Workflows are not terminated if errors are detected

[t0mdavid-m]

In FeatureFinderMetabo within the TOPP Workflow Framework, enabling the advanced parameter masstrace_snr_filtering (via Configure -> Show Advanced Parameter) results in an error when executing the workflow (as noted in issue #90). While this specific issue should be addressed separately, I observed another inconsistency:

When a TOPP tool encounters an error, the workflow continues running, and no error message is displayed in the minimal log.

To improve error handling and workflow stability, implement the following:

• Abort the workflow upon encountering an error.
  (Ensure that failures in individual TOPP tools result in the termination of the entire workflow.)

• Display error messages in the log.
  (Provide clear and informative error messages in the minimal log.)

[asterisk-ragavan]

@t0mdavid-m

Process finished:
FeatureFinderMetabo -in ..\workspaces-streamlit-template\default\topp-workflow\input-files\mzML-files\Pool.mzML -out ..\workspaces-streamlit-template\default\topp-workflow\results\feature-detection\Pool.featureXML -algorithm:epd:masstrace_snr_filtering false -ini ..\workspaces-streamlit-template\default\topp-workflow\ini\FeatureFinderMetabo.ini
Total time to run command: 0.04 seconds 

ERRORS OCCURRED:
Trailing text argument(s) '[false]' given. Aborting!

am I getting this error because of masstrace_snr_filtering false

[t0mdavid-m]

Yes, correct! This should of course not happen and be addressed in #90.

The issue here is that the workflow continues after encountering this error and at the minimal log level no error displayed to the user.

[asterisk-ragavan]

Yes, correct! This should of course not happen and be addressed in #90.

The issue here is that the workflow continues after encountering this error and at the minimal log level no error displayed to the user.

@t0mdavid-m okay I'll try to debug and stop the workflow and display a error when errors detected.

Once it's done I'll look into #90 to treat Boolean as value not as string.

[asterisk-ragavan]

@t0mdavid-m found the bug

• I have added line 108 which will raise an error and stop the process, and it has been logged into level 2 priority.
• raising error here aborts the further process.

• error from the line 108 will be captured here and logged in level 0, since its level 0, I am just logging the 1st line.

Tested and works as expected.

minimal

commands and run times

All

if this is fine, I can create a PR and push the changes.

[t0mdavid-m]

This looks good to me! Feel free to open a PR :)

[t0mdavid-m]

Unassigning as PR seems to be stale. Other students are welcome to work on this.

[subCode321]

@t0mdavid-m can this be assigned to me?

[jitendra-ky]

@t0mdavid-m , I submitted I approach to solve this issue please check #223