def test_all_filters(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
# Create a special Pixel Set which will match all filters
species = factories.SpeciesFactory()
strain = factories.StrainFactory(species=species)
omics_unit_type = factories.OmicsUnitTypeFactory()
omics_unit = factories.OmicsUnitFactory(
strain=strain,
type=omics_unit_type,
)
omics_area = factories.OmicsAreaFactory()
experiment = factories.ExperimentFactory(omics_area=omics_area)
experiment_tag = 'candida'
experiment.tags = experiment_tag
experiment.save()
analysis = factories.AnalysisFactory(experiments=[
experiment,
])
pixel_set = factories.PixelSetFactory(analysis=analysis)
factories.PixelFactory(
omics_unit=omics_unit,
pixel_set=pixel_set,
)
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=9)
# all filters
tag = models.Tag.objects.get(name=experiment_tag)
data = {
'species': [
species.id,
],
'omics_unit_types': [
omics_unit_type.id,
],
'omics_area': [
omics_area.id,
],
'tags': [
tag.id,
],
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
def setUp(self):
self.user = factories.PixelerFactory(
is_active=True,
is_staff=True,
is_superuser=True,
)
self.client.login(
username=self.user.username,
password=factories.PIXELER_PASSWORD,
)
self.pixel_set = factories.PixelSetFactory()
self.pixels = factories.PixelFactory.create_batch(
2, pixel_set=self.pixel_set)
self.url = self.pixel_set.get_absolute_url()
def setUp(self):
self.user = factories.PixelerFactory(
is_active=True,
is_staff=True,
is_superuser=True,
)
self.client.login(
username=self.user.username,
password=factories.PIXELER_PASSWORD,
)
self.pixel_set = factories.PixelSetFactory()
self.pixel_set.analysis.experiments.add(factories.ExperimentFactory())
factories.PixelFactory.create_batch(10, pixel_set=self.pixel_set)
self.url = self.pixel_set.get_export_pixels_url()
def test_pixels_limit(self):
response = self.client.get(self.url)
self.assertContains(response,
'<tr class="pixel">',
count=self.n_pixels)
# Generate a new pixelset with limit+ pixels
n_pixels = 101
pixel_set = factories.PixelSetFactory()
factories.PixelFactory.create_batch(n_pixels, pixel_set=pixel_set)
response = self.client.get(pixel_set.get_absolute_url())
self.assertContains(response,
'<tr class="pixel">',
count=PixelSetDetailView.pixels_limit)
self.assertNotContains(response,
'Download a CSV file with the selected Pixels')
def setUp(self):
self.user = factories.PixelerFactory(
is_active=True,
is_staff=True,
is_superuser=True,
)
self.client.login(
username=self.user.username,
password=factories.PIXELER_PASSWORD,
)
self.pixel_set = factories.PixelSetFactory()
self.pixels = factories.PixelFactory.create_batch(
2, pixel_set=self.pixel_set)
self.url = reverse('explorer:pixelset_detail_quality_scores',
kwargs={'pk': str(self.pixel_set.id)})
def setUp(self):
self.user = factories.PixelerFactory(
is_active=True,
is_staff=True,
is_superuser=True,
)
self.client.login(
username=self.user.username,
password=factories.PIXELER_PASSWORD,
)
self.pixel_set = factories.PixelSetFactory()
self.pixels = factories.PixelFactory.create_batch(
2,
pixel_set=self.pixel_set
)
self.url = reverse('explorer:pixelset_selection_cumulative_values')
def test_tags_filter(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
omics_area = factories.OmicsAreaFactory()
experiment = factories.ExperimentFactory(omics_area=omics_area)
experiment_tag = 'candida'
experiment.tags = experiment_tag
experiment.save()
analysis = factories.AnalysisFactory(experiments=[
experiment,
])
analysis_tag = 'msms/time'
analysis.tags = analysis_tag
analysis.save()
factories.PixelSetFactory(analysis=analysis)
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=9)
# tags filter
tag = models.Tag.objects.get(name=experiment_tag)
data = {
'tags': [
tag.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
tag = models.Tag.objects.get(name=analysis_tag)
data = {
'tags': [
tag.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
def test_omics_areas_filter(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
omics_area = factories.OmicsAreaFactory()
experiment = factories.ExperimentFactory(omics_area=omics_area)
analysis = factories.AnalysisFactory(experiments=[
experiment,
])
factories.PixelSetFactory(analysis=analysis)
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=9)
# omics_areas filter
data = {
'omics_areas': [
omics_area.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
def test_tags_tree_filter(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
# Create two pixelsets with tags
omics_area = factories.OmicsAreaFactory()
experiment = factories.ExperimentFactory(omics_area=omics_area)
first_analysis = factories.AnalysisFactory(experiments=[
experiment,
])
first_analysis_tags = 'candida/glabrata/cbs138'
first_analysis.tags = first_analysis_tags
first_analysis.save()
first_pixelset = factories.PixelSetFactory(analysis=first_analysis)
second_analysis = factories.AnalysisFactory(experiments=[
experiment,
])
second_analysis_tags = 'candida'
second_analysis.tags = second_analysis_tags
second_analysis.save()
second_pixelset = factories.PixelSetFactory(analysis=second_analysis)
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=10)
# tags filter
tag = models.Tag.objects.get(name=first_analysis_tags)
data = {
'tags': [
tag.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{first_pixelset.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(first_pixelset.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
tag = models.Tag.objects.get(name=second_analysis_tags)
data = {
'tags': [
tag.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=2)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{first_pixelset.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(first_pixelset.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{second_pixelset.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(second_pixelset.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
def test_omics_areas_tree_filter(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
# Create a parent omics area and link it to a Pixel Set
parent_omics_area = factories.OmicsAreaFactory()
first_experiment = factories.ExperimentFactory(
omics_area=parent_omics_area)
first_analysis = factories.AnalysisFactory(experiments=[
first_experiment,
])
first_pixelset = factories.PixelSetFactory(analysis=first_analysis)
# Create a child omics are and link it to a Pixel Set
child_omics_area = factories.OmicsAreaFactory(parent=parent_omics_area)
second_experiment = factories.ExperimentFactory(
omics_area=child_omics_area)
second_analysis = factories.AnalysisFactory(experiments=[
second_experiment,
])
second_pixelset = factories.PixelSetFactory(analysis=second_analysis)
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=10)
# omics_areas filter
data = {
'omics_areas': [
child_omics_area.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{second_pixelset.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(second_pixelset.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
data = {
'omics_areas': [
parent_omics_area.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=2)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{first_pixelset.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(first_pixelset.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{second_pixelset.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(second_pixelset.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)