6 import simplejson as json
8 from django.test import TestCase
9 from django.test.utils import setup_test_environment, \
10 teardown_test_environment
11 from django.db import connection
12 from django.conf import settings
14 from htsworkflow.frontend.samples.models import \
20 from htsworkflow.frontend.samples.views import \
24 from htsworkflow.frontend.auth import apidata
25 from htsworkflow.util.conversion import unicode_or_none
26 from htsworkflow.util.ethelp import validate_xhtml
28 class LibraryTestCase(TestCase):
29 fixtures = ['test_samples.json']
34 def testOrganism(self):
35 self.assertEquals(self.library_10001.organism(), 'human')
37 def testAffiliations(self):
38 self.library_10001.affiliations.add(self.affiliation_alice)
39 self.library_10002.affiliations.add(
40 self.affiliation_alice,
43 self.failUnless(len(self.library_10001.affiliations.all()), 1)
44 self.failUnless(self.library_10001.affiliation(), 'Alice')
46 self.failUnless(len(self.library_10002.affiliations.all()), 2)
47 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
50 class SampleWebTestCase(TestCase):
52 Test returning data from our database in rest like ways.
53 (like returning json objects)
55 fixtures = ['test_samples.json']
57 def test_library_info(self):
58 for lib in Library.objects.all():
59 lib_dict = library_dict(lib.id)
60 url = '/samples/library/%s/json' % (lib.id,)
61 lib_response = self.client.get(url, apidata)
62 self.failUnlessEqual(lib_response.status_code, 200)
63 lib_json = json.loads(lib_response.content)
65 for d in [lib_dict, lib_json]:
66 # amplified_from_sample is a link to the library table,
67 # I want to use the "id" for the data lookups not
68 # the embedded primary key.
69 # It gets slightly confusing on how to implement sending the right id
70 # since amplified_from_sample can be null
71 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
72 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
73 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
74 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
75 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
76 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
77 self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
78 self.failUnlessEqual(d['hidden'], lib.hidden)
79 self.failUnlessEqual(d['id'], lib.id)
80 self.failUnlessEqual(d['insert_size'], lib.insert_size)
81 self.failUnlessEqual(d['library_name'], lib.library_name)
82 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
83 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
84 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
85 if lib.library_type_id is not None:
86 self.failUnlessEqual(d['library_type'], lib.library_type.name)
88 self.failUnlessEqual(d['library_type'], None)
89 self.failUnlessEqual(d['made_for'], lib.made_for)
90 self.failUnlessEqual(d['made_by'], lib.made_by)
91 self.failUnlessEqual(d['notes'], lib.notes)
92 self.failUnlessEqual(d['replicate'], lib.replicate)
93 self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
94 self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
95 self.failUnlessEqual(d['undiluted_concentration'],
96 unicode(lib.undiluted_concentration))
99 # test a case where there is no known status
100 lane_set = {u'status': u'Unknown',
105 u'flowcell': u'303TUAAXX',
106 u'status_code': None}
107 self.failUnlessEqual(len(d['lane_set']), 1)
108 self.failUnlessEqual(d['lane_set'][0], lane_set)
109 elif lib.id == '11016':
110 # test a case where there is a status
111 lane_set = {u'status': 'Good',
116 u'flowcell': u'303TUAAXX',
118 self.failUnlessEqual(len(d['lane_set']), 1)
119 self.failUnlessEqual(d['lane_set'][0], lane_set)
122 def test_invalid_library_json(self):
124 Make sure we get a 404 if we request an invalid library id
126 response = self.client.get('/samples/library/nottheone/json', apidata)
127 self.failUnlessEqual(response.status_code, 404)
130 def test_invalid_library(self):
131 response = self.client.get('/library/nottheone/')
132 self.failUnlessEqual(response.status_code, 404)
135 def test_library_no_key(self):
137 Make sure we get a 302 if we're not logged in
139 response = self.client.get('/samples/library/10981/json')
140 self.failUnlessEqual(response.status_code, 403)
141 response = self.client.get('/samples/library/10981/json', apidata)
142 self.failUnlessEqual(response.status_code, 200)
144 def test_library_rdf(self):
146 from htsworkflow.util.rdfhelp import get_model, \
149 load_string_into_model, \
154 response = self.client.get('/library/10981/')
155 self.assertEqual(response.status_code, 200)
156 content = response.content
157 load_string_into_model(model, 'rdfa', content)
159 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
160 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
162 select ?library ?name ?library_id ?gel_cut ?made_by
164 ?library a libns:library ;
166 libns:library_id ?library_id ;
167 libns:gel_cut ?gel_cut ;
168 libns:made_by ?made_by
170 query = RDF.SPARQLQuery(body)
171 for r in query.execute(model):
172 self.assertEqual(fromTypedNode(r['library_id']), u'10981')
173 self.assertEqual(fromTypedNode(r['name']),
174 u'Paired End Multiplexed Sp-BAC')
175 self.assertEqual(fromTypedNode(r['gel_cut']), 400)
176 self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
178 state = validate_xhtml(content)
179 if state is not None:
180 self.assertTrue(state)
182 # validate a library page.
183 from htsworkflow.util.rdfhelp import add_default_schemas
184 from htsworkflow.util.rdfinfer import Infer
185 add_default_schemas(model)
186 inference = Infer(model)
187 errmsgs = list(inference.run_validation())
188 self.assertEqual(len(errmsgs), 0)
190 def test_library_index_rdfa(self):
191 from htsworkflow.util.rdfhelp import \
192 add_default_schemas, get_model, load_string_into_model, \
194 from htsworkflow.util.rdfinfer import Infer
197 add_default_schemas(model)
198 inference = Infer(model)
200 response = self.client.get('/library/')
201 self.assertEqual(response.status_code, 200)
202 load_string_into_model(model, 'rdfa', response.content)
204 errmsgs = list(inference.run_validation())
205 self.assertEqual(len(errmsgs), 0)
207 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
208 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
210 select ?library ?library_id ?name ?species ?species_name
212 ?library a libns:Library .
213 OPTIONAL { ?library libns:library_id ?library_id . }
214 OPTIONAL { ?library libns:species ?species .
215 ?species libns:species_name ?species_name . }
216 OPTIONAL { ?library libns:name ?name . }
218 bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
219 query = RDF.SPARQLQuery(body)
221 for r in query.execute(model):
223 for name, value in r.items():
224 self.assertTrue(name in bindings)
225 self.assertTrue(value is not None)
227 self.assertEqual(count, len(Library.objects.filter(hidden=False)))
229 state = validate_xhtml(response.content)
230 if state is not None: self.assertTrue(state)
233 # The django test runner flushes the database between test suites not cases,
234 # so to be more compatible with running via nose we flush the database tables
235 # of interest before creating our sample data.
237 obj.species_human = Species.objects.get(pk=8)
238 obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
239 obj.affiliation_alice = Affiliation.objects.get(pk=1)
240 obj.affiliation_bob = Affiliation.objects.get(pk=2)
242 Library.objects.all().delete()
243 obj.library_10001 = Library(
245 library_name = 'C2C12 named poorly',
246 library_species = obj.species_human,
247 experiment_type = obj.experiment_rna_seq,
248 creation_date = datetime.datetime.now(),
249 made_for = 'scientist unit 2007',
250 made_by = 'microfludics system 7321',
251 stopping_point = '2A',
252 undiluted_concentration = '5.01',
255 obj.library_10001.save()
256 obj.library_10002 = Library(
258 library_name = 'Worm named poorly',
259 library_species = obj.species_human,
260 experiment_type = obj.experiment_rna_seq,
261 creation_date = datetime.datetime.now(),
262 made_for = 'scientist unit 2007',
263 made_by = 'microfludics system 7321',
264 stopping_point = '2A',
265 undiluted_concentration = '5.01',
268 obj.library_10002.save()
274 rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
275 xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
276 libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
277 except ImportError,e:
281 class TestRDFaLibrary(TestCase):
282 fixtures = ['test_samples.json']
284 def test_parse_rdfa(self):
285 model = get_rdf_memory_model()
286 parser = RDF.Parser(name='rdfa')
287 url = '/library/10981/'
288 lib_response = self.client.get(url)
289 self.failIfEqual(len(lib_response.content), 0)
291 parser.parse_string_into_model(model,
292 lib_response.content,
293 'http://localhost'+url)
294 # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
295 self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
296 self.check_literal_object(model, ['Multiplexed'], p=libNS['experiment_type'])
297 self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
298 self.check_literal_object(model, ['Igor'], p=libNS['made_by'])
299 self.check_literal_object(model, ['Paired End Multiplexed Sp-BAC'], p=libNS['name'])
300 self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
302 self.check_uri_object(model,
303 [u'http://localhost/lane/1193'],
306 fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
307 self.check_literal_object(model,
309 s=fc_uri, p=libNS['flowcell_id'])
311 def check_literal_object(self, model, values, s=None, p=None, o=None):
312 statements = list(model.find_statements(
313 RDF.Statement(s,p,o)))
314 self.failUnlessEqual(len(statements), len(values),
315 "Couln't find %s %s %s" % (s,p,o))
317 self.failUnless(s.object.literal_value['string'] in values)
320 def check_uri_object(self, model, values, s=None, p=None, o=None):
321 statements = list(model.find_statements(
322 RDF.Statement(s,p,o)))
323 self.failUnlessEqual(len(statements), len(values),
324 "Couln't find %s %s %s" % (s,p,o))
326 self.failUnless(unicode(s.object.uri) in values)
330 def get_rdf_memory_model():
331 storage = RDF.MemoryStorage()
332 model = RDF.Model(storage)
335 OLD_DB = settings.DATABASES['default']['NAME']
337 setup_test_environment()
338 connection.creation.create_test_db()
340 def tearDownModule():
341 connection.creation.destroy_test_db(OLD_DB)
342 teardown_test_environment()
345 from unittest2 import TestSuite, defaultTestLoader
347 suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
348 suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
349 suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
352 if __name__ == "__main__":
353 from unittest2 import main
354 main(defaultTest="suite")