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imports does not respect local directory #2422

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ialarmedalien opened this issue Nov 21, 2024 · 1 comment · May be fixed by linkml/linkml-runtime#350
Open

imports does not respect local directory #2422

ialarmedalien opened this issue Nov 21, 2024 · 1 comment · May be fixed by linkml/linkml-runtime#350
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bug Something that should work but isn't, with an example and a test case. community-generated devops poetry, setuptools, actions, etc. related changes

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@ialarmedalien
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When importing from a local file which references another local file, the file path of the local file is not taken into account.

Example:

|- schema.yaml
|- parts/
|      A.yaml
|      B.yaml

parts/A.yaml file:

imports:
  - B

schema.yaml file:

imports:
  - parts/A

parts/A.yaml can be imported fine using the relative path, but the file it references, parts/B.yaml cannot be found as the SV is looking for it in the same directory as schema.yaml, rather than in parts/.
@ialarmedalien ialarmedalien added the bug Something that should work but isn't, with an example and a test case. label Nov 21, 2024
@ialarmedalien
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Looks like there's a condition missing when assessing whether an import is a relative link in SchemaView.imports_closure:

            if sn not in visited:
                for i in self.schema_map[sn].imports:
                    # no self imports ;)
                    if i == sn:
                        continue

                    # resolve relative imports relative to the importing schema, rather than the
                    # origin schema. Imports can be a URI or Curie, and imports from the same
                    # directory don't require a ./, so if the current (sn) import is a relative
                    # path, and the target import doesn't have : (as in a curie or a URI)
                    # we prepend the relative path. This WILL make the key in the `schema_map` not
                    # equal to the literal text specified in the importing schema, but this is
                    # essential to sensible deduplication:
                    # [...]
                    if sn.startswith(".") and ":" not in i:
                        i = os.path.normpath(str(Path(sn).parent / i))
                    todo.append(i)

Code assumes that relative links will be written as ./file_name -- need to add in a check for / to catch relative links that don't refer to .. It would probably make more sense to check for / instead of ..

@ialarmedalien ialarmedalien linked a pull request Nov 22, 2024 that will close this issue
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@nlharris nlharris added community-generated devops poetry, setuptools, actions, etc. related changes labels Nov 22, 2024
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@nlharris @ialarmedalien