miqatools 2.0.0rc0

No project description provided

Installing

pip3 install miqatools --upgrade

Usage

Multi-sample Test Execution

from miqatools.remoteexecution.triggertestandupload_python import trigger_test_and_upload_by_dsid
from miqatools.remoteexecution.triggertest_helpers import get_trigger_info

server_url = "YOURCO.miqa.io"
trigger_id = "YOUR_TRIGGER_ID"
api_key = "YOUR_API_KEY"

# First create the lookup of test result file locations for each dataset:
ds_id_mapping = get_trigger_info(server_url, trigger_id, api_key=api_key).get("ds_id_mapping", {}).get("results",{}).get("data",{})
locations_lookup_by_dsid = {ds_id_mapping.get(k):v for k,v in locations_lookup_by_samplename.items()}

# Use the dataset location lookup and trigger info to kick off "execution" of the trigger, uploading the outputs
run_id = trigger_test_and_upload_by_dsid(server_url, trigger_id, "YOUR_VERSION_NAME", locations_lookup_by_dsid, filepatterns=["*.vcf"], api_key=api_key)

Create and Tag Stand-In Datasets

from miqatools.datamanagement.datasethelpers import batch_create_datasets_and_tag_or_group

server_url = "YOURCO.miqa.io"
trigger_id = "YOUR_TRIGGER_ID"
api_key = "YOUR_API_KEY"

batch_create_datasets_and_tag_or_group(server_url, 1, 1, ["Sample1","Sample2"], ["BATCH_1","another_tag"], "BATCH_1", api_key=api_key)