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[owl]: erroneous ':' in generated URIs if no default_prefix #2578

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Silvanoc opened this issue Mar 24, 2025 · 6 comments · May be fixed by linkml/linkml-runtime#378
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[owl]: erroneous ':' in generated URIs if no default_prefix #2578

Silvanoc opened this issue Mar 24, 2025 · 6 comments · May be fixed by linkml/linkml-runtime#378
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bug Something that should work but isn't, with an example and a test case. community-generated schemaview

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@Silvanoc
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Silvanoc commented Mar 24, 2025 •
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Describe the bug

Element URIs contained in generated OWL contain erroneous :. For example: https://example.org/my-schema/:MySubclass for the below provided schema. The issue appears only if no default_prefix is explicitly declared.

Version of LinkML you are using

v1.8.7

Please provide a schema (and if applicable, a data file) that replicates the issue

id: https://example.org/my-schema
prefixes:
  linkml: https://w3id.org/linkml/
  rdl: https://rds.posccaesar.org/ontology/lis14/rdl/
imports:
  - linkml:types
default_range: string

classes:
  MySubclass:
    is_a: FunctionalObject
  FunctionalObject:
    class_uri: rdl:FunctionalObject
@Silvanoc Silvanoc added the bug Something that should work but isn't, with an example and a test case. label Mar 24, 2025
@Silvanoc Silvanoc mentioned this issue Mar 24, 2025
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@Silvanoc Silvanoc changed the title [owl]: erroneous ':' in generated URIs [owl]: erroneous ':' in generated URIs if no default_prefix Mar 24, 2025
@Silvanoc
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Silvanoc commented Mar 24, 2025 •
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@dalito since you appear to know the code probably involved in this issue, could you please have a look at this issue? Thanks!

I'm not blaming you! Your changes are posterior to the version of linkml-runtime (v1.8.3) integrated into the version of linkml (v1.8.7) that is showing this issue.

@dalito
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dalito commented Mar 24, 2025

@Silvanoc - With which linkml-runtime version did you see this? Did you try the dev version of linkml-runtime?

@Silvanoc
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@Silvanoc - With which linkml-runtime version did you see this? Did you try the dev version of linkml-runtime?

I have seen on linkml v1.8.7, which integrates linkml-runtime v1.8.3. I do not know what you mean with "dev version", is it the HEAD of main?

@dalito
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dalito commented Mar 24, 2025 •
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Yes, with "dev" I meant the current "main" branch. If I remember correctly, there were some changes made after v1.8.3 of linkml-runtime in code that could affect this. I don't have time right now but can have a look later.

@Silvanoc
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Yes, there were some changes in dev... done by you 😄 That's why I pulled you in. Because it does not look as if you were fixing the issue in your changes, but you appear to know that code.

@dalito dalito linked a pull request Mar 24, 2025 that will close this issue
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@dalito
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dalito commented Mar 24, 2025 •
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@Silvanoc - I made a PR with a fix and marked you as reviewer. This bug has been present since the creation of schemaview.py.

@dalito dalito mentioned this issue Mar 24, 2025
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Silvanoc added a commit to linkml/linkml-runtime that referenced this issue Mar 25, 2025
@Silvanoc
test(schemaview): schema without default_prefix
3039434 
Add regression test for issue #2578 [^1].

Issue was that SchemaView method `get_uri` was adding an errorneous ':'
when no `default_prefix` was being declared in the schema.

[^1]: linkml/linkml#2578

Signed-off-by: Silvano Cirujano Cuesta <[email protected]>
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Fix Schemaview.get_uri(...) for no default_prefix in schema dalito/linkml-runtime
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@nlharris @dalito @Silvanoc