From 2ee1299ca704cf3fcf5a48744db84274640c0176 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 19 Sep 2012 17:08:43 -0700 Subject: [PATCH] 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). --- htsworkflow/submission/condorfastq.py | 2 +- htsworkflow/util/rdfhelp.py | 1 + htsworkflow/util/rdfinfer.py | 4 ++-- htsworkflow/util/test/test_rdfhelp.py | 2 +- htsworkflow/util/test/test_rdfinfer.py | 6 ++++-- 5 files changed, 9 insertions(+), 6 deletions(-) diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py index 5ae4b7a..9f4f136 100644 --- 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 89d9e5b..6fa326d 100644 --- 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 aac3afa..92564a0 100644 --- 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 948bcf4..dfa4b97 100644 --- 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 380c1e6..faa7672 100644 --- 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 ' + 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 ' + 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] -- 2.30.2