6 import simplejson as json
8 from django.test import TestCase
10 from htsworkflow.frontend.samples.models import \
16 from htsworkflow.frontend.samples.views import \
20 from htsworkflow.frontend.auth import apidata
21 from htsworkflow.util.conversion import unicode_or_none
22 from htsworkflow.util.ethelp import validate_xhtml
24 class LibraryTestCase(TestCase):
25 fixtures = ['test_samples.json']
30 def testOrganism(self):
31 self.assertEquals(self.library_10001.organism(), 'human')
33 def testAffiliations(self):
34 self.library_10001.affiliations.add(self.affiliation_alice)
35 self.library_10002.affiliations.add(
36 self.affiliation_alice,
39 self.failUnless(len(self.library_10001.affiliations.all()), 1)
40 self.failUnless(self.library_10001.affiliation(), 'Alice')
42 self.failUnless(len(self.library_10002.affiliations.all()), 2)
43 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
46 class SampleWebTestCase(TestCase):
48 Test returning data from our database in rest like ways.
49 (like returning json objects)
51 fixtures = ['test_samples.json']
53 def test_library_info(self):
54 for lib in Library.objects.all():
55 lib_dict = library_dict(lib.id)
56 url = '/samples/library/%s/json' % (lib.id,)
57 lib_response = self.client.get(url, apidata)
58 self.failUnlessEqual(lib_response.status_code, 200)
59 lib_json = json.loads(lib_response.content)
61 for d in [lib_dict, lib_json]:
62 # amplified_from_sample is a link to the library table,
63 # I want to use the "id" for the data lookups not
64 # the embedded primary key.
65 # It gets slightly confusing on how to implement sending the right id
66 # since amplified_from_sample can be null
67 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
68 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
69 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
70 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
71 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
72 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
73 self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
74 self.failUnlessEqual(d['hidden'], lib.hidden)
75 self.failUnlessEqual(d['id'], lib.id)
76 self.failUnlessEqual(d['insert_size'], lib.insert_size)
77 self.failUnlessEqual(d['library_name'], lib.library_name)
78 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
79 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
80 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
81 if lib.library_type_id is not None:
82 self.failUnlessEqual(d['library_type'], lib.library_type.name)
84 self.failUnlessEqual(d['library_type'], None)
85 self.failUnlessEqual(d['made_for'], lib.made_for)
86 self.failUnlessEqual(d['made_by'], lib.made_by)
87 self.failUnlessEqual(d['notes'], lib.notes)
88 self.failUnlessEqual(d['replicate'], lib.replicate)
89 self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
90 self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
91 self.failUnlessEqual(d['undiluted_concentration'],
92 unicode(lib.undiluted_concentration))
95 # test a case where there is no known status
96 lane_set = {u'status': u'Unknown',
101 u'flowcell': u'303TUAAXX',
102 u'status_code': None}
103 self.failUnlessEqual(len(d['lane_set']), 1)
104 self.failUnlessEqual(d['lane_set'][0], lane_set)
105 elif lib.id == '11016':
106 # test a case where there is a status
107 lane_set = {u'status': 'Good',
112 u'flowcell': u'303TUAAXX',
114 self.failUnlessEqual(len(d['lane_set']), 1)
115 self.failUnlessEqual(d['lane_set'][0], lane_set)
118 def test_invalid_library_json(self):
120 Make sure we get a 404 if we request an invalid library id
122 response = self.client.get('/samples/library/nottheone/json', apidata)
123 self.failUnlessEqual(response.status_code, 404)
126 def test_invalid_library(self):
127 response = self.client.get('/library/nottheone/')
128 self.failUnlessEqual(response.status_code, 404)
131 def test_library_no_key(self):
133 Make sure we get a 302 if we're not logged in
135 response = self.client.get('/samples/library/10981/json')
136 self.failUnlessEqual(response.status_code, 403)
137 response = self.client.get('/samples/library/10981/json', apidata)
138 self.failUnlessEqual(response.status_code, 200)
140 def test_library_rdf(self):
142 from htsworkflow.util.rdfhelp import get_model, \
145 load_string_into_model, \
150 response = self.client.get('/library/10981/')
151 self.assertEqual(response.status_code, 200)
152 content = response.content
153 load_string_into_model(model, 'rdfa', content)
155 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
156 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
158 select ?library ?name ?library_id ?gel_cut ?made_by
160 ?library a libns:library ;
162 libns:library_id ?library_id ;
163 libns:gel_cut ?gel_cut ;
164 libns:made_by ?made_by
166 query = RDF.SPARQLQuery(body)
167 for r in query.execute(model):
168 self.assertEqual(fromTypedNode(r['library_id']), u'10981')
169 self.assertEqual(fromTypedNode(r['name']),
170 u'Paired End Multiplexed Sp-BAC')
171 self.assertEqual(fromTypedNode(r['gel_cut']), 400)
172 self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
174 state = validate_xhtml(content)
175 if state is not None:
176 self.assertTrue(state)
178 # validate a library page.
179 from htsworkflow.util.rdfhelp import add_default_schemas
180 from htsworkflow.util.rdfinfer import Infer
181 add_default_schemas(model)
182 inference = Infer(model)
183 errmsgs = list(inference.run_validation())
184 self.assertEqual(len(errmsgs), 0)
186 def test_library_index_rdfa(self):
187 from htsworkflow.util.rdfhelp import \
188 add_default_schemas, get_model, load_string_into_model, \
190 from htsworkflow.util.rdfinfer import Infer
193 add_default_schemas(model)
194 inference = Infer(model)
196 response = self.client.get('/library/')
197 self.assertEqual(response.status_code, 200)
198 load_string_into_model(model, 'rdfa', response.content)
200 errmsgs = list(inference.run_validation())
201 self.assertEqual(len(errmsgs), 0)
203 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
204 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
206 select ?library ?library_id ?name ?species ?species_name
208 ?library a libns:Library .
209 OPTIONAL { ?library libns:library_id ?library_id . }
210 OPTIONAL { ?library libns:species ?species .
211 ?species libns:species_name ?species_name . }
212 OPTIONAL { ?library libns:name ?name . }
214 bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
215 query = RDF.SPARQLQuery(body)
217 for r in query.execute(model):
219 for name, value in r.items():
220 self.assertTrue(name in bindings)
221 self.assertTrue(value is not None)
223 self.assertEqual(count, len(Library.objects.filter(hidden=False)))
225 state = validate_xhtml(response.content)
226 if state is not None: self.assertTrue(state)
229 # The django test runner flushes the database between test suites not cases,
230 # so to be more compatible with running via nose we flush the database tables
231 # of interest before creating our sample data.
233 obj.species_human = Species.objects.get(pk=8)
234 obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
235 obj.affiliation_alice = Affiliation.objects.get(pk=1)
236 obj.affiliation_bob = Affiliation.objects.get(pk=2)
238 Library.objects.all().delete()
239 obj.library_10001 = Library(
241 library_name = 'C2C12 named poorly',
242 library_species = obj.species_human,
243 experiment_type = obj.experiment_rna_seq,
244 creation_date = datetime.datetime.now(),
245 made_for = 'scientist unit 2007',
246 made_by = 'microfludics system 7321',
247 stopping_point = '2A',
248 undiluted_concentration = '5.01',
251 obj.library_10001.save()
252 obj.library_10002 = Library(
254 library_name = 'Worm named poorly',
255 library_species = obj.species_human,
256 experiment_type = obj.experiment_rna_seq,
257 creation_date = datetime.datetime.now(),
258 made_for = 'scientist unit 2007',
259 made_by = 'microfludics system 7321',
260 stopping_point = '2A',
261 undiluted_concentration = '5.01',
264 obj.library_10002.save()
270 rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
271 xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
272 libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
273 except ImportError,e:
277 class TestRDFaLibrary(TestCase):
278 fixtures = ['test_samples.json']
280 def test_parse_rdfa(self):
281 model = get_rdf_memory_model()
282 parser = RDF.Parser(name='rdfa')
283 url = '/library/10981/'
284 lib_response = self.client.get(url)
285 self.failIfEqual(len(lib_response.content), 0)
287 parser.parse_string_into_model(model,
288 lib_response.content,
289 'http://localhost'+url)
290 # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
291 self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
292 self.check_literal_object(model, ['Multiplexed'], p=libNS['experiment_type'])
293 self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
294 self.check_literal_object(model, ['Igor'], p=libNS['made_by'])
295 self.check_literal_object(model, ['Paired End Multiplexed Sp-BAC'], p=libNS['name'])
296 self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
298 self.check_uri_object(model,
299 [u'http://localhost/lane/1193'],
302 fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
303 self.check_literal_object(model,
305 s=fc_uri, p=libNS['flowcell_id'])
307 def check_literal_object(self, model, values, s=None, p=None, o=None):
308 statements = list(model.find_statements(
309 RDF.Statement(s,p,o)))
310 self.failUnlessEqual(len(statements), len(values),
311 "Couln't find %s %s %s" % (s,p,o))
313 self.failUnless(s.object.literal_value['string'] in values)
316 def check_uri_object(self, model, values, s=None, p=None, o=None):
317 statements = list(model.find_statements(
318 RDF.Statement(s,p,o)))
319 self.failUnlessEqual(len(statements), len(values),
320 "Couln't find %s %s %s" % (s,p,o))
322 self.failUnless(unicode(s.object.uri) in values)
326 def get_rdf_memory_model():
327 storage = RDF.MemoryStorage()
328 model = RDF.Model(storage)