password=getpass.getpass())
# report_events = client.report_events().get_report_events(panelName='cakut')
# [re.caseId for re in islice(report_events, 5)]
# report_events = client.report_events().get_report_events(caseId='2915')
# sum(1 for _ in report_events)
# report_events = client.report_events().get_report_events(caseId='2915')
# tiers = set([re.reportEvent.tier for re in report_events])
tiers
# client.cases().get_variants_by_panel('cakut', hasTiered=True, tiers=["TIER1"])
report_events = cva.report_events()
entities = cva.entities()
cases = cva.cases()
variants = cva.variants()
from pyark.cva_client import CvaClient
from protocols.reports_6_0_0 import Program, Assembly
import pandas as pd
import itertools
pd.options.display.float_format = '{:.3f}'.format
import matplotlib.pyplot as plt
import getpass
# %matplotlib inline
cva_url = "https://bio-prod-cva.gel.zone"
gel_user = "******"
consoleHandler = logging.StreamHandler()
consoleHandler.setFormatter(formatter)
logger.addHandler(consoleHandler)
cva_url = os.environ.get("CVA_URL_BASE", "http://localhost:8090")
gel_user = os.environ.get("CVA_USER", None)
if not gel_user:
gel_user = getpass.getpass("User:"******"CVA_PASSWORD", None)
if not gel_password:
gel_password = getpass.getpass("Password:"******"pyark version {}".format(pyark.VERSION))
def get_size(obj, seen=None):
"""Recursively finds size of objects"""
size = sys.getsizeof(obj)
if seen is None:
seen = set()
obj_id = id(obj)
if obj_id in seen:
return 0
# Important mark as seen *before* entering recursion to gracefully handle
# self-referential objects
seen.add(obj_id)