Make sure we can roundtrip unicode characters via converting to utf-8

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

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index 7b7870363cce0888d41bd047f521b127e37c05ff..4a40f0be0ddc1cae9242eb76461afaa7aa4dfe7f 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -1,10 +1,13 @@
 """Helper features for working with librdf
 """
+import logging
 import os
 import types
 
 import RDF
 
+logger = logging.getLogger(__name__)
+
 # standard ontology namespaces
 owlNS = RDF.NS('http://www.w3.org/2002/07/owl#')
 dublinCoreNS = RDF.NS("http://purl.org/dc/elements/1.1/")
@@ -21,6 +24,7 @@ submissionLog = RDF.NS("http://jumpgate.caltech.edu/wiki/SubmissionsLog/")
 def sparql_query(model, query_filename):
     """Execute sparql query from file
     """
+    logger.info("Opening: %s" % (query_filename,))
     query_body = open(query_filename,'r').read()
     query = RDF.SPARQLQuery(query_body)
     results = query.execute(model)
@@ -56,13 +60,15 @@ def toTypedNode(value):
     elif type(value) == types.FloatType:
         value_type = xsdNS['float'].uri
         value = unicode(value)
-    elif type(value) in types.StringTypes:
-        value_type = xsdNS['string'].uri
     else:
         value_type = None
         value = unicode(value)
 
-    return RDF.Node(literal=value, datatype=value_type)
+    if value_type is not None:
+        node = RDF.Node(literal=value, datatype=value_type)
+    else:
+        node = RDF.Node(literal=unicode(value).encode('utf-8'))
+    return node
 
 def fromTypedNode(node):
     if node is None:
@@ -92,16 +98,19 @@ def fromTypedNode(node):
 
     return literal
 
-
+    
 def get_model(model_name=None, directory=None):
     if directory is None:
         directory = os.getcwd()
         
     if model_name is None:
         storage = RDF.MemoryStorage()
+        logger.info("Using RDF Memory model")
     else:
+        options = "hash-type='bdb',dir='{0}'".format(directory)
         storage = RDF.HashStorage(model_name,
-                      options="hash-type='bdb',dir='{0}'".format(directory))
+                      options=options)
+        logger.info("Using {0} with options {1}".format(model_name, options))
     model = RDF.Model(storage)
     return model