snakemake-storage-plugin-pelican 0.1.1

A Snakemake Storage Plugin for Pelican Federations

Snakemake Pelican Storage Plugin

A Snakemake storage plugin for accessing data via the Pelican Platform, enabling integration with data federations like the Open Science Data Federation (OSDF).

Installation

pip install snakemake-storage-plugin-pelican

Or install from source:

git clone https://github.com/PelicanPlatform/snakemake-storage-plugin-pelican.git
cd snakemake-storage-plugin-pelican
pip install -e .

Usage

There are a few ways to use/configure the plugin. Broadly, they are:

• Wrapping pelican:// and osdf:// URLs with the storage() function
• Defining a default storage provider
• Multiple, tagged Pelican plugin instances

Using the storage() function

In your Snakefile, any files that should be fetched or written to a Pelican federation can be wrapped with the storage() function. This tells Snakemake it should automatically determine which storage plugins can be used to complete the required file operations. In this case, the Pelican storage plugin will be used whenever the storage string begins with a pelican:// or osdf:// URL.

For example:

rule download_data:
    input:
        storage("pelican://osg-htc.org/pelicanplatform/test/hello-world.txt")
    output:
		# Anything not wrapped with `storage()` is assumed to be a local file
        "local_output.txt"
    shell:
        "cp {input} {output}"

Defining a Default Storage Provider

If your workflow heavily relies on objects accessed with Pelican, you may not want to wrap everything explicitly with storage(). In this case, you can define the Pelican plugin as the default storage provider. This tells Snakemake to assume all files that aren't explicitly wrapped with a different storage provider are Pelican objects. Enable this feature by passing --default-storage-provider pelican to your Snakemake invocation.

Passing this argument also requires defining a default storage prefix to tell Snakemake what common prefix it should prepend to all relative file paths. This is done with the --default-storage-prefix flag.

If all of your files/objects come from the same federation, this prefix will often be the federation URL with a namespace, e.g. pelican://osg-htc.org/chtc/.

For example, with this Snakefile:

rule download_data:
    input:
        remote_input="/staging/jhiemstra/input.txt",  # Treated as Pelican (default provider)
        local_input=local("some-local-file.txt")   # Explicitly local with local() wrapper
    output:
        "/staging/jhiemstra/output.txt"  # Also treated as Pelican (default provider)
    shell:
        "cat {input.remote_input} {input.local_input} > {output}"

Run with default storage provider:

snakemake --cores 1 \
    --default-storage-provider pelican \
    --default-storage-prefix "pelican://osg-htc.org/ospool/" \
    --storage-pelican-token-file /path/to/token.txt

Snakemake will automatically treat "/staging/jhiemstra/input.txt" as "pelican://osg-htc.org/chtc/staging/jhiemstra/input.txt".

Tagged Plugin Instances

Advanced users can define multiple instances of the Pelican plugin with different configurations using tags. This is useful when working with multiple federations that require completely separate authentication or settings.

See the Snakemake storage plugin documentation for details on tagged plugin instances.

URL Formats

The plugin supports two URL schemes:

1. Pelican URLs: pelican://federation-hostname/namespace/path/to/object

   pelican://osg-htc.org/ospool/uchicago/public/data.txt
   

2. OSDF URLs: osdf:///namespace/path/to/file (automatically converted to pelican://osg-htc.org/...)

   osdf:///pelicanplatform/test/hello-world.txt
   

Authentication with Tokens

The Pelican storage plugin for Snakemake does not yet support automatic token management like other Pelican clients, but these are features that will be added in the future. In the meantime, whenever an operation on an object requires authorization, you must provide your own tokens.

For information about how to create namespace tokens, see the upstream Pelican documentation.

Single Token for All Requests

If all the Pelican objects in your Snakemake workflow that require authorization can be handled with a single token, that token can be provided to the plugin using the --storage-pelican-token-file flag, e.g.:

snakemake --cores 1 \
    --storage-pelican-token-file /path/to/token.txt

Multiple Tokens with URL Prefix Mapping

For workflows accessing multiple federations or namespaces with different credentials, tokens can be mapped to specific federation prefixes. This is done by passing the --storage-pelican-token-file flag a space-delimited string list of <URL prefix>:<token file> components.

For example, if your objects come from two different federations, you can specify which tokens should be used with which federations/prefixes:

snakemake --cores 1 \
    --storage-pelican-token-file "pelican://osg-htc.org/ospool:/path/to/ospool-token.txt pelican://itb-osdf-director.osdf-dev.chtc.io/chtc/itb:/path/to/itb-token.txt"

Note: There is a quotation requirement around the string list you pass with this flag. The entire list should be wrapped in either single or double quotes.

The plugin uses longest-prefix matching to select the appropriate token for each URL. You can use this feature to map tokens to specific federations or to specific namespaces within a federation.

With Default Fallback

snakemake --cores 1 \
    --storage-pelican-token-file 'pelican://osg-htc.org/chtc/itb:/path/to/itb-token.txt default:/path/to/default-token.txt'

URLs that don't match any prefix will use the default token.

Debug Logging

Enable detailed logging of the Pelican storage plugin and the underlying PelicanFS library for troubleshooting:

snakemake --cores 1 \
    --storage-pelican-debug true

Examples

Example 1: Reading from OSDF

rule process_osdf_data:
    input:
        storage("osdf:///pelicanplatform/test/hello-world.txt")
    output:
        "processed_output.txt"
    shell:
        "cat {input} | tr '[:lower:]' '[:upper:]' > {output}"

Run without authentication (for public data):

snakemake --cores 1

Example 2: Reading from Multiple Federations

Note: This example is for demonstration purposes -- the referenced objects do not actually exist, so this Snakefile will not work if copy-pasted.

rule combine_data:
    input:
        osdf_data=storage("pelican://osg-htc.org/ospool/data.txt"),
        itb_data=storage("pelican://itb-osdf-director.osdf-dev.chtc.io/chtc/itb/data.txt")
    output:
        "combined.txt"
    shell:
        "cat {input.osdf_data} {input.itb_data} > {output}"

Run with multiple tokens:

snakemake --cores 1 \
    --storage-pelican-token-file 'pelican://osg-htc.org/ospool:/path/to/ospool-token.txt pelican://itb-osdf-director.osdf-dev.chtc.io/chtc/itb:/path/to/itb-token.txt'

Example 3: Writing to Pelican

In this "write" example, the output is written back to the storage exposed by an Origin. Here, Snakemake creates an intermediary copy of output on the local disk and then uses PelicanFS to copy the data to the remote storage.

rule upload_results:
    input:
        "local_results.txt"
    output:
        storage("pelican://my-federation.org/myspace/results.txt")
    shell:
        "cp {input} {output}"

Run with write-enabled token:

snakemake --cores 1 \
    --storage-pelican-token-file /path/to/write-token.txt

Token File Format

Token files should contain a single line with the bearer token:

eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9...

Configuration Options

Option	Description	Example
--storage-pelican-token-file	Path(s) to token file(s), optionally with URL prefix mappings	--storage-pelican-token-file 'pelican://host/path:token.txt'
--storage-pelican-debug	Enable debug logging	--storage-pelican-debug true

Dependencies

• snakemake-interface-storage-plugins
• pelicanfs - Python filesystem interface for Pelican

Development

To contribute or modify the plugin:

git clone https://github.com/PelicanPlatform/snakemake-storage-plugin-pelican.git
cd snakemake-storage-plugin-pelican
pip install -e ".[dev]"

Run tests:

pytest