def add_resource(resource_info, update=True):
if 'trait' in resource_info['data']:
resource_id = hmac_creation('{}:{}:{}'.format(
str(resource_info['type']), str(resource_info['data']['dataset']),
str(resource_info['data']['trait'])))
else:
resource_id = hmac_creation('{}:{}'.format(
str(resource_info['type']), str(resource_info['data']['dataset'])))
if update or not Redis.hexists("resources", resource_id):
Redis.hset("resources", resource_id, json.dumps(resource_info))
return resource_info
def get_resource_id(dataset, trait_id=None):
resource_id = False
if dataset.type == "Publish":
if trait_id:
resource_id = hmac_creation("{}:{}:{}".format(
'dataset-publish', dataset.id, trait_id))
elif dataset.type == "ProbeSet":
resource_id = hmac_creation("{}:{}".format('dataset-probeset',
dataset.id))
elif dataset.type == "Geno":
resource_id = hmac_creation("{}:{}".format('dataset-geno', dataset.id))
return resource_id
def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
assert separator == ":", "Expected a : here"
assert the_signature == hmac.hmac_creation(
the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
def process_traits(unprocessed_traits):
if isinstance(unprocessed_traits, basestring):
unprocessed_traits = unprocessed_traits.split(",")
traits = set()
for trait in unprocessed_traits:
data, _separator, the_hmac = trait.rpartition(':')
data = data.strip()
if g.user_session.logged_in:
assert the_hmac == hmac.hmac_creation(data), "Data tampering?"
traits.add(str(data))
return traits
def create_signed_cookie():
the_uuid = str(uuid.uuid4())
signature = hmac.hmac_creation(the_uuid)
uuid_signed = the_uuid + ":" + signature
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
def generate_corr_json(corr_results,
this_trait,
dataset,
target_dataset,
for_api=False):
results_list = []
for i, trait in enumerate(corr_results):
results_dict = {}
if not for_api:
results_dict[
'checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + hmac.hmac_creation(
'{}:{}'.format(trait.name, trait.dataset.name)) + "'>"
results_dict['index'] = i + 1
results_dict['trait_id'] = "<a href='/show_trait?trait_id=" + str(
trait.name) + "&dataset=" + str(dataset.name) + "'>" + str(
trait.name) + "</a>"
else:
results_dict['trait_id'] = trait.name
if target_dataset.type == "ProbeSet":
results_dict['symbol'] = trait.symbol
results_dict['description'] = trait.description_display
results_dict['location'] = trait.location_repr
results_dict['mean'] = float(trait.mean)
if trait.LRS_score_repr != "N/A":
results_dict['lrs_score'] = "%.1f" % float(
trait.LRS_score_repr)
else:
results_dict['lrs_score'] = "N/A"
results_dict['lrs_location'] = trait.LRS_location_repr
if trait.additive != "":
results_dict['additive'] = "%0.3f" % float(trait.additive)
else:
results_dict['additive'] = "N/A"
if for_api:
results_dict['sample_r'] = "%0.3f" % float(trait.sample_r)
else:
results_dict[
'sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(
dataset.name) + "&dataset_2=" + str(
trait.dataset.name) + "&trait_1=" + str(
this_trait.name) + "&trait_2=" + str(
trait.name) + "'>" + "%0.3f" % float(
trait.sample_r) + "</a>"
results_dict['num_overlap'] = trait.num_overlap
results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
if trait.lit_corr == "" or trait.lit_corr == 0:
results_dict['lit_corr'] = "--"
else:
results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr)
if trait.tissue_corr == "" or trait.tissue_corr == 0:
results_dict['tissue_corr'] = "--"
else:
results_dict['tissue_corr'] = "%0.3f" % float(
trait.tissue_corr)
elif target_dataset.type == "Publish":
results_dict['description'] = trait.description_display
results_dict['authors'] = trait.authors
if trait.pubmed_id:
if for_api:
results_dict['pubmed_id'] = trait.pubmed_id
results_dict['year'] = trait.pubmed_text
else:
results_dict[
'pubmed'] = "<a href='" + trait.pubmed_link + "'> " + trait.pubmed_text + "</a>"
else:
if for_api:
results_dict['pubmed_id'] = "N/A"
results_dict['year'] = "N/A"
else:
results_dict['pubmed'] = "N/A"
results_dict['lrs_score'] = trait.LRS_score_repr
results_dict['lrs_location'] = trait.LRS_location_repr
if trait.additive != "":
results_dict['additive'] = "%0.3f" % float(trait.additive)
else:
results_dict['additive'] = "N/A"
if for_api:
results_dict['sample_r'] = "%0.3f" % trait.sample_r
else:
results_dict[
'sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(
dataset.name) + "&dataset_2=" + str(
trait.dataset.name) + "&trait_1=" + str(
this_trait.name) + "&trait_2=" + str(
trait.name
) + "'>" + "%0.3f" % trait.sample_r + "</a>"
results_dict['num_overlap'] = trait.num_overlap
results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
else:
results_dict['lrs_location'] = trait.LRS_location_repr
if for_api:
results_dict['sample_r'] = "%0.3f" % trait.sample_r
else:
results_dict[
'sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(
dataset.name) + "&dataset_2=" + str(
trait.dataset.name) + "&trait_1=" + str(
this_trait.name) + "&trait_2=" + str(
trait.name) + "'>" + "%0.3f" % float(
trait.sample_r) + "</a>"
results_dict['num_overlap'] = trait.num_overlap
results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
results_list.append(results_dict)
return json.dumps(results_list)
def test_hmac_creation_with_cookie(self):
"""Test hmac creation with a cookie"""
cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce"
uuid_, _, signature = cookie.partition(":")
self.assertEqual(hmac_creation(uuid_), "af4fcf5eace9e7c864ce")
def test_hmac_creation(self):
"""Test hmac creation with a utf-8 string"""
self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
