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

[htsworkflow.git] / htsworkflow / util / rdfhelp.py

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index fda8772f858601a0f488c61248da3d39d67c7be3..93b7ada645e876834319236359b3121c73f94c74 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -258,13 +258,14 @@ def load_into_model(model, parser_name, path, ns=None):
     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 @@ def load_into_model(model, parser_name, path, ns=None):
             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 @@ 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'