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WIP: Fix issues with changed IRIs effecting test_excelparser #697

Merged
merged 6 commits into from
Jan 2, 2024
Merged

WIP: Fix issues with changed IRIs effecting test_excelparser #697

merged 6 commits into from
Jan 2, 2024

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jesper-friis
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Description

Fix issues with changed IRIs effecting test_excelparser.

Added difference() method to Ontology for easier debugging. I think it is worth keeping.

Note that this branch is branched out from the directory-layout in PR #696.

Type of change

  • Bug fix.
  • New feature.
  • Documentation update.
  • Test update.

Checklist

This checklist can be used as a help for the reviewer.

  • Is the code easy to read and understand?
  • Are comments for humans to read, not computers to disregard?
  • Does a new feature has an accompanying new test (in the CI or unit testing schemes)?
  • Has the documentation been updated as necessary?
  • Does this close the issue?
  • Is the change limited to the issue?
  • Are errors handled for all outcomes?
  • Does the new feature provide new restrictions on dependencies, and if so is this documented?

Comments

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codecov bot commented Dec 21, 2023 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

❗ No coverage uploaded for pull request base (directory_layout@6c9bd2b). Click here to learn what that means.

Additional details and impacted files 
@@                 Coverage Diff                 @@
##             directory_layout     #697   +/-   ##
===================================================
  Coverage                    ?   71.46%           
===================================================
  Files                       ?       16           
  Lines                       ?     3385           
  Branches                    ?        0           
===================================================
  Hits                        ?     2419           
  Misses                      ?      966           
  Partials                    ?        0

☔ View full report in Codecov by Sentry.
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@jesper-friis jesper-friis changed the base branch from master to directory_layout December 21, 2023 16:36
francescalb
francescalb reviewed Dec 22, 2023
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ontopy/ontology.py
Comment on lines +1944 to +1951
def difference(self, other: owlready2.Ontology) -> set:
"""Return a set of triples that are in this, but not in the
`other` ontology."""
# pylint: disable=invalid-name
s1 = set(self.get_unabbreviated_triples(blank="_:b"))
s2 = set(other.get_unabbreviated_triples(blank="_:b"))
return s1.difference(s2)

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Nice.

francescalb
francescalb reviewed Dec 22, 2023
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ontopy/ontology.py
@@ -2008,31 +2016,31 @@ def _unabbreviate(


def _get_unabbreviated_triples(
self, subject=None, predicate=None, obj=None, blank=None
onto, subject=None, predicate=None, obj=None, blank=None
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Well spotted!

francescalb
francescalb reviewed Dec 22, 2023
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tests/test_excelparser/result_ontology/fromexcelonto.ttl
owl:imports <http://emmo.info/emmo-inferred>,
owl:imports <http://emmo.info/emmo>,
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I do not understand why. We import beta-4 which should not have changed as development is now happening in beta5.

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It is due to backward corrections of ontology IRIs on GitHub Pages. Probably a bad decision, but now it is done and should not be reverted again...

francescalb
francescalb reviewed Dec 22, 2023
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tests/test_excelparser/onto_only_classes.xlsx Outdated
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I have tried to compare the files visually, but can't spot the change. Can you explain?

francescalb
francescalb reviewed Dec 22, 2023
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tests/test_excelparser/test_excelparser.py Outdated
Comment on lines 128 to 133
print("----- only in onto -----")
print(onto.difference(ontology))

print("----- only in ontology -----")
print(ontology.difference(onto))

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Should be remobed

francescalb
francescalb reviewed Dec 22, 2023
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tests/test_excelparser/test_excelparser.py Outdated
Comment on lines 102 to 107

# if True:
# from pathlib import Path
#
# repo_dir = Path(__file__).resolve().parent.parent.parent

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Should be removed

francescalb
francescalb reviewed Dec 22, 2023
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tests/test_excelparser/test_excelparser.py
Comment on lines -146 to +158
assert updated_onto.Pattern.iri == onto.Pattern.iri
assert updated_onto.FinitePattern.iri == onto.FinitePattern.iri
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We should check both Pattern (in the imported ontology) and FinitePattern (newly created)

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Pattern doesn't exists in 1.0.0-beta5, which is the one we have here.

francescalb
francescalb requested changes Dec 22, 2023
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I like the difference function. Please see comments, though.

@francescalb francescalb self-requested a review January 2, 2024 07:35
francescalb
francescalb approved these changes Jan 2, 2024
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Good, but check that pylint passes.

@jesper-friis jesper-friis merged commit 4496126 into directory_layout Jan 2, 2024
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@jesper-friis jesper-friis deleted the directory-layout-test_excelparser branch January 2, 2024 08:00
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@jesper-friis @francescalb