From: Diane Trout <diane@testing.woldlab.caltech.edu>
Date: Wed, 8 Mar 2017 00:32:36 +0000 (-0800)
Subject: Make compatbile with rdflib and python 2/3
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=f181eb8ab89e0af5e8475340b65c4fbc66924f06

Make compatbile with rdflib and python 2/3

* remove old get_model redland code.
* add_default_namespaces needs ConjunctiveGraph
* serialize returns bytes in python 3, which needs to be
  converted to a string for later functions
---

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index be17dbe..28ce8c5 100644
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -316,9 +316,9 @@ def add_default_namespaces(model):
 def get_turtle_header():
     """Return a turtle header with our typical namespaces
     """
-    empty = get_model()
-    add_default_namespaces(model)
-    return model.serialize(format='turtle')
+    empty = ConjunctiveGraph()
+    add_default_namespaces(empty)
+    return empty.serialize(format='turtle').decode()
 
 def dump_model(model, destination=None):
     if destination is None: