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Added fix for adding annotations that are not strings in ontodoc #512

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merged 6 commits into from
Dec 14, 2022
Merged

Added fix for adding annotations that are not strings in ontodoc #512

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d7ec93c
Added fix for adding annotations that are not strings in ontodoc
francescalb Dec 12, 2022
09eafd3
Merge branch 'master' into 510-ontodoc-adding-annotations-that-are-no…
francescalb Dec 13, 2022
3d3c1d4
Merge branch 'master' into 510-ontodoc-adding-annotations-that-are-no…
francescalb Dec 13, 2022
16858f5
typo
francescalb Dec 13, 2022
9b7f13e
typo
francescalb Dec 13, 2022
9d29601
Merge branch 'master' into 510-ontodoc-adding-annotations-that-are-no…
CasperWA Dec 14, 2022
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3 changes: 2 additions & 1 deletion ontopy/ontodoc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -288,7 +288,8 @@ def itemdoc(
annotations.keys(), key=lambda key: order.get(key, key)
):
for value in annotations[key]:
if self.url_regex.match(value):
value = str(value)
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This could fail, I suppose, if the type of value cannot be cast to a str type.
You could instead wrap it in a try/except block, where you're catching TypeError and ValueError exceptions, re-raising them with an appropriate custom message?

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I discussed this with @jesper-friis , and we can't really see a situation in which this not enough. I think it is better to leave it as is, and update this if and when we find examples of situations in which a different handling is needed.

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As you wish. Casting to str is in general quite generous in this case, so it's fine I suppose. However, I'd argue it's good convention to consider possible edge cases and try to catch them if possible so exception messages are clear and helpful.

if self.url_regex.match(str(value)):
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doc.append(
annotation_style.format(
key=key, value=asstring(value, link_style)
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2 changes: 1 addition & 1 deletion tests/ontopy_tests/test_prefix.py
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Expand Up @@ -9,7 +9,7 @@
def test_prefix(testonto: "Ontology", emmo: "Ontology") -> None:
"""Test prefix in ontology"""

assert len(testonto.get_by_label_all("*")) == 2
assert len(testonto.get_by_label_all("*")) == 3
assert testonto.get_by_label_all("*", prefix="testonto") == [
testonto.TestClass
]
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3 changes: 2 additions & 1 deletion tests/testonto/models.ttl
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Expand Up @@ -18,4 +18,5 @@ skos:altLabel rdf:type owl:AnnotationProperty .

:testclass rdf:type owl:Class ;
rdfs:subClassOf owl:Thing ;
skos:prefLabel "TestClass"@en .
skos:prefLabel "TestClass"@en ;
skos:altLabel 25517 . # Test that values given as integers as still accepted by ontodoc
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4 changes: 3 additions & 1 deletion tests/tools/test_ontodoc.py
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Expand Up @@ -4,7 +4,6 @@
import pytest


@pytest.mark.skip("ontodoc is tested in other ways")
@pytest.mark.parametrize("tool", ["ontodoc"], indirect=True)
def test_run(tool, tmpdir: Path) -> None:
"""Check that running `ontodoc` works."""
Expand All @@ -13,3 +12,6 @@ def test_run(tool, tmpdir: Path) -> None:
)

tool.main([str(test_file), str(tmpdir / "test.md")])
tool.main(
[str(test_file), "--format=simple-html", str(tmpdir / "test.html")]
)