def from_http_request(args):
"""Returns list of Tag instances.
"""
tag_names = get_param_as_list(args, 'tags')
tags = []
for name in tag_names:
# If the name is not an empty string or just whitespace.
if bool(name.strip()):
tags.append(get_or_create(Tag, name=name))
return tags
def check_combination():
"""Checks if a combination of accession, dataset, and selected samples has
already been processed.
"""
try:
try:
tag = get_param_as_list(request.args, 'tags')[0]
except IndexError as e:
raise HttpRequestArgumentsException('Make sure you have exactly one tag.', e)
accession = request.args.get('dataset')
controls = get_param_as_list(request.args, 'A_cols')
conditions = get_param_as_list(request.args, 'B_cols')
if len(controls) == 0:
raise HttpRequestArgumentsException('Please select 2 or more control samples.')
if len(conditions) == 0:
raise HttpRequestArgumentsException('Please select 2 or more condition samples.')
soft_files = database.get_soft_files_by_accession(accession)
matching_ids = []
for sf in soft_files:
tag_matches = _tag_matches(sf.gene_signature, tag)
controls_match = _samples_match(controls, sf.samples, True)
conditions_match = _samples_match(conditions, sf.samples, False)
if tag_matches or controls_match or conditions_match:
matching_ids.append(sf.gene_signature.extraction_id)
if len(matching_ids) > 0:
links = []
for id_ in matching_ids:
link = '%s%s/%s' % (config.SERVER_URL,config.RESULTS_URL, id_)
links.append(link)
return jsonify({
'preexisting': True,
'links': links
})
else:
return jsonify({
'preexisting': False
})
except AttributeError as e:
raise HttpRequestArgumentsException('Illegal arguments. Make sure you have only input one tag.', e)
def check_combination():
"""Checks if a combination of accession, dataset, and selected samples has
already been processed.
"""
try:
try:
tag = get_param_as_list(request.args, 'tags')[0]
except IndexError as e:
raise HttpRequestArgumentsException(
'Make sure you have exactly one tag.', e)
accession = request.args.get('dataset')
controls = get_param_as_list(request.args, 'A_cols')
conditions = get_param_as_list(request.args, 'B_cols')
if len(controls) == 0:
raise HttpRequestArgumentsException(
'Please select 2 or more control samples.')
if len(conditions) == 0:
raise HttpRequestArgumentsException(
'Please select 2 or more condition samples.')
soft_files = database.get_soft_files_by_accession(accession)
matching_ids = []
for sf in soft_files:
tag_matches = _tag_matches(sf.gene_signature, tag)
controls_match = _samples_match(controls, sf.samples, True)
conditions_match = _samples_match(conditions, sf.samples, False)
if tag_matches or controls_match or conditions_match:
matching_ids.append(sf.gene_signature.extraction_id)
if len(matching_ids) > 0:
links = []
for id_ in matching_ids:
link = '%s%s/%s' % (config.SERVER_URL, config.RESULTS_URL, id_)
links.append(link)
return jsonify({'preexisting': True, 'links': links})
else:
return jsonify({'preexisting': False})
except AttributeError as e:
raise HttpRequestArgumentsException(
'Illegal arguments. Make sure you have only input one tag.', e)
def _user_is_authenticated_for_tag(args, is_authenticated):
"""Returns False if a tag is restricted and the user is not authenticated,
True otherwise.
"""
tag_names = get_param_as_list(args, 'tags')
for tag_name in tag_names:
tag = database.get_tag_by_name(tag_name)
# The tag may not exist yet. If so, we can safely assume it is not
# restricted.
if tag and tag.is_restricted and not is_authenticated:
return False
return True
def _user_is_authenticated_for_tag(args, is_authenticated):
"""Returns False if a tag is restricted and the user is not authenticated,
True otherwise.
"""
tag_names = get_param_as_list(args, 'tags')
for tag_name in tag_names:
tag = database.get_tag_by_name(tag_name)
# The tag may not exist yet. If so, we can safely assume it is not
# restricted.
if tag and tag.is_restricted and not is_authenticated:
return False
return True
def edit_result():
"""Edits gene signature, removing fields that are empty and adding new ones.
"""
extraction_id = request.form.get('extraction_id')
gene_signature = database.get_gene_signature(extraction_id)
for opt_meta in gene_signature.optional_metadata:
value = request.form.get(opt_meta.name)
if not value:
database.delete_object(opt_meta)
continue
opt_meta.value = value
database.update_object(opt_meta)
# Generate a new optional metadata field is requested.
new_meta_name = request.form.get('new_metadata_name')
new_meta_value = request.form.get('new_metadata_value')
if new_meta_name and new_meta_value:
new_opt_meta = OptionalMetadata(new_meta_name, new_meta_value)
gene_signature.optional_metadata.append(new_opt_meta)
database.update_object(gene_signature)
# Update existing tags.
tag_names = request_utils.get_param_as_list(request.form, 'tags')
for tag in gene_signature.tags:
if tag.name not in tag_names:
database.delete_object(tag)
else:
tag_names.remove(tag.name)
database.update_object(gene_signature)
# Create any new tags. Note that any leftover tags are new ones.
if len(tag_names) > 0:
for tag_name in tag_names:
tag = Tag(tag_name)
gene_signature.tags.append(tag)
database.update_object(gene_signature)
return redirect(
url_for('results_page.view_result', extraction_id=extraction_id))
def edit_result():
"""Edits gene signature, removing fields that are empty and adding new ones.
"""
extraction_id = request.form.get('extraction_id')
gene_signature = database.get_gene_signature(extraction_id)
for opt_meta in gene_signature.optional_metadata:
value = request.form.get(opt_meta.name)
if not value:
database.delete_object(opt_meta)
continue
opt_meta.value = value
database.update_object(opt_meta)
# Generate a new optional metadata field is requested.
new_meta_name = request.form.get('new_metadata_name')
new_meta_value = request.form.get('new_metadata_value')
if new_meta_name and new_meta_value:
new_opt_meta = OptionalMetadata(new_meta_name, new_meta_value)
gene_signature.optional_metadata.append(new_opt_meta)
database.update_object(gene_signature)
# Update existing tags.
tag_names = request_utils.get_param_as_list(request.form, 'tags')
for tag in gene_signature.tags:
if tag.name not in tag_names:
database.delete_object(tag)
else:
tag_names.remove(tag.name)
database.update_object(gene_signature)
# Create any new tags. Note that any leftover tags are new ones.
if len(tag_names) > 0:
for tag_name in tag_names:
tag = Tag(tag_name)
gene_signature.tags.append(tag)
database.update_object(gene_signature)
return redirect(url_for('results_page.view_result',
extraction_id=extraction_id))
def from_geo(args):
"""Constructs a SoftFile
"""
accession = args['dataset']
if not file_manager.file_exists(accession):
file_manager.download(accession)
dataset = database.get_geo_dataset(accession)
if not dataset:
platform = args['platform']
if platform.index('GPL') == 0:
platform = platform[3:]
title = args.get('title')
summary = args.get('summary')
if not title or not summary:
title, summary = eutils.get_title_and_summary(accession)
print('Fetched title and summary from EUtils API: %s, %s' %
(title, summary))
dataset = GeoDataset(accession=accession,
platform=platform,
organism=args['organism'],
title=title,
summary=summary)
else:
print('Dataset %s already exists!' % (accession))
a_cols = get_param_as_list(args, 'A_cols')
b_cols = get_param_as_list(args, 'B_cols')
# Use get_or_create to track GSMs. We don't do this for custom files.
control = [
database.get_or_create(SoftFileSample, name=sample, is_control=True)
for sample in a_cols
]
experimental = [
database.get_or_create(SoftFileSample, name=sample, is_control=False)
for sample in b_cols
]
samples = control + experimental
genes, a_vals, b_vals, selections, stats = parser.parse(
accession, True, dataset.platform, samples)
if 'normalize' not in args or args['normalize'] == 'True':
normalize = True
else:
normalize = False
genes, a_vals, b_vals = cleaner.clean(genes, a_vals, b_vals, normalize)
text_file = file_manager.write(accession, dataset.platform, normalize,
genes, a_vals, b_vals, samples, selections,
stats)
return SoftFile(samples,
dataset,
text_file,
genes,
a_vals,
b_vals,
stats=stats,
normalize=normalize)
def from_geo(args):
"""Constructs a SoftFile
"""
accession = args['dataset']
if not file_manager.file_exists(accession):
file_manager.download(accession)
dataset = database.get_geo_dataset(accession)
if not dataset:
platform = args['platform']
if platform.index('GPL') == 0:
platform = platform[3:]
title = args.get('title')
summary = args.get('summary')
if not title or not summary:
title, summary = eutils.get_title_and_summary(accession)
print('Fetched title and summary from EUtils API: %s, %s' % (title, summary))
dataset = GeoDataset(
accession=accession,
platform=platform,
organism=args['organism'],
title=title,
summary=summary
)
else:
print 'Dataset %s already exists!' % accession
a_cols = get_param_as_list(args, 'A_cols')
b_cols = get_param_as_list(args, 'B_cols')
# Use get_or_create to track GSMs. We don't do this for custom files.
control = [database.get_or_create(SoftFileSample,
name=sample,
is_control=True) for sample in a_cols]
experimental = [database.get_or_create(SoftFileSample,
name=sample,
is_control=False) for sample in b_cols]
samples = control + experimental
genes, a_vals, b_vals, selections, stats = parser.parse(accession,
True,
dataset.platform,
samples)
if 'normalize' not in args or args['normalize'] == 'True':
normalize = True
else:
normalize = False
genes, a_vals, b_vals = cleaner.clean(genes, a_vals, b_vals, normalize)
text_file = file_manager.write(accession, dataset.platform, normalize,
genes, a_vals, b_vals, samples, selections,
stats)
return SoftFile(
samples, dataset, text_file,
genes, a_vals, b_vals,
stats=stats, normalize=normalize
)
def test_with_brackets(self):
with app.test_request_context('/fake_endpoint?p[]=foo&p[]=bar', method='GET'):
x = get_param_as_list(request.args, 'p')
self.assertTrue(len(x), 2)
self.assertTrue(x[0], 'foo')
self.assertTrue(x[1], 'bar')