Use htsworkflow ontology to validate various RDF using components.

[htsworkflow.git] / htsworkflow / frontend / experiments / tests.py

diff --git a/htsworkflow/frontend/experiments/tests.py b/htsworkflow/frontend/experiments/tests.py
index 537e4b47c2ef871ea084a489ebf68eef6c2d43ef..93e1f3d452c32a5c6b74bae709794e1340a8e96b 100644 (file)
--- a/htsworkflow/frontend/experiments/tests.py
+++ b/htsworkflow/frontend/experiments/tests.py
@@ -8,6 +8,7 @@ import os
 import shutil
 import sys
 import tempfile
+from urlparse import urljoin
 
 from django.conf import settings
 from django.core import mail
@@ -280,7 +281,7 @@ class ExperimentsTestCases(TestCase):
         failed_fc_span = flowcell_spans[0]
         failed_fc_a = failed_fc_span.getparent()
         # make sure some of our RDF made it.
-        self.assertEqual(failed_fc_a.get('rel'), 'libns:flowcell')
+        self.assertEqual(failed_fc_a.get('typeof'), 'libns:IlluminaFlowcell')
         self.assertEqual(failed_fc_a.get('href'), '/flowcell/30012AAXX/')
         fc_response = self.client.get(failed_fc_a.get('href'))
         self.assertEqual(fc_response.status_code, 200)
@@ -411,6 +412,53 @@ class ExperimentsTestCases(TestCase):
 
             self.assertEqual(mimetype, response['content-type'])
 
+    def test_flowcell_rdf(self):
+        import RDF
+        from htsworkflow.util.rdfhelp import get_model, \
+             fromTypedNode, \
+             load_string_into_model, \
+             rdfNS, \
+             libraryOntology, \
+             dump_model
+
+        model = get_model()
+
+        expected = {1: ['11034'],
+                    2: ['11036'],
+                    3: ['12044','11045'],
+                    4: ['11047','13044'],
+                    5: ['11055'],
+                    6: ['11067'],
+                    7: ['11069'],
+                    8: ['11070']}
+        url = '/flowcell/42JU1AAXX/'
+        response = self.client.get(url)
+        self.assertEqual(response.status_code, 200)
+        ns = urljoin('http://localhost', url)
+        load_string_into_model(model, 'rdfa', response.content, ns=ns)
+        body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+
+        select ?flowcell ?flowcell_id ?lane_id ?library_id
+        where {
+          ?flowcell a libns:IlluminaFlowcell ;
+                    libns:flowcell_id ?flowcell_id ;
+                    libns:has_lane ?lane .
+          ?lane libns:lane_number ?lane_id ;
+                libns:library ?library .
+          ?library libns:library_id ?library_id .
+        }"""
+        query = RDF.SPARQLQuery(body)
+        count = 0
+        for r in query.execute(model):
+            count += 1
+            self.assertEqual(fromTypedNode(r['flowcell_id']), u'42JU1AAXX')
+            lane_id = fromTypedNode(r['lane_id'])
+            library_id = fromTypedNode(r['library_id'])
+            self.assertTrue(library_id in expected[lane_id])
+        self.assertEqual(count, 10)
+
+
 class TestFileType(TestCase):
     def test_file_type_unicode(self):
         file_type_objects = models.FileType.objects
@@ -535,24 +583,30 @@ class TestSequencer(TestCase):
                              "Illumina Genome Analyzer IIx")
         self.assertEqual(fc.sequencer.instrument_name,
                              "ILLUMINA-EC5D15")
+        # well actually we let the browser tack on the host name
+        url = fc.get_absolute_url()
+        self.assertEqual(url, '/flowcell/FC12150/')
 
     def test_rdf(self):
         response = self.client.get('/flowcell/FC12150/', apidata)
         tree = fromstring(response.content)
-        divs = tree.xpath('//div[@rel="libns:sequenced_by"]',
-                          namespaces=NSMAP)
-        self.assertEqual(len(divs), 1)
-        self.assertEqual(divs[0].attrib['rel'], 'libns:sequenced_by')
-        self.assertEqual(divs[0].attrib['resource'], '/sequencer/2')
-
-        name = divs[0].xpath('./span[@property="libns:sequencer_name"]')
+        seq_by = tree.xpath('//div[@rel="libns:sequenced_by"]',
+                            namespaces=NSMAP)
+        self.assertEqual(len(seq_by), 1)
+        self.assertEqual(seq_by[0].attrib['rel'], 'libns:sequenced_by')
+        seq = seq_by[0].getchildren()
+        self.assertEqual(len(seq), 1)
+        self.assertEqual(seq[0].attrib['about'], '/sequencer/2')
+        self.assertEqual(seq[0].attrib['typeof'], 'libns:Sequencer')
+
+        name = seq[0].xpath('./span[@property="libns:sequencer_name"]')
         self.assertEqual(len(name), 1)
         self.assertEqual(name[0].text, 'Tardigrade')
-        instrument = divs[0].xpath(
+        instrument = seq[0].xpath(
             './span[@property="libns:sequencer_instrument"]')
         self.assertEqual(len(instrument), 1)
         self.assertEqual(instrument[0].text, 'ILLUMINA-EC5D15')
-        model = divs[0].xpath(
+        model = seq[0].xpath(
             './span[@property="libns:sequencer_model"]')
         self.assertEqual(len(model), 1)
         self.assertEqual(model[0].text, 'Illumina Genome Analyzer IIx')