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import ovation.lab.constants as constants
import ovation.lab.results as results
import ovation.download as dowload
from ovation.lab.session import connect
Create an API key in the Ovation application at Account > Settings > API Keys (https://support.ovation.io/article/52-api-overview)
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s = connect(input("Email: "), api=constants.LAB_STAGING_HOST) # use constants.LAB_PRODUCTION_HOST for production
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batch = input("Batch (workflow ID): ")
results.get_sample_results pulls all WorkflowSampleResults for the given batch and result type. In the workflow, Ovation associated each file with its corresponding sample, and created a WorkflowSampleResult that referenced the uploaded file.
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fastq_results = results.get_sample_results(s, result_type='fastq', workflow_id=2418)
results.get_file_urls retrieves temporary, pre-signed download URLs for each file Resource described by the WorkflowSampleResults.
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urls = results.get_file_urls(s, fastq_results)
urls is a list of dictionaries that have a "url" attribute and an "etag" attribute. You can use the pre-signed "url" to read/download the file. The etag is like a "version" of the file. If the file has changed, the etag will change too.
Using download.download_urls, you can download all of the files to the local file system. download_urls runs downloads in parallel.
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download.download_urls([d['url'] for d in urls])