %s are different files' % \
-                           (source, destination))
+            logging.error('%s and %s are different files, skipping' % \
+                          (source, destination)) 
+            return 0
     logging.debug('Linking: %s -> %s' % (source, destination))
 
     # we would do something by this part