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 = ['initial_data.json',
35 def testOrganism(self):
36 self.assertEquals(self.library_10001.organism(), 'human')
38 def testAffiliations(self):
39 self.library_10001.affiliations.add(self.affiliation_alice)
40 self.library_10002.affiliations.add(
41 self.affiliation_alice,
44 self.failUnless(len(self.library_10001.affiliations.all()), 1)
45 self.failUnless(self.library_10001.affiliation(), 'Alice')
47 self.failUnless(len(self.library_10002.affiliations.all()), 2)
48 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
51 class SampleWebTestCase(TestCase):
53 Test returning data from our database in rest like ways.
54 (like returning json objects)
56 fixtures = ['initial_data.json',
59 def test_library_info(self):
60 for lib in Library.objects.all():
61 lib_dict = library_dict(lib.id)
62 url = '/samples/library/%s/json' % (lib.id,)
63 lib_response = self.client.get(url, apidata)
64 self.failUnlessEqual(lib_response.status_code, 200)
65 lib_json = json.loads(lib_response.content)
67 for d in [lib_dict, lib_json]:
68 # amplified_from_sample is a link to the library table,
69 # I want to use the "id" for the data lookups not
70 # the embedded primary key.
71 # It gets slightly confusing on how to implement sending the right id
72 # since amplified_from_sample can be null
73 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
74 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
75 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
76 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
77 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
78 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
79 self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
80 self.failUnlessEqual(d['hidden'], lib.hidden)
81 self.failUnlessEqual(d['id'], lib.id)
82 self.failUnlessEqual(d['insert_size'], lib.insert_size)
83 self.failUnlessEqual(d['library_name'], lib.library_name)
84 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
85 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
86 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
87 if lib.library_type_id is not None:
88 self.failUnlessEqual(d['library_type'], lib.library_type.name)
90 self.failUnlessEqual(d['library_type'], None)
91 self.failUnlessEqual(d['made_for'], lib.made_for)
92 self.failUnlessEqual(d['made_by'], lib.made_by)
93 self.failUnlessEqual(d['notes'], lib.notes)
94 self.failUnlessEqual(d['replicate'], lib.replicate)
95 self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
96 self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
97 self.failUnlessEqual(d['undiluted_concentration'],
98 unicode(lib.undiluted_concentration))
100 if lib.id == '10981':
101 # test a case where there is no known status
102 lane_set = {u'status': u'Unknown',
107 u'flowcell': u'303TUAAXX',
108 u'status_code': None}
109 self.failUnlessEqual(len(d['lane_set']), 1)
110 self.failUnlessEqual(d['lane_set'][0], lane_set)
111 elif lib.id == '11016':
112 # test a case where there is a status
113 lane_set = {u'status': 'Good',
118 u'flowcell': u'303TUAAXX',
120 self.failUnlessEqual(len(d['lane_set']), 1)
121 self.failUnlessEqual(d['lane_set'][0], lane_set)
124 def test_invalid_library_json(self):
126 Make sure we get a 404 if we request an invalid library id
128 response = self.client.get('/samples/library/nottheone/json', apidata)
129 self.failUnlessEqual(response.status_code, 404)
132 def test_invalid_library(self):
133 response = self.client.get('/library/nottheone/')
134 self.failUnlessEqual(response.status_code, 404)
137 def test_library_no_key(self):
139 Make sure we get a 302 if we're not logged in
141 response = self.client.get('/samples/library/10981/json')
142 self.failUnlessEqual(response.status_code, 403)
143 response = self.client.get('/samples/library/10981/json', apidata)
144 self.failUnlessEqual(response.status_code, 200)
146 def test_library_rdf(self):
148 from htsworkflow.util.rdfhelp import get_model, \
151 load_string_into_model, \
156 response = self.client.get('/library/10981/')
157 self.assertEqual(response.status_code, 200)
158 content = response.content
159 load_string_into_model(model, 'rdfa', content)
161 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
162 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
164 select ?library ?name ?library_id ?gel_cut ?made_by
166 ?library a libns:library ;
168 libns:library_id ?library_id ;
169 libns:gel_cut ?gel_cut ;
170 libns:made_by ?made_by
172 query = RDF.SPARQLQuery(body)
173 for r in query.execute(model):
174 self.assertEqual(fromTypedNode(r['library_id']), u'10981')
175 self.assertEqual(fromTypedNode(r['name']),
176 u'Paired End Multiplexed Sp-BAC')
177 self.assertEqual(fromTypedNode(r['gel_cut']), 400)
178 self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
180 state = validate_xhtml(content)
181 if state is not None:
182 self.assertTrue(state)
184 # validate a library page.
185 from htsworkflow.util.rdfhelp import add_default_schemas
186 from htsworkflow.util.rdfinfer import Infer
187 add_default_schemas(model)
188 inference = Infer(model)
189 errmsgs = list(inference.run_validation())
190 self.assertEqual(len(errmsgs), 0)
192 def test_library_index_rdfa(self):
193 from htsworkflow.util.rdfhelp import \
194 add_default_schemas, get_model, load_string_into_model, \
196 from htsworkflow.util.rdfinfer import Infer
199 add_default_schemas(model)
200 inference = Infer(model)
202 response = self.client.get('/library/')
203 self.assertEqual(response.status_code, 200)
204 load_string_into_model(model, 'rdfa', response.content)
206 errmsgs = list(inference.run_validation())
207 self.assertEqual(len(errmsgs), 0)
209 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
210 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
212 select ?library ?library_id ?name ?species ?species_name
214 ?library a libns:Library .
215 OPTIONAL { ?library libns:library_id ?library_id . }
216 OPTIONAL { ?library libns:species ?species .
217 ?species libns:species_name ?species_name . }
218 OPTIONAL { ?library libns:name ?name . }
220 bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
221 query = RDF.SPARQLQuery(body)
223 for r in query.execute(model):
225 for name, value in r.items():
226 self.assertTrue(name in bindings)
227 self.assertTrue(value is not None)
229 self.assertEqual(count, len(Library.objects.filter(hidden=False)))
231 state = validate_xhtml(response.content)
232 if state is not None: self.assertTrue(state)
235 # The django test runner flushes the database between test suites not cases,
236 # so to be more compatible with running via nose we flush the database tables
237 # of interest before creating our sample data.
239 obj.species_human = Species.objects.get(pk=8)
240 obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
241 obj.affiliation_alice = Affiliation.objects.get(pk=1)
242 obj.affiliation_bob = Affiliation.objects.get(pk=2)
244 Library.objects.all().delete()
245 obj.library_10001 = Library(
247 library_name = 'C2C12 named poorly',
248 library_species = obj.species_human,
249 experiment_type = obj.experiment_rna_seq,
250 creation_date = datetime.datetime.now(),
251 made_for = 'scientist unit 2007',
252 made_by = 'microfludics system 7321',
253 stopping_point = '2A',
254 undiluted_concentration = '5.01',
257 obj.library_10001.save()
258 obj.library_10002 = Library(
260 library_name = 'Worm named poorly',
261 library_species = obj.species_human,
262 experiment_type = obj.experiment_rna_seq,
263 creation_date = datetime.datetime.now(),
264 made_for = 'scientist unit 2007',
265 made_by = 'microfludics system 7321',
266 stopping_point = '2A',
267 undiluted_concentration = '5.01',
270 obj.library_10002.save()
276 rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
277 xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
278 libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
279 except ImportError,e:
283 class TestRDFaLibrary(TestCase):
284 fixtures = ['initial_data.json',
287 def test_parse_rdfa(self):
288 model = get_rdf_memory_model()
289 parser = RDF.Parser(name='rdfa')
290 url = '/library/10981/'
291 lib_response = self.client.get(url)
292 self.failIfEqual(len(lib_response.content), 0)
294 parser.parse_string_into_model(model,
295 lib_response.content,
296 'http://localhost'+url)
297 # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
298 self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
299 self.check_literal_object(model, ['Multiplexed'], p=libNS['experiment_type'])
300 self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
301 self.check_literal_object(model, ['Igor'], p=libNS['made_by'])
302 self.check_literal_object(model, ['Paired End Multiplexed Sp-BAC'], p=libNS['name'])
303 self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
305 self.check_uri_object(model,
306 [u'http://localhost/lane/1193'],
309 fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
310 self.check_literal_object(model,
312 s=fc_uri, p=libNS['flowcell_id'])
314 def check_literal_object(self, model, values, s=None, p=None, o=None):
315 statements = list(model.find_statements(
316 RDF.Statement(s,p,o)))
317 self.failUnlessEqual(len(statements), len(values),
318 "Couln't find %s %s %s" % (s,p,o))
320 self.failUnless(s.object.literal_value['string'] in values)
323 def check_uri_object(self, model, values, s=None, p=None, o=None):
324 statements = list(model.find_statements(
325 RDF.Statement(s,p,o)))
326 self.failUnlessEqual(len(statements), len(values),
327 "Couln't find %s %s %s" % (s,p,o))
329 self.failUnless(unicode(s.object.uri) in values)
333 def get_rdf_memory_model():
334 storage = RDF.MemoryStorage()
335 model = RDF.Model(storage)
339 from unittest2 import TestSuite, defaultTestLoader
341 suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
342 suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
343 suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
346 if __name__ == "__main__":
347 from unittest2 import main
348 main(defaultTest="suite")