Snakemake storage plugin: xrootd

A Snakemake storage plugin to read and write via the XRootD protocol.

Currently, only files can be used as inputs or outputs and not directories.

The plugin can be used without specifying any options relating to the URLs, in which case all information must be contained in the URL passed by the user.

The options for host, port, username, password and url_decorator can be specifed to make the URLs shorter and easier to use.

Please note: if the password option is supplied (even implicitly via the environment variable SNAKEMAKE_STORAGE_XROOTD_PASSWORD) it will be displayed in plaintext as part of the XRootD URLs when Snakemake prints information about a rule. Only use the password option in trusted environments.

Installation

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

pip install snakemake-storage-plugin-xrootd

Usage

Queries

Queries to this storage should have the following format:

Query type	Query	Description
any	root://eosuser.cern.ch//eos/user/s/someuser/somefile.txt	A file on a XrootD instance not specifying any arguments.
any	root://eos/user/s/someuser/somefile.txt	A file on an XrootD instance where the host has beenspecified in the storage object.

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 xrootd --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 xrootd --default-storage-prefix ... \
    --storage-xrootd-max-requests-per-second ... \        --storage-xrootd-host ... \        --storage-xrootd-port ... \        --storage-xrootd-username ... \        --storage-xrootd-password ... \        --storage-xrootd-url-decorator ...

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="xrootd",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-xrootd-..., 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=...,
    # The XrootD host to connect to
    host=...,
    # The XrootD port to connect to
    port=...,
    # The username to use for authentication
    username=...,
    # The password to use for authentication. NOTE: Only use this setting in trusted environments! Snakemake will print the password in plaintext as part of the XRootD URLs used in the inputs/outputs of jobs.
    password=...,
    # A function to decorate the URL e.g. wrapping an auth token.
    url_decorator=...,

rule example:
    input:
        storage.xrootd(
            # 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="xrootd",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-xrootd-..., 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=...,
    # The XrootD host to connect to
    host=...,
    # The XrootD port to connect to
    port=...,
    # The username to use for authentication
    username=...,
    # The password to use for authentication. NOTE: Only use this setting in trusted environments! Snakemake will print the password in plaintext as part of the XRootD URLs used in the inputs/outputs of jobs.
    password=...,
    # A function to decorate the URL e.g. wrapping an auth token.
    url_decorator=...,

# register multiple tagged entities
storage foo:
    provider="xrootd",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-xrootd-..., 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=...,
    # The XrootD host to connect to
    host=...,
    # The XrootD port to connect to
    port=...,
    # The username to use for authentication
    username=...,
    # The password to use for authentication. NOTE: Only use this setting in trusted environments! Snakemake will print the password in plaintext as part of the XRootD URLs used in the inputs/outputs of jobs.
    password=...,
    # A function to decorate the URL e.g. wrapping an auth token.
    url_decorator=...,

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-xrootd-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-xrootd-host VALUE	host		The XrootD host to connect to	None		✗	str
--storage-xrootd-port VALUE	port		The XrootD port to connect to	None		✗	str
--storage-xrootd-username VALUE	username	SNAKEMAKE_STORAGE_XROOTD_USERNAME	The username to use for authentication	None		✗	str
--storage-xrootd-password VALUE	password	SNAKEMAKE_STORAGE_XROOTD_PASSWORD	The password to use for authentication. NOTE: Only use this setting in trusted environments! Snakemake will print the password in plaintext as part of the XRootD URLs used in the inputs/outputs of jobs.	None		✗	str
--storage-xrootd-url-decorator VALUE	url_decorator		A function to decorate the URL e.g. wrapping an auth token.	'<function>'		✗	str

Further details

The username and password fields do not need to be specified if you use kerberos and/or a VOMS proxy for authentication.

The optional url_decorator argument can be used to pass a function to modify the root URL.

A possible use-case would be a function that wraps the URL with a token to allow for authentication.