htsworkflow/frontend/samples/test_samples.py

   1 import datetime
   2
   3 try:
   4     import json
   5 except ImportError, e:
   6     import simplejson as json
   7
   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
  13
  14 from htsworkflow.frontend.samples.models import \
  15         Affiliation, \
  16         ExperimentType, \
  17         Species, \
  18         Library
  19
  20 from htsworkflow.frontend.samples.views import \
  21      library_dict, \
  22      library_json
  23
  24 from htsworkflow.frontend.auth import apidata
  25 from htsworkflow.util.conversion import unicode_or_none
  26 from htsworkflow.util.ethelp import validate_xhtml
  27
  28 class LibraryTestCase(TestCase):
  29     fixtures = ['test_samples.json']
  30
  31     def setUp(self):
  32         create_db(self)
  33
  34     def testOrganism(self):
  35         self.assertEquals(self.library_10001.organism(), 'human')
  36
  37     def testAffiliations(self):
  38         self.library_10001.affiliations.add(self.affiliation_alice)
  39         self.library_10002.affiliations.add(
  40                 self.affiliation_alice,
  41                 self.affiliation_bob
  42         )
  43         self.failUnless(len(self.library_10001.affiliations.all()), 1)
  44         self.failUnless(self.library_10001.affiliation(), 'Alice')
  45
  46         self.failUnless(len(self.library_10002.affiliations.all()), 2)
  47         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
  48
  49
  50 class SampleWebTestCase(TestCase):
  51     """
  52     Test returning data from our database in rest like ways.
  53     (like returning json objects)
  54     """
  55     fixtures = ['test_samples.json']
  56
  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)
  64
  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)
  87                 else:
  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))
  97                 # some specific tests
  98                 if lib.id == '10981':
  99                     # test a case where there is no known status
 100                     lane_set = {u'status': u'Unknown',
 101                                 u'paired_end': True,
 102                                 u'read_length': 75,
 103                                 u'lane_number': 1,
 104                                 u'lane_id': 1193,
 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',
 112                                 u'paired_end': True,
 113                                 u'read_length': 75,
 114                                 u'lane_number': 5,
 115                                 u'lane_id': 1197,
 116                                 u'flowcell': u'303TUAAXX',
 117                                 u'status_code': 2}
 118                     self.failUnlessEqual(len(d['lane_set']), 1)
 119                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 120
 121
 122     def test_invalid_library_json(self):
 123         """
 124         Make sure we get a 404 if we request an invalid library id
 125         """
 126         response = self.client.get('/samples/library/nottheone/json', apidata)
 127         self.failUnlessEqual(response.status_code, 404)
 128
 129
 130     def test_invalid_library(self):
 131         response = self.client.get('/library/nottheone/')
 132         self.failUnlessEqual(response.status_code, 404)
 133
 134
 135     def test_library_no_key(self):
 136         """
 137         Make sure we get a 302 if we're not logged in
 138         """
 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)
 143
 144     def test_library_rdf(self):
 145         import RDF
 146         from htsworkflow.util.rdfhelp import get_model, \
 147              dump_model, \
 148              fromTypedNode, \
 149              load_string_into_model, \
 150              rdfNS, \
 151              libraryOntology
 152         model = get_model()
 153
 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)
 158
 159         body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 160         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 161
 162         select ?library ?name ?library_id ?gel_cut ?made_by
 163         where {
 164            ?library a libns:library ;
 165                     libns:name ?name ;
 166                     libns:library_id ?library_id ;
 167                     libns:gel_cut ?gel_cut ;
 168                     libns:made_by ?made_by
 169         }"""
 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')
 177
 178         state = validate_xhtml(content)
 179         if state is not None:
 180             self.assertTrue(state)
 181
 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)
 189
 190     def test_library_index_rdfa(self):
 191         from htsworkflow.util.rdfhelp import \
 192              add_default_schemas, get_model, load_string_into_model, \
 193              dump_model
 194         from htsworkflow.util.rdfinfer import Infer
 195
 196         model = get_model()
 197         add_default_schemas(model)
 198         inference = Infer(model)
 199
 200         response = self.client.get('/library/')
 201         self.assertEqual(response.status_code, 200)
 202         load_string_into_model(model, 'rdfa', response.content)
 203
 204         errmsgs = list(inference.run_validation())
 205         self.assertEqual(len(errmsgs), 0)
 206
 207         body =  """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 208         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 209
 210         select ?library ?library_id ?name ?species ?species_name
 211         where {
 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 . }
 217         }"""
 218         bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
 219         query = RDF.SPARQLQuery(body)
 220         count = 0
 221         for r in query.execute(model):
 222             count += 1
 223             for name, value in r.items():
 224                 self.assertTrue(name in bindings)
 225                 self.assertTrue(value is not None)
 226
 227         self.assertEqual(count, len(Library.objects.filter(hidden=False)))
 228
 229         state = validate_xhtml(response.content)
 230         if state is not None: self.assertTrue(state)
 231
 232
 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.
 236 def create_db(obj):
 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)
 241
 242     Library.objects.all().delete()
 243     obj.library_10001 = Library(
 244         id = "10001",
 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',
 253         hidden = False,
 254     )
 255     obj.library_10001.save()
 256     obj.library_10002 = Library(
 257         id = "10002",
 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',
 266         hidden = False,
 267     )
 268     obj.library_10002.save()
 269
 270 try:
 271     import RDF
 272     HAVE_RDF = True
 273
 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:
 278     HAVE_RDF = False
 279
 280
 281 class TestRDFaLibrary(TestCase):
 282     fixtures = ['test_samples.json']
 283
 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)
 290
 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'])
 301
 302         self.check_uri_object(model,
 303                               [u'http://localhost/lane/1193'],
 304                               p=libNS['has_lane'])
 305
 306         fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
 307         self.check_literal_object(model,
 308                                   [u"303TUAAXX"],
 309                                   s=fc_uri, p=libNS['flowcell_id'])
 310
 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))
 316         for s in statements:
 317             self.failUnless(s.object.literal_value['string'] in values)
 318
 319
 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))
 325         for s in statements:
 326             self.failUnless(unicode(s.object.uri) in values)
 327
 328
 329
 330 def get_rdf_memory_model():
 331     storage = RDF.MemoryStorage()
 332     model = RDF.Model(storage)
 333     return model
 334
 335 OLD_DB = settings.DATABASES['default']['NAME']
 336 def setUpModule():
 337     setup_test_environment()
 338     connection.creation.create_test_db()
 339
 340 def tearDownModule():
 341     connection.creation.destroy_test_db(OLD_DB)
 342     teardown_test_environment()
 343
 344 def suite():
 345     from unittest2 import TestSuite, defaultTestLoader
 346     suite = TestSuite()
 347     suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
 348     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
 349     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
 350     return suite
 351
 352 if __name__ == "__main__":
 353     from unittest2 import main
 354     main(defaultTest="suite")