Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

diff --git a/htsworkflow/frontend/experiments/test_experiments.py b/htsworkflow/frontend/experiments/test_experiments.py
index e6d7484151149b4f7f7ce147cbacf046c28bb9d9..631fb1b6ab8ca1fde67246f97f6a3c2836346970 100644 (file)
--- a/htsworkflow/frontend/experiments/test_experiments.py
+++ b/htsworkflow/frontend/experiments/test_experiments.py
@@ -649,9 +649,7 @@ class TestSequencer(TestCase):
         load_string_into_model(model, 'rdfa', response.content)
 
         errmsgs = list(inference.run_validation())
-        self.assertEqual(len(errmsgs), 2)
-        for errmsg in errmsgs:
-            self.assertEqual(errmsg, 'Missing type for: http://localhost/')
+        self.assertEqual(len(errmsgs), 0)
 
     def test_lane_with_rdf_validation(self):
         from htsworkflow.util.rdfhelp import add_default_schemas, \
@@ -673,6 +671,4 @@ class TestSequencer(TestCase):
         load_string_into_model(model, 'rdfa', response.content)
 
         errmsgs = list(inference.run_validation())
-        self.assertEqual(len(errmsgs), 2)
-        for errmsg in errmsgs:
-            self.assertEqual(errmsg, 'Missing type for: http://localhost/')
+        self.assertEqual(len(errmsgs), 0)

diff --git a/htsworkflow/frontend/samples/test_samples.py b/htsworkflow/frontend/samples/test_samples.py
index d64499d2d911ef201aecb9000407e25964314205..0320c0ad318f8266ae776ac13b867209ea69866a 100644 (file)
--- a/htsworkflow/frontend/samples/test_samples.py
+++ b/htsworkflow/frontend/samples/test_samples.py
@@ -181,9 +181,7 @@ class SampleWebTestCase(TestCase):
         from htsworkflow.util.rdfinfer import Infer
         add_default_schemas(model)
         inference = Infer(model)
-        ignored = {'Missing type for: http://localhost/'}
-        errmsgs = [msg for msg in inference.run_validation()
-                   if msg not in ignored ]
+        errmsgs = list(inference.run_validation())
         self.assertEqual(len(errmsgs), 0)
 
     def test_library_index_rdfa(self):
@@ -200,9 +198,7 @@ class SampleWebTestCase(TestCase):
         self.assertEqual(response.status_code, 200)
         load_string_into_model(model, 'rdfa', response.content)
 
-        ignored = {'Missing type for: http://localhost/'}
-        errmsgs = [msg for msg in inference.run_validation()
-                   if msg not in ignored ]
+        errmsgs = list(inference.run_validation())
         self.assertEqual(len(errmsgs), 0)
 
         body =  """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
@@ -216,7 +212,7 @@ class SampleWebTestCase(TestCase):
                       ?species libns:species_name ?species_name . }
            OPTIONAL { ?library libns:name ?name . }
         }"""
-        bindings = {'library', 'library_id', 'name', 'species', 'species_name'}
+        bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
         query = RDF.SPARQLQuery(body)
         count = 0
         for r in query.execute(model):

diff --git a/htsworkflow/util/rdfinfer.py b/htsworkflow/util/rdfinfer.py
index 1a0fb504181cdf4aed6ebf2aadf68271efbb5bb1..42957be4709a308ca8f563f6ab8b4cfbeedb043b 100644 (file)
--- a/htsworkflow/util/rdfinfer.py
+++ b/htsworkflow/util/rdfinfer.py
@@ -135,12 +135,14 @@ class Infer(object):
         prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
         prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
         prefix owl: <http://www.w3.org/2002/07/owl#>
+        prefix xhtmlv: <http://www.w3.org/1999/xhtml/vocab#>
 
         select ?subject ?predicate ?object
         where {
           ?subject ?predicate ?object
           OPTIONAL { ?subject a ?class }
           FILTER(!bound(?class))
+          FILTER(?predicate != xhtmlv:stylesheet)
         }
         """
         query = RDF.SPARQLQuery(body)