def functional_table():
form = FunctionClassFilterForm()
form.function_class.choices = [('cog', 'Cog'),
('pfam', 'Pfam'),
('tigrfam', 'TigrFam'),
('all', 'All')
]
form.select_sample_groups.choices = [(sample_set.name, sample_set.name) for sample_set in SampleSet.query.all()]
type_identifiers = []
if form.validate_on_submit():
function_class = form.function_class.data
if function_class == 'all':
function_class = None
limit = form.limit.data
if limit == 'all':
limit = None
else:
limit = int(limit)
filter_alternative = form.filter_alternative.data
if filter_alternative == 'filter_with_type_identifiers':
for type_identifier in form.type_identifiers.entries:
if type_identifier.data != '':
type_identifiers.append(type_identifier.data)
elif filter_alternative == 'filter_with_search':
search_string = form.search_annotations
if search_string.data != '':
q = _search_query(search_string.data)
type_identifiers = [a.type_identifier for a in q.all()]
sample_sets = form.select_sample_groups.data
if len(sample_sets) > 0:
samples = [sample.scilifelab_code for sample in Sample.all_from_sample_sets(sample_sets)]
else:
samples = None
download_action = False
if form.submit_download.data:
download_action = True
download_select = form.download_select.data
else:
function_class=None
limit=20
samples = None
download_action = False
if len(form.type_identifiers) == 0:
form.type_identifiers.append_entry()
if type_identifiers == []:
type_identifiers = None
samples, table = Annotation.rpkm_table(limit=limit, samples=samples, function_class=function_class, type_identifiers=type_identifiers)
samples = sorted(samples, key=lambda x: x.scilifelab_code)
sample_scilifelab_codes = [sample.scilifelab_code for sample in samples]
if download_action:
if download_select == 'Gene List':
# Fetch all contributing genes for all the annotations in the table
annotation_ids = [annotation.id for annotation, sample in table.items()]
genes_per_annotation = Annotation.genes_per_annotation(annotation_ids)
csv_output = '\n'.join(
[','.join([gene.name, annotation.type_identifier]) \
for gene, annotation in genes_per_annotation])
r = make_response(csv_output)
r.headers["Content-Disposition"] = "attachment; filename=gene_list.csv"
r.headers["Content-Type"] = "text/csv"
return r
return render_template('functional_table.html',
table=table,
samples=samples,
sample_scilifelab_codes = sample_scilifelab_codes,
form=form
)
def test_sample_sampleset(self):
#Test that sample and sample set references each other properly
sample_set = SampleSet("first_sampleset")
sample1 = Sample("P1993_101", sample_set, None)
self.session.add(sample1)
self.session.add(sample_set)
# Sample sets relations are created
assert Sample.query.filter_by(scilifelab_code='P1993_101').first().sample_set is sample_set
sample_set2 = SampleSet("second_sampleset")
sample2 = Sample("P1993_102", sample_set2, None)
sample3 = Sample("P1993_103", sample_set, None)
self.session.add(sample2)
self.session.add(sample3)
self.session.commit()
# Sample2 should have sample set 2
assert Sample.query.filter_by(scilifelab_code='P1993_102').first().sample_set is sample_set2
# There should be 2 sample sets and 3 samples in the db
assert len(SampleSet.query.all()) == 2
assert len(Sample.query.all()) == 3
# The reverse relationship for sample set 2 should have sample1 and sample3
assert len(sample_set.samples) == 2
assert sample2 not in sample_set.samples
assert sample1 in sample_set.samples
assert sample3 in sample_set.samples
assert len(Sample.all_from_sample_sets(['first_sampleset'])) == 2
assert sample1 in Sample.all_from_sample_sets(['first_sampleset'])
assert sample3 in Sample.all_from_sample_sets(['first_sampleset'])
assert sample2 not in Sample.all_from_sample_sets(['first_sampleset'])
assert len(Sample.all_from_sample_sets(['second_sampleset'])) == 1
assert sample1 not in Sample.all_from_sample_sets(['second_sampleset'])
assert sample3 not in Sample.all_from_sample_sets(['second_sampleset'])
assert sample2 in Sample.all_from_sample_sets(['second_sampleset'])
assert len(Sample.all_from_sample_sets(['second_sampleset', 'first_sampleset'])) == 3
assert sample1 in Sample.all_from_sample_sets(['second_sampleset', 'first_sampleset'])
assert sample3 in Sample.all_from_sample_sets(['second_sampleset', 'first_sampleset'])
assert sample2 in Sample.all_from_sample_sets(['second_sampleset', 'first_sampleset'])
