def make_clients():
api_key, device_key = get_api_key()
fw = flywheel.Flywheel(api_key)
if device_key:
fw_device = flywheel.Flywheel(device_key)
else:
fw_device = None
fw.enable_feature('beta')
# Mock cli login
home = os.environ['HOME']
os.environ['HOME'] = tmp_path = tempfile.mkdtemp()
cli_config_path = os.path.expanduser('~/.config/flywheel/')
if not os.path.exists(cli_config_path):
os.makedirs(cli_config_path)
with open(os.path.join(cli_config_path, 'user.json'), 'w') as cli_config:
json.dump({'key': api_key}, cli_config)
client = flywheel.Client()
client.enable_feature('beta')
# Don't need the login anymore
shutil.rmtree(tmp_path)
os.environ['HOME'] = home
return fw, client, fw_device
def main():
### Read in arguments
parser = argparse.ArgumentParser(description='BIDS Curation')
parser.add_argument('--api-key',
dest='api_key',
action='store',
required=True,
help='API key')
parser.add_argument('-p',
dest='project_label',
action='store',
required=False,
default=None,
help='Project Label on Flywheel instance')
parser.add_argument(
'--session',
dest='session_id',
action='store',
required=False,
default=None,
help=
'Session ID, used to look up project if project label is not readily available'
)
parser.add_argument('--reset',
dest='reset',
action='store_true',
default=False,
help='Reset BIDS data before running')
parser.add_argument('--session-only',
dest='session_only',
action='store_true',
default=False,
help='Only curate the session identified by --session')
parser.add_argument('--template-file',
dest='template_file',
action='store',
default=None,
help='Template file to use')
args = parser.parse_args()
### Prep
# Check API key - raises Error if key is invalid
fw = flywheel.Flywheel(args.api_key)
# Get project id from label
if args.project_label:
project_id = utils.validate_project_label(fw, args.project_label)
elif args.session_id:
project_id = utils.get_project_id_from_session_id(fw, args.session_id)
else:
print('Either project label or session id is required!')
sys.exit(1)
### Curate BIDS project
curate_bids_dir(fw,
project_id,
args.session_id,
reset=args.reset,
template_file=args.template_file,
session_only=args.session_only)
def test_validate_project_label_invalidproject(self):
""" Get project that does not exist. Assert function returns None.
NOTE: the environment variable $APIKEY needs to be defined with users API key
"""
client = flywheel.Flywheel(os.environ['APIKEY'])
label = 'doesnotexistdoesnotexistdoesnotexist89479587349'
with self.assertRaises(SystemExit):
utils.validate_project_label(client, label)
def test_client_isolation(self):
fw = self.fw
fw2 = flywheel.Flywheel('127.0.0.1:invalid-key')
try:
user = self.fw.get_current_user()
self.assertUserIsSane(user)
except flywheel.ApiException:
self.fail('Flywheel instance is not isolated!')
def test_validate_project_label_validproject(self):
""" Get project that DOES exist. Assert function returns the project.
NOTE: the environment variable $APIKEY needs to be defined with users API key
"""
client = flywheel.Flywheel(os.environ['APIKEY'])
label = 'Project Name'
project_id = utils.validate_project_label(client, label)
project_id_expected = u'58175ad3de26e00012c69306'
self.assertEqual(project_id, project_id_expected)
def make_clients():
api_key = None
if init_db.SCITRAN_PERSISTENT_DB_URI:
# Initialize database first
init_db.init_db()
site_url = urlparse(os.environ['SCITRAN_SITE_API_URL'])
api_key = '{}:__force_insecure:{}'.format(
site_url.netloc, init_db.SCITRAN_ADMIN_API_KEY)
else:
api_key = os.environ.get('SdkTestKey')
if not api_key:
print(
'Could not initialize test case, no api_key. Try setting the SdkTestKey environment variable!'
)
exit(1)
fw = flywheel.Flywheel(api_key)
fw.enable_feature('beta')
fw_root = flywheel.Flywheel(api_key, root=True)
fw_root.enable_feature('beta')
# Mock cli login
home = os.environ['HOME']
os.environ['HOME'] = tmp_path = tempfile.mkdtemp()
cli_config_path = os.path.expanduser('~/.config/flywheel/')
if not os.path.exists(cli_config_path):
os.makedirs(cli_config_path)
with open(os.path.join(cli_config_path, 'user.json'), 'w') as cli_config:
json.dump({'key': api_key}, cli_config)
client = flywheel.Client()
client.enable_feature('beta')
# Don't need the login anymore
shutil.rmtree(tmp_path)
os.environ['HOME'] = home
return fw, fw_root, client
def create_flywheel_client(require=True):
config = load_config()
if config is None or config.get('key') is None:
if require:
print(
'Not logged in, please login using `fw login` and your API key',
file=sys.stderr)
sys.exit(1)
return None
result = flywheel.Flywheel(config['key'])
log.debug('SDK Version: %s', flywheel.flywheel.SDK_VERSION)
log.debug('Flywheel Site URL: %s', result.api_client.configuration.host)
return result
def download_tabular_file_wrapper(filename, project_label, group_id, api_key):
api_key = get_fw_api(api_key)
fw = flywheel.Flywheel(api_key)
project = handle_project(fw, project_label, group_id, create=False,
raise_on="missing")
project_id = project["id"]
df = get_info_for_all(fw, project_id)
df.drop(columns=["BIDS.Label", "BIDS.Subject"], inplace=True)
Path(filename).parent.mkdir(parents=True, exist_ok=True)
df.to_csv(filename, index=False, sep="\t")
def main_with_args(api_key, session_id, reset, session_only):
### Prep
# Check API key - raises Error if key is invalid
fw = flywheel.Flywheel(api_key)
if session_id:
project_id = utils.get_project_id_from_session_id(fw, session_id)
else:
print('Session id is required!')
sys.exit(1)
### Curate BIDS project
curate_bids_dir(fw,
project_id,
session_id,
reset=reset,
session_only=session_only)
def generate_license(args):
license_file = '/opt/freesurfer/license.txt'
license_info = ''
# If the config file does not exist then exit
if not os.path.isfile(args.json_file):
raise SystemExit('File does not exist: %s!' % args.json_file)
# Read the config json file
with open(args.json_file, 'r') as jsonfile:
config = json.load(jsonfile)
# OPTION 1: Parse config for license elements
print(
'\tChecking for license in Gear Configuration (config.FREESURFER_LICENSE)...'
)
if config['config'].get('FREESURFER_LICENSE'):
license_info = ' '.join(
config['config']['FREESURFER_LICENSE'].split()).replace(" ", "\n")
print(
'\t-->Generating FREESURFER LICENSE file from Gear Configuration.')
# OPTION 2: Parse config for license elements
if not license_info:
print(
'\tChecking for license in project info (project.info.FREESURFER_LICENSE)...'
)
fw = flywheel.Flywheel(config['inputs']['api_key']['key'])
project_id = fw.get_analysis(
config['destination']['id']).parents.project
project = fw.get_project(project_id)
if project.info.get('FREESURFER_LICENSE'):
license_info = ' '.join(
project.info.get('FREESURFER_LICENSE').split()).replace(
" ", "\n")
print('\t-->Generating FREESURFER LICENSE file from Project Info.')
# Write the license info to a file.
if license_info:
with open(license_file, 'w') as lf:
lf.write(license_info)
return 0
else:
return 1
def get_flywheel_subjects(key, group_id, project_label, studyid, basedir):
# Create client
fw = flywheel.Flywheel(key) # API key
subs = []
# Iterates through given project
for project in fw.get_group_projects(group_id):
if project.label == project_label:
print('Project: %s: %s' % (project.id, project.label))
# Iterates through sessions in project
for session in fw.get_project_sessions(project.id):
# Finds subject id for session
if 'BIDS' in session.info:
sub = session.info['BIDS']['Subject']
for analysis in fw.get_session_analyses(session.id):
# looks for fmriprep analyses
if 'fmriprep' in analysis.label:
if analysis.files != None: # checks for output files - that fmriprep succeeded
if sub not in subs:
subs.append(sub)
subs.sort()
return subs
def main():
key = os.environ.get('FlywheelKey')
fw = flywheel.Flywheel(key)
manifest = load_json_from_file(manifest_path)
name = manifest['name']
version = manifest['name']
new_version = version
for gear in fw.get_all_gears():
if gear['gear']['name'] == name:
new_version = int(gear['gear']['version']) + 1
if new_version != version:
print 'New gear version will be ' + str(new_version)
manifest['version'] = str(new_version)
write_json_to_file(manifest_path, manifest)
if os.environ.get('CIRCLE_BRANCH') == 'master':
check(call(['fw', 'gear', 'upload']))
else:
print 'Not running on master, so not pushing.'
import shutil
import logging
from fw_heudiconv.cli import curate, export, tabulate
# logging stuff
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('fw-heudiconv-gear')
logger.info("=======: fw-heudiconv starting up :=======")
# start up inputs
invocation = json.loads(open('config.json').read())
config = invocation['config']
inputs = invocation['inputs']
destination = invocation['destination']
fw = flywheel.Flywheel(inputs['api_key']['key'])
user = fw.get_current_user()
# start up logic:
heuristic = None #inputs['heuristic']['location']['path']
analysis_container = fw.get(destination['id'])
project_container = fw.get(analysis_container.parents['project'])
project_label = project_container.label
dry_run = False #config['dry_run']
action = "Export" #config['action']
# whole project, single session?
do_whole_project = False #config['do_whole_project']
if not do_whole_project:
def main():
### Read in arguments
parser = argparse.ArgumentParser(description='BIDS Directory Export')
parser.add_argument(
'--bids-dir',
dest='bids_dir',
action='store',
required=True,
help='Name of directory in which to download BIDS hierarchy. \
NOTE: Directory must be empty.')
parser.add_argument('--api-key',
dest='api_key',
action='store',
required=True,
help='API key')
parser.add_argument('--source-data',
dest='source_data',
action='store_true',
default=False,
required=False,
help='Include source data in BIDS export')
parser.add_argument(
'--dry-run',
dest='dry_run',
action='store_true',
default=False,
required=False,
help=
'Don\'t actually export any data, just print what would be exported')
parser.add_argument(
'--replace',
dest='replace',
action='store_true',
default=False,
required=False,
help='Replace files if the modified timestamps do not match')
parser.add_argument('--subject',
dest='subjects',
action='append',
help='Limit export to the given subject')
parser.add_argument('--session',
dest='sessions',
action='append',
help='Limit export to the given session name')
parser.add_argument('--folder',
dest='folders',
action='append',
help='Limit export to the given folder. (e.g. func)')
parser.add_argument('-p',
dest='project_label',
action='store',
required=False,
default=None,
help='Project Label on Flywheel instance')
parser.add_argument(
'--container-type',
dest='container_type',
action='store',
required=False,
default=None,
help=
'Download single container (acquisition|session|project) in BIDS format. Must provide --container-id.'
)
parser.add_argument(
'--container-id',
dest='container_id',
action='store',
required=False,
default=None,
help=
'Download single container in BIDS format. Must provide --container-type.'
)
args = parser.parse_args()
# Check API key - raises Error if key is invalid
fw = flywheel.Flywheel(args.api_key)
try:
export_bids(fw,
args.bids_dir,
args.project_label,
subjects=args.subjects,
sessions=args.sessions,
folders=args.folders,
replace=args.replace,
dry_run=args.dry_run,
container_type=args.container_type,
container_id=args.container_id,
source_data=args.source_data)
except utils.BIDSException as bids_exception:
logger.error(bids_exception)
sys.exit(bids_exception.status_code)
import logging
from fw_heudiconv.cli import export
# logging stuff
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('reproin-checker-gear')
logger.info("{:=^70}\n".format(": reproin-checker gear manager starting up :"))
# start up inputs
invocation = json.loads(open('config.json').read())
config = invocation['config']
inputs = invocation['inputs']
destination = invocation['destination']
key = inputs['api-key']['key']
fw = flywheel.Flywheel(key)
user = fw.get_current_user()
# start up logic:
analysis_container = fw.get(destination['id'])
project_container = fw.get(analysis_container.parents['project'])
project_label = project_container.label
# find session object origin
session_container = fw.get(analysis_container.parent['id'])
sessions = [session_container.label]
# find subject object origin
subject_container = fw.get(session_container.parents['subject'])
subjects = [subject_container.label]
# logging stuff
os.makedirs(rootdir)
# Read in config file
config_file = os.path.join(flywheel_basedir, 'config.json')
if not os.path.exists(config_file):
raise Exception('Config file (%s) does not exist' % config_file)
fp = open(config_file, 'r')
config_contents = json.loads(fp.read())
fp.close()
# Get apikey and session ID number from config file
api_key = str(config_contents['inputs']['api_key']['key'])
analysis_id = str(config_contents['destination']['id'])
## Create SDK client
print("Create SDK client")
fw = flywheel.Flywheel(api_key)
# Get analysis
analysis = fw.get_analysis(analysis_id)
# Get container type and id from
container_type = analysis['parent']['type']
container_id = analysis['parent']['id']
# Check if curate-bids was ran
# Determine if ID is a project or a session ID
if container_type == 'project':
# Get list of sessions within project
container = fw.get_project(container_id)
elif container_type == 'session':
# If container type is a session, get the specific session
container = fw.get_session(container_id)
if __name__ == '__main__':
"""
Given a Flywheel job id, this script will generate a local testing directory
within which you can run the job locally, using Docker, as it ran in Flywheel.
Positional inputs:
[1] - Api Key
[2] - Job ID
[3] - (Optional) Directory to save job contents. Defaults to cwd.
"""
if not sys.argv[1]:
raise ValueError('API KEY required')
else:
api_key = sys.argv[1]
fw = flywheel.Flywheel(api_key)
if fw.get_current_user().root:
fw = flywheel.Flywheel(api_key, root=True)
else:
raise ValueError('This process requires site-admin priviliges!')
# Get the job
job = fw.get_job(sys.argv[2])
# Build the local test
if len(sys.argv) == 4:
test_path_root = sys.argv[3]
else:
test_path_root = os.getcwd()
build_local_test(job, test_path_root, api_key)
gear.log('input \"dicom\" is a ' + gear.data['inputs']['dicom']['base'])
gear.log('you can find your file at ' +
gear.data['inputs']['dicom']['location']['path'])
# as an example a file processing we rename and copy the input file to ./output for upload to Flywheel
copyfile(
gear.data['inputs']['dicom']['location']['path'],
'./output/copy_of_' + gear.data['inputs']['dicom']['location']['name'])
# Check if the flywheel SDK is installed
try:
import flywheel
# Make some simple calls to the API
fw = flywheel.Flywheel(gear.data['inputs']['api-key']['key'])
user = fw.get_current_user()
config = fw.get_config()
gear.log('You are logged in as ' + user.firstname + ' ' + user.lastname +
' at ' + config.site.api_url[:-4])
except ImportError:
gear.log(
'\nFlywheel SDK is not installed, try "fw gear modify" and then "pip install flywheel-sdk".\n'
)
#place output files in the gear output_folder
gear.log(
'Make sure to move any result files you want to preserve to the output folder'
)
def main():
### Read in arguments
parser = argparse.ArgumentParser(description='BIDS Directory Upload')
parser.add_argument('--bids-dir',
dest='bids_dir',
action='store',
required=True,
help='BIDS directory')
parser.add_argument('--api-key',
dest='api_key',
action='store',
required=True,
help='API key')
parser.add_argument('-g',
dest='group_id',
action='store',
required=True,
help='Group ID on Flywheel instance')
parser.add_argument('-p',
dest='project_label',
action='store',
required=False,
default=None,
help='Project Label on Flywheel instance')
parser.add_argument(
'--subject',
default=None,
help='Only upload data from single subject folder (i.e. sub-01)')
parser.add_argument(
'--session',
default=None,
help='Only upload data from single session fodler (i.e. ses-01)')
parser.add_argument(
'--type',
dest='hierarchy_type',
action='store',
required=False,
default='Flywheel',
choices=['BIDS', 'Flywheel'],
help="Hierarchy to load into, either 'BIDS' or 'Flywheel'")
parser.add_argument('--source-data',
dest='source_data',
action='store_true',
default=False,
required=False,
help='Include source data in BIDS upload')
parser.add_argument(
'--use-template-defaults',
dest='local_properties',
action='store_false',
default=True,
required=False,
help='Prioiritize template default values for BIDS information')
parser.add_argument('-y',
'--yes',
action='store_true',
help='Assume the answer is yes to all prompts')
args = parser.parse_args()
if args.session and not args.subject:
logger.error('Cannot only provide session without subject')
sys.exit(1)
# Check API key - raises Error if key is invalid
fw = flywheel.Flywheel(args.api_key)
upload_bids(fw,
args.bids_dir,
args.group_id,
project_label=args.project_label,
hierarchy_type=args.hierarchy_type,
include_source_data=args.source_data,
local_properties=args.local_properties,
assume_yes=args.yes,
subject_label=args.subject,
session_label=args.session)
def export_raw_bids(studyid, basedir, key, group_id, project_label):
studydir = os.path.join(basedir, studyid)
rawdir = os.path.join(studydir, 'raw')
if not os.path.exists(rawdir):
os.makedirs(rawdir)
# checks whether docker is installed (but not if docker is running)
dockerExists = False
try:
FNULL = open(os.devnull, 'w')
sp.call(['docker'], stdout=FNULL, stderr=sp.STDOUT)
dockerExists = True
except:
dockerExists = False
# check if fw CLI is installed - needed for exporting BIDS
fwExists = False
try:
FNULL = open(os.devnull, 'w')
sp.call(['fw'], stdout=FNULL, stderr=sp.STDOUT)
fwExists = True
except:
fwExists = False
print '\n## Exporting raw BIDS now ##\n'
if fwExists and dockerExists:
# Create client
fw = flywheel.Flywheel(key) # API key
sub_codes = []
for project in fw.get_group_projects(group_id):
if project.label == project_label:
print('Project: %s: %s' % (project.id, project.label))
for session in fw.get_project_sessions(project.id):
sub = session.subject.code
if sub not in sub_codes:
sub_codes.append(session.subject.code)
all_subs = get_all_subs(
studydir) # subjects with fmriprep outputs downloaded
sub_code_dict = {}
for code in sub_codes:
code_w_underscore_removed = code.replace("_", "")
# want to removed underscore from subject code because underscore in subject id is not compatible with BIDS
if code_w_underscore_removed in all_subs:
sub_code_dict[
code] = code_w_underscore_removed # key is subject code, value is subject id
# subject code is used to export BIDS, subject id used by the fmriprep output
sub_list = sub_code_dict.keys()
sub_list.sort()
for sub_code in sub_list:
sub = sub_code_dict[sub_code]
rawsubdir = os.path.join(rawdir, 'sub-%s' % sub)
if os.path.exists(rawsubdir):
print "Skipping download of raw bids for sub-%s" % sub
else:
# creates tmp dir specific to the subject
tmpsubdir = os.path.join(studydir, 'tmp_sub-%s_BIDS' % sub)
os.mkdir(tmpsubdir)
# call subprocess to export BIDS
commands = [
'fw', 'export', 'bids', tmpsubdir, '-p', project_label,
'--subject', sub_code
]
print 'Calling:', ' '.join(commands)
sp.call(commands)
# moves the exported directory into the raw directory
rawsubout = os.path.join(tmpsubdir, 'sub-%s' % sub)
print 'Moving %s to %s' % (rawsubout, rawdir)
sp.call(['mv', rawsubout, rawdir])
# removes tmp directory that was created
print 'Removing %s' % (tmpsubdir)
sp.call(['rm', '-rf', tmpsubdir])
"""
# gets all subjects with fmriprep directories
#all_subs=get_all_subs(studydir)
for sub in all_subs: # sub is missing the prefix 'sub-'
rawsubdir=os.path.join(rawdir,'sub-%s'%sub)
if os.path.exists(rawsubdir):
print "Skipping download of raw bids for sub-%s"%sub
else:
# creates tmp dir specific to the subject
tmpsubdir=os.path.join(studydir,'tmp_sub-%s_BIDS'%sub)
os.mkdir(tmpsubdir)
# call subprocess to export BIDS
commands=['fw','export','bids',tmpsubdir,'-p',project_label,'--subject',sub]
print 'Calling:',' '.join(commands)
sp.call(commands)
# moves the exported directory into the raw directory
rawsubout=os.path.join(tmpsubdir,'sub-%s'%sub)
print 'Moving %s to %s'%(rawsubout,rawdir)
sp.call(['mv',rawsubout,rawdir])
# removes tmp directory that was created
print 'Removing %s'%(tmpsubdir)
sp.call(['rm','-rf',tmpsubdir])
"""
# to download all raw bids rather than subject by subject
"""
tmpdir=os.path.join(studydir,'tmp_BIDS')
commands=['fw','export','bids',tmpdir,'-p',project_label]
sp.call(commands)
sp.call(['mv',tmpdir, rawdir])
subs = os.listdir(tmpdir)
for sub in subs:
rawsubout = os.path.join(tmpdir,sub)
if not os.path.exists(rawsubout):
sp.call(['mv',rawsubout,rawdir])
sp.call(['rm','-rf',tmpdir])
"""
else:
if not fwExists:
print 'Flywheel CLI is not installed, which is required for exporting raw BIDS.'
if not dockerExists:
print 'Docker is not installed. Docker is required to export raw BIDS from flywheel'
def download_flywheel_fmriprep(key, group_id, project_label, studyid, basedir,
downloadReports, downloadFmriprep,
downloadFreesurfer, ignoreSessionLabel,
subjectList, overwriteSubjectOutputs):
# Creates tmp, fmriprep, and reports directories if they don't exist
studydir = os.path.join(basedir, studyid)
if not os.path.exists(studydir):
os.mkdir(studydir)
tmpdir = os.path.join(studydir, 'tmp')
if not os.path.exists(tmpdir):
os.mkdir(os.path.join(tmpdir))
fmriprepdir = os.path.join(studydir, 'fmriprep')
if downloadFmriprep and not os.path.exists(fmriprepdir):
os.mkdir(fmriprepdir)
freesurferdir = os.path.join(studydir, 'freesurfer')
if downloadFreesurfer and not os.path.exists(freesurferdir):
os.mkdir(freesurferdir)
reportsdir = os.path.join(studydir, 'reports')
if downloadReports and not os.path.exists(reportsdir):
os.mkdir(reportsdir)
# Create client
fw = flywheel.Flywheel(key) # API key
if overwriteSubjectOutputs:
remove_existing_sub_dirs_to_overwrite_later(studyid, basedir,
subjectList,
downloadReports,
downloadFmriprep,
downloadFreesurfer)
print '\n## Downloading fmriprep outputs now ##\n'
# Iterates through given project
for project in fw.get_group_projects(group_id):
if project.label == project_label:
print('Project: %s: %s' % (project.id, project.label))
for session in fw.get_project_sessions(project.id):
if 'BIDS' not in session.info:
break
sub = session.info['BIDS']['Subject']
if sub in subjectList:
dates = []
analysis_ids = {} # key is date, value is analysis.id
analysis_objs = {
} # key is analysis.id, value is analysis object
for analysis in fw.get_session_analyses(session.id):
# looks for fmriprep analyses
if 'fmriprep' in analysis.label:
print('\tAnalysis: %s: %s' %
(analysis.id, analysis.label))
date_created = analysis.created
analysis_ids[date_created] = analysis.id
analysis_objs[analysis.id] = analysis
if analysis.files != None: # checks for output files - that fmriprep succeeded
dates.append(date_created)
if len(dates) != 0:
list.sort(dates)
most_recent_analysis_id = analysis_ids[dates[
-1]] # if fmriprep was run multiple times, uses most recent analysis
"""
# Doesn't work at the moment
try:
print "Downloading session analysis"
fw.download_session_analysis_outputs(session.id, analysis.id)
except flywheel.ApiException as e:
print 'Could not use fw.download_session_analysis_outputs'
print('API Error: %d -- %s' % (e.status, e.reason))
"""
for file in analysis_objs[
most_recent_analysis_id].files:
#print file.name
name = file.name
# assumes subject ID is between sub- and _ or between sub- and .
if 'sub-' in name:
i1 = name.find('sub-')
tmpname = name[i1:]
if '_' in tmpname:
i2 = tmpname.find('_')
else:
i2 = tmpname.find('.')
if i1 > -1 and i2 > -1:
sub = tmpname[:
i2] # sub is the subject ID with 'sub-' removed
#print "Subject ID:", sub
# get fmriprep reports (html and svg files)
if downloadReports and 'html' in file.name: # sub-<id>.html.zip
subreportsdir = os.path.join(
reportsdir, sub)
session_label = session['label']
session_label = re.sub(
r'[^a-zA-Z0-9]+', '', session_label
) # remove non-alphanumeric characters
subsesreportsdir = os.path.join(
reportsdir, sub,
'ses-' + session_label)
if not ignoreSessionLabel and os.path.exists(
subsesreportsdir
) and not overwriteSubjectOutputs:
print 'Skipping downloading and processing of fmriprep reports for %s/ses-%s' % (
sub, session_label)
elif ignoreSessionLabel and os.path.exists(
subreportsdir
) and not overwriteSubjectOutputs:
print 'Skipping downloading and processing of fmriprep reports for %s' % (
sub)
else:
downloadSessionOnly = False
if os.path.exists(
subreportsdir
) and not ignoreSessionLabel:
downloadSessionOnly = True
# download the file
outfile = sub + '.html.zip'
print 'Downloading', sub + '/ses-' + session_label + ':', file.name
filepath = os.path.join(
tmpdir, outfile)
fw.download_output_from_session_analysis(
session.id,
most_recent_analysis_id,
file.name, filepath)
#download_request = fw.download_session_analysis_outputs(session.id, most_recent_analysis_id, ticket='')
#fw.download_ticket(download_request.ticket, filepath)
unzippedfilepath = filepath[:-4]
# unzip the file
unzip_dir(filepath,
unzippedfilepath)
# Move sub folder in sub-<id>.html->flywheel->...->sub-<id> to the reportsdir
# iterates through the flywheel folder to find sub folder buried inside
# the variable i is used to avoid an infinite loop
i = 10
curdir = ''
fullcurdir = os.path.join(
unzippedfilepath, 'flywheel')
moved = False
while i > 0 and curdir != sub:
if sub in os.listdir(
fullcurdir):
desireddir = os.path.join(
fullcurdir, sub)
targetdir = reportsdir
if downloadSessionOnly:
desireddir = os.path.join(
fullcurdir, sub,
'ses-' +
session_label)
targetdir = os.path.join(
reportsdir, sub)
#if not os.path.exists(targetdir):
# os.mkdir(targetdir)
if os.path.exists(
desireddir):
move_dir(
desireddir,
targetdir)
moved = True
if len(os.listdir(
fullcurdir)) > 0:
# assuming only one directory in fullcurdir
for folder in os.listdir(
fullcurdir):
if os.path.isdir(
os.path.join(
fullcurdir,
folder)):
curdir = folder
fullcurdir = os.path.join(
fullcurdir,
folder)
i -= 1
if not moved:
print "Could not find %s in %s.html" % (
sub, sub)
# moves and renames index.html to sub-<id>.html
indexhtmlpath = os.path.join(
unzippedfilepath, 'index.html')
if os.path.exists(indexhtmlpath):
subreportsdir = os.path.join(
reportsdir, sub)
move_dir(
indexhtmlpath,
subreportsdir)
oldindexhtml = os.path.join(
subreportsdir,
'index.html')
#newindexhtml=os.path.join(subreportsdir,'ses-'+session_label,'%s.html'%sub)
newindexhtml = os.path.join(
reportsdir,
'%s.html' % sub)
move_dir(
oldindexhtml, newindexhtml)
# move figures directory
figurespath = os.path.join(
unzippedfilepath, sub,
'figures')
print figurespath
if os.path.exists(figurespath):
subreportsdir = os.path.join(
reportsdir, sub)
move_dir(
figurespath, subreportsdir)
# remove originally downloaded files
remove_dir(filepath)
remove_dir(unzippedfilepath)
# get fmriprep outputs
elif (
downloadFmriprep
or downloadFreesurfer
) and file.name.startswith(
'fmriprep_' + sub
): # fmriprep_sub-<subid>_<random alphanumericcode?>.zip
subfmriprepdir = os.path.join(
fmriprepdir, sub)
subfreesurferdir = os.path.join(
freesurferdir, sub)
session_label = session['label']
session_label = re.sub(
r'[^a-zA-Z0-9]+', '', session_label
) # remove non-alphanumeric characters
subsesfmriprepdir = os.path.join(
fmriprepdir, sub,
'ses-' + session_label)
continueFmriprepDownload = downloadFmriprep
continueFreesurferDownload = downloadFreesurfer
if not ignoreSessionLabel and downloadFmriprep and os.path.exists(
subsesfmriprepdir
) and not overwriteSubjectOutputs:
print 'Skipping downloading and processing of fmriprep outputs for %s/ses-%s' % (
sub, session_label)
continueFmriprepDownload = False
elif ignoreSessionLabel and downloadFmriprep and os.path.exists(
subfmriprepdir
) and not overwriteSubjectOutputs:
print 'Skipping downloading and processing of fmriprep outputs for %s' % (
sub)
continueFmriprepDownload = False
if not ignoreSessionLabel and downloadFreesurfer and os.path.exists(
subfreesurferdir
) and not overwriteSubjectOutputs:
print 'Skipping downloading and processing of freesurfer outputs for %s' % sub
continueFreesurferDownload = False
if continueFmriprepDownload or continueFreesurferDownload:
downloadSessionOnly = False
if os.path.exists(
subfmriprepdir
) and not ignoreSessionLabel:
downloadSessionOnly = True
outfile = sub + '.zip'
# downloads outputs
print 'Downloading', sub + '/ses-' + session_label + ':', file.name
filepath = os.path.join(
tmpdir, outfile)
fw.download_output_from_session_analysis(
session.id,
most_recent_analysis_id,
file.name, filepath)
#download_request = fw.download_session_analysis_outputs(session.id, most_recent_analysis_id, ticket='')
#fw.download_ticket(download_request.ticket, filepath)
# unzips outputs
unzippedfilepath = filepath[:
-4] # removes .zip from name
unzip_dir(filepath,
unzippedfilepath)
# Move downloaded fmriprep folder to fmriprep
unzippedfmriprep = os.path.join(
unzippedfilepath, 'fmriprep',
sub)
newsubfmriprep = os.path.join(
fmriprepdir, '%s' % sub)
# iterates through the unzipped sub folder to find fmriprep folder buried inside
# the variable i is used to avoid an infinite loop
i = 3
curdir = ''
fullcurdir = unzippedfilepath
desireddir = os.path.join(
fullcurdir, 'fmriprep', sub)
moved = False
while i > 0 and curdir != 'fmriprep' and curdir != 'freesurfer':
if downloadFmriprep and continueFmriprepDownload and 'fmriprep' in os.listdir(
fullcurdir):
desireddir = os.path.join(
fullcurdir, 'fmriprep',
sub)
targetdir = fmriprepdir
if downloadSessionOnly:
desireddir = os.path.join(
fullcurdir,
'fmriprep', sub,
'ses-' +
session_label)
targetdir = os.path.join(
fmriprepdir, sub)
tmpsubfmriprepdir = os.path.join(
fullcurdir, 'fmriprep',
sub)
if os.path.exists(
desireddir):
move_dir(
desireddir,
targetdir)
moved = True
if downloadFreesurfer and continueFreesurferDownload and 'freesurfer' in os.listdir(
fullcurdir):
tmpsubfreesurferdir = os.path.join(
fullcurdir,
'freesurfer', sub)
if os.path.exists(
tmpsubfreesurferdir
) and not os.path.exists(
os.path.join(
freesurferdir,
sub)):
move_dir(
tmpsubfreesurferdir,
freesurferdir)
moved = True
if len(os.listdir(
fullcurdir)) > 0:
# assuming only one directory in fullcurdir
for folder in os.listdir(
fullcurdir):
if os.path.isdir(
os.path.join(
fullcurdir,
folder)):
curdir = folder
fullcurdir = os.path.join(
fullcurdir,
folder)
i -= 1
if downloadFmriprep and not moved:
print "Could not find fmriprep in %s" % fullcurdir
# Remove figures directory from sub folder in fmriprep
# the figures directory is a duplicate of the fmriprep reports, which are downloaded separately into the reports directory
fmriprepsubfigures = os.path.join(
newsubfmriprep, 'figures')
remove_dir(fmriprepsubfigures)
remove_dir(filepath)
remove_dir(unzippedfilepath)
# remove the tmp directory
if os.path.exists(tmpdir):
remove_dir(tmpdir)
def main():
### SETUP
# Define variables
flywheel_basedir = os.environ['FLYWHEEL']
rootdir = os.path.join(flywheel_basedir, 'input', 'bids_dataset')
if not os.path.exists(rootdir):
os.makedirs(rootdir)
# Read in config file
config_file = os.path.join(flywheel_basedir, 'config.json')
if not os.path.exists(config_file):
raise Exception('Config file (%s) does not exist' % config_file)
fp = open(config_file, 'r')
config_contents = json.loads(fp.read())
fp.close()
# Get apikey and session ID number from config file
api_key = str(config_contents['inputs']['api_key']['key'])
analysis_id = str(config_contents['destination']['id'])
## Create SDK client
print("Create SDK client")
fw = flywheel.Flywheel(api_key)
# Get analysis
analysis = fw.get_analysis(analysis_id)
# Get container type and id from
container_type = analysis['parent']['type']
container_id = analysis['parent']['id']
# Check if curate-bids was ran
# Determine if ID is a project or a session ID
if container_type == 'project':
# Get list of sessions within project
project = fw.get_project(container_id)
BIDS_metadata = project.get('info', {}).get('BIDS')
elif container_type == 'session':
# If container type is a session, get the specific session
session = fw.get_session(container_id)
project = fw.get_project(session.project)
BIDS_metadata = session.get('info', {}).get('BIDS')
if BIDS_metadata:
try:
export_bids.export_bids(fw,
rootdir,
project.label,
subjects=[session.subject.code],
sessions=[session.label],
validate=False)
if BIDS_metadata != 'NA':
if container_type == 'session':
download_optional_inputs(
flywheel_basedir,
"sub-{}".format(BIDS_metadata.get('Subject')),
"ses-{}".format(BIDS_metadata.get('Label')))
else:
print(
'BIDS Curation was not valid, will not download additional files.'
)
except SystemExit: # This is a necessary evil until bids_export doesn't call sys.exit(1)
print('Curated BIDS export failed, using on-the-fly bids-export')
# Clean rootdir
shutil.rmtree(rootdir)
os.makedirs(rootdir)
create_and_download_bids(fw, rootdir, flywheel_basedir,
analysis_id)
else:
create_and_download_bids(fw, rootdir, flywheel_basedir, analysis_id)
ts2 = other.acq.get('timestamp')
if ts1 and ts2:
return int((ts1 - ts2).total_seconds())
return int((self.acq['created'] - other.acq['created']).total_seconds())
def to_dict(fw, obj):
return fw.api_client.sanitize_for_serialization(obj.to_dict())
if __name__ == '__main__':
import argparse
import flywheel
import json
parser = argparse.ArgumentParser(description='Dump project tree to json')
parser.add_argument('--api-key', dest='api_key', action='store',
required=True, help='API key')
parser.add_argument('-p', dest='project_label', action='store',
required=False, default=None, help='Project Label on Flywheel instance')
parser.add_argument('output_file', help='The output file destination')
args = parser.parse_args()
fw = flywheel.Flywheel(args.api_key)
project_id = utils.validate_project_label(fw, args.project_label)
project_tree = get_project_tree(fw, project_id)
with open(args.output_file, 'w') as f:
json.dump(project_tree.to_json(), f, indent=2)
