import datetime
-import unittest
try:
import json
-except ImportError, e:
+except ImportError as e:
import simplejson as json
from django.test import TestCase
+from django.test.utils import setup_test_environment, \
+ teardown_test_environment
+from django.db import connection
+from django.conf import settings
from htsworkflow.frontend.samples.models import \
Affiliation, \
self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
self.failUnlessEqual(d['undiluted_concentration'],
- unicode(lib.undiluted_concentration))
+ str(lib.undiluted_concentration))
# some specific tests
if lib.id == '10981':
# test a case where there is no known status
- lane_set = {u'status': u'Unknown',
- u'paired_end': True,
- u'read_length': 75,
- u'lane_number': 1,
- u'lane_id': 1193,
- u'flowcell': u'303TUAAXX',
- u'status_code': None}
+ lane_set = {'status': 'Unknown',
+ 'paired_end': True,
+ 'read_length': 75,
+ 'lane_number': 1,
+ 'lane_id': 1193,
+ 'flowcell': '303TUAAXX',
+ 'status_code': None}
self.failUnlessEqual(len(d['lane_set']), 1)
self.failUnlessEqual(d['lane_set'][0], lane_set)
elif lib.id == '11016':
# test a case where there is a status
- lane_set = {u'status': 'Good',
- u'paired_end': True,
- u'read_length': 75,
- u'lane_number': 5,
- u'lane_id': 1197,
- u'flowcell': u'303TUAAXX',
- u'status_code': 2}
+ lane_set = {'status': 'Good',
+ 'paired_end': True,
+ 'read_length': 75,
+ 'lane_number': 5,
+ 'lane_id': 1197,
+ 'flowcell': '303TUAAXX',
+ 'status_code': 2}
self.failUnlessEqual(len(d['lane_set']), 1)
self.failUnlessEqual(d['lane_set'][0], lane_set)
}"""
query = RDF.SPARQLQuery(body)
for r in query.execute(model):
- self.assertEqual(fromTypedNode(r['library_id']), u'10981')
+ self.assertEqual(fromTypedNode(r['library_id']), '10981')
self.assertEqual(fromTypedNode(r['name']),
- u'Paired End Multiplexed Sp-BAC')
+ 'Paired End Multiplexed Sp-BAC')
self.assertEqual(fromTypedNode(r['gel_cut']), 400)
- self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
+ self.assertEqual(fromTypedNode(r['made_by']), 'Igor')
state = validate_xhtml(content)
if state is not None:
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):
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#>
prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
- select ?library ?library_id ?name ?species_name
+ select ?library ?library_id ?name ?species ?species_name
where {
?library a libns:Library .
OPTIONAL { ?library libns:library_id ?library_id . }
- OPTIONAL { ?library libns:species_name ?species_name . }
+ OPTIONAL { ?library libns:species ?species .
+ ?species libns:species_name ?species_name . }
OPTIONAL { ?library libns:name ?name . }
}"""
- bindings = set(['library', 'library_id', 'name', 'species_name'])
+ bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
query = RDF.SPARQLQuery(body)
count = 0
for r in query.execute(model):
count += 1
- for name, value in r.items():
+ for name, value in list(r.items()):
self.assertTrue(name in bindings)
self.assertTrue(value is not None)
state = validate_xhtml(response.content)
if state is not None: self.assertTrue(state)
-
+
# The django test runner flushes the database between test suites not cases,
# so to be more compatible with running via nose we flush the database tables
# of interest before creating our sample data.
rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
-except ImportError,e:
+except ImportError as e:
HAVE_RDF = False
self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
self.check_uri_object(model,
- [u'http://localhost/lane/1193'],
+ ['http://localhost/lane/1193'],
p=libNS['has_lane'])
fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
self.check_literal_object(model,
- [u"303TUAAXX"],
+ ["303TUAAXX"],
s=fc_uri, p=libNS['flowcell_id'])
def check_literal_object(self, model, values, s=None, p=None, o=None):
self.failUnlessEqual(len(statements), len(values),
"Couln't find %s %s %s" % (s,p,o))
for s in statements:
- self.failUnless(unicode(s.object.uri) in values)
+ self.failUnless(str(s.object.uri) in values)
storage = RDF.MemoryStorage()
model = RDF.Model(storage)
return model
+
+OLD_DB = settings.DATABASES['default']['NAME']
+def setUpModule():
+ setup_test_environment()
+ connection.creation.create_test_db()
+
+def tearDownModule():
+ connection.creation.destroy_test_db(OLD_DB)
+ teardown_test_environment()
+
+def suite():
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
+ return suite
+
+if __name__ == "__main__":
+ from unittest import main
+ main(defaultTest="suite")
projects / htsworkflow.git / blobdiff