Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

diff --combined htsworkflow/util/rdfhelp.py
index cb445b6b0cb4f5f1d9abab3d13ae7edad483b931,93b7ada645e876834319236359b3121c73f94c74..89d9e5b4d16290e940878d7cc6844d8b64d80c79
--- 1/htsworkflow/util/rdfhelp.py
--- 2/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@@ -258,13 -258,14 +258,14 @@@ def load_into_model(model, parser_name
      if len(url_parts[0]) == 0 or url_parts[0] == 'file':
          url_parts[0] = 'file'
          url_parts[2] = os.path.abspath(url_parts[2])
-         if parser_name is None or parser_name == 'guess':
-             parser_name = guess_parser_by_extension(path)
+     if parser_name is None or parser_name == 'guess':
+         parser_name = guess_parser_by_extension(path)
      url = urlunparse(url_parts)
      logger.info("Opening {0} with parser {1}".format(url, parser_name))
  
      rdf_parser = RDF.Parser(name=parser_name)
  
+     statements = []
      retries = 3
      while retries > 0:
          try:
@@@ -273,7 -274,7 +274,7 @@@
              retries = 0
          except RDF.RedlandError, e:
              errmsg = "RDF.RedlandError: {0} {1} tries remaining"
-             logger.error(errmsg.format(str(e), tries))
+             logger.error(errmsg.format(str(e), retries))
  
      for s in statements:
          conditionally_add_statement(model, s, ns)
@@@ -384,16 -385,16 +385,16 @@@ def guess_parser(content_type, pathname
          return 'turtle'
      elif content_type in ('text/html',):
          return 'rdfa'
-     elif content_type is None:
+     elif content_type is None or content_type in ('text/plain',):
          return guess_parser_by_extension(pathname)
  
  def guess_parser_by_extension(pathname):
      _, ext = os.path.splitext(pathname)
      if ext in ('.xml', '.rdf'):
          return 'rdfxml'
-     elif ext in ('.html'):
+     elif ext in ('.html',):
          return 'rdfa'
-     elif ext in ('.turtle'):
+     elif ext in ('.turtle',):
          return 'turtle'
      return 'guess'
  
@@@ -418,9 -419,6 +419,9 @@@ def get_serializer(name='turtle')
      return writer
  
  
 -def dump_model(model):
 +def dump_model(model, destination=None):
 +    if destination is None:
 +        destination = sys.stdout
      serializer = get_serializer()
 -    print serializer.serialize_model_to_string(model)
 +    destination.write(serializer.serialize_model_to_string(model))
 +    destination.write(os.linesep)