Metadata-Version: 1.1
Name: fs-basespace
Version: 1.3.0
Summary: Illumina Basespace filesystem for PyFilesystem2
Home-page: https://github.com/emedgene/fs_basespace
Author: emedgene
Author-email: pypi@emedgene.com
License: MIT
Download-URL: https://github.com/emedgene/fs_basespace/tarball/0.2.0
Description: 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.
        
Keywords: pyfilesystem,Illumina,Basespace
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: System :: Filesystems
