# Example script to execute the "labcas-test" workflow
from gov.nasa.jpl.edrn.labcas.labcas_client import LabcasClient
if __name__ == '__main__':
# submit workflow
# ./wmgr-client --url http://localhost:9001 --operation --sendEvent --eventName labcas-test --metaData --key experiment 11 --key species snakes
labcasClient = LabcasClient()
wInstId = labcasClient.executeWorkflow(['urn:edrn:LabcasTestInit','urn:edrn:LabcasTestTask'],
{'experiment':'11',
'species':'snakes' } )
# monitor workflow instance
labcasClient.waitForCompletion(wInstId)
# list all files of this product type
labcasClient.listProducts('LabCAS_Test_Product')
# Python script for programmatic execution of the AF workflow
# (and consequent publishing of UnivColoLungImages)
from gov.nasa.jpl.edrn.labcas.labcas_client import LabcasClient
if __name__ == '__main__':
# upload these datasets
#dataset_names = ['UCHSC_1467', 'UCHSC_8798']
#dataset_names = ['UCHSC_1467']
dataset_names = ['UCHSC_8798']
product_type = 'University_of_Colorado_Lung_Image'
for dataset_name in dataset_names:
# submit workflow
# ./wmgr-client --url http://localhost:9001 --operation --sendEvent --eventName waf --metaData --key DatasetId UCHSC_1001
labcasClient = LabcasClient()
wInstId = labcasClient.executeWorkflow(['urn:edrn:WafInitTask',
'urn:edrn:WafCrawlTask'],
{ 'DatasetName':dataset_name },
)
# monitor workflow instance
labcasClient.waitForCompletion(wInstId)
# list all products for given product type
labcasClient.listProducts(product_type)
# product type metadata (to be submitted as part of upload workflow)
metadata = {
# required
'DatasetName':'Autoantibody Biomarkers',
'ProtocolId':'138',
'ProtocolName':'Validation of Protein Markers for Lung Cancer Using CARET Sera and Proteomics Techniques',
'LeadPI':'Samir Hanash',
'DataCustodian':'Ji Qiu',
'DataCustodianEmail':'*****@*****.**',
'CollaborativeGroup':'Lung and Upper Aerodigestive',
'OwnerPrincipal':'/Samir/Hanash',
# optional
'OrganSite':'Lung',
'SiteName':'Fred Hutchinson Cancer Research Center (Biomarker Developmental Laboratories)',
'SiteShortName':'FHCRC',
'QAState':'Accepted',
'PubMedId':'http://www.ncbi.nlm.nih.gov/pubmed/18794547',
'DateDatasetFrozen':'2007/05/29',
}
# upload dataset staged in directory 'mydata'
labcasClient.uploadDataset(datasetId, metadata)
# query the product types from the XML/RPC File Manager interface
labcasClient.getProductTypeByName(datasetId)
# list all products for given dataset == product type
labcasClient.listProducts(datasetId)