def download(clientKey=None, clientSecret=None, accessToken=None, runId=None, runName=None, outputDirectory='\.', createBsDir=True):
'''
Downloads run-level files.
Run Id and run name should not be specified together.
All files for a given run will be downloaded based on either the unique run ID, or
the first run found with matching experiment name.
:param clientKey the Illumina developer app client key
:param clientSecret the Illumina developer app client secret
:param accessToken the Illumina developer app access token
:param runId the BaseSpace run identifier
:param runName the BaseSpace run experiment name
:param outputDirectory the root output directory
:param createBsDir true to recreate the path structure within BaseSpace, false otherwise
'''
appSessionId = ''
apiServer = 'https://api.basespace.illumina.com/' # or 'https://api.cloud-hoth.illumina.com/'
apiVersion = 'v1pre3'
fileLimit = 1024
runLimit = 100
# init the API
if None != clientKey:
myAPI = BaseSpaceAPI(clientKey, clientSecret, apiServer, apiVersion, appSessionId, accessToken)
else:
myAPI = BaseSpaceAPI(profile='DEFAULT')
# get the current user
user = myAPI.getUserById('current')
expName = None
if runId:
run = myAPI.getRunById(Id=runId)
runFiles = Runs.__get_files_to_download(myAPI, run.Id, fileLimit)
expName = run.ExperimentName
else:
runs = myAPI.getAccessibleRunsByUser(qp({'Limit' : runLimit}))
for run in runs:
runId = run.Id
if runName and runName == run.ExperimentName:
expName = run.ExperimentName
runFiles = Samples.__get_files_to_download(myAPI, runId)
if 0 < len(runFiles):
break
if not expName:
if runName:
print 'Could not find a run with name: %s' % runName
else:
print 'Could not find a run for user'
sys.exit(1)
numFiles = len(runFiles)
print "Will download files from %d ." % numFiles
i = 0
for runFile in runFiles:
outDir = os.path.join(outputDirectory, expName)
print 'Downloading (%d/%d): %s' % ((i+1), numFiles, str())
print "BaseSpace File Path: %s" % runFile.Path
print "Destination File Path: %s" % os.path.join(outDir, runFile.Name)
if not options.dryRun:
runFile.downloadFile(myAPI, outDir, createBsDir=createBsDir)
i = i + 1
print "Download complete."
