CLI command reference: Ingest folder

The ingest folder command should be used if you are importing data that you previously downloaded from Flywheel, or if you are importing data that was shared from another Flywheel site. The folder import command uses the folder structure to map your data to the Flywheel hierarchy. Learn how to run the ingest folder command.

Below is the basic Flywheel hierarchy:

Usage

fw ingest folder [SRC] [optional arguments]

Required arguments

Required argument	Description
SRC	The parent folder for the directory you want to import

Optional arguments

Tip

If you are using multiple optional arguments in your command, consider creating a config file. See our article for more information on creating and using a config file.

Optional argument	Description
-h, --help	show this help message and exit
-g ID, --group ID	The id of the group, if not in folder structure
-p LABEL, --project LABE	The label of the project, if not in folder structure
--dicom NAME	The name of dicom subfolders to be zipped prior to upload
--pack-acquisitions TYPE	Acquisition folders only contain acquisitions of TYPE and are zipped prior to upload
--root-dirs ROOT_DIRS	The number of directories to discard before matching
--no-subjects	no subject level (create a subject for every session)
--no-sessions	no session level (create a session for every subject)
--group-override ID	Force using this group id
--project-override LABEL	Force using this project label
--include-dirs PATTERN	Patterns of directories to include Note When S3 bucket is configured as source, this flag does not support regex wildcard match, only “starts with.” `Include-dirs: OHM/101-10` `Will match:OHM/101-105, OHM/101-106, etc`
--exclude-dirs PATTERN	Patterns of directories to exclude
--include PATTERN	Patterns of filenames to include
--exclude PATTERN	Patterns of filenames to exclude
--compression-level COMPRESSION_LEVEL	The compression level to use for packfiles -1 by default. 0 for store. A higher compression level number means more compression
--ignore-unknown-tags	Ignore unknown dicom tags when parsing dicom files
--encodings ENCODINGS	Set character encoding aliases. E.g. win_1251=cp1251
--de-identify	De-identify DICOM files
--deid-profile NAME	Use the De-identify profile by name. Learn more about how to create a de-id profile.
--skip-existing	Skip import of existing files
--no-audit-log	Skip uploading audit log to the target projects
--load-subjects PATH	Load subjects from the specified file
--detect-duplicates	Identify duplicate data conflicts within source data and duplicates between source data and data in Flywheel. Duplicates are skipped and noted in audit log
--require-project	Proceed with the ingest process only if the resolved group and project exists (default: False) Note A new group/project will be created if the resolved group/project do not exist and this command is not invoked.
--enable-project-files	Enable file uploads to project container (default: False)

Reporter

These config options are only available when using cluster mode with the --follow argument or when using local worker.

Optional argument	Description
--save-audit-logs PATH	Save audit log to the specified path on the current machine
--save-deid-logs PATH	Save deid log to the specified path on the current machine
--save-subjects PATH	Save subjects to the specified file

Cluster config

These config options apply when using a cluster to ingest data.

Optional argument	Description
--cluster CLUSTER	Ingest cluster url (default: None)
-f, --follow	Follow the progress of the ingest (default: False)

Worker config

These config options are only available when using local worker (--cluster is not defined)

Optional argument	Description
--jobs JOBS	The number of concurrent jobs to run (e.g. scan jobs), ignored when using cluster (default: 4)
--sleep-time SECONDS	Number of seconds to wait before trying to get a task (default: 1)
--max-tempfile MAX_TEMPFILE	The max in-memory tempfile size, in MB, or 0 to always use disk (default: 50)The max in-memory tempfile size, in MB, or 0 to always use disk (default: 50)

General

Optional argument	Description
-C PATH, --config-file	Specify configuration options via config file. Learn more about how to create this file.
--no-config	Do NOT load the default configuration file
-y, --yes	Assume the answer is yes to all prompts
--ca-certs CA_CERTS	Set the effective local timezone for imports
--timezone TIMEZONE	Set the effective local timezone for imports
-q, --quiet	Squelch log messages to the console
-d, --debug	Turn on debug logging
-v, --verbose	Get more detailed output

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