From 8d05c774372d51ed72ae51d18c20f97379dd4861 Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@sib.swiss>
Date: Mon, 18 Dec 2023 23:09:34 +0100
Subject: [PATCH] API change in Ruamel >=0.15

---
 workflow/envs/timeline.yaml     |  2 +-
 workflow/scripts/file_parser.py | 10 ++++------
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/workflow/envs/timeline.yaml b/workflow/envs/timeline.yaml
index c6563fcc..77fcfed4 100644
--- a/workflow/envs/timeline.yaml
+++ b/workflow/envs/timeline.yaml
@@ -6,5 +6,5 @@ dependencies:
   - python
   - numpy
   - pandas
-  - ruamel.yaml
+  - ruamel.yaml>=0.15
   - regex
diff --git a/workflow/scripts/file_parser.py b/workflow/scripts/file_parser.py
index 7b974afc..2acbb904 100755
--- a/workflow/scripts/file_parser.py
+++ b/workflow/scripts/file_parser.py
@@ -202,11 +202,8 @@ def main():
     datefmt = None
     if args.config_file:
         with open(args.config_file, "r") as stream:
-            try:
-                reg_data = ruamel.yaml.load(stream, Loader=ruamel.yaml.Loader)
-            except yaml.YAMLError as exc:
-                print(exc)
-                sys.exit(1)
+            yaml = ruamel.yaml.YAML(typ='rt')
+            reg_data = yaml.load(stream)
         if "sample" in reg_data:
             rxsam = regex.compile(reg_data.get("sample"))
         if "batch" in reg_data:
@@ -266,7 +263,8 @@ def main():
 
     if args.out_loc:
         with open(args.out_loc, "w") as outf:
-            ruamel.yaml.round_trip_dump(
+            yaml = ruamel.yaml.YAML()
+            yaml.dump(
                 {
                     "locations_list": list(
                         set(