From 96d312d41b3d703f028a9e57388c588acf08feda Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 6 Oct 2020 12:57:22 +0200
Subject: [PATCH] Fix workflows on Windows.
---
Applications/Utils/ExtractBoundary.py | 8 +++++---
scripts/snakemake/vtkdiff/wrapper.py | 7 ++++---
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/Applications/Utils/ExtractBoundary.py b/Applications/Utils/ExtractBoundary.py
index 57dd8b36981..008b042dc0c 100644
--- a/Applications/Utils/ExtractBoundary.py
+++ b/Applications/Utils/ExtractBoundary.py
@@ -41,7 +41,10 @@ def extract_boundary(elem_type, inputs=[], outputs=[],
@bash_app
def vtk_diff(fields, inputs=[], outputs=[],
stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME):
+ import os
script = ""
+ if os.path.exists(outputs[0]):
+ os.remove(outputs[0])
for field in fields:
field_a = field[0]
offset = 0
@@ -51,10 +54,9 @@ def vtk_diff(fields, inputs=[], outputs=[],
abs_tol = field[1 + offset]
rel_tol = field[2 + offset]
- script += f"""rm {outputs[0]} || true
- vtkdiff {inputs[0]} {inputs[1]} \
+ script += f"""vtkdiff {inputs[0]} {inputs[1]} \
-a {field_a} -b {field_b} \
- --abs {abs_tol} --rel {rel_tol} > {outputs[0]}
+ --abs {abs_tol} --rel {rel_tol} >> {outputs[0]}
"""
return script
diff --git a/scripts/snakemake/vtkdiff/wrapper.py b/scripts/snakemake/vtkdiff/wrapper.py
index 2347d1bc31c..013a2bed78c 100644
--- a/scripts/snakemake/vtkdiff/wrapper.py
+++ b/scripts/snakemake/vtkdiff/wrapper.py
@@ -7,7 +7,9 @@ __license__ = "BSD"
import os
from snakemake.shell import shell
-output_path = os.getcwd().replace(snakemake.config['Data_BINARY_DIR'], "")
+output_path = os.getcwd().replace("\\", "/").replace(snakemake.config["Data_BINARY_DIR"], "")
+if os.path.exists(snakemake.output[0]):
+ os.remove(snakemake.output[0])
for field in snakemake.params.fields:
field_a = field[0]
@@ -20,10 +22,9 @@ for field in snakemake.params.fields:
shell(
"""
- rm {snakemake.output[0]} || true
vtkdiff {snakemake.input[0]} \
{snakemake.config[Data_SOURCE_DIR]}/{output_path}/{snakemake.input[0]} \
-a {field_a} -b {field_b} \
- --abs {abs_tol} --rel {rel_tol} > {snakemake.output[0]}
+ --abs {abs_tol} --rel {rel_tol} >> {snakemake.output[0]}
"""
)
--
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