YAML checker catches pipelines omitting required params #677
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Note that one exception is the `standard_tomo` loader. If any of the required parameters representing paths in the data are omitted, then the check of the data paths within the data will itself run into an error when the omitted parameter is attempted to be checked for the `auto` value. Addressing this edge case could be done by introducing a dependency between some of the checks being performed (ie, if the check of omitted parameter values not being required fails for the loader, then don't try to check the data paths in the loader). For the moment, introducing such a dependency between the checks likely adds complexity that isn't worth it, so has been left out.
Collaborator
Author
|
For some context, a pipeline that has the majority of parameters omitted such as the following: - method: standard_tomo
module_path: httomo.data.hdf.loaders
parameters:
data_path: auto
image_key_path: auto
rotation_angles: auto
- method: find_center_vo
module_path: httomolibgpu.recon.rotation
parameters: {}
id: centering
side_outputs:
cor: centre_of_rotation
- method: remove_outlier
module_path: httomolibgpu.misc.corr
parameters: {}
- method: dark_flat_field_correction
module_path: httomolibgpu.prep.normalize
parameters: {}
- method: minus_log
module_path: httomolibgpu.prep.normalize
parameters: {}
- method: remove_stripe_based_sorting
module_path: httomolibgpu.prep.stripe
parameters: {}
- method: FBP3d_tomobar
module_path: httomolibgpu.recon.algorithm
parameters:
center: ${{centering.side_outputs.centre_of_rotation}}
save_result: true
- method: rescale_to_int
module_path: httomolibgpu.misc.rescale
parameters: {}
- method: save_to_images
module_path: httomolib.misc.images
parameters: {}is able to pass the YAML checker: and be executed by httomo: |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Part of the work needed for IMGDA-517
Should be merged with the following PR in httomo-backends: DiamondLightSource/httomo-backends#90
Note that one exception for the feature working is the
standard_tomoloader. If any of the required parameters representing paths in the data are omitted, then the check of the data paths within the data will itself run into an error when the omitted parameter is attempted to be checked for theautovalue.Addressing this edge case could be done by introducing a dependency between some of the checks being performed (ie, if the check of omitted parameter values not being required fails for the loader, then don't try to check the data paths in the loader). For the moment, introducing such a dependency between the checks likely adds complexity that isn't worth it, so has been left out.
Checklist