def main(uargs):
uargs['--config'] = os.path.abspath(os.path.expanduser(uargs['--config']))
conf = ConfigObj(uargs['--config'], configspec=get_configspec())
try:
conf_args = conf[uargs['--profile']]
except KeyError:
msg = 'Profile "{}" not found in config file'
raise KeyError, msg.format(uargs['--profile'])
# selecting config args
keys = ['clientKey', 'clientSecret', 'apiServer', 'apiVersion', 'appSessionId', 'accessToken']
conf_args = [conf_args[x] for x in keys]
myAPI = BaseSpaceAPI(*conf_args)
# setting user
if uargs['--user'] is not None:
user = myAPI.getUserById(uargs['--user'])
else:
user = myAPI.getUserById('current')
# all samples for project
if uargs['project']:
samples = myAPI.getSamplesByProject(uargs['<Id>'])
for sample in samples:
file_download(myAPI, sample.Id)
if uargs['sample']:
file_download(myAPI, uargs['<Id>'])
def download_Project(project_Name, output_folder):
# initialize an authentication object using the key and secret from your app
# Fill in with your own values
'''
client_key = <my key>
client_secret = <my secret>
AppSessionId = <my appSession id>
BaseSpaceUrl = 'https://api.basespace.illumina.com/'
version = 'v1pre3'
accessToken = <my acceseToken>
'''
myAPI = BaseSpaceAPI(client_key, client_secret, BaseSpaceUrl, version, AppSessionId,AccessToken=accessToken)
# Retrieve current user
user = myAPI.getUserById('current')
user=str(user)
id_name=user.split(':')
#print id_name[0]
# Retrieve all the project associated to that user
projects=myAPI.getProjectByUser(id_name[0], queryPars=QueryParameters( {'Limit': '100'}))
project_found=0
for project in projects:
project=str(project)
nameProject_id=project.split('-')
if str(project_Name) in str(nameProject_id):
project_found=1
id_project=nameProject_id[1].split('=')
id_project=id_project[1]
samples=myAPI.getSamplesByProject(id_project, queryPars=QueryParameters( {'Limit': '100'}))
print "There are "+str(len(samples))+" samples in the requested project ("+str(project_Name)+" - ID_PROJECT "+str(id_project)+")"
if not os.path.exists(output_folder):
os.makedirs(output_folder)
print time.ctime()+" START DOWNLOADING"
for file in samples:
file_out=file.getFiles(myAPI)
#print file_out
for fastq in file_out:
fastq.downloadFile(myAPI,output_folder)
print time.ctime()+" FILE "+str(fastq)+" DOWNLOADED"
path_file=join(output_folder,str(fastq))
path_S3=join(str(project_Name),str(fastq))
s3_upload(path_file,"bmi-ngs",path_S3)
print time.ctime()+" DOWNLOAD COMPLETED"
if project_found==0:
print "Project Not Found"
def main(uargs):
uargs['--config'] = os.path.abspath(os.path.expanduser(uargs['--config']))
conf = ConfigObj(uargs['--config'], configspec=get_configspec())
try:
conf_args = conf[uargs['--profile']]
except KeyError:
msg = 'Profile "{}" not found in config file'
raise KeyError, msg.format(uargs['--profile'])
# selecting config args
keys = ['clientKey', 'clientSecret', 'apiServer', 'apiVersion', 'appSessionId', 'accessToken']
conf_args = [conf_args[x] for x in keys]
myAPI = BaseSpaceAPI(*conf_args)
# setting user
if uargs['--user'] is not None:
user = myAPI.getUserById(uargs['--user'])
else:
user = myAPI.getUserById('current')
# user projects
projects = myAPI.getProjectByUser()
print "## The projects for this user are:"
project_headers = ['ProjectID','Name','UserOwnedBy','DateCreated']
sample_headers = ['SampleID','NumReadsRaw','NumReadsPF','IsPairedEnd','Status']
print '\t'.join(project_headers + sample_headers)
for project in projects:
project_data = [project.Id,
project.Name,
project.UserOwnedBy,
project.DateCreated]
samples = myAPI.getSamplesByProject(project.Id)
for sample in samples:
sample_data = [sample.Id,
sample.NumReadsRaw,
sample.NumReadsPF,
sample.IsPairedEnd,
sample.Status]
print '\t'.join([str(x) for x in project_data + sample_data])
#files = myAPI.getSampleFilesById(sample.Id)
#for f in files:
#fo = myAPI.getFileById(f.Id)
# myAPI.fileDownload(f.Id, '.')
# user runs
print "## The runs for this user are:"
print '\t'.join(['RunID','ExperimentName','UserOwnedBy',
'DateCreated', 'Status'])
runs = user.getRuns(myAPI)
for run in runs:
data = [run.Id,
run.ExperimentName,
run.UserOwnedBy,
run.DateCreated,
run.Status]
print '\t'.join([str(x) for x in data])
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))
