fs-basespace 1.2.0.dev2024102100

Illumina Basespace filesystem for PyFilesystem2

Readonly pyfilesystem2 interface to Illumina Basespace

Installing

pip install fs-basespace

Requires python3 version of basespace-python-sdk which can be installed from the develop branch.

pip install 'git+https://github.com/basespace/basespace-python-sdk#egg=BaseSpacePy-0.3&subdirectory=src'

Opening FS Basespace

With class constructor

from fs_basespace import BASESPACEFS
basespacefs = BASESPACEFS("/projects/{project-id}/appresults/{result-id}/files/{file-id}",
                          client_id = "{client-key}",
                          client_secret = "{client-secret}",
                          access_token = "{access_token}",
                          server_name = "{server_name} optional")

Default server name for Illumina is https://api.basespace.illumina.com/

With connection string

import fs
basespacefs = fs.open_fs("basespace://{clientKey}:{clientSecret}:{appToken}@{server}")

Advanced connection strings

Access to server root directory:

basespace://{clientKey}:{clientSecret}:{appToken}@{server}

Accessing projects:

basespace://{clientKey}:{clientSecret}:{appToken}@{server}!/projects/{projectId}

Accessing project sample files:

basespace://{clientKey}:{clientSecret}:{appToken}@{server}!/projects/{projectId}/samples/{sampleId}/files/{fileId}

Accessing project appResult files (bam, vcf, …):

basespace://{clientKey}:{clientSecret}:{appToken}@{server}!/projects/{projectId}/appresults/{resultId}/files/{fileId}

Downloading files

with open("local_file", "wb") as local_file:
    basespacefs.download("path/to/remote/file/id", local_file)

Uploading files

Only readonly access to Basespace is implemented in this package. No upload possible yet.