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))