larssono

from bs4 import BeautifulSoup
from urllib.request import urlopen, HTTPError
import string
import time
import random

url = 'https://www.mayoclinic.org/diseases-conditions/index?letter=%s'
output = 'diseases.txt'

fp = open(output,'w')

larssono

import synapseclient
import synapsebridgehelpers as sb

FILTER_QUERY = "SELECT distinct healthCode FROM syn7841519 where substudyMemberships like '%Cirrhosis_pilot%'"
ORIG_PROJECT = 'syn7838471'
DESTINATION_PROJECT = 'syn18589808'
TABLE_MAPPING = {'syn7841519': 'syn18632063'}


syn = synapseclient.login()

larssono

import pandas as pd
import bridgeclient
import synapseclient 
from multiprocessing.dummy import Pool
from synapseutils.monitor import with_progress_bar

mp = Pool(4)
bridge = bridgeclient.bridgeConnector(<email>, <password>, study='journey-pro')
syn = synapseclient.login()

larssono

import synapseclient
import pandas as pd
from multiprocessing.dummy import Pool

def with_progress_bar(func, totalCalls, prefix = '', postfix='', isBytes=False):
    """Adds a progress bar to calls to func

    :param func: Function being wrapped with progress Bar
    :param totalCalls: total number of items/bytes when completed
    :param prefix: String printed before progress bar

larssono

import synapseclient
syn=synapseclient.Synapse()
syn.login() 

def determineNewSampleCount():
    """
    """
    table = syn.tableQuery('SELECT * FROM syn3281840')
    df = table.asDataFrame()

larssono

import sys
import synapseclient


syn=synapseclient.Synapse()
syn.login(silent=True) 
md5 = sys.argv[1]

files =  syn.restGET('/entity/md5/%s' % md5)
for f in files['results']:

larssono

import pandas as pd
import json
graph = json.load(open('graph.json'))
df = pd.DataFrame(graph['vertices'])
df.to_csv('vertices.csv')

larssono

##Load graph into memory g = new TinkerGraph() g.loadGraphSON('/Users/lom/Downloads/graph.json')

##Find all activities g.V('concreteType', 'activity').name nActivities = g.V('concreteType', 'activity').count()

larssono

"""Get permalink to git commit for a specific path.

"""

import os
import ConfigParser
import github

def getToken(cfgfile="~/.pygit"):
    """Authenticate using a token.

larssono

ids = [i['file.id'] for i in syn.chunkedQuery('select id from file where parentId=="syn5521815"')]
for i in ids:
    e = syn.get(i, downloadFile=False)
    e.properties.fileNameOverride = e.name
    syn.store(e, forceVersion=False)