Library Usage by kchason · Pull Request #118 · casework/CASE-Utilities-Python

kchason · 2023-07-25T00:37:35Z

Example usage of the programmatic usage of the CASE utilities.

importosfromcase_utils.case_validateimportvalidate, ValidationResult# Validate a case fileresult: ValidationResult=validate(os.path.abspath("location.json"), 'case-1.2.0')
print("Valid"ifresult.conformselse"Invalid")

ajnelson-nist

There are at least three can't-pass-as-is issues. It looks like a few parts of this PR can be filed on their own while we work those out.

This patch partially implements a small piece of PR 118. References: * #118 Requested-by: kchason <keith.chason@gmail.com> Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

@kchason

AJN: This is a partial application of @kchason 's work in PR 118, and is being pulled into its own patch series to focus review. References: * #118 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

It seems to me like `--disallow-untyped-defs`, enabled in `mypy --strict`, should have flagged this as an error. However, from documentation on `no-untyped-def`, `mypy` only requires `__init__(...) -> None` when there is any argument aside from the first `self`. This patch follows the parenthetical recommendation from PEP 484 that `-> None` be given anyways. References: * https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-disallow-untyped-defs * https://mypy.readthedocs.io/en/stable/error_code_list2.html#check-that-every-function-has-an-annotation-no-untyped-def * https://peps.python.org/pep-0484/#the-meaning-of-annotations Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

… type Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist · 2023-08-21T18:22:31Z

- validate_result = pyshacl.validate(
+ validate_result: Tuple[
+ bool, Union[Exception, bytes, str, rdflib.Graph], str
+ ] = pyshacl.validate(


I think this call needs to be replaced with the validate() method this PR is adding to this file, but only after logistics related to #123 are settled.

I believe this is addressed in 15f00c9.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

…n "none" This is a continuation of PR 123. References: * #123 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist · 2023-08-23T15:14:03Z


-class NonExistentCDOConceptWarning(UserWarning):
+def validate(
+ input_file: str,


For our awareness, this is a narrower argument than the first argument of pyshacl.validate; here's today's definition:
https://github.com/RDFLib/pySHACL/blob/v0.23.0/pyshacl/validate.py#L369-L370
pyshacl.validate's first argument seems to permit a string to be a file path or URL, OR a full string dump of a graph. See these lines for heuristics in pyshacl.rdfutil.load.load_from_graph:
https://github.com/RDFLib/pySHACL/blob/v0.23.0/pyshacl/rdfutil/load.py#L222-L227
Should we implement "str means path" now, or just adopt the load_from_graph usage now from these lines:
https://github.com/RDFLib/pySHACL/blob/v0.23.0/pyshacl/validate.py#L424-L428

Welp, I found an issue pushing us towards expanding input_file from str. case_validate is written to take multiple input files as data graphs (as well as multiple input files as ontology graphs). I believe this behavior should be preserved, because otherwise a user that needs to read two data graphs at once needs to do some intermediary graph compilation before calling case_validate.
So, I think the first argument needs to become at least either Union[str, List[str]] or Union[str, Graph]. The current code path from the CLI entry point I think favors Union[str, List[str]].

I believe this is addressed in 15f00c9.

…idate This patch separates implementation points between functionality distinct to `case_utils.validate` and `pyshacl.validate`. The `allow_warnings` and `inference` parameters provide CASE-specific documentation as an augmentation to `pyshacl.validate`'s documentation, but otherwise other documentation on `pyshacl.validate`'s keyword arguments is delegated to their upstream function. This patch removes some hardcoded parameter values in `pyshacl.validate`, letting the `case_validate` CLI or caller provide any runtime-requested values. Also, without functional impact, this patch sorts keyword parameters alphabetically. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist

I'm fine with this merging once CI passes. Also open to discussing any of the last revisions I made.

Add validate() function for programmatic access
2df147a

kchason requested a review from a team as a code owner July 25, 2023 00:37

kchason added 4 commits July 24, 2023 20:40

Fix pre-commit formatting
f485161

Fix property reference
b509dc5

Make type generic to account for multiple return types
8c40df1

Fix List vs list for casting
f6d48e2

ajnelson-nist requested changes Jul 25, 2023
View reviewed changes

ajnelson-nist added a commit that referenced this pull request Jul 25, 2023
Use typing symbols directly
7621f7f
This patch partially implements a small piece of PR 118. References: * #118 Requested-by: kchason <keith.chason@gmail.com> Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

kchason added 3 commits July 25, 2023 20:59

Feedback from PR
2d3a65b

Merge branch 'develop' into library-usage
bfe9992

Instantiate properties as instance variables instead of class
86ed417

ajnelson-nist mentioned this pull request Aug 9, 2023
case_validate: Expose CDO IRI typo-checker as function #121
Merged

ajnelson-nist added this to the 0.12.0 milestone Aug 14, 2023

Fix None vs "none" ontology version specification
40be311
No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist requested changes Aug 19, 2023
View reviewed changes

Comment threadcase_utils/case_validate/__init__.py Outdated
Comment threadcase_utils/case_validate/__init__.py Outdated
Comment threadcase_utils/case_validate/__init__.py Outdated

ajnelson-nist added 2 commits August 21, 2023 11:31

Constrain ValidationResult.graph type to pyshacl.validate(...)[1]…
97d7fbb
… type Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist reviewed Aug 21, 2023
View reviewed changes

Comment threadcase_utils/case_validate/__init__.py Outdated

ajnelson-nist reviewed Aug 21, 2023
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kchasonand others added 7 commits August 22, 2023 13:36

Merge branch 'develop' into library-usage
64bd95c

Wrap errors and positional arg signature support
4208a99

Separate types and utils into discrete files
73e4683

Fix import reference
d41a418

Forward arguments with unpacking syntax
8f957dc
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

Merge branch 'develop' into library-usage
6f9b6c9

Default case_validate.validate inference parameter to None rather tha…
00f1360
…n "none" This is a continuation of PR 123. References: * #123 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist reviewed Aug 23, 2023
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ajnelson-nist added 2 commits August 23, 2023 17:41

Add new case_validate source files to Make dependencies
eccaad4
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

case_validate: Update NIST inlined license text
90f5c8c
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

ajnelson-nist approved these changes Aug 23, 2023
View reviewed changes

kchason merged commit bded343 into developAug 24, 2023

kchason deleted the library-usage branch August 24, 2023 11:34

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Library Usage - #118

Library Usage#118
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