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#275: check that spatial dimensions match before running test #276

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merged 5 commits into from
Oct 28, 2022

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fbergmann
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Description

before testing whether the unitsize is between 0 and 1, we should check, that the spatial dimensions match first.

Motivation and Context

fixes #275

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to change)
  • Change in documentation

Checklist:

  • I have updated all documentation necessary.
  • I have checked spelling in (new) comments.

Testing

  • Testing is done automatically and codecov shows test coverage
  • This cannot be tested automatically

@fbergmann fbergmann marked this pull request as ready for review October 27, 2022 13:27
@luciansmith
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We can change the wording to whatever, but it should match sbmlteam/sbml-specifications#392

The rule already was flagged as a 'warning' anyway.
@luciansmith
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@fbergmann : We also need to apply the caveat to rule 21351. I looked at the code, but I got stymied; can you look at it? It's the function:

SpatialCompartmentMappingUnitSizesCheck::check_

@skeating skeating merged commit efc1992 into development Oct 28, 2022
@skeating skeating deleted the spatial-validation-issue branch October 28, 2022 07:53
@luciansmith
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We still need checks for rule 21351, not just 21350.

@fbergmann
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@fbergmann : We also need to apply the caveat to rule 21351. I looked at the code, but I got stymied; can you look at it? It's the function:

SpatialCompartmentMappingUnitSizesCheck::check_

@luciansmith that code should probably be adjusted such that it only sums up the compartmentmappings, for which their compartmetns spatialDimensions match. Though i'm unsure of how that fix would actually look like. Since it is a warning, it didnt stop the exchange between tools.

Maybe one idea could be to change the check such that it would only try and sum up fractional unitSizes < 1. As that check was probably be intended to tell you when you added too many fractions.

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spatial validation rule 1221350 is to stringent
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