Command Line Interface#

modo#

Multi-Omics Digital Objects command line interface.

modo [OPTIONS] COMMAND [ARGS]...

Options

--endpoint <endpoint>#

URL of modos server.

--version#

Print version of modos client.

--debug#

Enable debug logging.

Environment variables

MODOS_ENDPOINT

Provide a default for --endpoint

add#

Add elements to a modo.

modo add [OPTIONS] OBJECT_PATH ELEMENT_TYPE:{sample|assay|data|reference}

Options

-p, --parent <parent>#

Parent object in the zarr store.

-e, --element <element>#

Create instance from element metadata provided as a json string.

-f, --from-file <from_file>#

Read instance metadata from a file. The file must be in json or yaml format.

-s, --source-file <source_file>#

Specify a data file (if any) to copy into the digital object and associate with the instance.

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

ELEMENT_TYPE#

Required argument

Type of element to add to the digital object.

c4gh#

Local encryption via crypt4gh.

modo c4gh [OPTIONS] COMMAND [ARGS]...

decrypt#

Decrypt a local MODO.

modo c4gh decrypt [OPTIONS] OBJECT_PATH

Options

-s, --secret-key <secret_key>#

Required Secret key of the recipient to decrypt files in the MODO.

-pw, --passphrase <passphrase>#

Path to file with passphrase to unlock secret key.

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

encrypt#

Encrypt a local MODO.

modo c4gh encrypt [OPTIONS] OBJECT_PATH

Options

-p, --public-key <public_key>#

Required Public key(s) of the recipent(s) to decrypt files in the MODO.

-s, --secret-key <secret_key>#

Secret key of the sender to encrypt files in the MODO.

-pw, --passphrase <passphrase>#

Path to file with passphrase to unlock secret key.

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

codes#

Terminology codes utilities.

modo codes [OPTIONS] COMMAND [ARGS]...

create#

Create a modo interactively or from a file.

modo create [OPTIONS] OBJECT_PATH

Options

-f, --from-file <from_file>#

Create a modo from a file. The file must be in json or yaml format.

-m, --meta <meta>#

Create instance from metadata provided as a json string.

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

enrich#

Enrich metadata of a digital object using file contents.

modo enrich [OPTIONS] OBJECT_PATH

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

publish#

Export a modo as linked data. Turns all paths into URIs.

modo publish [OPTIONS] OBJECT_PATH

Options

--output-format <output_format>#
Default:

RdfFormat.TURTLE

Options:

turtle | xml | json-ld

--base-uri <base_uri>#

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

remote#

Remote object management.

modo remote [OPTIONS] COMMAND [ARGS]...

download#

Download a modo from a remote endpoint.

modo remote download [OPTIONS] OBJECT_PATH

Options

-t, --target <target_path>#

Required Path where to download the digital object.

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

list#

List remote modos on the endpoint.

modo remote list [OPTIONS]

stream#

Stream genomic file from a remote modo into stdout.

modo remote stream [OPTIONS] FILE_PATH

Options

-r, --region <region>#

Restrict stream to genomic region (chr:start-end).

Arguments

FILE_PATH#

Required argument

The s3 path of the file to stream . Use modos show –files to check it.

upload#

Upload a local modo to a remote endpoint.

modo remote upload [OPTIONS] OBJECT_PATH

Options

-t, --target <target_path>#

Required S3 path where to upload the digital object (format: s3://bucket/name).

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

remove#

Removes an element and its files from the modo.

modo remove [OPTIONS] OBJECT_PATH [ELEMENT_ID]

Options

-f, --force#

Skip confirmation for file deletion and allow deletion of the root object.

Default:

False

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

ELEMENT_ID#

Optional argument

The identifier within the modo. Use modos show to check it. Leave empty to remove the whole object.

show#

Show the contents of a modo.

modo show [OPTIONS] OBJECT_PATH [ELEMENT_ID]

Options

-z, --zarr#

Show the structure of the zarr archive

Default:

False

-f, --files#

Show data files in the digital object.

Default:

False

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path

ELEMENT_ID#

Optional argument

The identifier within the modo. Use modos show to check it.

update#

Update a modo based on a yaml file.

modo update [OPTIONS] OBJECT_PATH

Options

-c, --config <config_file>#

Required File defining the updated modo. The file must be in json or yaml format.

-f, --force#

Force deletion of elements that are missing in the config_file.

Default:

False

Arguments

OBJECT_PATH#

Required argument

Path to the digital object. Remote paths should have format s3://bucket/path