def login(*args, **kwargs):
"""
Prompt user for login information (domain/email/password).
Domain, email and password are used to get the user's API key.
Always updates the stored credentials file.
"""
if args and args[0].api_key:
# Handle command-line arguments if provided.
solvebio.login(api_key=args[0].api_key)
elif kwargs:
# Run the global login() if kwargs are provided
# or local credentials are found.
solvebio.login(**kwargs)
else:
interactive_login()
# Print information about the current user
user = client.whoami()
if user:
print_user(user)
save_credentials(user['email'].lower(), solvebio.api_key)
_print_msg('Updated local credentials.')
return True
else:
_print_msg('Invalid credentials. You may not be logged-in.')
return False
def login(*args, **kwargs):
"""
Prompt user for login information (domain/email/password).
Domain, email and password are used to get the user's API key.
Always updates the stored credentials file.
"""
if args and args[0].api_key:
# Handle command-line arguments if provided.
solvebio.login(api_key=args[0].api_key)
elif kwargs:
# Run the global login() if kwargs are provided
# or local credentials are found.
solvebio.login(**kwargs)
else:
interactive_login()
# Print information about the current user
user = client.whoami()
if user:
print_user(user)
save_credentials(user['email'].lower(), solvebio.api_key)
_print_msg('Updated local credentials.')
return True
else:
_print_msg('Invalid credentials. You may not be logged-in.')
return False
def main():
if len(sys.argv) < 3:
print('Usage: {} <vault path> <local path>'.format(sys.argv[0]))
sys.exit(1)
solvebio.login()
download_vault_folder(sys.argv[1], sys.argv[2], dry_run=True)
def main():
if len(sys.argv) < 3:
print('Usage: {} <vault path> <local path>'.format(sys.argv[0]))
sys.exit(1)
solvebio.login()
download_vault_folder(sys.argv[1], sys.argv[2], dry_run=True)
def login_and_save_credentials(*args, **kwargs):
"""
Domain, email and password are used to get the user's API key.
"""
if args and args[0].api_key:
# Handle command-line arguments if provided.
logged_in = solvebio.login(api_key=args[0].api_key,
api_host=solvebio.api_host)
elif args and args[0].access_token:
# Handle command-line arguments if provided.
logged_in = solvebio.login(access_token=args[0].access_token,
api_host=solvebio.api_host)
elif solvebio.login(**kwargs):
logged_in = True
else:
logged_in = False
if logged_in:
# Print information about the current user
user = client.whoami()
print_user(user)
save_credentials(
user['email'].lower(), client._auth.token,
client._auth.token_type, solvebio.api_host)
print('Updated local credentials file.')
else:
print('You are not logged-in. Visit '
'https://docs.solvebio.com/#authentication to get started.')
def main(argv=sys.argv[1:]):
""" Main entry point for SolveBio CLI """
parser = SolveArgumentParser()
args = parser.parse_solvebio_args(argv)
solvebio.login(api_host=args.api_host or solvebio.api_host,
api_key=args.api_key or solvebio.api_key,
access_token=args.access_token or solvebio.access_token)
return args.func(args)
def test_init_login(self):
from solvebio import login
from solvebio.client import client
_auth = client._auth
client._auth = None
login(api_key="TEST_KEY")
self.assertEqual(client._auth.token, "TEST_KEY")
# Reset the key
client._auth = _auth
def import_file(args):
"""
Given a dataset and a local path, upload and import the file(s).
Command arguments (args):
* create_dataset
* template_id
* genome_build
* follow (default: False)
* auto_approve (default: False)
* dataset
* file (list)
"""
if not solvebio.api_key:
solvebio.login()
# Ensure the dataset exists. Create if necessary.
try:
dataset = solvebio.Dataset.retrieve(args.dataset)
except solvebio.SolveError as e:
if e.status_code != 404:
raise e
print("Dataset not found: {0}".format(args.dataset))
if args.create_dataset:
dataset = create_dataset(args)
else:
print("Tip: use the --create-dataset flag "
"to create one automatically")
sys.exit(1)
# Generate a manifest from the local files
manifest = solvebio.Manifest()
manifest.add(*args.file)
# Create the manifest-based import
imp = solvebio.DatasetImport.create(
dataset_id=dataset.id,
manifest=manifest.manifest,
genome_build=args.genome_build,
auto_approve=args.auto_approve)
if args.follow:
imp.follow()
else:
mesh_url = 'https://my.solvebio.com/jobs/imports/{0}'.format(imp.id)
print("Your import has been submitted, view details at: {0}"
.format(mesh_url))
import sys
import operator
import rebuildanal_helper
from collections import Counter
import Queue
import logging
import simplejson as json
import os
import bisect
import solvebio
solvebio.login()
###
# do it from json files
# chrom, start_position, rsid, reference_allele, alt (list), hugo_symbol,
# variant_classification
# amino acid residue (gene:pos)
###
#mutations = json.load(open('mutations.json'))
residues = json.load(open('residues.json'))
### dictionary format
file = open('tcga_residues_dictionary')
tcga_residues = json.load(file)
file.close()
class Rows(object):
def __init__(self,object):
for x in object.keys():
setattr(self, x, object[x])
import solvebio
solvebio.login()
vault = solvebio.Vault.get_personal_vault()
# The folders that will contain your dataset
path = '/SampleImport/1.0.0'
# The name of your dataset
dataset_name = 'SampleDataset'
# Create a dataset
dataset = solvebio.Dataset.get_or_create_by_full_path(
'{0}:/{1}/{2}'.format(vault.name, path, dataset_name), )
# Create a manifest object and a file to it
manifest = solvebio.Manifest()
manifest.add_file('path/to/file.vcf.gz')
# Create the import
imp = solvebio.DatasetImport.create(dataset_id=dataset.id,
manifest=manifest.manifest)
# Prints updates as the data is processed
# and indexed into SolveBio
imp.follow()
#
# You now have data!
#
def query_mutations(cnf, mutations):
if not verify_module('solvebio'):
err('Cannot import solvebio')
return None
saves_fpath = join(cnf.work_dir, 'solvebio.txt')
if cnf.debug:
if verify_file(saves_fpath, silent=True):
info('Debug, reading hits from ' + saves_fpath)
with open(saves_fpath) as f:
for mut, l in zip(mutations, f):
if l:
l = l.strip().split('\t')
if len(l) == 2:
mut.solvebio = SolvebioRecord(clinsig=l[0],
url=l[1])
info('Done, read ' + str(sum(1 for m in mutations if m.solvebio)) +
' hits')
return mutations
ds = None
from solvebio import login, Dataset, BatchQuery, SolveError
try:
login()
ds = Dataset.retrieve('ClinVar/Variants')
except SolveError:
err(format_exc())
err('Could not retrieve information for SolveBio, skipping')
MAX_BATCH_SIZE = 250
batches = []
batch = None
for i, m in enumerate(mutations):
if i % MAX_BATCH_SIZE == 0:
batch = []
batches.append(batch)
batch.append(ds.query().filter(gene_symbol=m.gene.name) \
.position(m.chrom, position=m.pos) \
.filter(allele=m.alt, reference_allele=m.ref))
info('Querying mutations against SolveBio ClinVar depository...')
try:
for i, batch in enumerate(batches):
if len(batches) > 1:
info(' batch ' + str(i) + '...')
for mut, res in zip(mutations, BatchQuery(batch).execute()):
if res['results']:
solvebio_record = parse_response(res['results'][0], mut)
if solvebio_record:
mut.solvebio = solvebio_record
info(' done, found ' +
str(sum(1 for m in mutations if m.solvebio)) + ' hits')
except SolveError:
err(format_exc())
err('Could not retrieve information for SolveBio, skipping')
if cnf.debug:
with open(saves_fpath, 'w') as f:
for mut in mutations:
if mut.solvebio:
f.write(mut.solvebio.clinsig)
f.write('\t')
f.write(mut.solvebio.url)
f.write('\n')
info('Saved to ' + saves_fpath)
info('-' * 70)
return mutations