library_json
from htsworkflow.frontend.auth import apidata
+from htsworkflow.util.conversion import unicode_or_none
-# 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)
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.
# 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))
+ 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'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'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(self):
"""
Make sure we get a 404 if we request an invalid library id
self.failUnlessEqual(response.status_code, 403)
response = self.client.get('/samples/library/10981/json', apidata)
self.failUnlessEqual(response.status_code, 200)
+
+# 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'])
+
+ self.check_literal_object(model,
+ [u"303TUAAXX"],
+ s=RDF.Uri('http://localhost/flowcell/303TUAAXX/'))
+
+ 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