def __init__(self, debug=False):
self.drsClients = {
"insdc": sdlDRSClient('~/.keys/prj_11218_D17199.ngc'),
"crdc": crdcDRSClient('~/.keys/crdc_credentials.json','s3'),
"bdc": bdcDRSClient('~/.keys/bdc_credentials.json','gs'),
"anv": anvilDRSClient('~/.keys/anvil_credentials.json', '', 'gs'),
"insdc": sdlDRSClient('~/.keys/prj_11218_D17199.ngc'),
"sbcgc": sbcgcDRSClient('~/.keys/sevenbridges_keys.json','s3'),
"sbcav": cavaticaDRSClient('~/.keys/sevenbridges_keys.json','s3'),
"srapub": DRSClient('https://locate.ncbi.nlm.nih.gov', debug=False)
}
self.registeredClients = []
self.hostNameIndex = {}
self.debug = debug
def __init__(self, debug=False, getReg=True):
self.drsClients = {
"insdc": sdlDRSClient('~/.keys/prj_11218_D17199.ngc'),
"crdc": crdcDRSClient('~/.keys/crdc_credentials.json', 's3'),
"bdc": bdcDRSClient('~/.keys/bdc_credentials.json', 'gs'),
"anv": anvilDRSClient('~/.keys/anvil_credentials.json', '', 'gs'),
"insdc": sdlDRSClient('~/.keys/prj_11218_D17199.ngc'),
"sbcgc": sbcgcDRSClient('~/.keys/sevenbridges_keys.json', 's3'),
"sbcav": cavaticaDRSClient('~/.keys/sevenbridges_keys.json', 'gs'),
'sbbdc': sbbdcDRSClient('~/.keys/sevenbridges_keys.json', 's3'),
"sradrs": SRADRSClient('https://locate.be-md.ncbi.nlm.nih.gov')
}
self.registeredClients = []
self.hostNameIndex = {}
self.debug = debug
if getReg: self.getRegisteredDRSServices()
def DRSClientFromRegistryEntry(self, service, prefix):
if prefix == "crdc":
drsClient = crdcDRSClient('~/.keys/crdc_credentials.json','s3')
elif prefix == "bdc":
drsClient = bdcDRSClient('~/.keys/bdc_credentials.json','gs')
elif prefix == "insdc":
drsClient = sdlDRSClient('~/.keys/prj_11218_D17199.ngc')
elif prefix == "sbcgc":
drsClient = sbcgcDRSClient('~/.keys/sevenbridges_keys.json','s3')
elif prefix == "sbcav":
drsClient = cavaticaDRSClient('~/.keys/sevenbridges_keys.json','s3')
else:
drsClient = DRSClient.fromRegistryEntry(service)
return drsClient
def main(argv):
# edit the following line for where you put your ngc credentials file from dbGaP
credentials_file = '~/.keys/prj_14565.ngc'
faspRunner = FASPRunner(pauseSecs=0)
settings = faspRunner.settings
# Step 1 - Discovery
# query for relevant DRS objects
searchClient = localSearchClient()
query_job = searchClient.runQuery('')
drsClient = drsClient = sdlDRSClient(credentials_file, debug=True)
location = 'projects/{}/locations/{}'.format(settings['GCPProject'],
settings['GCPPipelineRegion'])
mysam = GCPLSsamtools(location, settings['GCPOutputBucket'], debug=True)
faspRunner = FASPRunner()
# repeat steps 2 and 3 for each row of the query
for row in query_job:
print("subject={}, drsID={}".format(row[0], row[1]))
# Step 2 - Use DRS to get the URL
#objInfo = drsClient.getObject(row[1])
# for testing
objInfo = drsClient.getObject(row[1])
fileSize = objInfo['size']
print(fileSize)
# we've predetermined we want to use the gs copy in this case
#url = drsClient.getAccessURL(row[1], 'gs')
res = drsClient.getAccessURL(row[1], 'gs.us')
url = res['url']
print(url)
# Step 3 - Run a pipeline on the file at the drs url
outfile = "{}.txt".format(row[0])
pipeline_id = mysam.runWorkflow(url, outfile)
print('submitted:{}'.format(pipeline_id))
via = ''
note = 'Anvil GTEX Test via SDL'
time = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S")
faspRunner.logRun(time, via, note, pipeline_id, outfile, str(fileSize),
searchClient, drsClient, mysam)
def main(argv):
# Step 1 - Discovery
# query for relevant DRS objects
searchClient = DiscoverySearchClient(
'https://ga4gh-search-adapter-presto-public.prod.dnastack.com/')
query = "select submitter_id, read_drs_id drsid from thousand_genomes.onek_genomes.ssd_drs where population = 'ACB' limit 1"
query_job = searchClient.runQuery(query)
# Step 2 - DRS - set up a DRS Client
# CRDC
drsClient = sdlDRSClient('~/.keys/prj_11218_D17199.ngc')
# Step 3 - set up a class that run a compute for us
wesClient = DNAStackWESClient('~/.keys/DNAStackWESkey.json')
# A log is helpful to keep track of the computes we've submitted
faspRunner = FASPRunner()
# repeat steps 2 and 3 for each row of the query
for row in query_job:
print("subject={}, drsID={}".format(row[0], row[1]))
# Step 2 - Use DRS to get the URL
#objInfo = drsClient.getObject(row[1])
# for testing
acc = 'SRR5368359.sra'
objInfo = drsClient.getObject(acc)
fileSize = objInfo['size']
print(fileSize)
# we've predetermined we want to use the gs copy in this case
#url = drsClient.getAccessURL(row[1], 'gs')
res = drsClient.getAccessURL(acc, 'gs.us')
url = res['url']
print(url)
# Step 3 - Run a pipeline on the file at the drs url
outfile = "{}.txt".format(row[0])
pipeline_id = wesClient.runWorkflow(url, outfile)
print('submitted:{}'.format(pipeline_id))
via = 'WES'
note = 'WES MD5 on NCBI SDL'
time = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S")
faspRunner.logRun(time, via, note, pipeline_id, outfile, str(fileSize),
searchClient, drsClient, wesClient)
def main(argv):
faspRunner = FASPRunner(pauseSecs=0)
# Step 1 - Discovery
# query for relevant DRS objects
searchClient = BigQuerySearchClient()
query = """SELECT sra.biosample, sra.acc||'.cram'
FROM `isbcgc-216220.GECCO_CRC_Susceptibility.Subject_Phenotypes` sp
join `isbcgc-216220.GECCO_CRC_Susceptibility.Sample_MULTI` sm on
sm.dbgap_subject_id = sp.dbgap_subject_id
join `nih-sra-datastore.sra.metadata` sra on sm.BioSample_Accession = sra.biosample
where AGE between 45 and 55 and sex = 'Female' limit 3"""
query_job = searchClient.runQuery(query)
# Step 2 - DRS - set up a DRS Client
# CRDC
drsClient = sdlDRSClient('~/.keys/prj_14565.ngc', True)
# Step 3 - set up a class that run a compute for us
wesClient = DNAStackWESClient('~/.keys/dnastack_wes_credentials.json')
# repeat steps 2 and 3 for each row of the query
for row in query_job:
print("sample={}, drsID={}".format(row[0], row[1]))
# Step 2 - Use DRS to get the URL
objInfo = drsClient.getObject(row[1])
fileSize = objInfo['size']
print(fileSize)
# we've predetermined we want to use the gs copy in this case
#url = drsClient.getAccessURL(row[1], 'gs')
res = drsClient.getAccessURL(row[1],'gs.us')
url = res['url']
print(url)
# Step 3 - Run a pipeline on the file at the drs url
outfile = "{}.txt".format(row[0])
pipeline_id = wesClient.runWorkflow(url, outfile)
print('submitted:{}'.format(pipeline_id))
via = 'WES'
note = 'WES MD5 on NCBI SDL'
time = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S")
faspRunner.logRun(time, via, note, pipeline_id, outfile, str(fileSize),
searchClient, drsClient, wesClient)
print('in download')
file_name = 'test_file.bam'
req = requests.get(url)
print(req)
file = open(file_name, 'wb')
for chunk in req.iter_content(100000):
print('writing a chunk')
file.write(chunk)
file.close()
if __name__ == "__main__":
# client1 = sdlDRSClient('~/.keys/prj_14565.ngc')
# res = client1.getObject('SRR1999478.bam')
# print('--Get Info--')
# print (res)
# print('--Get a URL--')
# res = client1.getAccessURL('SRR1999478.bam','gs.us')
# print (res)
# print ('-----------------')
client2 = sdlDRSClient('~/.keys/prj_11218_D17199.ngc', debug=True)
res = client2.getObject('SRR5368359.sra')
print('--Get Info--')
print(res)
print('--Get a URL--')
res = client2.getAccessURL('SRR5368359.sra', 'gs.us')
#print (json.dumps(res, indent=2))
print(res['url'])
download(res['url'])