1 from __future__ import absolute_import, print_function
7 from django.test import TestCase, RequestFactory
8 from django.conf import settings
9 from django.utils.encoding import smart_text, smart_str
11 from .models import Affiliation, ExperimentType, Species, Library
12 from .views import library_dict, library_json, library
13 from .samples_factory import *
15 from htsworkflow.auth import apidata
16 from htsworkflow.util.conversion import str_or_none
17 from htsworkflow.util.ethelp import validate_xhtml
19 class LibraryTestCase(TestCase):
20 def testOrganism(self):
21 human = SpeciesFactory(common_name='human')
22 self.assertEquals(human.common_name, 'human')
23 library = LibraryFactory(library_species=human)
24 self.assertEquals(library.organism(), 'human')
26 def testAddingOneAffiliation(self):
27 affiliation = AffiliationFactory.create(name='Alice')
28 library = LibraryFactory()
29 library.affiliations.add(affiliation)
31 self.assertEqual(len(library.affiliations.all()), 1)
32 self.assertEqual(library.affiliation(), 'Alice (contact name)')
34 def testMultipleAffiliations(self):
35 alice = AffiliationFactory.create(name='Alice')
36 bob = AffiliationFactory.create(name='Bob')
38 library = LibraryFactory()
39 library.affiliations.add(alice, bob)
41 self.assertEqual(len(library.affiliations.all()), 2)
42 self.assertEqual(library.affiliation(),
43 'Alice (contact name), Bob (contact name)')
46 class SampleWebTestCase(TestCase):
48 Test returning data from our database in rest like ways.
49 (like returning json objects)
51 def test_library_dict(self):
52 library = LibraryFactory.create()
53 lib_dict = library_dict(library.id)
54 url = '/samples/library/%s/json' % (library.id,)
55 lib_response = self.client.get(url, apidata)
56 lib_json = json.loads(smart_text(lib_response.content))['result']
58 for d in [lib_dict, lib_json]:
59 # amplified_from_sample is a link to the library table,
60 # I want to use the "id" for the data lookups not
61 # the embedded primary key.
62 # It gets slightly confusing on how to implement sending the right id
63 # since amplified_from_sample can be null
64 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
65 self.failUnlessEqual(d['antibody_id'], library.antibody_id)
66 self.failUnlessEqual(d['cell_line_id'], library.cell_line_id)
67 self.failUnlessEqual(d['cell_line'], str_or_none(library.cell_line))
68 self.failUnlessEqual(d['experiment_type'], library.experiment_type.name)
69 self.failUnlessEqual(d['experiment_type_id'], library.experiment_type_id)
70 self.failUnlessEqual(d['gel_cut_size'], library.gel_cut_size)
71 self.failUnlessEqual(d['hidden'], library.hidden)
72 self.failUnlessEqual(d['id'], library.id)
73 self.failUnlessEqual(d['insert_size'], library.insert_size)
74 self.failUnlessEqual(d['library_name'], library.library_name)
75 self.failUnlessEqual(d['library_species'], library.library_species.scientific_name)
76 self.failUnlessEqual(d['library_species_id'], library.library_species_id)
77 self.failUnlessEqual(d['library_type_id'], library.library_type_id)
78 self.assertTrue(d['library_type'].startswith('library type'))
79 self.failUnlessEqual(d['made_for'], library.made_for)
80 self.failUnlessEqual(d['made_by'], library.made_by)
81 self.failUnlessEqual(d['notes'], library.notes)
82 self.failUnlessEqual(d['replicate'], library.replicate)
83 self.failUnlessEqual(d['stopping_point'], library.stopping_point)
84 self.failUnlessEqual(d['successful_pM'], library.successful_pM)
85 self.failUnlessEqual(d['undiluted_concentration'],
86 str(library.undiluted_concentration))
91 if library.id == '10981':
92 # test a case where there is no known status
93 lane_set = {u'status': u'Unknown',
98 u'flowcell': u'303TUAAXX',
100 self.failUnlessEqual(len(d['lane_set']), 1)
101 self.failUnlessEqual(d['lane_set'][0], lane_set)
102 elif library.id == '11016':
103 # test a case where there is a status
104 lane_set = {u'status': 'Good',
109 u'flowcell': u'303TUAAXX',
111 self.failUnlessEqual(len(d['lane_set']), 1)
112 self.failUnlessEqual(d['lane_set'][0], lane_set)
115 def test_invalid_library_json(self):
117 Make sure we get a 404 if we request an invalid library id
119 response = self.client.get('/samples/library/nottheone/json', apidata)
120 self.failUnlessEqual(response.status_code, 404)
123 def test_invalid_library(self):
124 response = self.client.get('/library/nottheone/')
125 self.failUnlessEqual(response.status_code, 404)
128 def test_library_no_key(self):
130 Make sure we get a 403 if we're not logged in
132 library = LibraryFactory.create()
134 url = '/samples/library/{}/json'.format(library.id)
135 response = self.client.get(url, apidata)
136 self.failUnlessEqual(response.status_code, 200)
137 response = self.client.get(url)
138 self.failUnlessEqual(response.status_code, 403)
140 def test_library_rdf(self):
141 library = LibraryFactory.create()
144 from htsworkflow.util.rdfhelp import get_model, \
147 load_string_into_model, \
152 response = self.client.get(library.get_absolute_url())
153 self.assertEqual(response.status_code, 200)
154 content = smart_text(response.content)
155 load_string_into_model(model, 'rdfa', content)
157 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
158 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
160 select ?library ?name ?library_id ?gel_cut ?made_by
162 ?library a libns:library ;
164 libns:library_id ?library_id ;
165 libns:gel_cut ?gel_cut ;
166 libns:made_by ?made_by
168 query = RDF.SPARQLQuery(body)
169 for r in query.execute(model):
170 self.assertEqual(fromTypedNode(r['library_id']),
172 self.assertEqual(fromTypedNode(r['name']),
174 self.assertEqual(fromTypedNode(r['gel_cut']),
176 self.assertEqual(fromTypedNode(r['made_by']),
179 state = validate_xhtml(content)
180 if state is not None:
181 self.assertTrue(state)
183 # validate a library page.
184 from htsworkflow.util.rdfhelp import add_default_schemas
185 from htsworkflow.util.rdfinfer import Infer
186 add_default_schemas(model)
187 inference = Infer(model)
188 errmsgs = list(inference.run_validation())
189 self.assertEqual(len(errmsgs), 0)
191 def test_library_index_rdfa(self):
192 from htsworkflow.util.rdfhelp import \
193 add_default_schemas, get_model, load_string_into_model, \
195 from htsworkflow.util.rdfinfer import Infer
198 add_default_schemas(model)
199 inference = Infer(model)
201 response = self.client.get('/library/')
202 self.assertEqual(response.status_code, 200)
203 load_string_into_model(model, 'rdfa', smart_text(response.content))
205 errmsgs = list(inference.run_validation())
206 self.assertEqual(len(errmsgs), 0)
208 body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
209 prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
211 select ?library ?library_id ?name ?species ?species_name
213 ?library a libns:Library .
214 OPTIONAL { ?library libns:library_id ?library_id . }
215 OPTIONAL { ?library libns:species ?species .
216 ?species libns:species_name ?species_name . }
217 OPTIONAL { ?library libns:name ?name . }
219 bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
220 query = RDF.SPARQLQuery(body)
222 for r in query.execute(model):
224 for name, value in r.items():
225 self.assertTrue(name in bindings)
226 self.assertTrue(value is not None)
228 self.assertEqual(count, len(Library.objects.filter(hidden=False)))
230 state = validate_xhtml(response.content)
231 if state is not None: self.assertTrue(state)
234 # The django test runner flushes the database between test suites not cases,
235 # so to be more compatible with running via nose we flush the database tables
236 # of interest before creating our sample data.
238 obj.species_human = Species.objects.get(pk=8)
239 obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
240 obj.affiliation_alice = Affiliation.objects.get(pk=1)
241 obj.affiliation_bob = Affiliation.objects.get(pk=2)
243 Library.objects.all().delete()
244 obj.library_10001 = Library(
246 library_name = 'C2C12 named poorly',
247 library_species = obj.species_human,
248 experiment_type = obj.experiment_rna_seq,
249 creation_date = datetime.datetime.now(),
250 made_for = 'scientist unit 2007',
251 made_by = 'microfludics system 7321',
252 stopping_point = '2A',
253 undiluted_concentration = '5.01',
256 obj.library_10001.save()
257 obj.library_10002 = Library(
259 library_name = 'Worm named poorly',
260 library_species = obj.species_human,
261 experiment_type = obj.experiment_rna_seq,
262 creation_date = datetime.datetime.now(),
263 made_for = 'scientist unit 2007',
264 made_by = 'microfludics system 7321',
265 stopping_point = '2A',
266 undiluted_concentration = '5.01',
269 obj.library_10002.save()
275 rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
276 xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
277 libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
279 from htsworkflow.util.rdfhelp import dump_model
280 except ImportError as e:
284 class TestRDFaLibrary(TestCase):
287 self.request = RequestFactory()
289 def test_parse_rdfa(self):
291 model = get_rdf_memory_model()
292 parser = RDF.Parser(name='rdfa')
294 bob = AffiliationFactory.create(name='Bob')
296 lib_object = LibraryFactory()
297 lib_object.affiliations.add(bob)
298 url = '/library/{}/'.format(lib_object.id)
299 ## request = self.request.get(url)
300 ## lib_response = library(request)
301 lib_response = self.client.get(url)
302 lib_body = smart_str(lib_response.content)
303 self.failIfEqual(len(lib_body), 0)
304 with open('/tmp/body.html', 'wt') as outstream:
305 outstream.write(lib_body)
307 parser.parse_string_into_model(model,
309 'http://localhost'+url)
310 # help debugging rdf errrors
311 #with open('/tmp/test.ttl', 'w') as outstream:
312 # dump_model(model, outstream)
313 # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
314 self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
315 self.check_literal_object(model,
316 ['experiment type name'],
317 p=libNS['experiment_type'])
318 self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
319 self.check_literal_object(model,
320 ['microfluidics bot 7321'],
322 self.check_literal_object(model,
323 [lib_object.library_name],
325 self.check_literal_object(model,
326 [lib_object.library_species.scientific_name],
327 p=libNS['species_name'])
330 def check_literal_object(self, model, values, s=None, p=None, o=None):
331 statements = list(model.find_statements(
332 RDF.Statement(s,p,o)))
333 self.failUnlessEqual(len(statements), len(values),
334 "Couln't find %s %s %s" % (s,p,o))
336 self.failUnless(s.object.literal_value['string'] in values)
339 def check_uri_object(self, model, values, s=None, p=None, o=None):
340 statements = list(model.find_statements(
341 RDF.Statement(s,p,o)))
342 self.failUnlessEqual(len(statements), len(values),
343 "Couln't find %s %s %s" % (s,p,o))
345 self.failUnless(str(s.object.uri) in values)
349 def get_rdf_memory_model():
350 storage = RDF.MemoryStorage()
351 model = RDF.Model(storage)
355 from unittest import TestSuite, defaultTestLoader
357 suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
358 suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
359 suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
362 if __name__ == "__main__":
363 from unittest import main
364 main(defaultTest="suite")