Mantle SDK Guide
Pipeline runs
Introduction
A Mantle pipeline run object describes a specific time a pipeline was run on Mantle. It contains links to the pipeline run’s inputs, as well as its output datasets and files.
Getting a pipeline run by unique ID
Get a pipeline run object by its unique ID
import mantlebio
mantle = mantlebio.MantleClient()
# Get a pipeline run
pipeline_run = mantle.pipeline_run.get('pipeline-run-id')
Accessing files associated with pipeline run inputs
Downloading dataset input files for a pipeline run
Download dataset input files
import mantlebio
mantle = mantlebio.MantleClient()
# Download input files for a pipeline run
pipeline_run = mantle.pipeline_run.get('pipeline-run-id')
input_dataset = pipeline_run.get_input_dataset('input-dataset-key')
input_dataset.download_s3('dataset_property','local/file/path/to/download/to')
Downloading S3 input files for a pipeline run
Download S3 input files
import mantlebio
mantle = mantlebio.MantleClient()
# Download input files for a pipeline run
pipeline_run = mantle.pipeline_run.get('pipeline-run-id')
pipeline_run.get_s3_input('input-key','local/file/path/to/download/to')
Adding outputs to pipeline runs
Adding a dataset output to a pipeline run
Add dataset output
import mantlebio
mantle = mantlebio.MantleClient()
# Create a dataset
dataset = mantle.dataset.create(
name="4XP1",
local=False,
properties={
"description": "X-ray structure of Drosophila dopamine transporter bound to neurotransmitter dopamine",
"resolution": 2.5,
"r_value": 0.2,
}
)
# Add dataset output to a pipeline run
pipeline_run = mantle.pipeline_run.get('pipeline-run-id')
pipeline_run.add_dataset_output('my_output_dataset', dataset)
Adding a file output to a pipeline run
Add file output
import mantlebio
mantle = mantlebio.MantleClient()
# Add file output to a pipeline run
pipeline_run = mantle.pipeline_run.get('pipeline-run-id')
pipeline_run.add_file_output('my_output_file','local/file/path/to/upload_file.txt')