Snakemake storage plugin: zenodo

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Warning

No documentation found in repository https://github.com/snakemake/snakemake-storage-plugin-zenodo. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instractions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-storage-plugin-zenodo

Usage

Queries

Queries to this storage should have the following format:

Query type

Query

Description

input

zenodo://record/123456/path/to/file_or_dir

A published zenodo record, starting with the ID, followed by the path to a file or directory in the record.

any

zenodo://deposition/123456/path/to/file_or_dir

A unpublished (still writable) zenodo record, starting with the ID, followed by the path to a file or directory in the record.

As default provider

If you want all your input and output (which is not explicitly marked to come from another storage) to be written to and read from this storage, you can use it as a default provider via:

snakemake --default-storage-provider zenodo --default-storage-prefix ...

with ... being the prefix of a query under which you want to store all your results. You can also pass custom settings via command line arguments:

snakemake --default-storage-provider zenodo --default-storage-prefix ... \
    --storage-zenodo-max-requests-per-second ... \        --storage-zenodo-access-token ... \        --storage-zenodo-restricted-access-token ... \        --storage-zenodo-sandbox ...

Within the workflow

If you want to use this storage plugin only for specific items, you can register it inside of your workflow:

# register storage provider (not needed if no custom settings are to be defined here)
storage:
    provider="zenodo",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-zenodo-..., see
    # snakemake --help
    # Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.
    max_requests_per_second=...,
    # Zenodo personal access token. Separate registration and access token is needed for Zenodo sandbox environment at https://sandbox.zenodo.org.
    access_token=...,
    # Zenodo restricted access token. This is needed for access to restricted records.
    restricted_access_token=...,
    # Whether to use sandbox.zenodo.org instead of the production instance.
    sandbox=...,

rule example:
    input:
        storage.zenodo(
            # define query to the storage backend here
            ...
        ),
    output:
        "example.txt"
    shell:
        "..."

Using multiple entities of the same storage plugin

In case you have to use this storage plugin multiple times, but with different settings (e.g. to connect to different storage servers), you can register it multiple times, each time providing a different tag:

# register shared settings
storage:
    provider="zenodo",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-zenodo-..., see below
    # Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.
    max_requests_per_second=...,
    # Zenodo personal access token. Separate registration and access token is needed for Zenodo sandbox environment at https://sandbox.zenodo.org.
    access_token=...,
    # Zenodo restricted access token. This is needed for access to restricted records.
    restricted_access_token=...,
    # Whether to use sandbox.zenodo.org instead of the production instance.
    sandbox=...,

# register multiple tagged entities
storage foo:
    provider="zenodo",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-zenodo-..., see below.
    # To only pass a setting to this tagged entity, prefix the given value with
    # the tag name, i.e. foo:max_requests_per_second=...
    # Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.
    max_requests_per_second=...,
    # Zenodo personal access token. Separate registration and access token is needed for Zenodo sandbox environment at https://sandbox.zenodo.org.
    access_token=...,
    # Zenodo restricted access token. This is needed for access to restricted records.
    restricted_access_token=...,
    # Whether to use sandbox.zenodo.org instead of the production instance.
    sandbox=...,

rule example:
    input:
        storage.foo(
            # define query to the storage backend here
            ...
        ),
    output:
        "example.txt"
    shell:
        "..."

Settings

The storage plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):

CLI setting

Workflow setting

Envvar setting

Description

Default

Choices

Required

Type

--storage-zenodo-max-requests-per-second VALUE

max_requests_per_second

Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.

None

str

--storage-zenodo-access-token VALUE

access_token

SNAKEMAKE_STORAGE_ZENODO_ACCESS_TOKEN

Zenodo personal access token. Separate registration and access token is needed for Zenodo sandbox environment at https://sandbox.zenodo.org.

None

str

--storage-zenodo-restricted-access-token VALUE

restricted_access_token

SNAKEMAKE_STORAGE_ZENODO_RESTRICTED_ACCESS_TOKEN

Zenodo restricted access token. This is needed for access to restricted records.

None

str

--storage-zenodo-sandbox VALUE

sandbox

Whether to use sandbox.zenodo.org instead of the production instance.

False

str