fs\_basespace
=============
Readonly `pyfilesystem2 <https://github.com/PyFilesystem/pyfilesystem2>`_ interface to `Illumina Basespace <https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview>`_
Installing
----------
::
pip install fs-basespace
Requires python3 version of `basespace-python-sdk <https://github.com/basespace/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
.. code-block:: python
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/ <https://api.basespace.illumina.com/>`_
With connection string
.. code-block:: python
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
-----------------
.. code-block:: python
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.
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