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If there are altLabels that match, get_by_label_all returns only the prefLabels. #511

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francescalb opened this issue Dec 12, 2022 · 1 comment
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If there are altLabels that match, get_by_label_all returns only the prefLabels. #511

francescalb opened this issue Dec 12, 2022 · 1 comment

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@francescalb
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Example:
´´´
from ontopy import get_ontology
onto = get_ontology()
onto = get_ontology().load()
onto.get_by_label_all('Concentration')
´´´

How to solve this should be consdered. Alternative labels should be returned as well, I think, but I am not sure if we should specifiy which are altLabels and which are prefLabels.

When this is fixed test_prefix should be corrected.
francescalb added a commit that referenced this issue Dec 12, 2022
@francescalb
Added fix for adding annotations that are not strings in ontodoc
d7ec93c 
Furthermore, reenabled test for ontodoc. This is still aminimal test,
but I think can be gradually expanded.

Lastlt - because a new altLabel was added in the testontology, it was revieled that
the same entity is returned twice in by get_by_label_all in test_prefix. Issue #511 was
made bacause of this.
@francescalb francescalb mentioned this issue Dec 12, 2022
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@francescalb
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I disagree with myself, I think it makes sense that each class is returned once and as it is returned with prefLabel(or label)

TEAM4-0 pushed a commit that referenced this issue Apr 12, 2024
@dependabot @francescalb
Update pytest-cov requirement from ~=4.1 to ~=5.0 (#738)
10833d6 
Updates the requirements on
[pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the
latest version.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst">pytest-cov's
changelog</a>.</em></p>
<blockquote>
<h2>5.0.0 (2024-03-24)</h2>
<ul>
<li>Removed support for xdist rsync (now deprecated).
Contributed by Matthias Reichenbach in
<code>[#623](pytest-dev/pytest-cov#623)
&lt;https://github.com/pytest-dev/pytest-cov/pull/623&gt;</code>_.</li>
<li>Switched docs theme to Furo.</li>
<li>Various legacy Python cleanup and CI improvements.
Contributed by Christian Clauss and Hugo van Kemenade in
<code>[#630](pytest-dev/pytest-cov#630)
&lt;https://github.com/pytest-dev/pytest-cov/pull/630&gt;</code><em>,
<code>[#631](pytest-dev/pytest-cov#631)
&lt;https://github.com/pytest-dev/pytest-cov/pull/631&gt;</code></em>,
<code>[#632](pytest-dev/pytest-cov#632)
&lt;https://github.com/pytest-dev/pytest-cov/pull/632&gt;</code>_ and
<code>[#633](pytest-dev/pytest-cov#633)
&lt;https://github.com/pytest-dev/pytest-cov/pull/633&gt;</code>_.</li>
<li>Added a <code>pyproject.toml</code> example in the docs.
Contributed by Dawn James in
<code>[#626](pytest-dev/pytest-cov#626)
&lt;https://github.com/pytest-dev/pytest-cov/pull/626&gt;</code>_.</li>
<li>Modernized project's pre-commit hooks to use ruff. Initial POC
contributed by
Christian Clauss in
<code>[#584](pytest-dev/pytest-cov#584)
&lt;https://github.com/pytest-dev/pytest-cov/pull/584&gt;</code>_.</li>
</ul>
<h2>4.1.0 (2023-05-24)</h2>
<ul>
<li>Updated CI with new Pythons and dependencies.</li>
<li>Removed rsyncdir support. This makes pytest-cov compatible with
xdist 3.0.
Contributed by Sorin Sbarnea in
<code>[#558](pytest-dev/pytest-cov#558)
&lt;https://github.com/pytest-dev/pytest-cov/pull/558&gt;</code>_.</li>
<li>Optimized summary generation to not be performed if no reporting is
active (for example,
when <code>--cov-report=''</code> is used without
<code>--cov-fail-under</code>).
Contributed by Jonathan Stewmon in
<code>[#589](pytest-dev/pytest-cov#589)
&lt;https://github.com/pytest-dev/pytest-cov/pull/589&gt;</code>_.</li>
<li>Added support for JSON reporting.
Contributed by Matthew Gamble in
<code>[#582](pytest-dev/pytest-cov#582)
&lt;https://github.com/pytest-dev/pytest-cov/pull/582&gt;</code>_.</li>
<li>Refactored code to use f-strings.
Contributed by Mark Mayo in
<code>[#572](pytest-dev/pytest-cov#572)
&lt;https://github.com/pytest-dev/pytest-cov/pull/572&gt;</code>_.</li>
<li>Fixed a skip in the test suite for some old xdist.
Contributed by a bunch of people in
<code>[#565](pytest-dev/pytest-cov#565)
&lt;https://github.com/pytest-dev/pytest-cov/pull/565&gt;</code>_.</li>
</ul>
<h2>4.0.0 (2022-09-28)</h2>
<p><strong>Note that this release drops support for
multiprocessing.</strong></p>
<ul>
<li>
<p><code>--cov-fail-under</code> no longer causes <code>pytest
--collect-only</code> to fail
Contributed by Zac Hatfield-Dodds in
<code>[#511](pytest-dev/pytest-cov#511)
&lt;https://github.com/pytest-dev/pytest-cov/pull/511&gt;</code>_.</p>
</li>
<li>
<p>Dropped support for multiprocessing (mostly because <code>issue 82408
&lt;https://github.com/python/cpython/issues/82408&gt;</code>_). This
feature was
mostly working but very broken in certain scenarios and made the test
suite very flaky and slow.</p>
<p>There is builtin multiprocessing support in coverage and you can
migrate to that. All you need is this in your
<code>.coveragerc</code>::</p>
<p>[run]
concurrency = multiprocessing</p>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/5295ce01c84262cec88f31255e9ac538718f3047"><code>5295ce0</code></a>
Bump version: 4.1.0 → 5.0.0</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/1181b067972bf94569f8011f3b18f271690f9ab1"><code>1181b06</code></a>
Update changelog.</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/9757222e2e044361e70125ebdd96e5eb87395983"><code>9757222</code></a>
Fix a minor grammar error (<a
href="https://github.com/pytest-dev/pytest-cov/issues/636">#636</a>)</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/9f5cd81a0dbe3fe41681efdbef516c08988fe8ff"><code>9f5cd81</code></a>
Cleanup releasing instructions. Closes <a
href="https://github.com/pytest-dev/pytest-cov/issues/616">#616</a>.</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/93b5047ec5050d63c10a6fe16a09b671a7a03df8"><code>93b5047</code></a>
Add test for pyproject.toml loading without explicit --cov-config. Ref
<a
href="https://github.com/pytest-dev/pytest-cov/issues/508">#508</a>.</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/ff50860d7c67b920503745d92a3f0944cf41f982"><code>ff50860</code></a>
docs: add config instructions for pyproject.toml.</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/4a5a4b5fa4b1c63ddcab5cbc1813798c9b6f1d36"><code>4a5a4b5</code></a>
Keep GitHub Actions up to date with GitHub's Dependabot</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/1d7f55963d5138f41c452a946f7cca7e0b6ee8b2"><code>1d7f559</code></a>
Fix or remove URLs that are causing docs tests to fail</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/6a5af8e85b8242ac815f33e26adf9068f5f0ebc3"><code>6a5af8e</code></a>
Update changelog.</li>
<li><a
href="https://github.com/pytest-dev/pytest-cov/commit/d9fe8dfed15023d3410dd299c5092e755b8981c2"><code>d9fe8df</code></a>
Switch to furo. Closes <a
href="https://github.com/pytest-dev/pytest-cov/issues/618">#618</a>.</li>
<li>Additional commits viewable in <a
href="https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0">compare
view</a></li>
</ul>
</details>
<br />


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</details>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com>
Co-authored-by: francescalb <francesca.l.bleken@sintef.no>
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