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Fix Knime Subprocess #22

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Merged
tduigou merged 2 commits into from
Sep 29, 2025
Merged

Fix Knime Subprocess #22

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a316382
fix: since str arguments in cmd-line, args for Knime must be a list
guillaume-gricourt Sep 29, 2025
c2ef9bd
fix: add import
guillaume-gricourt Sep 29, 2025
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7 changes: 5 additions & 2 deletions retropath2_wrapper/knime.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import os
import requests
import shutil
import subprocess
import sys
import tempfile
import urllib.parse
Expand All @@ -20,7 +21,7 @@
download,
download_and_unzip,
chown_r,
subprocess_call
subprocess_call,
)
from retropath2_wrapper.Args import (
DEFAULTS,
Expand Down Expand Up @@ -526,6 +527,7 @@ def call(
args += ['-workflow.variable=output.dir,"%s",String' % (self.standardize_path(files['outdir']),)]
args += ['-workflow.variable=output.solutionfile,"%s",String' % (self.standardize_path(files['results']),)]
args += ['-workflow.variable=output.sourceinsinkfile,"%s",String' % (self.standardize_path(files['src-in-sk']),)]
print("Hydrogen:", params["std_hydrogen"])
args += ['-workflow.variable=input.std_mode,"%s",String' % (params["std_hydrogen"],)]
if preference and preference.is_init():
preference.to_file()
Expand All @@ -550,7 +552,8 @@ def call(
)
is_ld_path_modified = True

CPE = subprocess_call(cmd=" ".join(args), logger=logger)
CPE = subprocess.run(args)
logger.debug(CPE)
if is_ld_path_modified:
os.environ['LD_LIBRARY_PATH'] = ':'.join(
os.environ['LD_LIBRARY_PATH'].split(':')[:-1]
Expand Down
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