class GSGeneLabClient:
myGeneLabClient = None
def testMethod(self):
print("GSGetFile test called")
# create the client which we need to have cache the user/pass
def GeneLabLogin(self, username, password):
self.myGeneLabClient = GenomeSpaceClient(username, password)
return self.myGeneLabClient
def downloadFile(self, genelabUrl, localFileName):
self.myGeneLabClient._download_file(genelabUrl, localFileName)
def download_from_genomespace_importer(json_parameter_file, root, data_conf,
custom_token):
with open(json_parameter_file, 'r') as param_file:
json_params = json.load(param_file)
# Add in missing job config properties that could not be set in the exec_before_job hook
json_params['job_config']['GALAXY_ROOT_DIR'] = root
json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'] = data_conf
# Extract input_urls and token (format is input_urls^token). If a custom_token is
# provided, use that instead.
url_with_token = json_params.get('param_dict', {}).get("URL", "")
if custom_token:
input_urls = url_with_token.split('^')[0]
token = custom_token
else:
input_urls, token = url_with_token.split('^')
input_url_list = input_urls.split(",")
gs_client = GenomeSpaceClient(token=token)
for idx, input_url in enumerate(input_url_list):
download_single_file(gs_client,
input_url,
json_params,
primary_dataset=(idx == 0))
def target_selector(request):
# if the user has no files selected for upload, select them first
if not request.session.get(S_CHOSEN_FILES, None):
messages.add_message(request, messages.INFO,
'Please choose the files you want to upload')
return HttpResponseRedirect('/files')
# the user has files selected, has selected a genomespace, and the
# directories the files are to go to, so move the files...
if request.method == 'POST' and request.session[S_TARGETS]:
target_directories = request.session[S_TARGETS]
targets = tuple((s['path'], s['name']) for s in target_directories)
form = TargetChooserForm(targets, request.POST)
if form.is_valid():
selected_dir = form.cleaned_data['target_directories']
return _move_files_to_gs(target_directories, selected_dir, request)
# else just show them the form again, populated with their choices
else:
# the user has files selected, has selected a genomespace, but we
# don't know what their target directory will be, so ask them...
client = GenomeSpaceClient(token=request.session[S_GS_TOKEN])
xrd_location = request.session[S_LOCATION]
dm_server = AgrfFeedConfig.get_dm_server(xrd_location)
home_dir = dm_server + '/v1.0/file/Home/'
try:
target_directories = _list_directories(
client, home_dir, request.session[S_GS_USERNAME])
request.session[S_TARGETS] = target_directories
targets = tuple((s['path'], s['path']) for s in target_directories)
if not len(targets):
messages.add_message(
request, messages.ERROR,
'No writeable GenomeSpace directory '
'has been found? Please check your '
'GenomeSpace account.')
return HttpResponseRedirect('/files')
except HTTPError as e:
status_code = e.response.status_code
if status_code == 403:
messages.add_message(
request, messages.ERROR,
'The GenomeSpace has forbidden access! '
'You may be able to fix this by '
're-entering your cloud '
'credentials in the GenomeSpace.')
return HttpResponseRedirect('/files')
elif status_code == 500:
messages.add_message(
request, messages.ERROR,
'The GenomeSpace has experienced an '
'internal server error! '
'Please report this to '
'*****@*****.**')
return HttpResponseRedirect('/files')
else:
raise
form = TargetChooserForm(targets)
return render(request, 'agrf_feed/targets.html', {'form': form})
def celery_move_files(chosen_files, target_dir, token):
client = GenomeSpaceClient(token=token)
# common prefix doesn't return the common path: but rather
# all the characters that match. So we need to trim it back to the path
# separator...
base = os.path.commonprefix(chosen_files).rpartition(os.sep)[0]
for path in chosen_files:
# there will always be a leading '/', as the base doesn't include it
# so remove it from the file name
file_name = path[len(base) + 1 if len(base) else 0:]
# the genomespace will expect a '/' in a file name to be a directory
file_name = file_name.replace('/', '_')
bucket = target_dir['url'] + '/' + file_name
fd = FileDescriptor.get_file_descriptor_for(path)
try:
logging.info('About to move %s to %s' % (path, bucket))
start_time = time.time()
client.copy(path, bucket)
elapsed_time = time.time() - start_time
bytes_moved = os.path.getsize(path)
logging.info('%s bytes moved in %.2f seconds' %
(bytes_moved, elapsed_time))
except GSClientException as error:
logging.error('Error uploading %s: %s' % (file_name, error))
fd.set_failed_upload()
except SoftTimeLimitExceeded:
logging.error('Soft time limit exceed for %s' % path)
fd.set_failed_upload()
except Exception as exp:
# all other errors should be logged and the upload marked as failed
logging.exception('On uploading %s' % path)
fd.set_failed_upload()
else:
logging.info('Successfully uploaded %s' % file_name)
fd.set_uploaded()
fd.save()
def upload_to_genomespace(token, input_file, target_url):
token = token or os.environ.get('GS_TOKEN')
gs_client = GenomeSpaceClient(token=token)
gs_client.copy(input_file, target_url)
print("File successfully copied.")
def upload_to_genomespace(token, input_file, target_url):
token = token or os.environ.get('GS_TOKEN')
gs_client = GenomeSpaceClient(token=token)
gs_client.copy(input_file, target_url)
print("File successfully copied.")
def get_genomespace_client():
return GenomeSpaceClient(username=get_test_username(),
password=get_test_password())
def GeneLabLogin(self, username, password):
self.myGeneLabClient = GenomeSpaceClient(username, password)
return self.myGeneLabClient
def get_client(args):
return GenomeSpaceClient(username=args.user,
password=args.password,
token=args.token)