diff --git a/retropath2_wrapper/knime.py b/retropath2_wrapper/knime.py index ca5c9f4..e99fe90 100644 --- a/retropath2_wrapper/knime.py +++ b/retropath2_wrapper/knime.py @@ -1,6 +1,7 @@ import os import requests import shutil +import subprocess import sys import tempfile import urllib.parse @@ -20,7 +21,7 @@ download, download_and_unzip, chown_r, - subprocess_call + subprocess_call, ) from retropath2_wrapper.Args import ( DEFAULTS, @@ -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() @@ -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]