From fd4033205a62174cfaf65154e58b1763be05bfed Mon Sep 17 00:00:00 2001
From: Nils Giordano <nils.giordano@integrative-phenomics.com>
Date: Fri, 21 May 2021 17:06:36 +0200
Subject: [PATCH] Fix #300 by sorting output targets before uploading

---
 awsf3/utils.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/awsf3/utils.py b/awsf3/utils.py
index 2daa4cd2..0f10f4ed 100644
--- a/awsf3/utils.py
+++ b/awsf3/utils.py
@@ -379,6 +379,16 @@ def upload_to_output_target(prj_out, encrypt_s3_upload=False):
     output_argnames = prj_out.output_files.keys()
     output_target = prj_out.alt_output_target(output_argnames)
 
+    # sorting outputs by mtime in order to upload in the right order.
+    # arbitrary order created issues with workflow managers (snakemake)
+    # because S3 does not save the modification time of uploaded objects
+    output_target = dict(
+        sorted(
+            output_target.items(),
+            key=lambda i: os.path.getmtime(i[0].replace('file://', ''))
+        )
+    )
+
     for k in output_target:
         target = Target(output_bucket)