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
  10 from htsworkflow.frontend.samples.models import \
  11         Affiliation, \
  12         ExperimentType, \
  13         Species, \
  14         Library
  15
  16 from htsworkflow.frontend.samples.views import \
  17      library_dict, \
  18      library_json
  19
  20 from htsworkflow.frontend.auth import apidata
  21 from htsworkflow.util.conversion import unicode_or_none
  22 from htsworkflow.util.ethelp import validate_xhtml
  23
  24 class LibraryTestCase(TestCase):
  25     fixtures = ['test_samples.json']
  26
  27     def setUp(self):
  28         create_db(self)
  29
  30     def testOrganism(self):
  31         self.assertEquals(self.library_10001.organism(), 'human')
  32
  33     def testAffiliations(self):
  34         self.library_10001.affiliations.add(self.affiliation_alice)
  35         self.library_10002.affiliations.add(
  36                 self.affiliation_alice,
  37                 self.affiliation_bob
  38         )
  39         self.failUnless(len(self.library_10001.affiliations.all()), 1)
  40         self.failUnless(self.library_10001.affiliation(), 'Alice')
  41
  42         self.failUnless(len(self.library_10002.affiliations.all()), 2)
  43         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
  44
  45
  46 class SampleWebTestCase(TestCase):
  47     """
  48     Test returning data from our database in rest like ways.
  49     (like returning json objects)
  50     """
  51     fixtures = ['test_samples.json']
  52
  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)
  60
  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)
  83                 else:
  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))
  93                 # some specific tests
  94                 if lib.id == '10981':
  95                     # test a case where there is no known status
  96                     lane_set = {u'status': u'Unknown',
  97                                 u'paired_end': True,
  98                                 u'read_length': 75,
  99                                 u'lane_number': 1,
 100                                 u'lane_id': 1193,
 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',
 108                                 u'paired_end': True,
 109                                 u'read_length': 75,
 110                                 u'lane_number': 5,
 111                                 u'lane_id': 1197,
 112                                 u'flowcell': u'303TUAAXX',
 113                                 u'status_code': 2}
 114                     self.failUnlessEqual(len(d['lane_set']), 1)
 115                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 116
 117
 118     def test_invalid_library_json(self):
 119         """
 120         Make sure we get a 404 if we request an invalid library id
 121         """
 122         response = self.client.get('/samples/library/nottheone/json', apidata)
 123         self.failUnlessEqual(response.status_code, 404)
 124
 125
 126     def test_invalid_library(self):
 127         response = self.client.get('/library/nottheone/')
 128         self.failUnlessEqual(response.status_code, 404)
 129
 130
 131     def test_library_no_key(self):
 132         """
 133         Make sure we get a 302 if we're not logged in
 134         """
 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)
 139
 140     def test_library_rdf(self):
 141         import RDF
 142         from htsworkflow.util.rdfhelp import get_model, \
 143              dump_model, \
 144              fromTypedNode, \
 145              load_string_into_model, \
 146              rdfNS, \
 147              libraryOntology
 148         model = get_model()
 149
 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)
 154
 155         body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 156         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 157
 158         select ?library ?name ?library_id ?gel_cut ?made_by
 159         where {
 160            ?library a libns:library ;
 161                     libns:name ?name ;
 162                     libns:library_id ?library_id ;
 163                     libns:gel_cut ?gel_cut ;
 164                     libns:made_by ?made_by
 165         }"""
 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')
 173
 174         state = validate_xhtml(content)
 175         if state is not None:
 176             self.assertTrue(state)
 177
 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)
 185
 186     def test_library_index_rdfa(self):
 187         from htsworkflow.util.rdfhelp import \
 188              add_default_schemas, get_model, load_string_into_model, \
 189              dump_model
 190         from htsworkflow.util.rdfinfer import Infer
 191
 192         model = get_model()
 193         add_default_schemas(model)
 194         inference = Infer(model)
 195
 196         response = self.client.get('/library/')
 197         self.assertEqual(response.status_code, 200)
 198         load_string_into_model(model, 'rdfa', response.content)
 199
 200         errmsgs = list(inference.run_validation())
 201         self.assertEqual(len(errmsgs), 0)
 202
 203         body =  """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 204         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 205
 206         select ?library ?library_id ?name ?species ?species_name
 207         where {
 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 . }
 213         }"""
 214         bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
 215         query = RDF.SPARQLQuery(body)
 216         count = 0
 217         for r in query.execute(model):
 218             count += 1
 219             for name, value in r.items():
 220                 self.assertTrue(name in bindings)
 221                 self.assertTrue(value is not None)
 222
 223         self.assertEqual(count, len(Library.objects.filter(hidden=False)))
 224
 225         state = validate_xhtml(response.content)
 226         if state is not None: self.assertTrue(state)
 227
 228
 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.
 232 def create_db(obj):
 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)
 237
 238     Library.objects.all().delete()
 239     obj.library_10001 = Library(
 240         id = "10001",
 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',
 249         hidden = False,
 250     )
 251     obj.library_10001.save()
 252     obj.library_10002 = Library(
 253         id = "10002",
 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',
 262         hidden = False,
 263     )
 264     obj.library_10002.save()
 265
 266 try:
 267     import RDF
 268     HAVE_RDF = True
 269
 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:
 274     HAVE_RDF = False
 275
 276
 277 class TestRDFaLibrary(TestCase):
 278     fixtures = ['test_samples.json']
 279
 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)
 286
 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'])
 297
 298         self.check_uri_object(model,
 299                               [u'http://localhost/lane/1193'],
 300                               p=libNS['has_lane'])
 301
 302         fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
 303         self.check_literal_object(model,
 304                                   [u"303TUAAXX"],
 305                                   s=fc_uri, p=libNS['flowcell_id'])
 306
 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))
 312         for s in statements:
 313             self.failUnless(s.object.literal_value['string'] in values)
 314
 315
 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))
 321         for s in statements:
 322             self.failUnless(unicode(s.object.uri) in values)
 323
 324
 325
 326 def get_rdf_memory_model():
 327     storage = RDF.MemoryStorage()
 328     model = RDF.Model(storage)
 329     return model