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 = ['initial_data.json',
  30                 'test_samples.json']
  31
  32     def setUp(self):
  33         create_db(self)
  34
  35     def testOrganism(self):
  36         self.assertEquals(self.library_10001.organism(), 'human')
  37
  38     def testAffiliations(self):
  39         self.library_10001.affiliations.add(self.affiliation_alice)
  40         self.library_10002.affiliations.add(
  41                 self.affiliation_alice,
  42                 self.affiliation_bob
  43         )
  44         self.failUnless(len(self.library_10001.affiliations.all()), 1)
  45         self.failUnless(self.library_10001.affiliation(), 'Alice')
  46
  47         self.failUnless(len(self.library_10002.affiliations.all()), 2)
  48         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
  49
  50
  51 class SampleWebTestCase(TestCase):
  52     """
  53     Test returning data from our database in rest like ways.
  54     (like returning json objects)
  55     """
  56     fixtures = ['initial_data.json',
  57                 'test_samples.json']
  58
  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)
  66
  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)
  89                 else:
  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))
  99                 # some specific tests
 100                 if lib.id == '10981':
 101                     # test a case where there is no known status
 102                     lane_set = {u'status': u'Unknown',
 103                                 u'paired_end': True,
 104                                 u'read_length': 75,
 105                                 u'lane_number': 1,
 106                                 u'lane_id': 1193,
 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',
 114                                 u'paired_end': True,
 115                                 u'read_length': 75,
 116                                 u'lane_number': 5,
 117                                 u'lane_id': 1197,
 118                                 u'flowcell': u'303TUAAXX',
 119                                 u'status_code': 2}
 120                     self.failUnlessEqual(len(d['lane_set']), 1)
 121                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 122
 123
 124     def test_invalid_library_json(self):
 125         """
 126         Make sure we get a 404 if we request an invalid library id
 127         """
 128         response = self.client.get('/samples/library/nottheone/json', apidata)
 129         self.failUnlessEqual(response.status_code, 404)
 130
 131
 132     def test_invalid_library(self):
 133         response = self.client.get('/library/nottheone/')
 134         self.failUnlessEqual(response.status_code, 404)
 135
 136
 137     def test_library_no_key(self):
 138         """
 139         Make sure we get a 302 if we're not logged in
 140         """
 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)
 145
 146     def test_library_rdf(self):
 147         import RDF
 148         from htsworkflow.util.rdfhelp import get_model, \
 149              dump_model, \
 150              fromTypedNode, \
 151              load_string_into_model, \
 152              rdfNS, \
 153              libraryOntology
 154         model = get_model()
 155
 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)
 160
 161         body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 162         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 163
 164         select ?library ?name ?library_id ?gel_cut ?made_by
 165         where {
 166            ?library a libns:library ;
 167                     libns:name ?name ;
 168                     libns:library_id ?library_id ;
 169                     libns:gel_cut ?gel_cut ;
 170                     libns:made_by ?made_by
 171         }"""
 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')
 179
 180         state = validate_xhtml(content)
 181         if state is not None:
 182             self.assertTrue(state)
 183
 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)
 191
 192     def test_library_index_rdfa(self):
 193         from htsworkflow.util.rdfhelp import \
 194              add_default_schemas, get_model, load_string_into_model, \
 195              dump_model
 196         from htsworkflow.util.rdfinfer import Infer
 197
 198         model = get_model()
 199         add_default_schemas(model)
 200         inference = Infer(model)
 201
 202         response = self.client.get('/library/')
 203         self.assertEqual(response.status_code, 200)
 204         load_string_into_model(model, 'rdfa', response.content)
 205
 206         errmsgs = list(inference.run_validation())
 207         self.assertEqual(len(errmsgs), 0)
 208
 209         body =  """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 210         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 211
 212         select ?library ?library_id ?name ?species ?species_name
 213         where {
 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 . }
 219         }"""
 220         bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
 221         query = RDF.SPARQLQuery(body)
 222         count = 0
 223         for r in query.execute(model):
 224             count += 1
 225             for name, value in r.items():
 226                 self.assertTrue(name in bindings)
 227                 self.assertTrue(value is not None)
 228
 229         self.assertEqual(count, len(Library.objects.filter(hidden=False)))
 230
 231         state = validate_xhtml(response.content)
 232         if state is not None: self.assertTrue(state)
 233
 234
 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.
 238 def create_db(obj):
 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)
 243
 244     Library.objects.all().delete()
 245     obj.library_10001 = Library(
 246         id = "10001",
 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',
 255         hidden = False,
 256     )
 257     obj.library_10001.save()
 258     obj.library_10002 = Library(
 259         id = "10002",
 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',
 268         hidden = False,
 269     )
 270     obj.library_10002.save()
 271
 272 try:
 273     import RDF
 274     HAVE_RDF = True
 275
 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:
 280     HAVE_RDF = False
 281
 282
 283 class TestRDFaLibrary(TestCase):
 284     fixtures = ['initial_data.json',
 285                 'test_samples.json']
 286
 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)
 293
 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'])
 304
 305         self.check_uri_object(model,
 306                               [u'http://localhost/lane/1193'],
 307                               p=libNS['has_lane'])
 308
 309         fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
 310         self.check_literal_object(model,
 311                                   [u"303TUAAXX"],
 312                                   s=fc_uri, p=libNS['flowcell_id'])
 313
 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))
 319         for s in statements:
 320             self.failUnless(s.object.literal_value['string'] in values)
 321
 322
 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))
 328         for s in statements:
 329             self.failUnless(unicode(s.object.uri) in values)
 330
 331
 332
 333 def get_rdf_memory_model():
 334     storage = RDF.MemoryStorage()
 335     model = RDF.Model(storage)
 336     return model
 337
 338 def suite():
 339     from unittest2 import TestSuite, defaultTestLoader
 340     suite = TestSuite()
 341     suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
 342     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
 343     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
 344     return suite
 345
 346 if __name__ == "__main__":
 347     from unittest2 import main
 348     main(defaultTest="suite")