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Raise more informative ROBOT error#37

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cthoyt merged 14 commits into
mainfrom
robot_error
Jul 6, 2025
Merged

Raise more informative ROBOT error#37
cthoyt merged 14 commits into
mainfrom
robot_error

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@bgyori

@bgyori bgyori commented May 3, 2025

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I've often been confused by the error shown if Robot conversion fails since it doesn't show the actual output from Robot so the reason for the error is unclear:

CalledProcessError: Command '['java', '-jar', '/Users/ben/.data/robot/1.9.7/robot.jar', 'merge', '-i',
 '/Users/ben/.data/pyobo/raw/bao/bao_complete.owl', 'convert', '-o', 
'/Users/ben/.data/pyobo/raw/bao/bao_complete.obo']' returned non-zero exit status 1.

There are two challenges: subprocess.CalledProcessError doesn't surface the output by default and the output can be very long which if fully displayed would be disruptive. So this PR adds a custom RobotError class which is raised instead of subprocess.CalledProcessError and creates a nicer and easier-to-customize output:

RobotError: Command ['java', '-jar', '/Users/ben/.data/robot/1.9.7/robot.jar', 'merge', '-i', 
'/Users/ben/.data/pyobo/raw/bao/bao_complete.owl', 'convert', '-o', 
'/Users/ben/.data/pyobo/raw/bao/bao_complete.obo'] returned non-zero exit status 1.
Output: OBO STRUCTURE ERROR Ontology does not conform to OBO structure rules:
multiple name tags not allowed. in frame:Frame(null ontology( http://www.bioassayontology.org/
bao/bao_complete.owl)data-version( http://www.bioassayontology.org/bao/bao_complete.owl)
property_value( dc:date March20, 2025 xsd:string)property_value( dc:license 
https://creativecommons.org/licenses/by-sa/4.0/)remark( Contact: Stephan Schurer stephan 
dot schurer at med dot miami dot edu)remark( Created by: Caty Chung, Nicolette Ross...

by default showing up to 500 characters of the actual Robot error.

Fixes #10 though taking a different approach to the one suggested there.

@cthoyt cthoyt changed the title Raise more informative Robot error Raise more informative ROBOT error Jul 6, 2025
@cthoyt cthoyt merged commit ac99273 into main Jul 6, 2025
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@cthoyt cthoyt deleted the robot_error branch July 6, 2025 09:37
@cthoyt

cthoyt commented Jul 6, 2025

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thanks!

@joeflack4

joeflack4 commented Jul 6, 2025

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@bgyori Much appreciated!

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Gracefully handle robot exceptions

3 participants

@bgyori @cthoyt @joeflack4