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."
class BaseSpace(object):
def __init__(self,
project_id=None,
project_name=None,
get_all_projects=False):
super(BaseSpace, self).__init__()
# BaseSpace credentials
creds = self._get_credentials()
self.client_key = creds['client_id']
self.client_secret = creds['client_secret']
self.access_token = creds['access_token']
self.version = creds['version']
self.api_server = creds['api_server']
self.api = BaseSpaceAPI(self.client_key,
self.client_secret,
self.api_server,
self.version,
AccessToken=self.access_token)
self.params = qp(pars={'Limit': 1024, 'SortDir': 'Desc'})
if project_id is not None:
self.project_id = project_id
self.project_name = None
elif project_name is not None:
self.project_name = project_name
self.project_id = self._get_project_id_from_name(project_name)
else:
self.project_id = None
self.project_name = None
# self.project_id, self.project_name = self._user_selected_project_id()
self._runs = None
@property
def runs(self):
if self._runs is None:
self._runs = self.api.getAccessibleRunsByUser(
queryPars=self.params)
return self._runs
def _get_credentials(self):
# BaseSpace credentials file should be in JSON format
cred_file = os.path.expanduser('~/.abstar/basespace_credentials')
cred_handle = open(cred_file, 'r')
return json.load(cred_handle)
def _get_project_id_from_name(self):
projects = self.api.getProjectByUser(queryPars=self.params)
for project in projects:
name = project.Name.encode('ascii', 'ignore')
if name == self.project_name:
return project.Id
print('No projects matched the given project name ({})'.format(name))
sys.exit(1)
def _user_selected_project_id(self):
projects = self.api.getProjectByUser(queryPars=self.params)
self.print_basespace_project()
offset = 0
while True:
for i, project in enumerate(projects[offset * 25:(offset * 25) +
25]):
project_name = project.Name.encode('ascii', 'ignore')
print('[ {} ] {}'.format(i + (offset * 25), project_name))
print('')
project_index = raw_input(
"Select the project number (or 'next' to see more projects): ")
try:
project_index = int(project_index)
return projects[project_index].Id, projects[
project_index].Name.encode('ascii', 'ignore')
except:
offset += 1
return projects[project_index].Id, projects[project_index].Name.encode(
'ascii', 'ignore')
def _get_projects(self, start=0):
projects = self.api.getProjectByUser(queryPars=self.params)
self.print_basespace_project()
for i, project in enumerate(projects[:25]):
project_name = project.Name.encode('ascii', 'ignore')
print('[ {} ] {}'.format(i, project_name))
print('')
return projects
def _get_samples(self, project_id):
samples = []
offset = 0
while True:
query_params = qp(pars={
'Limit': 1024,
'SortDir': 'Asc',
'Offset': offset * 1024
})
s = self.api.getSamplesByProject(self.project_id,
queryPars=query_params)
if not s:
break
samples.extend(s)
offset += 1
return samples
def _get_files(self):
files = []
samples = self._get_samples(self.project_id)
for sample in samples:
files.extend(
self.api.getFilesBySample(sample.Id, queryPars=self.params))
return files
def download(self, direc):
if all([self.project_id is None, self.project_name is None]):
self.project_id, self.project_name = self._user_selected_project_id(
)
files = self._get_files()
self.print_download_info(files)
start = time.time()
for i, f in enumerate(files):
# self.log.write('[ {} ] {}\n'.format(i, str(f)))
logger.info('[ {} ] {}'.format(i, str(f)))
f.downloadFile(self.api, direc)
end = time.time()
self.print_completed_download_info(start, end)
return len(files)
def print_basespace_project(self):
print('')
print('')
print('========================================')
print('BaseSpace Project Selection')
print('========================================')
print('')
def print_download_info(self, files):
logger.info('')
logger.info('')
logger.info('========================================')
logger.info('Downloading files from BaseSpace')
logger.info('========================================')
logger.info('')
logger.info('Identified {0} files for download.'.format(len(files)))
logger.info('')
def print_completed_download_info(self, start, end):
logger.info('')
logger.info('Download completed in {0} seconds'.format(end - start))
