To run this example, you'll need the Ovation Python API. Install with pip:
pip install ovation
In [1]:
import ovation.core as core
from ovation.session import connect
from ovation.upload import upload_revision, upload_file, upload_folder
from ovation.download import download_revision
from pprint import pprint
from getpass import getpass
from tqdm import tqdm_notebook as tqdm
You use a connection.Session to interact with the Ovaiton REST API. Use the connect method to create an authenticated Session.
In [2]:
session = connect(input('Ovation email: '), org=input('Organization (enter for default): ') or 0)
The Python API wraps the Ovation REST API, using the awesome requests library. The Session provides some convenient additions to make working with Ovation's API a little easier. For example, it automatically sets the content type to JSON and handles URL creation from path and host.
The example below shows retrieving a project by ID, adding a new File and uploading a new Revision (a version) of that file using the ovation.revisions.upload_revision convenience method.
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project_id = input('Project UUID: ')
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# Get a project by ID
proj = session.get(session.path('project', project_id))
You can upload an entire folder or individual files to the Project. First, let's upload a folder:
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folder = upload_folder(session, proj, '/path/to/project_fastq_folder')
Alternatively, we can create a folder and upload individual files:
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import os
folder = core.create_folder(session, proj, 'FASTQ')
for f in os.glob('/path/to/project_fastq_folder/*.fastq')
For advanced users, we can create a File and then upload a Revision.
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# Create a new File
r = session.post(project_url,
data={'entities': [{'type': 'File',
'attributes': {'name': 'example.vcf'}}]})
file = r[0]
pprint(file)
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# Create a new Revision (version) of the new File by uploading a local file
revision = upload_revision(session, file, '/Users/barry/Desktop/example.vcf')
pprint(revision)
upload_revision is also how you can upload a new Revision to an existing file.
The Ovation API generates a temporary authenticated URL for downloading a Revision. This example uses the ovation.revisions.download_revision function to get this authenticated URL and then to download it to the local file system, returning the downloaded file's path:
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file_path = download_revision(session, revision._id)