def main(argv):
faspRunner = FASPRunner(pauseSecs=0)
settings = faspRunner.settings
# Step 1 - Discovery
# query for relevant DRS objects
searchClient = BigQuerySearchClient()
# query = """
# SELECT subject_id, read_drs_id
# FROM `isbcgc-216220.COPDGene.phenotype_drs`
# where weight_kg between 91.8 and 93.0
# LIMIT 1"""
query = """
SELECT submitter_id, read_drs_id
FROM `isbcgc-216220.onek_genomes.ssd_drs`
where population = 'BEB'
LIMIT 1"""
# BioDataCatalyst
drsClient = bdcDRSClient('~/.keys/bdc_credentials.json', 'gs')
location = 'projects/{}/locations/{}'.format(settings['GCPProject'],
settings['GCPPipelineRegion'])
mysam = GCPLSsamtools(location, settings['GCPOutputBucket'])
faspRunner.configure(searchClient, drsClient, mysam)
faspRunner.runQuery(query, 'One k query ')
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 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 __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 main(argv):
faspRunner = FASPRunner(pauseSecs=0)
# 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 3"
# Step 2 - DRS - set up a DRS Client
drsClient = bdcDRSClient('~/.keys/bdc_credentials.json', 'gs')
# Step 3 - set up a class that run a compute for us
wesClient = DNAStackWESClient('~/.keys/dnastack_wes_credentials.json')
faspRunner.configure(searchClient, drsClient, wesClient)
faspRunner.runQuery(query, 'One k query using Search and WES')
def main(argv):
faspRunner = FASPRunner(pauseSecs=0)
settings =faspRunner.settings
# 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 = 'BEB' limit 3"
# Step 2 - DRS - set up a DRS Client
# CRDC
drsClient = bdcDRSClient('~/.keys/bdc_credentials.json', 'gs')
# Step 3 - set up a class that runs samtools for us
# providing the location where we the results to go
location = 'projects/{}/locations/{}'.format(settings['GCPProject'], settings['GCPPipelineRegion'])
mysam = GCPLSsamtools(location, settings['GCPOutputBucket'])
faspRunner.configure(searchClient, drsClient, mysam)
faspRunner.runQuery(query, 'One k query using Search')
def main(argv):
faspRunner = FASPRunner(pauseSecs=0)
creditor = faspRunner.creditor
settings = faspRunner.settings
# set your Seven Bridges CGC project using what you have put in FASP Settings
sbProject = settings['SevenBridgesProject']
sbInstance = settings['SevenBridgesInstance']
# Step 1 - Discovery
# query for relevant DRS objects
discoveryClients = {
"sb": DiscoverySearchClient('https://ga4gh-search-adapter-presto-public.prod.dnastack.com/'),
"bdc": BigQuerySearchClient()
}
crdcquery = "SELECT sp.dbGaP_Subject_ID, 'sb:'||sb_drs_id FROM dbgap_demo.scr_gecco_susceptibility.subject_phenotypes_multi sp join dbgap_demo.scr_gecco_susceptibility.sample_multi sm on sm.dbgap_subject_id = sp.dbgap_subject_id join dbgap_demo.scr_gecco_susceptibility.sb_drs_index di on di.sample_id = sm.sample_id where AGE between 45 and 55 and sex = 'Female' and file_type = 'cram' limit 3"
bdcquery = """
SELECT sp.dbGaP_Subject_ID, 'bdc:'||read_drs_id
FROM `isbcgc-216220.COPDGene.Subject_MULTI` sm
join `isbcgc-216220.COPDGene.Subject_Phenotypes_HMB` sp on sp.dbgap_subject_id = sm.dbgap_subject_id
join `isbcgc-216220.COPDGene.COPD_DRS` drs on drs.su_submitter_id = sm.subject_id
where gender = '2'
and Age_Enroll between 45 and 55
LIMIT 3"""
results = discoveryClients['sb'].runQuery(crdcquery) # Send the query
creditor.creditFromList('dbGapSSD')
creditor.creditClass(discoveryClients['sb'])
results += discoveryClients['bdc'].runQuery(bdcquery)
creditor.creditFromList('BDCData')
# Step 2 - DRS - set up DRS Clients
drsClients = {
"sb": sbcgcDRSClient('~/.keys/sevenbridges_keys.json', 's3'),
"bdc": bdcDRSClient('~/.keys/bdc_credentials.json', 'gs')
}
print('setting credentials ')
creditor.creditFromList('dbGaPFence')
# Step 3 - set up a class that runs samtools for us
# providing the location for the results
location = 'projects/{}/locations/{}'.format(settings['GCPProject'], settings['GCPPipelineRegion'])
sam2 = GCPLSsamtools(location, settings['GCPOutputBucket'])
samClients = {
"sb": samtoolsSBClient(sbInstance, sbProject),
"bdc": sam2
}
# repeat steps 2 and 3 for each row of the query
for row in results:
print("subject={}, drsID={}".format(row[0], row[1]))
resRow = [row[0], row[1]]
# Step 2 - Use DRS to get the URL
# get the prefix
prefix, drsid = row[1].split(":", 1)
drsClient = drsClients[prefix]
searchClient = discoveryClients[prefix]
creditor.creditClass(drsClient)
url = drsClient.getAccessURL(drsid)
print(url)
#objInfo = drsClient.getObject(drsid)
#print (objInfo)
#fileSize = objInfo['size']
fileSize = 0
# Step 3 - Run a pipeline on the file at the drs url
if url != None:
outfile = "{}.txt".format(row[0])
mysam = samClients[prefix]
creditor.creditClass(mysam)
via = 'sh'
note = 'Two dbGaP sources'
time = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S")
run_id = mysam.runWorkflow(url, outfile)
faspRunner.logRun(time, via, note, run_id, outfile, fileSize,
searchClient, drsClient, mysam)
resRow.append('OK')
else:
print('could not get DRS url')
resRow.append('unauthorized')
def main(argv):
faspRunner = FASPRunner(pauseSecs=0)
creditor = faspRunner.creditor
settings = faspRunner.settings
# Step 1 - Discovery
# query for relevant DRS objects
searchClient = BigQuerySearchClient()
# TCGA Query - CRDC
crdcquery = """
SELECT 'case_'||associated_entities__case_gdc_id , 'crdc:'||file_id
FROM `isb-cgc.GDC_metadata.rel24_fileData_active`
where data_format = 'BAM'
and project_disease_type = 'Breast Invasive Carcinoma'
limit 3"""
#COPD query - Topmed
bdcquery = """
SELECT SUBJECT_ID, 'bdc:'||read_drs_id
FROM `isbcgc-216220.COPDGene.phenotype_drs`
where Weight_KG between 92.5 and 93.0
LIMIT 3"""
results = searchClient.runQuery(crdcquery) # Send the query
creditor.creditFromList('ISBGDCData')
results += searchClient.runQuery(bdcquery)
creditor.creditFromList('BDCData')
# Step 2 - DRS - set up DRS Clients
drsClients = {
"crdc": crdcDRSClient('~/.keys/crdc_credentials.json', ''),
"bdc": bdcDRSClient('~/.keys/bdc_credentials.json', '')
}
print('setting credentials ')
creditor.creditFromList('dbGaPFence')
# Step 3 - set up a class that runs samtools for us
# providing the location for the results
location = 'projects/{}/locations/{}'.format(settings['GCPProject'], settings['GCPPipelineRegion'])
mysam = GCPLSsamtools(location, settings['GCPOutputBucket'])
# repeat steps 2 and 3 for each row of the query
for row in results:
print("subject={}, drsID={}".format(row[0], row[1]))
# Step 2 - Use DRS to get the URL
# get the prefix
prefix, drsid = row[1].split(":", 1)
url = drsClients[prefix].getAccessURL(drsid, 'gs')
drsClient = drsClients[prefix]
creditor.creditClass(drsClient)
objInfo = drsClient.getObject(drsid)
fileSize = objInfo['size']
# Step 3 - Run a pipeline on the file at the drs url
outfile = "{}.txt".format(row[0])
mysam.runWorkflow(url, outfile)
creditor.creditClass(mysam)
via = 'sh'
pipeline_id = 'paste here'
note = 'Two sources'
time = datetime.datetime.now().strftime("%m/%d/%Y, %H:%M:%S")
faspRunner.logRun(time, via, note, pipeline_id, outfile, fileSize,
searchClient, drsClient, mysam)
creditor.creditFromList('FASPScript2_sdrf', closeImage=False)
