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

this was needed to support the make-library-tree script

diff --git a/htsworkflow/util/fctracker.py b/htsworkflow/util/fctracker.py
index 57b5dcfa647a1815a28c9cd0b08a216ecdef3302..5ba33892f741213bb1932292e5821551df379295 100644 (file)
--- a/htsworkflow/util/fctracker.py
+++ b/htsworkflow/util/fctracker.py
@@ -81,8 +81,8 @@ class fctracker:
         attach the library dictionary to the instance
         """
         self.library = self._make_dict_from_table(
-                         'fctracker_library', 
-                         'library_id')
+                         'samples_library', 
+                         'id')
                                                   
         
     def _get_species(self):
@@ -90,7 +90,7 @@ class fctracker:
         attach the species dictionary to the instance
         """
         self.species = self._make_dict_from_table(
-                         'fctracker_species',
+                         'samples_species',
                          'id'
                        )
         
@@ -106,7 +106,7 @@ class fctracker:
             where = ""
         self.flowcells = {}
         c = self.conn.cursor()
-        c.execute('select * from fctracker_flowcell %s;' % (where))
+        c.execute('select * from experiments_flowcell %s;' % (where))
         # extract just the field name
         description = [ f[0] for f in c.description ]
         for row in c:

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('_')
-        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]
@@ -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.
     """
-    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)
@@ -72,6 +74,7 @@ def carefully_make_hardlink(source, destination, dry_run=False):
 
     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' % \