def create_test_dataset(owner=None):
from search.mutation import MutationSearch
search = MutationSearch(text_query=test_query)
dataset = UsersMutationsDataset(name='test', data=search, owner=owner)
db.session.add(dataset)
db.session.commit()
return dataset
def user_mutations(self, uri):
filter_manager = SearchViewFilters()
dataset = UsersMutationsDataset.by_uri(uri)
if dataset.owner and dataset.owner != current_user:
current_app.login_manager.unauthorized()
response = make_response(
template('search/dataset.html',
mutation_types=Mutation.types,
results=dataset.data.results,
widgets=make_widgets(filter_manager),
without_mutations=dataset.data.without_mutations,
query=dataset.data.query,
badly_formatted=dataset.data.badly_formatted,
dataset=dataset))
return response
def remove_user_mutations(self, uri):
dataset = UsersMutationsDataset.by_uri(uri)
name = dataset.name
if not dataset.owner or dataset.owner != current_user:
current_app.login_manager.unauthorized()
try:
dataset.remove()
except Exception as e:
message = 'Failed to remove dataset <b>%s</b> (%s).' % (name, uri)
print(message, e)
message += '<br>If the message reappears, please contact us.'
flash(message, category='danger')
raise abort(500)
flash('Successfully removed <b>%s</b> dataset.' % name,
category='success')
return redirect(url_for('ContentManagementSystem:my_datasets'))
def test_init(self):
user = User('user@domain', 'password')
dataset = create_test_dataset(owner=user)
assert user.datasets == [dataset]
public_id = dataset.uri
d = UsersMutationsDataset.query.filter_by(uri=public_id).one()
assert d == dataset
assert UsersMutationsDataset.by_uri(public_id) == dataset
assert dataset.data
assert dataset.query_size == 3
# should be empty as no mutations where imported
assert not dataset.mutations
assert dataset.name == 'test'
assert dataset.life_expectancy < timedelta(days=7)
assert not dataset.is_expired
update(dataset, store_until=utc_now())
db.session.commit()
time.sleep(2)
assert dataset.is_expired
d = UsersMutationsDataset.query.filter_by(is_expired=True).one()
assert d == dataset
u = User.query.filter_by(email='user@domain').one()
assert u.datasets == []
def mutations(self):
"""Render search form and results (if any) for proteins or mutations"""
task_id = request.args.get('task_id', None)
use_celery = current_app.config.get('USE_CELERY', False)
filter_manager = SearchViewFilters()
if request.method == 'POST':
textarea_query = request.form.get('mutations', False)
vcf_file = request.files.get('vcf-file', False)
store_on_server = request.form.get('store_on_server', False)
if not use_celery:
mutation_search = MutationSearch(vcf_file, textarea_query,
filter_manager)
if store_on_server:
name = request.form.get('dataset_name', None)
if not name:
name = 'Custom Dataset'
if current_user.is_authenticated:
user = current_user
else:
user = None
flash(
'To browse uploaded mutations easily in the '
'future, please <a href="/register">register</a> or <a href="login">log in</a>.',
'warning')
dataset = UsersMutationsDataset(
name=name,
data=mutation_search if not use_celery else None,
owner=user)
db.session.add(dataset)
db.session.commit()
if use_celery:
mutation_search = search_task.delay(
# vcf_file is not serializable but list of lines is
vcf_file.readlines() if vcf_file else None,
textarea_query,
filter_manager,
dataset.uri if store_on_server else None)
return redirect(
url_for('SearchView:progress',
task_id=mutation_search.task_id))
elif task_id:
celery_task = celery.AsyncResult(task_id)
if celery_task.status == 'PENDING':
flash(
'This search either expired or does not exist. Please try specifying a new one',
'warning')
return redirect(url_for('SearchView:mutations'))
mutation_search, dataset_uri = celery_task.result
if dataset_uri:
url = url_for('SearchView:user_mutations',
uri=dataset_uri,
_external=True)
flash(
'Your mutations have been saved on the server.'
'<p>You can access the results later using following URL: '
'<a href="' + url + '">' + url + '</a></p>', 'success')
celery_task.forget()
else:
mutation_search = MutationSearch()
response = make_response(
template('search/index.html',
target='mutations',
mutation_types=Mutation.types,
hidden_results_cnt=mutation_search.hidden_results_cnt,
results=mutation_search.results,
widgets=make_widgets(filter_manager),
without_mutations=mutation_search.without_mutations,
query=mutation_search.query,
badly_formatted=mutation_search.badly_formatted))
return response