import json
except ImportError, e:
import simplejson as json
-
+
from django.test import TestCase
from htsworkflow.frontend.samples.models import \
library_json
from htsworkflow.frontend.auth import apidata
+from htsworkflow.util.conversion import unicode_or_none
+from htsworkflow.util.ethelp import validate_xhtml
-# 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.
-def create_db(obj):
- Species.objects.all().delete()
- obj.species_human = Species(
- scientific_name = 'Homo Sapeins',
- common_name = 'human',
- )
- obj.species_human.save()
- obj.species_worm = Species(
- scientific_name = 'C. Elegans',
- common_name = 'worm',
- )
- obj.species_worm.save()
- obj.species_phix = Species(
- scientific_name = 'PhiX',
- common_name = 'PhiX'
- )
- obj.species_phix.save()
-
- ExperimentType.objects.all().delete()
- obj.experiment_de_novo = ExperimentType(
- name = 'De Novo',
- )
- obj.experiment_de_novo.save()
- obj.experiment_chip_seq = ExperimentType(
- name = 'ChIP-Seq'
- )
- obj.experiment_chip_seq.save()
- obj.experiment_rna_seq = ExperimentType(
- name = 'RNA-Seq'
- )
- obj.experiment_rna_seq.save()
-
- Affiliation.objects.all().delete()
- obj.affiliation_alice = Affiliation(
- name = 'Alice',
- contact = 'Lab Boss',
- email = 'alice@some.where.else.'
- )
- obj.affiliation_alice.save()
- obj.affiliation_bob = Affiliation(
- name = 'Bob',
- contact = 'Other Lab Boss',
- email = 'bob@some.where.else',
- )
- obj.affiliation_bob.save()
-
- Library.objects.all().delete()
- obj.library_10001 = Library(
- id = "10001",
- library_name = 'C2C12 named poorly',
- library_species = obj.species_human,
- experiment_type = obj.experiment_rna_seq,
- creation_date = datetime.datetime.now(),
- made_for = 'scientist unit 2007',
- made_by = 'microfludics system 7321',
- stopping_point = '2A',
- undiluted_concentration = '5.01',
- )
- obj.library_10001.save()
- obj.library_10002 = Library(
- id = "10002",
- library_name = 'Worm named poorly',
- library_species = obj.species_human,
- experiment_type = obj.experiment_rna_seq,
- creation_date = datetime.datetime.now(),
- made_for = 'scientist unit 2007',
- made_by = 'microfludics system 7321',
- stopping_point = '2A',
- undiluted_concentration = '5.01',
- )
- obj.library_10002.save()
-
class LibraryTestCase(TestCase):
+ fixtures = ['test_samples.json']
+
def setUp(self):
create_db(self)
-
+
def testOrganism(self):
self.assertEquals(self.library_10001.organism(), 'human')
def testAffiliations(self):
self.library_10001.affiliations.add(self.affiliation_alice)
self.library_10002.affiliations.add(
- self.affiliation_alice,
+ self.affiliation_alice,
self.affiliation_bob
)
self.failUnless(len(self.library_10001.affiliations.all()), 1)
self.failUnless(len(self.library_10002.affiliations.all()), 2)
self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
+
class SampleWebTestCase(TestCase):
"""
Test returning data from our database in rest like ways.
fixtures = ['test_samples.json']
def test_library_info(self):
-
for lib in Library.objects.all():
lib_dict = library_dict(lib.id)
url = '/samples/library/%s/json' % (lib.id,)
# since amplified_from_sample can be null
#self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
- self.failUnlessEqual(d['avg_lib_size'], lib.avg_lib_size)
- self.failUnlessEqual(d['cell_line'], lib.cell_line.cellline_name)
self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
+ self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
+ self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
+ self.failUnlessEqual(d['hidden'], lib.hidden)
self.failUnlessEqual(d['id'], lib.id)
+ self.failUnlessEqual(d['insert_size'], lib.insert_size)
self.failUnlessEqual(d['library_name'], lib.library_name)
self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
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))
- def test_invalid_library(self):
+ unicode(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}
+ 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}
+ self.failUnlessEqual(len(d['lane_set']), 1)
+ self.failUnlessEqual(d['lane_set'][0], lane_set)
+
+
+ def test_invalid_library_json(self):
"""
Make sure we get a 404 if we request an invalid library id
"""
response = self.client.get('/samples/library/nottheone/json', apidata)
self.failUnlessEqual(response.status_code, 404)
-
+
+ def test_invalid_library(self):
+ response = self.client.get('/library/nottheone/')
+ self.failUnlessEqual(response.status_code, 404)
+
+
def test_library_no_key(self):
"""
Make sure we get a 302 if we're not logged in
self.failUnlessEqual(response.status_code, 403)
response = self.client.get('/samples/library/10981/json', apidata)
self.failUnlessEqual(response.status_code, 200)
+
+ def test_library_rdf(self):
+ import RDF
+ from htsworkflow.util.rdfhelp import get_model, \
+ dump_model, \
+ fromTypedNode, \
+ load_string_into_model, \
+ rdfNS, \
+ libraryOntology
+ model = get_model()
+
+ response = self.client.get('/library/10981/')
+ self.assertEqual(response.status_code, 200)
+ content = response.content
+ load_string_into_model(model, 'rdfa', content)
+
+ body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+
+ select ?library ?name ?library_id ?gel_cut ?made_by
+ where {
+ ?library a libns:library ;
+ libns:name ?name ;
+ libns:library_id ?library_id ;
+ libns:gel_cut ?gel_cut ;
+ libns:made_by ?made_by
+ }"""
+ query = RDF.SPARQLQuery(body)
+ for r in query.execute(model):
+ self.assertEqual(fromTypedNode(r['library_id']), u'10981')
+ self.assertEqual(fromTypedNode(r['name']),
+ u'Paired End Multiplexed Sp-BAC')
+ self.assertEqual(fromTypedNode(r['gel_cut']), 400)
+ self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
+
+ state = validate_xhtml(content)
+ if state is not None:
+ self.assertTrue(state)
+
+ # validate a library page.
+ from htsworkflow.util.rdfhelp import add_default_schemas
+ 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 ]
+ self.assertEqual(len(errmsgs), 0)
+
+ def test_library_index_rdfa(self):
+ from htsworkflow.util.rdfhelp import \
+ add_default_schemas, get_model, load_string_into_model, \
+ dump_model
+ from htsworkflow.util.rdfinfer import Infer
+
+ model = get_model()
+ add_default_schemas(model)
+ inference = Infer(model)
+
+ response = self.client.get('/library/')
+ 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 ]
+ 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
+ where {
+ ?library a libns:Library .
+ OPTIONAL { ?library libns:library_id ?library_id . }
+ OPTIONAL { ?library libns:species ?species . }
+ OPTIONAL { ?library libns:name ?name . }
+ }"""
+ bindings = set(['library', 'library_id', 'name', 'species'])
+ query = RDF.SPARQLQuery(body)
+ count = 0
+ for r in query.execute(model):
+ count += 1
+ for name, value in r.items():
+ self.assertTrue(name in bindings)
+ self.assertTrue(value is not None)
+
+ self.assertEqual(count, len(Library.objects.filter(hidden=False)))
+
+ 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.
+def create_db(obj):
+ obj.species_human = Species.objects.get(pk=8)
+ obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
+ obj.affiliation_alice = Affiliation.objects.get(pk=1)
+ obj.affiliation_bob = Affiliation.objects.get(pk=2)
+
+ Library.objects.all().delete()
+ obj.library_10001 = Library(
+ id = "10001",
+ library_name = 'C2C12 named poorly',
+ library_species = obj.species_human,
+ experiment_type = obj.experiment_rna_seq,
+ creation_date = datetime.datetime.now(),
+ made_for = 'scientist unit 2007',
+ made_by = 'microfludics system 7321',
+ stopping_point = '2A',
+ undiluted_concentration = '5.01',
+ hidden = False,
+ )
+ obj.library_10001.save()
+ obj.library_10002 = Library(
+ id = "10002",
+ library_name = 'Worm named poorly',
+ library_species = obj.species_human,
+ experiment_type = obj.experiment_rna_seq,
+ creation_date = datetime.datetime.now(),
+ made_for = 'scientist unit 2007',
+ made_by = 'microfludics system 7321',
+ stopping_point = '2A',
+ undiluted_concentration = '5.01',
+ hidden = False,
+ )
+ obj.library_10002.save()
+
+try:
+ import RDF
+ HAVE_RDF = True
+
+ 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:
+ HAVE_RDF = False
+
+
+class TestRDFaLibrary(TestCase):
+ fixtures = ['test_samples.json']
+
+ def test_parse_rdfa(self):
+ model = get_rdf_memory_model()
+ parser = RDF.Parser(name='rdfa')
+ url = '/library/10981/'
+ lib_response = self.client.get(url)
+ self.failIfEqual(len(lib_response.content), 0)
+
+ parser.parse_string_into_model(model,
+ lib_response.content,
+ 'http://localhost'+url)
+ # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
+ self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
+ self.check_literal_object(model, ['Multiplexed'], p=libNS['experiment_type'])
+ self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
+ self.check_literal_object(model, ['Igor'], p=libNS['made_by'])
+ self.check_literal_object(model, ['Paired End Multiplexed Sp-BAC'], p=libNS['name'])
+ self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species'])
+
+ self.check_uri_object(model,
+ [u'http://localhost/lane/1193'],
+ p=libNS['has_lane'])
+
+ fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
+ self.check_literal_object(model,
+ [u"303TUAAXX"],
+ s=fc_uri, p=libNS['flowcell_id'])
+
+ def check_literal_object(self, model, values, s=None, p=None, o=None):
+ statements = list(model.find_statements(
+ RDF.Statement(s,p,o)))
+ self.failUnlessEqual(len(statements), len(values),
+ "Couln't find %s %s %s" % (s,p,o))
+ for s in statements:
+ self.failUnless(s.object.literal_value['string'] in values)
+
+
+ def check_uri_object(self, model, values, s=None, p=None, o=None):
+ statements = list(model.find_statements(
+ RDF.Statement(s,p,o)))
+ 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)
+
+
+
+def get_rdf_memory_model():
+ storage = RDF.MemoryStorage()
+ model = RDF.Model(storage)
+ return model
projects / htsworkflow.git / blobdiff