samples/test_samples.py

   1 from __future__ import absolute_import, print_function, unicode_literals
   2
   3 import datetime
   4 import unittest
   5 import json
   6
   7 from django.test import TestCase, RequestFactory
   8 from django.conf import settings
   9 from django.utils.encoding import smart_text, smart_str
  10
  11 from .models import Affiliation, ExperimentType, Species, Library
  12 from .views import library_dict, library_json, library
  13 from .samples_factory import *
  14
  15 from htsworkflow.auth import apidata
  16 from htsworkflow.util.conversion import str_or_none
  17 from htsworkflow.util.ethelp import validate_xhtml
  18
  19 class LibraryTestCase(TestCase):
  20     def testOrganism(self):
  21         human = SpeciesFactory(common_name='human')
  22         self.assertEquals(human.common_name, 'human')
  23         library = LibraryFactory(library_species=human)
  24         self.assertEquals(library.organism(), 'human')
  25
  26     def testAddingOneAffiliation(self):
  27         affiliation = AffiliationFactory.create(name='Alice')
  28         library = LibraryFactory()
  29         library.affiliations.add(affiliation)
  30
  31         self.assertEqual(len(library.affiliations.all()), 1)
  32         self.assertEqual(library.affiliation(), 'Alice (contact name)')
  33
  34     def testMultipleAffiliations(self):
  35         alice = AffiliationFactory.create(name='Alice')
  36         bob = AffiliationFactory.create(name='Bob')
  37
  38         library = LibraryFactory()
  39         library.affiliations.add(alice, bob)
  40
  41         self.assertEqual(len(library.affiliations.all()), 2)
  42         self.assertEqual(library.affiliation(),
  43                          'Alice (contact name), Bob (contact name)')
  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     def test_library_dict(self):
  52         library = LibraryFactory.create()
  53         lib_dict = library_dict(library.id)
  54         url = '/samples/library/%s/json' % (library.id,)
  55         lib_response = self.client.get(url, apidata)
  56         lib_json = json.loads(smart_text(lib_response.content))['result']
  57
  58         for d in [lib_dict, lib_json]:
  59             # amplified_from_sample is a link to the library table,
  60             # I want to use the "id" for the data lookups not
  61             # the embedded primary key.
  62             # It gets slightly confusing on how to implement sending the right id
  63             # since amplified_from_sample can be null
  64             #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
  65             self.failUnlessEqual(d['antibody_id'], library.antibody_id)
  66             self.failUnlessEqual(d['cell_line_id'], library.cell_line_id)
  67             self.failUnlessEqual(d['cell_line'], str_or_none(library.cell_line))
  68             self.failUnlessEqual(d['experiment_type'], library.experiment_type.name)
  69             self.failUnlessEqual(d['experiment_type_id'], library.experiment_type_id)
  70             self.failUnlessEqual(d['gel_cut_size'], library.gel_cut_size)
  71             self.failUnlessEqual(d['hidden'], library.hidden)
  72             self.failUnlessEqual(d['id'], library.id)
  73             self.failUnlessEqual(d['insert_size'], library.insert_size)
  74             self.failUnlessEqual(d['library_name'], library.library_name)
  75             self.failUnlessEqual(d['library_species'], library.library_species.scientific_name)
  76             self.failUnlessEqual(d['library_species_id'], library.library_species_id)
  77             self.failUnlessEqual(d['library_type_id'], library.library_type_id)
  78             self.assertTrue(d['library_type'].startswith('library type'))
  79             self.failUnlessEqual(d['made_for'], library.made_for)
  80             self.failUnlessEqual(d['made_by'], library.made_by)
  81             self.failUnlessEqual(d['notes'], library.notes)
  82             self.failUnlessEqual(d['replicate'], library.replicate)
  83             self.failUnlessEqual(d['stopping_point'], library.stopping_point)
  84             self.failUnlessEqual(d['successful_pM'], library.successful_pM)
  85             self.failUnlessEqual(d['undiluted_concentration'],
  86                                  str(library.undiluted_concentration))
  87
  88
  89         def junk(self):
  90                 # some specific tests
  91                 if library.id == '10981':
  92                     # test a case where there is no known status
  93                     lane_set = {u'status': u'Unknown',
  94                                 u'paired_end': True,
  95                                 u'read_length': 75,
  96                                 u'lane_number': 1,
  97                                 u'lane_id': 1193,
  98                                 u'flowcell': u'303TUAAXX',
  99                                 u'status_code': None}
 100                     self.failUnlessEqual(len(d['lane_set']), 1)
 101                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 102                 elif library.id == '11016':
 103                     # test a case where there is a status
 104                     lane_set = {u'status': 'Good',
 105                                 u'paired_end': True,
 106                                 u'read_length': 75,
 107                                 u'lane_number': 5,
 108                                 u'lane_id': 1197,
 109                                 u'flowcell': u'303TUAAXX',
 110                                 u'status_code': 2}
 111                     self.failUnlessEqual(len(d['lane_set']), 1)
 112                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 113
 114
 115     def test_invalid_library_json(self):
 116         """
 117         Make sure we get a 404 if we request an invalid library id
 118         """
 119         response = self.client.get('/samples/library/nottheone/json', apidata)
 120         self.failUnlessEqual(response.status_code, 404)
 121
 122
 123     def test_invalid_library(self):
 124         response = self.client.get('/library/nottheone/')
 125         self.failUnlessEqual(response.status_code, 404)
 126
 127
 128     def test_library_no_key(self):
 129         """
 130         Make sure we get a 403 if we're not logged in
 131         """
 132         library = LibraryFactory.create()
 133
 134         url = '/samples/library/{}/json'.format(library.id)
 135         response = self.client.get(url, apidata)
 136         self.failUnlessEqual(response.status_code, 200)
 137         response = self.client.get(url)
 138         self.failUnlessEqual(response.status_code, 403)
 139
 140     def test_library_rdf(self):
 141         library = LibraryFactory.create()
 142
 143         import RDF
 144         from htsworkflow.util.rdfhelp import get_model, \
 145              dump_model, \
 146              fromTypedNode, \
 147              load_string_into_model, \
 148              rdfNS, \
 149              libraryOntology
 150         model = get_model()
 151
 152         response = self.client.get(library.get_absolute_url())
 153         self.assertEqual(response.status_code, 200)
 154         content = smart_text(response.content)
 155         load_string_into_model(model, 'rdfa', content)
 156
 157         body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 158         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 159
 160         select ?library ?name ?library_id ?gel_cut ?made_by
 161         where {
 162            ?library a libns:library ;
 163                     libns:name ?name ;
 164                     libns:library_id ?library_id ;
 165                     libns:gel_cut ?gel_cut ;
 166                     libns:made_by ?made_by
 167         }"""
 168         query = RDF.SPARQLQuery(body)
 169         for r in query.execute(model):
 170             self.assertEqual(fromTypedNode(r['library_id']),
 171                              library.id)
 172             self.assertEqual(fromTypedNode(r['name']),
 173                              library.name)
 174             self.assertEqual(fromTypedNode(r['gel_cut']),
 175                              library.gel_cut)
 176             self.assertEqual(fromTypedNode(r['made_by']),
 177                              library.made_by)
 178
 179         state = validate_xhtml(content)
 180         if state is not None:
 181             self.assertTrue(state)
 182
 183         # validate a library page.
 184         from htsworkflow.util.rdfhelp import add_default_schemas
 185         from htsworkflow.util.rdfinfer import Infer
 186         add_default_schemas(model)
 187         inference = Infer(model)
 188         errmsgs = list(inference.run_validation())
 189         self.assertEqual(len(errmsgs), 0)
 190
 191     def test_library_index_rdfa(self):
 192         from htsworkflow.util.rdfhelp import \
 193              add_default_schemas, get_model, load_string_into_model, \
 194              dump_model
 195         from htsworkflow.util.rdfinfer import Infer
 196
 197         model = get_model()
 198         add_default_schemas(model)
 199         inference = Infer(model)
 200
 201         response = self.client.get('/library/')
 202         self.assertEqual(response.status_code, 200)
 203         load_string_into_model(model, 'rdfa', smart_text(response.content))
 204
 205         errmsgs = list(inference.run_validation())
 206         self.assertEqual(len(errmsgs), 0)
 207
 208         body =  """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 209         prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
 210
 211         select ?library ?library_id ?name ?species ?species_name
 212         where {
 213            ?library a libns:Library .
 214            OPTIONAL { ?library libns:library_id ?library_id . }
 215            OPTIONAL { ?library libns:species ?species .
 216                       ?species libns:species_name ?species_name . }
 217            OPTIONAL { ?library libns:name ?name . }
 218         }"""
 219         bindings = set(['library', 'library_id', 'name', 'species', 'species_name'])
 220         query = RDF.SPARQLQuery(body)
 221         count = 0
 222         for r in query.execute(model):
 223             count += 1
 224             for name, value in r.items():
 225                 self.assertTrue(name in bindings)
 226                 self.assertTrue(value is not None)
 227
 228         self.assertEqual(count, len(Library.objects.filter(hidden=False)))
 229
 230         state = validate_xhtml(response.content)
 231         if state is not None: self.assertTrue(state)
 232
 233
 234 # The django test runner flushes the database between test suites not cases,
 235 # so to be more compatible with running via nose we flush the database tables
 236 # of interest before creating our sample data.
 237 def create_db(obj):
 238     obj.species_human = Species.objects.get(pk=8)
 239     obj.experiment_rna_seq = ExperimentType.objects.get(pk=4)
 240     obj.affiliation_alice = Affiliation.objects.get(pk=1)
 241     obj.affiliation_bob = Affiliation.objects.get(pk=2)
 242
 243     Library.objects.all().delete()
 244     obj.library_10001 = Library(
 245         id = "10001",
 246         library_name = 'C2C12 named poorly',
 247         library_species = obj.species_human,
 248         experiment_type = obj.experiment_rna_seq,
 249         creation_date = datetime.datetime.now(),
 250         made_for = 'scientist unit 2007',
 251         made_by = 'microfludics system 7321',
 252         stopping_point = '2A',
 253         undiluted_concentration = '5.01',
 254         hidden = False,
 255     )
 256     obj.library_10001.save()
 257     obj.library_10002 = Library(
 258         id = "10002",
 259         library_name = 'Worm named poorly',
 260         library_species = obj.species_human,
 261         experiment_type = obj.experiment_rna_seq,
 262         creation_date = datetime.datetime.now(),
 263         made_for = 'scientist unit 2007',
 264         made_by = 'microfludics system 7321',
 265         stopping_point = '2A',
 266         undiluted_concentration = '5.01',
 267         hidden = False,
 268     )
 269     obj.library_10002.save()
 270
 271 try:
 272     import RDF
 273     HAVE_RDF = True
 274
 275     rdfNS = RDF.NS(b"http://www.w3.org/1999/02/22-rdf-syntax-ns#")
 276     xsdNS = RDF.NS(b"http://www.w3.org/2001/XMLSchema#")
 277     libNS = RDF.NS(b"http://jumpgate.caltech.edu/wiki/LibraryOntology#")
 278
 279     from htsworkflow.util.rdfhelp import dump_model
 280 except ImportError as e:
 281     HAVE_RDF = False
 282
 283
 284 class TestRDFaLibrary(TestCase):
 285
 286     def setUp(self):
 287         self.request = RequestFactory()
 288
 289     def test_parse_rdfa(self):
 290
 291         model = get_rdf_memory_model()
 292         parser = RDF.Parser(name=b'rdfa')
 293
 294         bob = AffiliationFactory.create(name='Bob')
 295
 296         lib_object = LibraryFactory()
 297         lib_object.affiliations.add(bob)
 298         url = '/library/{}/'.format(lib_object.id)
 299         ## request = self.request.get(url)
 300         ## lib_response = library(request)
 301         lib_response = self.client.get(url)
 302         lib_body = smart_str(lib_response.content)
 303         self.failIfEqual(len(lib_body), 0)
 304         with open('/tmp/body.html', 'wt') as outstream:
 305             outstream.write(lib_body)
 306
 307         parser.parse_string_into_model(model,
 308                                        lib_body,
 309                                        'http://localhost'+url)
 310         # help debugging rdf errrors
 311         #with open('/tmp/test.ttl', 'w') as outstream:
 312         #    dump_model(model, outstream)
 313         # http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
 314         self.check_literal_object(model, ['Bob'], p=libNS[b'affiliation'])
 315         self.check_literal_object(model,
 316                                   ['experiment type name'],
 317                                   p=libNS[b'experiment_type'])
 318         self.check_literal_object(model, ['400'], p=libNS[b'gel_cut'])
 319         self.check_literal_object(model,
 320                                   ['microfluidics bot 7321'],
 321                                   p=libNS[b'made_by'])
 322         self.check_literal_object(model,
 323                                   [lib_object.library_name],
 324                                   p=libNS[b'name'])
 325         self.check_literal_object(model,
 326                                   [lib_object.library_species.scientific_name],
 327                                   p=libNS[b'species_name'])
 328
 329
 330     def check_literal_object(self, model, values, s=None, p=None, o=None):
 331         statements = list(model.find_statements(
 332             RDF.Statement(s,p,o)))
 333         self.failUnlessEqual(len(statements), len(values),
 334                         "Couln't find %s %s %s" % (s,p,o))
 335         for s in statements:
 336             self.failUnless(s.object.literal_value['string'] in values)
 337
 338
 339     def check_uri_object(self, model, values, s=None, p=None, o=None):
 340         statements = list(model.find_statements(
 341             RDF.Statement(s,p,o)))
 342         self.failUnlessEqual(len(statements), len(values),
 343                         "Couln't find %s %s %s" % (s,p,o))
 344         for s in statements:
 345             self.failUnless(str(s.object.uri) in values)
 346
 347
 348
 349 def get_rdf_memory_model():
 350     storage = RDF.MemoryStorage()
 351     model = RDF.Model(storage)
 352     return model
 353
 354 def suite():
 355     from unittest import TestSuite, defaultTestLoader
 356     suite = TestSuite()
 357     suite.addTests(defaultTestLoader.loadTestsFromTestCase(LibraryTestCase))
 358     suite.addTests(defaultTestLoader.loadTestsFromTestCase(SampleWebTestCase))
 359     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestRDFaLibrary))
 360     return suite
 361
 362 if __name__ == "__main__":
 363     from unittest import main
 364     main(defaultTest="suite")