Use the get_runs from htsworkflow.pipelines.runfolder

On the plus side this means it'll handle IPAR files, on the downside
it means that the srf program will crash if there's something wrong with
the summary.htm file or if there's an ipar directory that doesn't have
a run in it.
(I really need to add some code to get_runs to skip over IPAR directories that
are being ignored.)

diff --git a/scripts/srf b/scripts/srf
index 248728f824fac0441c6a5b088d3387a78eebfa75..9e0fff8de22fd6fd68bc2680f7af97cdee5d8980 100644 (file)
--- a/scripts/srf
+++ b/scripts/srf
@@ -8,6 +8,7 @@ import subprocess
 import sys
 
 from htsworkflow.util import queuecommands
+from htsworkflow.pipelines import runfolder
 
 def make_commands(run_name, lanes, site_name, destdir):
   """
@@ -50,22 +51,6 @@ def pathname_to_run_name(base):
       return None
   return name
 
-def find_bustard_dir(pathname):
-  # fixme: for don't repeat yourself this should some how be related 
-  # fixme: to pipelines.runfolder
-
-  datadir = os.path.join(pathname, 'Data')
-  logging.info("searching in %s" % (datadir,))
-  
-  bustard_dirs = []
-  for firecrest_pathname in glob(os.path.join(datadir,"*Firecrest*")):
-    bustard_glob = os.path.join(firecrest_pathname, "Bustard*")
-    for bustard_pathname in glob(bustard_glob):
-      bustard_dirs.append(bustard_pathname)
-  return bustard_dirs
-    
-
-
 def make_parser():
   usage = '%prog: [options] runfolder -l 1,2,3 [runfolder -l 5,6 ...]'
 
@@ -132,15 +117,13 @@ def main(cmdline=None):
         # the last part of the path should be a runfolder name
         name = pathname_to_run_name(runfolder_path)
         # so any bustard directories?
-        bustard_dir = find_bustard_dir(runfolder_path)
-        # give up if there are anything other than 1 bustard dir
-        if len(bustard_dir) > 1:
-          print 'ERROR: Too many bustard directories',
-          print "\n ".join(bustard_dir)
+        runs = runfolder.get_runs(runfolder_path)
+        # give up if there are anything other than 1 run
+        if len(runs) > 1:
+          print 'ERROR: Too many run directories in %s' %(runfolder_path,)
           return 1
-
-        elif len(bustard_dir) == 1:
-          bustard_dir = bustard_dir[0]
+        elif len(runs) == 1:
+          bustard_dir = runs[0].bustard.pathname
           cmds[bustard_dir] = make_commands(name, lanes, opts.site, opts.dest_dir)
         else:
           print "ERROR: Couldn't find a bustard directory in", runfolder_path