htsworkflow/frontend/samples/tests.py

   1 import datetime
   2 import unittest
   3
   4 try:
   5     import json
   6 except ImportError, e:
   7     import simplejson as json
   8
   9 from django.test import TestCase
  10
  11 from htsworkflow.frontend.samples.models import \
  12         Affiliation, \
  13         ExperimentType, \
  14         Species, \
  15         Library
  16
  17 from htsworkflow.frontend.samples.views import \
  18      library_dict, \
  19      library_json
  20
  21 from htsworkflow.frontend.auth import apidata
  22 from htsworkflow.util.conversion import unicode_or_none
  23
  24
  25 class LibraryTestCase(TestCase):
  26     fixtures = ['test_samples.json']
  27
  28     def setUp(self):
  29         create_db(self)
  30
  31     def testOrganism(self):
  32         self.assertEquals(self.library_10001.organism(), 'human')
  33
  34     def testAffiliations(self):
  35         self.library_10001.affiliations.add(self.affiliation_alice)
  36         self.library_10002.affiliations.add(
  37                 self.affiliation_alice,
  38                 self.affiliation_bob
  39         )
  40         self.failUnless(len(self.library_10001.affiliations.all()), 1)
  41         self.failUnless(self.library_10001.affiliation(), 'Alice')
  42
  43         self.failUnless(len(self.library_10002.affiliations.all()), 2)
  44         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
  45
  46
  47 class SampleWebTestCase(TestCase):
  48     """
  49     Test returning data from our database in rest like ways.
  50     (like returning json objects)
  51     """
  52     fixtures = ['test_samples.json']
  53
  54     def test_library_info(self):
  55
  56         for lib in Library.objects.all():
  57             lib_dict = library_dict(lib.id)
  58             url = '/samples/library/%s/json' % (lib.id,)
  59             lib_response = self.client.get(url, apidata)
  60             self.failUnlessEqual(lib_response.status_code, 200)
  61             lib_json = json.loads(lib_response.content)
  62
  63             for d in [lib_dict, lib_json]:
  64                 # amplified_from_sample is a link to the library table,
  65                 # I want to use the "id" for the data lookups not
  66                 # the embedded primary key.
  67                 # It gets slightly confusing on how to implement sending the right id
  68                 # since amplified_from_sample can be null
  69                 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
  70                 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
  71                 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
  72                 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
  73                 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
  74                 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
  75                 self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
  76                 self.failUnlessEqual(d['hidden'], lib.hidden)
  77                 self.failUnlessEqual(d['id'], lib.id)
  78                 self.failUnlessEqual(d['insert_size'], lib.insert_size)
  79                 self.failUnlessEqual(d['library_name'], lib.library_name)
  80                 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
  81                 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
  82                 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
  83                 if lib.library_type_id is not None:
  84                     self.failUnlessEqual(d['library_type'], lib.library_type.name)
  85                 else:
  86                     self.failUnlessEqual(d['library_type'], None)
  87                     self.failUnlessEqual(d['made_for'], lib.made_for)
  88                     self.failUnlessEqual(d['made_by'], lib.made_by)
  89                     self.failUnlessEqual(d['notes'], lib.notes)
  90                     self.failUnlessEqual(d['replicate'], lib.replicate)
  91                     self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
  92                     self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
  93                     self.failUnlessEqual(d['undiluted_concentration'],
  94                                          unicode(lib.undiluted_concentration))
  95                 # some specific tests
  96                 if lib.id == '10981':
  97                     # test a case where there is no known status
  98                     lane_set = {u'status': u'Unknown',
  99                                 u'paired_end': True,
 100                                 u'read_length': 75,
 101                                 u'lane_number': 1,
 102                                 u'lane_id': 1193,
 103                                 u'flowcell': u'303TUAAXX',
 104                                 u'status_code': None}
 105                     self.failUnlessEqual(len(d['lane_set']), 1)
 106                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 107                 elif lib.id == '11016':
 108                     # test a case where there is a status
 109                     lane_set = {u'status': 'Good',
 110                                 u'paired_end': True,
 111                                 u'read_length': 75,
 112                                 u'lane_number': 5,
 113                                 u'lane_id': 1197,
 114                                 u'flowcell': u'303TUAAXX',
 115                                 u'status_code': 2}
 116                     self.failUnlessEqual(len(d['lane_set']), 1)
 117                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 118
 119
 120     def test_invalid_library_json(self):
 121         """
 122         Make sure we get a 404 if we request an invalid library id
 123         """
 124         response = self.client.get('/samples/library/nottheone/json', apidata)
 125         self.failUnlessEqual(response.status_code, 404)
 126
 127
 128     def test_invalid_library(self):
 129         response = self.client.get('/library/nottheone/')
 130         self.failUnlessEqual(response.status_code, 404)
 131
 132
 133     def test_library_no_key(self):
 134         """
 135         Make sure we get a 302 if we're not logged in
 136         """
 137         response = self.client.get('/samples/library/10981/json')
 138         self.failUnlessEqual(response.status_code, 403)
 139         response = self.client.get('/samples/library/10981/json', apidata)
 140         self.failUnlessEqual(response.status_code, 200)
 141
 142     def test_library_rdf(self):
 143         import RDF
 144         from htsworkflow.util.rdfhelp import get_model, \
 145              fromTypedNode, \
 146              load_string_into_model, \
 147              rdfNS, \
 148              libraryOntology
 149         model = get_model()
 150
 151         response = self.client.get('/library/10981/')
 152         self.assertEqual(response.status_code, 200)
 153         load_string_into_model(model, 'rdfa', response.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 # The django test runner flushes the database between test suites not cases,
 175 # so to be more compatible with running via nose we flush the database tables
 176 # of interest before creating our sample data.
 177 def create_db(obj):
 178     obj.species_human = Species.objects.get(pk=8)
 179     obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
 180     obj.affiliation_alice = Affiliation.objects.get(pk=1)
 181     obj.affiliation_bob = Affiliation.objects.get(pk=2)
 182
 183     Library.objects.all().delete()
 184     obj.library_10001 = Library(
 185         id = "10001",
 186         library_name = 'C2C12 named poorly',
 187         library_species = obj.species_human,
 188         experiment_type = obj.experiment_rna_seq,
 189         creation_date = datetime.datetime.now(),
 190         made_for = 'scientist unit 2007',
 191         made_by = 'microfludics system 7321',
 192         stopping_point = '2A',
 193         undiluted_concentration = '5.01',
 194         hidden = False,
 195     )
 196     obj.library_10001.save()
 197     obj.library_10002 = Library(
 198         id = "10002",
 199         library_name = 'Worm named poorly',
 200         library_species = obj.species_human,
 201         experiment_type = obj.experiment_rna_seq,
 202         creation_date = datetime.datetime.now(),
 203         made_for = 'scientist unit 2007',
 204         made_by = 'microfludics system 7321',
 205         stopping_point = '2A',
 206         undiluted_concentration = '5.01',
 207         hidden = False,
 208     )
 209     obj.library_10002.save()
 210
 211 try:
 212     import RDF
 213     HAVE_RDF = True
 214
 215     rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
 216     xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
 217     libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
 218 except ImportError,e:
 219     HAVE_RDF = False
 220
 221
 222 class TestRDFaLibrary(TestCase):
 223     fixtures = ['test_samples.json']
 224
 225     def test_parse_rdfa(self):
 226         model = get_rdf_memory_model()
 227         parser = RDF.Parser(name='rdfa')
 228         url = '/library/10981/'
 229         lib_response = self.client.get(url)
 230         self.failIfEqual(len(lib_response.content), 0)
 231
 232         parser.parse_string_into_model(model,
 233                                        lib_response.content,
 234                                        'http://localhost'+url)
 235         # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
 236         self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
 237         self.check_literal_object(model, ['Multiplexed'], p=libNS['experiment_type'])
 238         self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
 239         self.check_literal_object(model, ['Igor'], p=libNS['made_by'])
 240         self.check_literal_object(model, ['Paired End Multiplexed Sp-BAC'], p=libNS['name'])
 241         self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species'])
 242
 243         self.check_uri_object(model,
 244                               [u'http://localhost/lane/1193'],
 245                               p=libNS['has_lane'])
 246
 247         fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
 248         self.check_literal_object(model,
 249                                   [u"303TUAAXX"],
 250                                   s=fc_uri, p=libNS['flowcell_id'])
 251
 252     def check_literal_object(self, model, values, s=None, p=None, o=None):
 253         statements = list(model.find_statements(
 254             RDF.Statement(s,p,o)))
 255         self.failUnlessEqual(len(statements), len(values),
 256                         "Couln't find %s %s %s" % (s,p,o))
 257         for s in statements:
 258             self.failUnless(s.object.literal_value['string'] in values)
 259
 260
 261     def check_uri_object(self, model, values, s=None, p=None, o=None):
 262         statements = list(model.find_statements(
 263             RDF.Statement(s,p,o)))
 264         self.failUnlessEqual(len(statements), len(values),
 265                         "Couln't find %s %s %s" % (s,p,o))
 266         for s in statements:
 267             self.failUnless(unicode(s.object.uri) in values)
 268
 269
 270
 271 def get_rdf_memory_model():
 272     storage = RDF.MemoryStorage()
 273     model = RDF.Model(storage)
 274     return model
 275