def test_search_filter_with_analysis_id(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
pixel_set = models.PixelSet.objects.all()[4]
analysis_id = pixel_set.analysis.id
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=8)
data = {
# search by short uuid
'search': str(analysis_id.hex[:7])
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{pixel_set.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(pixel_set.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
def test_species_filter(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
# Create our special ones
species = factories.SpeciesFactory()
strain = factories.StrainFactory(species=species)
n_new_pixel_sets = 2
pixel_sets = factories.PixelSetFactory.create_batch(n_new_pixel_sets)
omics_units = factories.OmicsUnitFactory.create_batch(n_new_pixel_sets,
strain=strain)
for omics_unit, pixel_set in zip(omics_units, pixel_sets):
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=10)
# species filter
data = {
'species': [
species.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response,
'<tr class="pixelset">',
count=n_new_pixel_sets)
def test_filters_with_no_match(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
# Create a new species
species = factories.SpeciesFactory()
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=8)
# filter with no possible result
data = {
'species': [
species.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=0)
self.assertContains(
response,
('<td colspan="8" class="empty">'
'No Pixel Set matches your query'
'</td>'),
count=1,
html=True,
)
def test_search_filter_with_omics_unit_reference(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
pixel_set = models.PixelSet.objects.all()[4]
reference = pixel_set.pixels.get().omics_unit.reference.identifier
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=8)
# filter with Omics Unit reference identifier search
data = {'search': reference}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=1)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{pixel_set.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(pixel_set.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
def test_omics_unit_types_filter(self):
# We generate one pixel per pixelset so that half of Pixel Sets
# contains pixels with 'mRNA' omics unit type and the other half
# 'protein' omics unit type
n_pixel_sets = 8
make_development_fixtures(n_pixel_sets=n_pixel_sets,
n_pixels_per_set=1)
# no filter
response = self.client.get(self.url)
self.assertContains(response,
'<tr class="pixelset">',
count=n_pixel_sets)
# omics_unit_types filter
omics_unit_type = models.OmicsUnitType.objects.first()
data = {
'omics_unit_types': [
omics_unit_type.id,
]
}
response = self.client.get(self.url, data)
self.assertContains(response,
'<tr class="pixelset">',
count=(n_pixel_sets // 2))
def test_unexpected_filter_value(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=8)
self.assertNotContains(
response,
'<small class="error">\'fakeid\' is not a valid UUID.</small>',
html=True,
)
# odd filter query
data = {
'species': [
'fakeid',
],
}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=8)
self.assertContains(
response,
('<small class="error">'
''fakeid' is not a valid UUID.'
'</small>'),
html=True,
)
def test_renders_pixelset_list(self):
make_development_fixtures(n_pixel_sets=12)
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=10)
self.assertContains(
response,
'<button type="submit" class="button">',
)
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 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_search_is_case_insensitive(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
first_pixel_set = models.PixelSet.objects.all().first()
second_pixel_set = models.PixelSet.objects.all().last()
# Add custom descriptions written in Klingon so that we are pretty
# sure nothing will match our query 🤓
#
# Lorem ipsum source:
# http://shooshee.tumblr.com/post/212964026/klingon-lorem-ipsum
first_analysis = factories.AnalysisFactory(description=(
'Qapla. Dah tlhingan hol mu ghom a dalegh. Qawhaqvam '
'chenmohlu di wiqipe diya ohvad ponglu. Ach jinmolvamvad '
'Saghbe law tlhingan hol, dis, oh mevmohlu.'))
first_pixel_set.analysis = first_analysis
first_pixel_set.save()
experiment = factories.ExperimentFactory(description=(
'Qapla. Dah tlhingan hol mu ghom a dalegh. Qawhaqvam '
'chenmohlu di wiqipe diya ohvad ponglu. Ach jinmolvamvad '
'Saghbe law tlhingan hol, dis, oh mevmohlu.'))
second_analysis = factories.AnalysisFactory(experiments=[
experiment,
])
second_pixel_set.analysis = second_analysis
second_pixel_set.save()
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=8)
# filter with keyword search
data = {'search': 'JINMOLVAMVAD'}
response = self.client.get(self.url, data)
self.assertContains(response, '<tr class="pixelset">', count=2)
def test_renders_completion_dates(self):
make_development_fixtures(n_pixel_sets=1)
response = self.client.get(self.url)
expected = ('<span class="completed-at">'
'Completion date: {}'
'</span>')
pixelset = models.PixelSet.objects.get()
self.assertContains(response,
expected.format(
date_filter(pixelset.analysis.completed_at)),
count=1,
html=True)
self.assertContains(
response,
expected.format(
date_filter(pixelset.analysis.experiments.get().completed_at)),
count=1,
html=True)
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_search_filter_with_keywords(self):
# Create 8 pixelset
make_development_fixtures(n_pixel_sets=8, n_pixels_per_set=1)
first_pixel_set = models.PixelSet.objects.all().first()
second_pixel_set = models.PixelSet.objects.all().last()
# Add custom descriptions written in Klingon so that we are pretty
# sure nothing will match our query 🤓
#
# Lorem ipsum source:
# http://shooshee.tumblr.com/post/212964026/klingon-lorem-ipsum
first_analysis = factories.AnalysisFactory(description=(
'Qapla. Dah tlhingan hol mu ghom a dalegh. Qawhaqvam '
'chenmohlu di wiqipe diya ohvad ponglu. Ach jinmolvamvad '
'Saghbe law tlhingan hol, dis, oh mevmohlu.'))
first_pixel_set.analysis = first_analysis
first_pixel_set.save()
experiment = factories.ExperimentFactory(description=(
'Qapla. Dah tlhingan hol mu ghom a dalegh. Qawhaqvam '
'chenmohlu di wiqipe diya ohvad ponglu. Ach jinmolvamvad '
'Saghbe law tlhingan hol, dis, oh mevmohlu.'))
second_analysis = factories.AnalysisFactory(experiments=[
experiment,
])
second_pixel_set.analysis = second_analysis
second_pixel_set.save()
# no filter
response = self.client.get(self.url)
self.assertContains(response, '<tr class="pixelset">', count=8)
# filter with keyword search
data = {'search': 'jinmolvamvad'}
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_pixel_set.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(first_pixel_set.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
self.assertContains(
response,
('<td class="filename">'
'<a'
f' href="{second_pixel_set.get_absolute_url()}"'
' title="More information about this Pixel Set"'
'>'
'<!-- Pixel Set file name -->'
f'{filename(second_pixel_set.pixels_file.name)}'
'</a>'
'</td>'),
count=1,
html=True,
)
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,
)