Command Line Interface

modos

Multi-Omics Digital Objects command line interface.

modos [OPTIONS] COMMAND [ARGS]...

Options

--endpoint <endpoint>

URL of modos server.

--anon

Use anonymous access for S3 connections.

Default:

False

--version

Print version of modos client.

--debug

Enable debug logging.

Environment variables

MODOS_ENDPOINT

Provide a default for --endpoint

AWS_SKIP_SIGNATURE

Provide a default for --anon

add

Add elements to a modo.

modos 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.

modos c4gh [OPTIONS] COMMAND [ARGS]...

decrypt

Decrypt a local MODO.

modos 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.

modos 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.

modos codes [OPTIONS] COMMAND [ARGS]...

search

Search for terminology codes using free text.

modos codes search [OPTIONS] SLOT

Options

-q, --query <query>

Predefined text to use when search codes.

-t, --top <top>

Show at most N codes when using a prefedined query.

Default:

50

Arguments

SLOT

Required argument

The slot to search for codes. Possible values are cell_type, source_material, taxon_id, sample_processing

create

Create a modo interactively or from a file.

modos 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.

modos 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.

modos 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.

modos remote [OPTIONS] COMMAND [ARGS]...

download

Download a modo from a remote endpoint.

modos 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.

modos remote list [OPTIONS]

login

Oauth device flow to login into a remote endpoint.

Once the flow is completed, the JWT token is cached locally for future requests. The JWT is then used to request temporary S3 credentials from the remote endpoint.

modos remote login [OPTIONS]

Options

-c, --client-id <client_id>

Specify OAuth Client ID explicitely.

-a, --auth-url <auth_url>

Specify OAuth Authorization URL explicitely.

Environment variables

MODOS_OAUTH_CLIENT_ID

Provide a default for --client-id

MODOS_OAUTH_AUTH_URL

Provide a default for --auth-url

stream

Stream genomic file from a remote modo into stdout.

modos remote stream [OPTIONS] OBJECT_PATH FILE_PATH

Options

-r, --region <region>

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

Arguments

OBJECT_PATH

Required argument

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

FILE_PATH

Required argument

The path of the file to stream, within the modo. Use modos show –files to check it.

upload

Upload a local modo to a remote endpoint.

modos 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.

modos 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.

modos 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.

modos 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