mavedb-fsspec 0.1.0

fsspec filesystem adapter for accessing MaveDB score set data through the MaveDB API.

mavedb-fsspec

mavedb-fsspec is a read-only fsspec filesystem adapter for MaveDB. It exposes MaveDB score set data as filesystem-like paths so Python tools that understand fsspec can browse and read MaveDB data without using MaveDB API endpoints directly.

What is fsspec?

fsspec is a Python interface for working with many storage systems through a common filesystem API. Code can use familiar operations such as ls, info, open, and cat against local files, HTTP resources, cloud buckets, and custom filesystems.

mavedb-fsspec registers the mavedb:// protocol with fsspec. This lets code access MaveDB data like:

mavedb://score-sets/urn:mavedb:00000670-a-1/scores.csv

instead of manually constructing API requests.

Installation

Install from PyPI:

pip install mavedb-fsspec

Or with uv:

uv add mavedb-fsspec

fsspec and the other runtime dependencies are installed automatically.

Filesystem layout

The filesystem currently exposes score set data:

mavedb://
  score-sets/
    {urn}/
      scores.csv
      counts.csv
      variants.csv
      metadata.json
      mapped-variants.json
  my-score-sets/
    {urn}/
      scores.csv
      counts.csv
      variants.csv
      metadata.json
      mapped-variants.json

score-sets/ lists public published score sets using the MaveDB search API.

my-score-sets/ is only available when an API key is provided. It lists score sets associated with the authenticated MaveDB user.

mapped-variants.json is only listed for a score set when MaveDB has mapped variants for that score set.

Basic usage

import fsspec

fs = fsspec.filesystem("mavedb")

print(fs.ls("mavedb://", detail=False))
print(fs.ls("mavedb://score-sets", detail=False, limit=25, offset=0))

data = fs.cat("mavedb://score-sets/urn:mavedb:00000670-a-1/scores.csv")
print(data[:500].decode())

The filesystem class can also be instantiated directly:

from mavedb_fsspec import MaveDBFileSystem

fs = MaveDBFileSystem()
print(fs.ls("score-sets", detail=False, limit=25))

Authenticated usage

Use an API key to access my-score-sets/ and private score set files that your MaveDB account can read:

import fsspec

fs = fsspec.filesystem("mavedb", api_key="YOUR_MAVEDB_API_KEY")

print(fs.ls("mavedb://", detail=False))
print(fs.ls("mavedb://my-score-sets", detail=False, limit=25, offset=0))

Reading with file-like objects

mavedb-fsspec supports fsspec's file-like API:

import fsspec

with fsspec.open("mavedb://score-sets/urn:mavedb:00000670-a-1/metadata.json", "rb") as handle:
    metadata = handle.read()

Files are currently downloaded completely into memory when opened. Similarly, cat_file() downloads the complete file before applying start and end slicing; these operations do not issue HTTP range requests.

Configuration

The public MaveDB API is used by default:

fs = fsspec.filesystem("mavedb")

Advanced options:

fs = fsspec.filesystem(
    "mavedb",
    base_url="https://api.mavedb.org/api/v1",
    api_key="YOUR_MAVEDB_API_KEY",
    timeout=30.0,
)

Development

Install this repository in editable mode with the development dependencies:

python -m pip install -e ".[dev]"

Run tests with:

python -m pytest

Run Ruff with:

python -m ruff check .

Notes

This filesystem is read-only. It does not upload data to MaveDB.

File information uses -1 when the size is unknown. MaveDB endpoints can return 405 Method Not Allowed for HEAD requests, so a size may remain unknown until the file has been read.

The JSON files returned by this adapter escape literal <, >, and & characters. This keeps JSON safe for consumers that reject HTML-like content during upload, while preserving equivalent JSON string values.

License

MIT. See LICENSE.