cbare

##
## A script to add permission on a synapse entity
## for a whole bunch of emails
############################################################
import synapseclient
import re, sys
import requests
import json

cbare

## Example code for getting gene information from NCBI
## using EUTILS.
## To install dependencies:
##   pip install lxml
##   pip install requests
############################################################

import requests
from lxml import etree as ET
import re

cbare

from __future__ import print_function
from __future__ import unicode_literals
import synapseclient
import re
import sys

## make sure we really want to delete stuff
not_kidding = len(sys.argv) > 1 and sys.argv[1] == '--not-kidding'

if not not_kidding:

cbare

##
## Try out support for external file handles in Synapse
######################################################################
import synapseclient
from synapseclient.entity import File, Project, Folder
syn = synapseclient.Synapse()
syn.login()

## create a sandbox project
project = Project('Uniquely named temporary project')

cbare

import argparse
import os
import shutil
import sys
import synapseclient
from synapseclient import Activity
import synapseclient.version_check as version_check
import signal
import json

cbare

import filecmp
import os
import random
import synapseclient
from synapseclient import Activity, File, Folder, Project
import uuid

## create synapse object and log in
syn = synapseclient.Synapse()
syn.login()

cbare

## Version 4 UUIDs have the form xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx
## where x is any hexadecimal digit and y is one of 8, 9, A, or B
## e.g., f47ac10b-58cc-4372-a567-0e02b2c3d479
uuid <- function(uppercase=FALSE) {

  hex_digits <- c(as.character(0:9), letters[1:6])
  hex_digits <- if (uppercase) toupper(hex_digits) else hex_digits

  y_digits <- hex_digits[9:12]

cbare

from __future__ import print_function
from IPython.core.magic import (Magics, magics_class, line_magic)

@magics_class
class SynapseMagics(Magics):
    """
    IPython magic for Synapse. In an interactive IPython session, you can
    conveniently import the key Synapse objects and log in.

    To log in as your default user (according to your ~/.synapseCache/.session file)::

cbare

##
## Collect statistics for auditing Synapse usage and governance
######################################################################
import synapseclient
from synapseclient.utils import id_of
from datetime import datetime as Datetime
import re, sys
import requests

ROOT = 'syn4489'

cbare

import numpy as np
import random
import uuid

import synapseclient
from synapseclient import File, Folder, Project
from synapseclient import Evaluation, Submission, SubmissionStatus


def read_matrix(filepath):