synapse_upload_vcf

#!/usr/bin/python

import argparse
import sys
import os
import json
import synapseclient
from synapseclient import File, Activity, Wiki



def build_parser():
    """Set up argument parser and returns"""
    parser = argparse.ArgumentParser(description='Uploads files to Synapse by using a json document for meta data.')
    parser.add_argument('--parentId', dest='parentId', required=True, 
                        help='Id for Folder where to store files (example DKFZ: syn2898426, Sanger: syn2897245)')
    parser.add_argument('--url', dest='url', default = None, 
                        help=('Overides the url/path where file is uploaded. '
                              'Ex: sftp://tcgaftps.nci.nih.gov/tcgapancan/pancan/variants/'))
    parser.add_argument('json_file', type=argparse.FileType('r'),
                        help='json file with parameters')
    return parser

    


if __name__ == '__main__':
    args = build_parser().parse_args()
    params = json.load(args.json_file)

    ##Login into Synapse if you have not logged in before you can use (to cache your credentials) 
    #  syn.login('username', 'secret_password', rememberMe=True)
    syn = synapseclient.login()
    

    ##Build up provenance and store to Synapse
    provenance = Activity(name = params['annotations']['workflow_name'],
                          description='Variant calling for indels, SNVs, and copy numbers.',
                          used = params['used_urls'],
                          executed = params['executed_urls'])

    #Step through list of files and store in Synapse
    for path in params['files']:
        if args.url is not None:
            url = syn._sftpUploadFile(path, args.url)
            f = File(url, parentId=args.parentId)
        else:
            f = File(path, parentId=args.parentId)
        print f.path
        #Set storage option if it is a URL
        if synapseclient.utils.is_url(f.path):
            f['synapseStore'] = False

        #Set annotations
        f.annotations = params['annotations']

        #Add file specific annotations
        filename = os.path.split(path)[-1]
        sample_id, pipeline_version, date, call_type, dataType  =  filename.split('.')[:5]
        fileType =  [i for i in filename.split('.')[5:] if i != 'gz'][-1]
        file_md5 = synapseclient.utils.md5_for_file(path).hexdigest()
        f.sample_id = sample_id
        f.pipeline_version = pipeline_version
        f.date = date
        f.call_type = call_type
        f.dataSubType = dataType
        f.dataType = 'DNA'
        f.disease = 'Cancer'
        f.fileType = fileType
        f.file_md5 = file_md5

        #Persist up to Synapse
        f = syn.store(f)
        provenance = syn.setProvenance(f, provenance)

        #Add Description Wiki
        try:
            wiki = syn.getWiki(f)
        except synapseclient.exceptions.SynapseHTTPError as err:
            if err.response.status_code == 404:
                wiki = Wiki(title = params['wiki_content']['title'], owner=f, markdown=params['wiki_content']['description'])
            else:
                raise err
        else:
            wiki.title = params['wiki_content']['title']
            wiki.owner=f
            wiki.markdown=params['wiki_content']['description']
        syn.store(wiki)