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.)
         """
         """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)
         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
 from urllib2 import urlopen
 import logging
 import os

+import sys

 import types
 
 import lxml.html
 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(
             """
             # 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
                 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
                 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)
             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)
 
             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)
         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.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]
         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)
 
         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.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]
         endswith = 'http://www.w3.org/2002/07/owl#Thing'
         self.assertEqual(errors[0][-len(endswith):], endswith)
         del self.model[s]