Minor tweaks to deal with the older version of librdf on ubuntu 10.04

things like utf-8 escaping a string, using str(node.uri) instead
of str(node).

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 5ae4b7a01f481f1b75e181c50d919010fb4b3d26..9f4f1368176fa1aa1bccec47b4c302831e56e30b 100644 (file)
--- a/htsworkflow/submission/condorfastq.py
+++ b/htsworkflow/submission/condorfastq.py
@@ -250,7 +250,7 @@ WHERE {
         """Add link between target pathname and the 'lane' that produced it
         (note lane objects are now post demultiplexing.)
         """
-        target_uri = 'file://' + target
+        target_uri = 'file://' + target.encode('utf-8')
         target_node = RDF.Node(RDF.Uri(target_uri))
         source_stmt = RDF.Statement(target_node, dcNS['source'], seq.filenode)
         self.model.add_statement(source_stmt)

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index 89d9e5b4d16290e940878d7cc6844d8b64d80c79..6fa326d576c97d18a6e50d15998e6c866db5d6a2 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -7,6 +7,7 @@ from urlparse import urlparse, urlunparse
 from urllib2 import urlopen
 import logging
 import os
+import sys
 import types
 
 import lxml.html

diff --git a/htsworkflow/util/rdfinfer.py b/htsworkflow/util/rdfinfer.py
index aac3afa849178cecffa7f8185c29144f554ebe23..92564a0d80b25b684ad54d31226776ae1eeebd00 100644 (file)
--- a/htsworkflow/util/rdfinfer.py
+++ b/htsworkflow/util/rdfinfer.py
@@ -187,13 +187,13 @@ class Infer(object):
             """
             # check domain
             query = RDF.SPARQLQuery(property_template.format(
-                predicate=predicate,
+                predicate=predicate.uri,
                 space=space))
             seen = []
             for r in query.execute(self.model):
                 if r['type'] == rdfsNS['Resource']:
                     continue
-                seen.append(str(r['type']))
+                seen.append(str(r['type'].uri))
                 check = RDF.Statement(node, rdfNS['type'], r['type'])
                 if self.model.contains_statement(check):
                     return

diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py
index 948bcf407cf976eea74c44b0ff095b475f02770e..dfa4b971c70c1bcd28723d8b3b416c331d6d84c5 100644 (file)
--- a/htsworkflow/util/test/test_rdfhelp.py
+++ b/htsworkflow/util/test/test_rdfhelp.py
@@ -231,7 +231,7 @@ _:a owl:imports "{loc}extra.turtle" .
             model = get_model()
             self.assertEqual(model.size(), 0)
             add_default_schemas(model)
-            self.assertGreater(model.size(), 0)
+            self.assertTrue(model.size() > 0)
             remove_schemas(model)
             self.assertEqual(model.size(), 0)
 

diff --git a/htsworkflow/util/test/test_rdfinfer.py b/htsworkflow/util/test/test_rdfinfer.py
index 380c1e640bd8133aadf5ff8ce7325026a1981814..faa76727cf21a5f59f2c26b056579af1ba8a0f18 100644 (file)
--- a/htsworkflow/util/test/test_rdfinfer.py
+++ b/htsworkflow/util/test/test_rdfinfer.py
@@ -172,8 +172,9 @@ class TestInfer(unittest.TestCase):
         self.model.append(s)
         errors = list(inference._validate_property_types())
         self.assertEqual(len(errors), 1)
-        startswith = 'Domain of <http://example.org/me.jpg>'
+        startswith = 'Domain of '
         self.assertEqual(errors[0][:len(startswith)], startswith)
+        self.assertTrue('http://example.org/me.jpg' in errors[0])
         endswith = 'http://xmlns.com/foaf/0.1/Person'
         self.assertEqual(errors[0][-len(endswith):], endswith)
         del self.model[s]
@@ -189,8 +190,9 @@ class TestInfer(unittest.TestCase):
 
         errors = list(inference._validate_property_types())
         self.assertEqual(len(errors), 1)
-        startswith = 'Range of <http://example.org/me.jpg>'
+        startswith = 'Range of '
         self.assertEqual(errors[0][:len(startswith)], startswith)
+        self.assertTrue('http://example.org/me.jpg' in errors[0])
         endswith = 'http://www.w3.org/2002/07/owl#Thing'
         self.assertEqual(errors[0][-len(endswith):], endswith)
         del self.model[s]