Update htsworkflow.util.fctracker module to work with the newer django db

[htsworkflow.git] / scripts / make-library-tree

diff --git a/scripts/make-library-tree b/scripts/make-library-tree
index 1c3772efb9f6050086f79138dfae8e4c03ebb967..50ce7a932ef263300c70d2e9483f18431ced6f5d 100644 (file)
--- a/scripts/make-library-tree
+++ b/scripts/make-library-tree
@@ -42,7 +42,9 @@ def parse_srf_directory(srf_dir):
         path, filename = os.path.split(pathname)
         basename, ext = os.path.splitext(filename)
         record = basename.split('_')
         path, filename = os.path.split(pathname)
         basename, ext = os.path.splitext(filename)
         record = basename.split('_')

-        assert len(record) == 6
+        if len(record) != 6:
+            logging.error("Unrecognized srf file: %s expected 6 fields got %d" % (pathname,len(record)))
+            continue

 
         site = record[0]
         date = record[1]
 
         site = record[0]
         date = record[1]


@@ -64,7 +66,7 @@ def carefully_make_hardlink(source, destination, dry_run=False):
     the same as the link we want to make.
     If the link already exists and is different, throw an error.
     """
     the same as the link we want to make.
     If the link already exists and is different, throw an error.
     """

-    logging.debug("%s -> %s", source, destination)
+    logging.debug("CHECKING: %s -> %s", source, destination)

 
     if not os.path.exists(source):
         logging.warning("%s doesn't exist", source)
 
     if not os.path.exists(source):
         logging.warning("%s doesn't exist", source)


@@ -72,6 +74,7 @@ def carefully_make_hardlink(source, destination, dry_run=False):
 
     if os.path.exists(destination):
         if os.path.samefile(source, destination):
 
     if os.path.exists(destination):
         if os.path.samefile(source, destination):

+            logging.debug('SAME: %s -> %s' % (source, destination))

             return
         else:
             raise IOError('%s and %s are different files' % \
             return
         else:
             raise IOError('%s and %s are different files' % \