samples/test_samples.py

   1 from __future__ import absolute_import, print_function
   2
   3 import datetime
   4 import json
   5
   6 from django.test import TestCase, RequestFactory
   7 from django.utils.encoding import smart_text, smart_str
   8
   9 from .models import Affiliation, ExperimentType, Species, Library
  10 from .views import library_dict, library_json, library
  11 from .samples_factory import *
  12
  13 from htsworkflow.auth import apidata
  14 from htsworkflow.util.conversion import str_or_none
  15 from htsworkflow.util.ethelp import validate_xhtml
  16
  17 class LibraryTestCase(TestCase):
  18     def testOrganism(self):
  19         human = SpeciesFactory(common_name='human')
  20         self.assertEquals(human.common_name, 'human')
  21         library = LibraryFactory(library_species=human)
  22         self.assertEquals(library.organism(), 'human')
  23
  24     def testAddingOneAffiliation(self):
  25         affiliation = AffiliationFactory.create(name='Alice')
  26         library = LibraryFactory()
  27         library.affiliations.add(affiliation)
  28
  29         self.assertEqual(len(library.affiliations.all()), 1)
  30         self.assertEqual(library.affiliation(), 'Alice (contact name)')
  31
  32     def testMultipleAffiliations(self):
  33         alice = AffiliationFactory.create(name='Alice')
  34         bob = AffiliationFactory.create(name='Bob')
  35
  36         library = LibraryFactory()
  37         library.affiliations.add(alice, bob)
  38
  39         self.assertEqual(len(library.affiliations.all()), 2)
  40         self.assertEqual(library.affiliation(),
  41                          'Alice (contact name), Bob (contact name)')
  42
  43
  44 class SampleWebTestCase(TestCase):
  45     """
  46     Test returning data from our database in rest like ways.
  47     (like returning json objects)
  48     """
  49     def test_library_dict(self):
  50         library = LibraryFactory.create()
  51         lib_dict = library_dict(library.id)
  52         url = '/samples/library/%s/json' % (library.id,)
  53         lib_response = self.client.get(url, apidata)
  54         lib_json = json.loads(smart_text(lib_response.content))['result']
  55
  56         for d in [lib_dict, lib_json]:
  57             # amplified_from_sample is a link to the library table,
  58             # I want to use the "id" for the data lookups not
  59             # the embedded primary key.
  60             # It gets slightly confusing on how to implement sending the right id
  61             # since amplified_from_sample can be null
  62             #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
  63             self.failUnlessEqual(d['antibody_id'], library.antibody_id)
  64             self.failUnlessEqual(d['cell_line_id'], library.cell_line_id)
  65             self.failUnlessEqual(d['cell_line'], str_or_none(library.cell_line))
  66             self.failUnlessEqual(d['experiment_type'], library.experiment_type.name)
  67             self.failUnlessEqual(d['experiment_type_id'], library.experiment_type_id)
  68             self.failUnlessEqual(d['gel_cut_size'], library.gel_cut_size)
  69             self.failUnlessEqual(d['hidden'], library.hidden)
  70             self.failUnlessEqual(d['id'], library.id)
  71             self.failUnlessEqual(d['insert_size'], library.insert_size)
  72             self.failUnlessEqual(d['library_name'], library.library_name)
  73             self.failUnlessEqual(d['library_species'], library.library_species.scientific_name)
  74             self.failUnlessEqual(d['library_species_id'], library.library_species_id)
  75             self.failUnlessEqual(d['library_type_id'], library.library_type_id)
  76             self.assertTrue(d['library_type'].startswith('library type'))
  77             self.failUnlessEqual(d['made_for'], library.made_for)
  78             self.failUnlessEqual(d['made_by'], library.made_by)
  79             self.failUnlessEqual(d['notes'], library.notes)
  80             self.failUnlessEqual(d['replicate'], library.replicate)
  81             self.failUnlessEqual(d['stopping_point'], library.stopping_point)
  82             self.failUnlessEqual(d['successful_pM'], library.successful_pM)
  83             self.failUnlessEqual(d['undiluted_concentration'],
  84                                  str(library.undiluted_concentration))
  85
  86
  87         def junk(self):
  88                 # some specific tests
  89                 if library.id == '10981':
  90                     # test a case where there is no known status
  91                     lane_set = {u'status': u'Unknown',
  92                                 u'paired_end': True,
  93                                 u'read_length': 75,
  94                                 u'lane_number': 1,
  95                                 u'lane_id': 1193,
  96                                 u'flowcell': u'303TUAAXX',
  97                                 u'status_code': None}
  98                     self.failUnlessEqual(len(d['lane_set']), 1)
  99                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 100                 elif library.id == '11016':
 101                     # test a case where there is a status
 102                     lane_set = {u'status': 'Good',
 103                                 u'paired_end': True,
 104                                 u'read_length': 75,
 105                                 u'lane_number': 5,
 106                                 u'lane_id': 1197,
 107                                 u'flowcell': u'303TUAAXX',
 108                                 u'status_code': 2}
 109                     self.failUnlessEqual(len(d['lane_set']), 1)
 110                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 111
 112
 113     def test_invalid_library_json(self):
 114         """
 115         Make sure we get a 404 if we request an invalid library id
 116         """
 117         response = self.client.get('/samples/library/nottheone/json', apidata)
 118         self.failUnlessEqual(response.status_code, 404)
 119
 120
 121     def test_invalid_library(self):
 122         response = self.client.get('/library/nottheone/')
 123         self.failUnlessEqual(response.status_code, 404)
 124
 125
 126     def test_library_no_key(self):
 127         """
 128         Make sure we get a 403 if we're not logged in
 129         """
 130         library = LibraryFactory.create()
 131
 132         url = '/samples/library/{}/json'.format(library.id)
 133         response = self.client.get(url, apidata)
 134         self.failUnlessEqual(response.status_code, 200)
 135         response = self.client.get(url)
 136         self.failUnlessEqual(response.status_code, 403)
 137
 138     def test_library_rdf(self):
 139         library = LibraryFactory.create()
 140
 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.get_absolute_url())
 151         self.assertEqual(response.status_code, 200)
 152         content = smart_text(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']),
 169                              library.id)
 170             self.assertEqual(fromTypedNode(r['name']),
 171                              library.name)
 172             self.assertEqual(fromTypedNode(r['gel_cut']),
 173                              library.gel_cut)
 174             self.assertEqual(fromTypedNode(r['made_by']),
 175                              library.made_by)
 176
 177         state = validate_xhtml(content)
 178         if state is not None:
 179             self.assertTrue(state)
 180
 181         # validate a library page.
 182         from htsworkflow.util.rdfhelp import add_default_schemas
 183         from htsworkflow.util.rdfinfer import Infer
 184         add_default_schemas(model)
 185         inference = Infer(model)
 186         errmsgs = list(inference.run_validation())
 187         self.assertEqual(len(errmsgs), 0)
 188
 189     def test_library_index_rdfa(self):
 190         from htsworkflow.util.rdfhelp import \
 191              add_default_schemas, get_model, load_string_into_model, \
 192              dump_model
 193         from htsworkflow.util.rdfinfer import Infer
 194
 195         model = get_model()
 196         add_default_schemas(model)
 197         inference = Infer(model)
 198
 199         response = self.client.get('/library/')
 200         self.assertEqual(response.status_code, 200)
 201         load_string_into_model(model, 'rdfa', smart_text(response.content))
 202
 203         errmsgs = list(inference.run_validation())
 204         self.assertEqual(len(errmsgs), 0)
 205
 206         body =  """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 207         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 208
 209         select ?library ?library_id ?name ?species ?species_name
 210         where {
 211            ?library a libns:Library .
 212            OPTIONAL { ?library libns:library_id ?library_id . }
 213            OPTIONAL { ?library libns:species ?species .
 214                       ?species libns:species_name ?species_name . }
 215            OPTIONAL { ?library libns:name ?name . }
 216         }"""
 217         bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
 218         query = RDF.SPARQLQuery(body)
 219         count = 0
 220         for r in query.execute(model):
 221             count += 1
 222             for name, value in r.items():
 223                 self.assertTrue(name in bindings)
 224                 self.assertTrue(value is not None)
 225
 226         self.assertEqual(count, len(Library.objects.filter(hidden=False)))
 227
 228         state = validate_xhtml(response.content)
 229         if state is not None: self.assertTrue(state)
 230
 231
 232 # The django test runner flushes the database between test suites not cases,
 233 # so to be more compatible with running via nose we flush the database tables
 234 # of interest before creating our sample data.
 235 def create_db(obj):
 236     obj.species_human = Species.objects.get(pk=8)
 237     obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
 238     obj.affiliation_alice = Affiliation.objects.get(pk=1)
 239     obj.affiliation_bob = Affiliation.objects.get(pk=2)
 240
 241     Library.objects.all().delete()
 242     obj.library_10001 = Library(
 243         id = "10001",
 244         library_name = 'C2C12 named poorly',
 245         library_species = obj.species_human,
 246         experiment_type = obj.experiment_rna_seq,
 247         creation_date = datetime.datetime.now(),
 248         made_for = 'scientist unit 2007',
 249         made_by = 'microfludics system 7321',
 250         stopping_point = '2A',
 251         undiluted_concentration = '5.01',
 252         hidden = False,
 253     )
 254     obj.library_10001.save()
 255     obj.library_10002 = Library(
 256         id = "10002",
 257         library_name = 'Worm named poorly',
 258         library_species = obj.species_human,
 259         experiment_type = obj.experiment_rna_seq,
 260         creation_date = datetime.datetime.now(),
 261         made_for = 'scientist unit 2007',
 262         made_by = 'microfludics system 7321',
 263         stopping_point = '2A',
 264         undiluted_concentration = '5.01',
 265         hidden = False,
 266     )
 267     obj.library_10002.save()
 268
 269 try:
 270     import RDF
 271     HAVE_RDF = True
 272
 273     rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
 274     xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
 275     libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
 276
 277     from htsworkflow.util.rdfhelp import dump_model
 278 except ImportError as e:
 279     HAVE_RDF = False
 280
 281
 282 class TestRDFaLibrary(TestCase):
 283
 284     def setUp(self):
 285         self.request = RequestFactory()
 286
 287     def test_parse_rdfa(self):
 288
 289         model = get_rdf_memory_model()
 290         parser = RDF.Parser(name='rdfa')
 291
 292         bob = AffiliationFactory.create(name='Bob')
 293
 294         lib_object = LibraryFactory()
 295         lib_object.affiliations.add(bob)
 296         url = '/library/{}/'.format(lib_object.id)
 297         ## request = self.request.get(url)
 298         ## lib_response = library(request)
 299         lib_response = self.client.get(url)
 300         lib_body = smart_str(lib_response.content)
 301         self.failIfEqual(len(lib_body), 0)
 302         with open('/tmp/body.html', 'wt') as outstream:
 303             outstream.write(lib_body)
 304
 305         parser.parse_string_into_model(model,
 306                                        lib_body,
 307                                        'http://localhost'+url)
 308         # help debugging rdf errrors
 309         #with open('/tmp/test.ttl', 'w') as outstream:
 310         #    dump_model(model, outstream)
 311         # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
 312         self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
 313         self.check_literal_object(model,
 314                                   ['experiment type name'],
 315                                   p=libNS['experiment_type'])
 316         self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
 317         self.check_literal_object(model,
 318                                   ['microfluidics bot 7321'],
 319                                   p=libNS['made_by'])
 320         self.check_literal_object(model,
 321                                   [lib_object.library_name],
 322                                   p=libNS['name'])
 323         self.check_literal_object(model,
 324                                   [lib_object.library_species.scientific_name],
 325                                   p=libNS['species_name'])
 326
 327
 328     def check_literal_object(self, model, values, s=None, p=None, o=None):
 329         statements = list(model.find_statements(
 330             RDF.Statement(s,p,o)))
 331         self.failUnlessEqual(len(statements), len(values),
 332                         "Couln't find %s %s %s" % (s,p,o))
 333         for s in statements:
 334             self.failUnless(s.object.literal_value['string'] in values)
 335
 336
 337     def check_uri_object(self, model, values, s=None, p=None, o=None):
 338         statements = list(model.find_statements(
 339             RDF.Statement(s,p,o)))
 340         self.failUnlessEqual(len(statements), len(values),
 341                         "Couln't find %s %s %s" % (s,p,o))
 342         for s in statements:
 343             self.failUnless(str(s.object.uri) in values)
 344
 345
 346
 347 def get_rdf_memory_model():
 348     storage = RDF.MemoryStorage()
 349     model = RDF.Model(storage)
 350     return model
 351
 352 def suite():
 353     from unittest import TestSuite, defaultTestLoader
 354     suite = TestSuite()
 355     suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
 356     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
 357     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
 358     return suite
 359
 360 if __name__ == "__main__":
 361     from unittest import main
 362     main(defaultTest="suite")