def test_save_with_same_reference_omics_units(self):
# Create two OmicsUnits with the same identifier but for different
# strains/types
identifier = 'CAGL0B00990g'
OmicsUnitFactory(reference=EntryFactory(identifier=identifier),
strain=StrainFactory(),
type=OmicsUnitTypeFactory())
OmicsUnitFactory(reference=EntryFactory(identifier=identifier),
strain=self.strain,
type=self.omics_unit_type)
parser = PixelSetParser(
Path('apps/submission/fixtures/dataset-0002/data.txt'),
description=self.description,
analysis=self.analysis,
omics_unit_type=self.omics_unit_type,
strain=self.strain,
)
parser.parse()
self._load_cgd_entries()
self.assertEqual(Pixel.objects.count(), 0)
parser.save()
# Even if we've created two OmicsUnits with the same reference
# identifier, only the pixel corresponding to the OmicsUnit with the
# relevant strain & OmicsUnitType will be imported. Hence, we expect
# to have created 7 pixels and not 8, see:
# - https://github.com/Candihub/pixel/pull/292
# - https://github.com/Candihub/pixel/pull/296
self.assertEqual(Pixel.objects.count(), 7)
def setUp(self):
species = models.Species.objects.create(
name='Saccharomyces cerevisiae',
reference=EntryFactory(),
description='lorem ipsum',
)
self.strain = models.Strain.objects.create(
name='S288c / XJ24-24a',
species=species,
)
self.reference = EntryFactory()
self.type = models.OmicsUnitType.objects.create(name='Promoter', )
def test_fills_rows_correctly(self):
entity = EntryFactory.create()
pixel_sets = factories.PixelSetFactory.create_batch(2)
pixel_1 = factories.PixelFactory.create(omics_unit__reference=entity,
pixel_set=pixel_sets[0])
pixel_2 = factories.PixelFactory.create(omics_unit__reference=entity,
pixel_set=pixel_sets[1])
pixel_set_ids = [pixel_set.id for pixel_set in pixel_sets]
expected_row = """
<tr>
<th>0</th>
<td><a href="{url}">{identifier}</a></td>
<td>{description}</td>
<td>{value_1}</td>
<td>{quality_score_1}</td>
<td>{value_2}</td>
<td>{quality_score_2}</td>
</tr>
""".format(
url=entity.url,
identifier=entity.identifier,
description=entity.description,
value_1=pixel_1.value,
quality_score_1=pixel_1.quality_score,
value_2=pixel_2.value,
quality_score_2=pixel_2.quality_score,
)
html = export_pixelsets_as_html(pixel_set_ids=pixel_set_ids)
self.assertInHTML(expected_row, html)
self.assertNotIn('<span class="highlight">', html)
def setUp(self):
self.species_name = 'Saccharomyces cerevisiae'
self.species_reference = EntryFactory()
self.species_description = 'lorem ipsum'
self.species = models.Species.objects.create(
name=self.species_name,
reference=self.species_reference,
description=self.species_description)
def setUp(self):
# OmicsUnit
species = models.Species.objects.create(
name='Saccharomyces cerevisiae',
reference=EntryFactory(),
description='lorem ipsum',
)
strain = models.Strain.objects.create(
name='S288c / XJ24-24a',
species=species,
)
reference = EntryFactory()
type = models.OmicsUnitType.objects.create(name='Promoter')
self.omics_unit = models.OmicsUnit.objects.create(
reference=reference,
strain=strain,
type=type,
)
# Analysis
omics_area = models.OmicsArea.objects.create(name='RNAseq')
experiment = models.Experiment.objects.create(
omics_area=omics_area,
completed_at=datetime.date(1980, 10, 14),
released_at=datetime.date(1980, 10, 14),
)
pixeler = models.Pixeler.objects.create(username='******',
email='*****@*****.**',
password='******')
self.analysis = models.Analysis.objects.create(
pixeler=pixeler,
completed_at=datetime.date(1980, 10, 14),
)
self.analysis.secondary_data.name = (
factories.SECONDARY_DATA_DEFAULT_PATH)
self.analysis.save()
self.analysis.experiments.add(experiment)
# Pixel set
self.pixel_set = factories.PixelSetFactory(
analysis=self.analysis,
pixels_file__from_path=factories.PIXELS_DEFAULT_PATH,
)
def test_model_representation(self):
name = 'Saccharomyces cerevisiae'
reference = EntryFactory()
species = models.Species.objects.create(
name=name,
reference=reference,
)
self.assertEqual(str(species), name)
def test_can_add_entries_to_experiment(self):
experiment = models.Experiment.objects.create(
description='lorem ipsum',
omics_area=self.omics_area,
completed_at=datetime.date(1980, 10, 14),
released_at=datetime.date(1980, 10, 14),
)
entries = [EntryFactory() for e in range(2)]
experiment.entries.add(*entries)
self.assertEqual(experiment.entries.count(), len(entries))
def test_can_create_species_without_description(self):
name = 'Saccharomyces cerevisiae'
reference = EntryFactory()
qs = models.Species.objects.all()
self.assertEqual(qs.count(), 0)
species = models.Species.objects.create(
name=name,
reference=reference,
)
self.assertEqual(species.name, name)
self.assertEqual(species.reference.id, reference.id)
self.assertEqual(qs.count(), 1)
def test_can_create_species(self):
name = 'Saccharomyces cerevisiae'
reference = EntryFactory()
description = 'lorem ipsum'
qs = models.Species.objects.all()
self.assertEqual(qs.count(), 0)
species = models.Species.objects.create(
name=name,
reference=reference,
description=description,
)
self.assertEqual(species.name, name)
self.assertEqual(species.reference.id, reference.id)
self.assertEqual(species.description, description)
self.assertEqual(qs.count(), 1)
def _create_pixel_from_set(self, pixelset):
entry = EntryFactory(
identifier='CAGL0K09834g',
description=(
'Ortholog(s) have role in response to salt stress and '
'cytoplasm localization'),
url=('http://www.candidagenome.org/cgi-bin/locus.pl?dbid=/'
'CAL0134577'),
repository=Repository.objects.get(name='CGD'))
omics_unit = OmicsUnitFactory(
reference=entry,
strain=self.strain,
type=self.omics_unit_type,
)
return PixelFactory(
value=4.2,
quality_score=0.8,
omics_unit=omics_unit,
pixel_set=pixelset,
)
def test_can_create_strain(self):
name = 'S288c / XJ24-24a'
description = 'lorem ipsum'
reference = EntryFactory()
qs = models.Strain.objects.all()
self.assertEqual(qs.count(), 0)
strain = models.Strain.objects.create(
name=name,
description=description,
species=self.species,
reference=reference,
)
self.assertEqual(strain.name, name)
self.assertEqual(strain.description, description)
self.assertEqual(strain.species.id, self.species.id)
self.assertEqual(strain.reference.id, reference.id)
self.assertEqual(qs.count(), 1)