def upload_tabular_file_wrapper(filename, project_label, group_id, api_key=None, create=False, raise_on=None,
update_values=False, create_emtpy_entry=False, subject_col="subject_id",
session_col="session_id"):
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
project = handle_project(fw, project_label, group_id, create, raise_on)
project_id = project["id"]
upload_tabular_file(fw, filename, project_id, update_values, create_emtpy_entry, subject_col, session_col)
def main():
logger.info("{:=^70}\n".format(": fw-heudiconv exporter starting up :"))
parser = get_parser()
args = parser.parse_args()
with warnings.catch_warnings():
warnings.simplefilter("ignore")
if args.api_key:
fw = flywheel.Client(args.api_key)
else:
fw = flywheel.Client()
assert fw, "Your Flywheel CLI credentials aren't set!"
if args.path:
destination = args.path
else:
destination = args.destination
if not os.path.exists(destination):
logger.info("Creating destination directory...")
os.makedirs(args.destination)
downloads = gather_bids(
client=fw, project_label=args.project, session_labels=args.session,
subject_labels=args.subject
)
if args.attachments is not None and args.verbose:
logger.info("Filtering attachments...")
logger.info(args.attachments)
download_bids(
client=fw, to_download=downloads, root_path=destination,
folders_to_download=args.folders, dry_run=args.dry_run,
attachments=args.attachments, name=args.directory_name
)
if args.dry_run:
shutil.rmtree(Path(args.destination, args.directory_name))
logger.info("Done!")
logger.info("{:=^70}".format(": Exiting fw-heudiconv exporter :"))
def upload_subject_dir(path,
project_name,
permissions=None,
fw=None,
projectId=None):
if permissions is None: permissions = []
if fw is None: fw = flywheel.Client()
#if fw is None: fw = Client(environ['FLYWHEEL_TOKEN'])
if projectId is None:
projectId = find_project_id(project_name, permissions, fw=fw)
path = pathlib.Path(path)
subjectId = {
'code': path.name[4:],
'_id': None,
}
for session in path.iterdir():
if session.is_file():
lg.warning(
f'It is probably better to only upload inside session, so skip {session}'
)
continue
# a weird way because first you generate the session, which gives you the subject_id.
# then you reuse the same subject_id across session
info = {
'label': session.name,
'project': projectId,
}
if subjectId['_id'] is not None:
info['subject'] = subjectId
sessionId = fw.add_session(info)
if subjectId['_id'] is None:
subjectId['_id'] = fw.get_session(sessionId)['subject']['_id']
fw.modify_session(sessionId, {'subject': subjectId})
for acquisition in session.iterdir():
if acquisition.is_file():
lg.warning(
f'Uploading file {acquisition.name} from {session} as attachment'
)
fw.upload_file_to_project(projectId, str(acquisition))
continue
acquisitionId = fw.add_acquisition({
'label': acquisition.name,
'session': sessionId,
})
for filepath in acquisition.iterdir():
lg.debug(
f'Uploading {filepath.name} to {path.name}/{session.name}/{acquisition.name}'
)
if filepath.suffix in ('.vhdr', '.vmrk'):
continue
#if filepath.suffix == '.eeg':
# _zip_and_upload(filepath, fw, acquisitionId)
# continue
fw.upload_file_to_acquisition(acquisitionId, str(filepath))
def test_handle_sessions_no_changes(group='scien',
project='Nate-BIDS-pre-curate'):
fw = flywheel.Client()
proj = fw.lookup(f'{group}/{project}')
path = Path(__file__).parents[
1] / 'assets/project/session_labels_Nate-BIDS-pre-curate.csv'
ses_df = pd.read_csv(path.resolve())
handle_sessions(ses_df, fw, proj, dry_run=True)
# This test only checks for errors, so if we get here, we can assert True
# Integration testing checks for functionality
assert True
def delete_analyses(group_id, project_label, analysis_label, api_key=None):
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
project = fw.lookup(f"{group_id}/{project_label}")
for subject in project.subjects():
print(subject.label)
ana_list = fw.get_container_analyses(
subject.id, filter=f'label="{analysis_label}"')
for analysis in ana_list:
print(analysis.id)
fw.delete_container_analysis(subject.id, analysis.id)
def delete_canceled_analysis(group_id, project_label, api_key=None):
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
project = fw.lookup(f"{group_id}/{project_label}")
for subject in project.subjects():
print(subject.label)
ana_list = fw.get_container_analyses(subject.id)
for analysis in ana_list:
job = fw.get_job(analysis.job)
if (job.state == "cancelled") or (job.state == "failed"):
print(analysis.id)
fw.delete_container_analysis(subject.id, analysis.id)
def test_handle_subjects_no_changes(group='scien',
project='Nate-BIDS-pre-curate'):
fw = flywheel.Client()
proj = fw.lookup(f'{group}/{project}')
path = Path(__file__).parents[
1] / 'assets/project/subject_codes_Nate-BIDS-pre-curate.csv'
sub_df = pd.read_csv(path.resolve())
with pytest.raises(flywheel.rest.ApiException) as api_info:
handle_subjects(sub_df, fw, proj, dry_run=True)
# This test only checks for errors, so if we get here, we can assert True
# Integration testing checks for functionality
# Subject id is stale so it won't find
assert "not found" in api_info
def upload_analysis(group_id, project_label, root_dir, api_key=None, level="subject", subjects=[],
search_strings_template=["{subject}*"], note="", check_ignored_files=True):
"""
:param group_id:
:param project_label:
:param root_dir:
:param api_key:
:param level:
:param subjects:
:return:
"""
assert level in ["subject", "project"], f'level needs to be "subject" or "project", not {level}'
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
project = fw.lookup(f"{group_id}/{project_label}")
root_dir = Path(root_dir)
os.chdir(root_dir)
analysis_label = root_dir.name
files_uploaded = []
if level == "subject":
containers = get_subject_containers(project, subjects)
print(f"Uploading {root_dir} into {project_label} for {len(containers)} subject.")
cont()
for container in containers:
subject = container.label
print(subject)
search_strings = [s.format(subject=subject) for s in search_strings_template]
files_uploaded += zip_and_upload_data(fw, container, root_dir, analysis_label,
search_strings=search_strings, note=note)
elif level == "project":
container = project
search_strings = search_strings_template
print(f"Uploading {root_dir} into {project_label} for group data.")
cont()
files_uploaded += zip_and_upload_data(fw, container, root_dir, analysis_label,
search_strings=search_strings, note=note)
print("Upload done")
# check for files that have not been uploaded
if check_ignored_files:
all_files = set(list_files(root_dir, ["*"]))
files_not_uploaded = all_files - set(files_uploaded)
if files_not_uploaded:
files_not_uploaded_ = [str(f) for f in files_not_uploaded]
warn(f"\n\n\n{len(files_not_uploaded)} files not uploaded {files_not_uploaded_}")
def init_gear(gear_name):
"""
Initializes a gear from name. Returns the flywheel client and gear object.
Args:
gear_name (str): Name of gear in instance reference by API-Key.
Returns:
tuple: fw_client (flywheel.Client), gear (flywheel.GearDoc)
"""
fw_client = flywheel.Client()
gear = fw_client.gears.find_one(f'gear.name="{gear_name}"')
return fw_client, gear
def get_meica_data(context, output_directory="/flywheel/v0/output"):
"""
For a given input dicom file, grab all of the nifti files from that acquisition.
Return MEICA data which is a sorted list of file objects.
"""
# Flywheel Object
fw = flywheel.Client(context.get_input("api_key")["key"])
# For this acquisition find each nifti file, download it and note its echo time
acquisition = fw.get_acquisition(
context.get_input("functional")["hierarchy"]["id"])
nifti_files = [
x for x in acquisition.files
if x.type == "nifti" and "Functional" in x.classification["Intent"]
]
log.info("Found %d Functional NIfTI files in %s" %
(len(nifti_files), acquisition.label))
# Compile meica_data structure
meica_data = []
repetition_time = ""
for n in nifti_files:
file_path = os.path.join(output_directory, n.name)
log.info("Downloading %s" % (n.name))
fw.download_file_from_acquisition(acquisition.id, n.name, file_path)
echo_time = n.info.get("EchoTime")
# TODO: Handle case where EchoTime is not here
# or classification is not correct
# Or not multi echo data
# Or if coronavirus attacks
meica_data.append({
"path": n.name,
"te": echo_time * 1000
}) # Convert to ms
# Generate prefix
sub_code = (fw.get_session(
acquisition.parents.session).subject.code.strip().replace(" ", ""))
label = acquisition.label.strip().replace(" ", "")
prefix = "%s_%s" % (sub_code, label)
meica_data = sorted(meica_data, key=lambda k: k["te"])
datasets = [Path(meica["path"]) for meica in meica_data]
tes = [meica["te"] for meica in meica_data]
return (datasets, tes)
def test_dcm2niix_nifti():
sd.clean_working_dir()
input_file = sd.get_zipped_t1()
work_dir = Path(sd.WORKING_DIR) / "work"
work_dir.mkdir(exist_ok=True)
output_dir = Path(sd.WORKING_DIR) / "output"
output_dir.mkdir(exist_ok=True)
fw = flywheel.Client()
# Get configuration, acquisition, and file info
file_id = "626037fe7cc96261fa295c75"
file_obj = fw.get_file(file_id)
# destination_type = "nrrd" if config.get("save_NRRD") else "nifti"
input_file = Path(input_file)
destination_type = "nifti"
combine = False
bitmask = False
method = "dcm2niix"
exporter = MeasurementExport(
fw_client=fw,
fw_file=file_obj,
work_dir=work_dir,
output_dir=output_dir,
input_file_path=input_file,
dest_file_type=destination_type,
combine=combine,
bitmask=bitmask,
method=method,
)
ohifviewer_info, labels, affine = exporter.process_file()
globpath = output_dir / "*"
output_files = glob.glob(globpath.as_posix())
assert len(output_files) == 3
output_files = [os.path.basename(a) for a in output_files]
doggy = [d for d in output_files if d.startswith("ROI_Doggy")]
potato = [d for d in output_files if d.startswith("ROI_Potato")]
lesion = [d for d in output_files if d.startswith("ROI_Lesion")]
assert len(doggy) == 1
assert len(potato) == 1
assert len(lesion) == 1
sd.clean_working_dir()
def main():
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fw = flywheel.Client()
assert fw, "Your Flywheel CLI credentials aren't set!"
parser = argparse.ArgumentParser(description=(
"Use this to query Flywheel for the gears available to you, or get the config file for a gear."
))
parser.add_argument("-name",
"--gear-name",
dest='name',
help="Shorthand name of the gear on Flywheel",
required=True,
default='all')
parser.add_argument(
"-config",
"--output-config",
dest='config',
help="True/False; Whether to output configuration file for running",
required=False,
default='False')
args = parser.parse_args()
config = str2bool(args.config)
if args.name == 'all':
gears = fw.gears()
gears_table = [nested_to_record(g.to_dict(), sep='_') for g in gears]
df = pd.DataFrame(gears_table)
df = df.filter(regex=r'gear_label$|gear_name$|^category$', axis=1)
print(tabulate(
df,
headers='keys',
tablefmt='psql',
))
else:
gear = find_gear(args.name, fw)
config_file = collect_gear_config(gear['_id'], fw)
if config:
with open('gear_config.json', 'w') as outfile:
json.dump(config_file, outfile)
print("Config file written.")
else:
print(json.dumps(config_file, indent=4))
def login(args):
fw = flywheel.Client(args.api_key)
try:
# Get current user
login_id = sdk_impl.get_login_id(fw)
# Save credentials
sdk_impl.save_api_key(args.api_key, root=user['root'])
print('You are now logged in as: {}!'.format(login_id))
except Exception as e:
log.debug('Login error', exc_info=True)
perror('Error logging in: {}'.format(str(e)))
sys.exit(1)
def find_project_id(project_name, permissions, fw=None):
if fw is None: fw = flywheel.Client()
#fw = Flywheel(environ['FLYWHEEL_TOKEN'])
projects = [
x['_id'] for x in fw.get_all_projects() if x['label'] == project_name
]
if len(projects) == 1:
projectId = projects[0]
lg.debug(f'Adding to data to project "{project_name}"')
else:
projectId = fw.add_project({'label': project_name, 'group': GROUPID})
lg.debug(f'Creating project "{project_name}" to group "{GROUPID}"')
for perm in permissions[1:]:
fw.add_project_permission(projectId, perm)
return projectId
def fix_session_labels(group="pennftdcenter",
projectLabel="HUP6",
matchString="BRAIN RESEARCH^GROSSMAN"):
fw = flywheel.Client()
proj = fw.lookup("{}/{}".format(group, projectLabel))
must_fix = [s for s in proj.sessions() if matchString in s.label]
for s in must_fix:
# Create a new session label by piecing together year/month/day/hour/minute info
# from the session timestamp.
tstamp = s.timestamp
lab = '{}{}{}x{}{}'.format(tstamp.year, f'{tstamp.month:02}',
f'{tstamp.day:02}', f'{tstamp.hour:02}',
f'{tstamp.minute:02}')
# Update the session label using the update() method, whose input is a dictionary
# of the fields to be changed and their new values.
s.update({'label': lab})
def generate_gear_args(gear_context):
"""Generate gear arguments."""
log.info("Preparing arguments for dicom-send gear.")
gear_kwargs = {
"work_dir": gear_context.work_dir,
"destination": gear_context.config["destination"],
"called_ae": gear_context.config["called_ae"],
"port": gear_context.config["port"],
"calling_ae": gear_context.config["calling_ae"],
"group": "0x0021",
"identifier": "Flywheel",
"tag_value": "DICOM Send",
'api_key': gear_context.get_input("api_key")["key"]
}
fw = flywheel.Client(gear_kwargs['api_key'])
# Input is a tgz or zip DICOM archive, or a single DICOM file
try:
infile = Path(gear_context.get_input_path("file"))
download = not infile.is_file()
except TypeError:
download = True
log.info(
"No input provided. Will use files of type DICOM from session.")
if download is False:
gear_kwargs["infile"] = infile
gear_kwargs["parent_acq"] = gear_context.get_input(
"file")["hierarchy"].get("id")
# When a file is provided as input, destination ID is the acquisition ID
gear_kwargs['session_id'] = fw.get_acquisition(
gear_kwargs["parent_acq"]).parents.session
else:
# Alternatively, if no input is provided, all DICOM files in the session are
# downloaded and used as input
# In this case the destination ID is the session ID.
gear_kwargs['session_id'] = gear_context.destination["id"]
gear_kwargs['input_dir'] = "/flywheel/v0/input"
print_kwargs = dict(gear_kwargs)
print_kwargs.pop('api_key')
gear_args_formatted = pprint.pformat(print_kwargs)
log.info(f"Prepared gear stage arguments: \n\n{gear_args_formatted}\n")
return gear_kwargs, download
def fix_timestamps(project_label, group_id, api_key=None):
from datetime import datetime, timezone
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
project = fw.lookup(f"{group_id}/{project_label}")
print(f"Fixing timestamps for {group_id} {project_label}.")
for subject in project.subjects():
for session in subject.sessions():
print(f"{subject.label} {session.label}")
session_num = int(session.label.replace("ses-tp", ""))
if not session_num:
raise RuntimeError(f"Session cannot be determined: {session.label}")
session.update({"timestamp": datetime(1900, 1, session_num, 0, 0, tzinfo=timezone.utc)})
print("Done")
def cancle_jobs(pending=True, running=True, api_key=None):
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
searches = []
if pending:
searches.append('state=pending')
if running:
searches.append('state=running')
for search_str in searches:
jobs = fw.jobs.find(search_str)
print(f"Cancelling {len(jobs)} jobs")
for job in jobs:
print(job.id)
job.change_state('cancelled')
def main():
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fw = flywheel.Client()
assert fw, "Your Flywheel CLI credentials aren't set!"
parser = get_parser()
args = parser.parse_args()
# Print a lot if requested
if args.verbose:
logger.setLevel(logging.DEBUG)
project_label = ' '.join(args.project)
convert_to_bids(client=fw,
project_label=project_label,
heuristic_path=args.heuristic,
session_labels=args.session,
subject_labels=args.subject,
dry_run=args.dry_run)
def gather_session_indeces():
# use flywheel to gather a dict of all session session_labels
# with their corresponding index by time, within the subject
# query subjects
import flywheel
fw = flywheel.Client()
'''
lg = fw.projects.find_first('label="{}"'.format("PNC_LG_810336"))
lg_subjects = lg.subjects()
lg_subject_labs = [int(x.label) for x in lg_subjects]
'''
cs = fw.projects.find_first('label="{}"'.format("PNC_CS_810336"))
cs_subjects = cs.subjects()
cs_subject_labs = [int(x.label) for x in cs_subjects]
# initialise dict
sess_dict = {}
for x in range(len(cs_subjects)):
'''
# if they already have a session in the CS project
if lg_subject_labs[x] in cs_subject_labs:
n = 1
else:
n = 0
'''
# get a list of their sessions
sess_list = cs_subjects[x].sessions()
if sess_list:
# sort that list by timestamp
sess_list = sorted(sess_list, key=lambda x: x.timestamp)
# loop through the sessions and assign the session label an index
for i, y in enumerate(sess_list):
sess_dict[y.label] = "PNC" + str(i + 1)
return sess_dict
def test_data2csv_ses_duplicate(group='scien', project='Nate-BIDS-pre-curate'):
fw = flywheel.Client()
proj = fw.lookup(f'{group}/{project}')
sess = [ses.to_dict() for ses in fw.get_project_sessions(proj.id)]
path, df = data2csv(sess,
project,
keep_keys=['label'],
prefix='session_labels',
regex='[^A-Za-z0-9]',
column_rename=['existing_session_label'],
user_columns=['new_session_label'],
unique=['label'],
no_print=True)
print(df.values)
supposedly_unique = df.index.values
unique = np.unique(
pd.DataFrame.from_records(session_object)['label'].values)
#assert set(unique) == set(supposedly_unique)
assert (set(df.columns) == set(
['existing_session_label', 'new_session_label']))
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 main():
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fw = flywheel.Client()
assert fw, "Your Flywheel CLI credentials aren't set!"
parser = get_parser()
args = parser.parse_args()
project_label = ' '.join(args.project)
assert os.path.exists(args.path), "Path does not exist!"
downloads = gather_bids(client=fw,
project_label=project_label,
session_labels=args.session,
subject_labels=args.subject)
download_bids(client=fw,
to_download=downloads,
root_path=args.path,
folders_to_download=args.folders,
dry_run=args.dry_run)
def upload_project_dir(bids_root, project_name, permissions=None, fw=None):
if permissions is None: permissions = []
#if fw is None: fw = Flywheel(environ['FLYWHEEL_TOKEN'])
if fw is None: fw = flywheel.Client()
projectId = find_project_id(project_name, permissions, fw=fw)
bids_root = pathlib.Path(bids_root)
for extra in bids_root.iterdir():
if extra.is_file():
fw.upload_file_to_project(projectId, str(extra))
continue
if not extra.name.startswith('sub-'):
lg.debug(f'Uploading directory {extra.name} as zipped file')
_zip_and_upload(extra, fw, projectId)
continue
else:
upload_subject_dir(extra,
project_name,
projectId=projectId,
fw=fw,
permissions=permissions)
def main(context):
#fw = flywheel.Client()
config = context.config
for inp in context.config_json["inputs"].values():
if inp["base"] == "api-key" and inp["key"]:
api_key = inp["key"]
fw = flywheel.Client(api_key)
# Setup basic logging and log the configuration for this job
if config["gear_log_level"] == "INFO":
context.init_logging("info")
else:
context.init_logging("debug")
context.log_config()
dry_run = config.get('dry-run', False)
log.debug(f"dry_run is {dry_run}")
try:
destination_id = context.destination.get('id')
dest_container = fw.get(destination_id)
project_id = dest_container.parents.project
project = fw.get_project(project_id)
output_dict = ar.acquire_rois(fw, project)
output_path = Path(
context.output_dir
) / f"{project.label}_ROI-Export_{datetime.now().strftime('%d-%m-%Y_%H-%M-%S')}.csv"
ar.save_csv(output_dict, output_path)
except Exception as e:
log.exception(e)
return 1
return 0
def test_main():
import os
import flywheel
fw = flywheel.Client(os.environ["FWGA_API"])
# Get configuration, acquisition, and file info
from pathlib import Path
parent_acq = "621d449c559d4f2a0d1468e0"
file_id = "621d449f332f06de9645fd7a"
file_obj = fw.get_file(file_id)
input_file = "/Users/davidparker/Documents/Flywheel/SSE/MyWork/Gears/roi2nix/tests/test_ax_cor_sag/Scans/T1_SE_AX.zip"
# destination_type = "nrrd" if config.get("save_NRRD") else "nifti"
work_dir = "/Users/davidparker/Documents/Flywheel/SSE/MyWork/Gears/roi2nix/tests/test_ax_cor_sag/work"
output_dir = "/Users/davidparker/Documents/Flywheel/SSE/MyWork/Gears/roi2nix/tests/test_ax_cor_sag/output"
input_file = Path(input_file)
work_dir = Path(work_dir)
output_dir = Path(output_dir)
destination_type = "nifti"
combine = False
bitmask = False
method = "dcm2niix"
exporter = MeasurementExport(
fw_client=fw,
fw_file=file_obj,
work_dir=work_dir,
output_dir=output_dir,
input_file_path=input_file,
dest_file_type=destination_type,
combine=combine,
bitmask=bitmask,
method=method,
)
ohifviewer_info, labels, affine = exporter.process_file()
def make_clients():
api_key = get_api_key()
fw = flywheel.Flywheel(api_key)
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
def main():
fw = flywheel.Client()
parser = argparse.ArgumentParser()
parser.add_argument("-orig",
help="Path to the original flywheel query CSV",
dest="original",
required=True)
parser.add_argument("-mod",
help="Path to the modified flywheel query CSV",
dest="modified",
required=True)
args = parser.parse_args()
# original df
df_original = read_flywheel_csv(args.original)
# edited df
df_modified = read_flywheel_csv(args.modified)
# check for equality of each cell between the original and modified
unequal = get_unequal_cells(df_original, df_modified)
# if any unequal, assess the validity of the modification
res = validate_on_unequal_cells(unequal, df_modified)
if len(ERROR_MESSAGES) is 0 and res is True:
print("Changes appear to be valid! Uploading...")
diff = df_modified.fillna(9999) != df_original.fillna(9999)
#drop_downs = ['classification_Measurement', 'classification_Intent', 'classification_Features']
#df_modified.loc[:, drop_downs] = df_modified.loc[:, drop_downs].applymap(relist_item)
upload_to_flywheel(df_modified.loc[diff.any(axis=1), ], unequal, fw)
print("Done!")
sys.exit(0)
else:
print("Exiting...")
sys.exit(0)
def test_data2csv_acq_duplicate(group='scien', project='Nate-BIDS-pre-curate'):
fw = flywheel.Client()
proj = fw.lookup(f'{group}/{project}')
acqs = [acq.to_dict() for acq in fw.get_project_acquisitions(proj.id)]
path, df = data2csv(acqs,
project,
keep_keys=['label'],
prefix='acquisition_labels',
regex='[^A-Za-z0-9]',
column_rename=['existing_acquisition_label'],
user_columns=[
'new_acquisition_label', 'modality', 'task', 'run',
'ignore'
],
unique=['label'],
no_print=True)
supposedly_unique = np.sort(df['existing_acquisition_label'].values)
unique = np.unique(
pd.DataFrame.from_records(acquistions_object)['label'].values)
# assert unique.shape == supposedly_unique.shape
assert (df.columns == [
'existing_acquisition_label', 'new_acquisition_label', 'modality',
'task', 'run', 'ignore'
]).all()
def delete_lhab_info(group_id, project_label, api_key=None, delete_subject_info_keys=["missing_info"],
delete_session_info_keys=['cognition', 'health', 'demographics', 'motorskills',
'questionnaires']):
"""
Removes keys from the info dict on subject and session levels
Needs to be run in case variables are discontinued
"""
api_key = get_fw_api(api_key)
fw = flywheel.Client(api_key)
project = fw.lookup(f"{group_id}/{project_label}")
print(f"Deleting LHAB-related values (phenotype) in info dict for {group_id} {project_label}.")
for subject in project.subjects():
for k in delete_subject_info_keys:
print(f"{subject.label} {k}")
subject.delete_info(k)
for session in subject.sessions():
for k in delete_session_info_keys:
print(f"{subject.label} {session.label} {k}")
session.delete_info(k)
print("DONE")