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import json

## First we'll create a terms-of-use object that refers to the participant
## team for the challenge, which in this case has ID 3328713. The termsOfUse
## contains the HTML that will be displayed in a panel of the registration
## wizard.
## http://rest.synapse.org/org/sagebionetworks/repo/model/AccessRequirement.html
tou = {
    'accessType': 'PARTICIPATE',
    'concreteType': 'org.sagebionetworks.repo.model.TermsOfUseAccessRequirement',

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## SMC-DNA challenges are configured by entries in the table smc-dna-config,
## which lives in the MutationCallingChallengeStaging project, here:
## https://www.synapse.org/#!Synapse:syn4686078

## To add a new sample:


## create new evaluation queue (one for each of SNV, SV and possibly indel)
evaluation_snv = syn.store(Evaluation(
    name="synthetic.challenge.set6.snv",

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##==========================================================
## Tables Pipeline Example
## 
## An example of using Synapse tables to store raw data and
## intermediate steps to extract features for downstream
## analysis
##==========================================================
import synapseclient
from synapseclient import Activity
from synapseclient import Entity, Project, Folder, File

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library(plyr)
library(synapseClient)
synapseLogin('chris.bare')


## Q1a = 3317421, Q1b = 3317433, Q2 = 3317446
## https://www.synapse.org/#!Synapse:syn2762531/wiki/72477
## metrics in the query may need to change for different questions
eid = '3317421'

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#!/usr/bin/env python                                                                                                       
"""                                                                                                                         
Recursively upload a directory structure to a Synapse project (synapse.org).                                                
                                                                                                                            
Examples::                                                                                                                  
                                                                                                                            
    synapse_upload_directory_tree <PROJECT ID> -user <EMAIL> --pass <PASS> --top <TOP DIRECTORY>
    synapse_upload_directory_tree syn3207152 --user [email protected] --pass XXXXXX --top brains

    synapse_upload_directory_tree syn3207152 --user [email protected]

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import synapseclient

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

## create the entity
e = syn.store(File("http://google.com/", name="google", parent="syn3361147", synapseStore=False))

## should work, but doesn't
## e = syn.store(File("http://google.com/testing1", name="google", parent="syn3361147"), synapseStore=False)

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import synapseclient
from synapseclient.exceptions import SynapseError


team_id = "3325290"
approved_participant_ids = ["377358", "3321663"]

syn = synapseclient.Synapse()

## log in using cached API key.

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from itertools import izip
import argparse
import os
import re
import sys
import synapseclient
import synapseclient.utils as utils
from synapseclient import Project, File, Folder, Activity
from synapseclient import Schema, Column, Table, Row, RowSet, as_table_columns
import pandas as pd

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

# ID for challenge participants team
team_id = ??
results = list(syn._GET_paginated('/teamMembers/{id}'.format(id=team_id)))

print "Number of participants:", len(results)

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################################################################
## get submissions and metadata for Synthetic challenge 4
################################################################

import synapseclient
from synapseclient import Activity
from synapseclient import Entity, Project, Folder, File
from synapseclient import Evaluation, Submission, SubmissionStatus
import os
import pandas as pd