From d9a21a0dc66102801fcac6a7ffa3fc48c15c9b3c Mon Sep 17 00:00:00 2001 From: npetrill Date: Wed, 20 Nov 2024 15:00:43 -0500 Subject: [PATCH] methoduri --- .github/workflows/test_illumina_genotyping_array.yml | 1 + scripts/firecloud_api/firecloud_api.py | 7 +++++++ 2 files changed, 8 insertions(+) diff --git a/.github/workflows/test_illumina_genotyping_array.yml b/.github/workflows/test_illumina_genotyping_array.yml index 47f4def20e..8346626ed1 100644 --- a/.github/workflows/test_illumina_genotyping_array.yml +++ b/.github/workflows/test_illumina_genotyping_array.yml @@ -159,6 +159,7 @@ jobs: --inputs_json "$input_file" \ --update_truth "$UPDATE_TRUTH_BOOL") echo "Uploading test input file: $test_input_file" + firecloud_action upload_test_inputs --pipeline_name $PIPELINE_NAME --test_input_file "$test_input_file" --branch_name "${{ github.head_ref }}" echo "Submitting job for input file: $input_file" diff --git a/scripts/firecloud_api/firecloud_api.py b/scripts/firecloud_api/firecloud_api.py index 622b22a8e1..0ea03e6e5d 100644 --- a/scripts/firecloud_api/firecloud_api.py +++ b/scripts/firecloud_api/firecloud_api.py @@ -171,6 +171,13 @@ def upload_test_inputs(self, pipeline_name, test_inputs, branch_name): config["inputs"] = inputs_json # update the config with the new branch name + + # Construct the methodUri with the branch name + base_url = "github.com/broadinstitute/warp/TestIlluminaGenotypingArray" + method_uri = f"dockstore://{quote(base_url)}/{branch_name}" + print(f"Updating methodUri with branch name: {method_uri}") + config["methodRepoMethod"]["methodUri"] = method_uri + print(f"Updating methodVersion with branch name: {branch_name}") config["methodRepoMethod"]["methodVersion"] = branch_name