From 5a0fc00af23bcead51f332fdc3e4b2da214e32c8 Mon Sep 17 00:00:00 2001 From: frederick Date: Thu, 7 May 2026 14:46:18 +0100 Subject: [PATCH] changing bash commands in e02/templates/mib2x-auto-virtual-images.yaml from exec to eval such that the string is parsed correctly --- e02/templates/mib2x-auto-virtual-images.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/e02/templates/mib2x-auto-virtual-images.yaml b/e02/templates/mib2x-auto-virtual-images.yaml index 1c19b65..70f5c36 100644 --- a/e02/templates/mib2x-auto-virtual-images.yaml +++ b/e02/templates/mib2x-auto-virtual-images.yaml @@ -181,8 +181,8 @@ spec: todo, checks = check_dataset(hdf5_files,hdf5_timestamps,[no_vir,no_dpc,no_par]) for item,x in enumerate(todo): - cmd_list.append('/usr/bin/python /home/ruska/py4DSTEM_Virtual_Image.py --hdf5-path %s --disk-thrs-low %f --disk-thrs-up %f --virtual-images %s --dpc-images %s --plax %s --mask-path %s' %(hdf5_files[todo[item]],0.05,0.2,checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]],"/home/ruska/29042024_12bitmask2.h5")) - logging.append('/usr/bin/python /home/ruska/py4DSTEM_Virtual_Image.py --hdf5-path %s --disk-thrs-low %f --disk-thrs-up %f --virtual-images %s --dpc-images %s --plax %s --mask-path %s' %(hdf5_files[todo[item]],0.05,0.2,checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]],"/home/ruska/29042024_12bitmask2.h5")) + cmd_list.append('python py4DSTEM_Virtual_Image.py --hdf5-path=%s --disk-thrs-low=%f --disk-thrs-up=%f --virtual-images=%s --dpc-images=%s --plax=%s --mask-path=%s' %(hdf5_files[todo[item]],0.05,0.2,checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]],"/home/ruska/29042024_12bitmask2.h5")) + logging.append('python py4DSTEM_Virtual_Image.py --hdf5-path=%s --disk-thrs-low=%f --disk-thrs-up=%f --virtual-images=%s --dpc-images=%s --plax=%s --mask-path=%s' %(hdf5_files[todo[item]],0.05,0.2,checks[0][todo[item]],checks[1][todo[item]],checks[2][todo[item]],"/home/ruska/29042024_12bitmask2.h5")) #ToDo think about this printing in the context of an Error #this should be try statement @@ -222,10 +222,9 @@ spec: source: | #!/bin/sh #set -e - pwd - cmd=("{{`{{inputs.parameters.hdf5_files}}`}}") + cmd="{{`{{inputs.parameters.hdf5_files}}`}}" echo "Executing: ${cmd}" - exec "${cmd}" + eval "${cmd}" podSpecPatch: | containers: