From 4af1c0a6ccd06f925abdd89c6e6677e8dfe9a969 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 30 Apr 2019 18:27:45 +0200 Subject: [PATCH] Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset To test this run a tool that generates discovered datsets twice, with the second run taking the first output as input. --- lib/galaxy/workflow/extract.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index bf2f4165787..80f02b00258 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -141,7 +141,7 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c hid = None for implicit_pair in jobs[job]: query_assoc_name, dataset_collection = implicit_pair - if query_assoc_name == assoc_name: + if query_assoc_name == assoc_name or assoc_name.startswith("__new_primary_file_%s|" % query_assoc_name): hid = dataset_collection.hid if hid is None: template = "Failed to find matching implicit job - job id is %s, implicit pairs are %s, assoc_name is %s."