jsonprofile 0.1.1__tar.gz

jsonprofile-0.1.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: jsonprofile
+Version: 0.1.1
+Summary: Dynamic profile management for json files share same schema
+Requires-Dist: bioregistry>=0.13.64
+Requires-Dist: cachetools>=7.1.4
+Requires-Dist: email-validator>=2.3.0
+Requires-Dist: httpx2>=0.28.1
+Requires-Dist: jsonpath-ng>=1.8.0
+Requires-Dist: jsonschema-rs>=0.46.9
+Requires-Dist: ontology-lookup>=0.1.1
+Requires-Dist: orjson>=3.11.9
+Requires-Dist: pydantic>=2.12.4
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: rfc3986>=2.0.0
+Requires-Dist: opa-wasmtime>=0.1.1 ; extra == 'opa'
+Requires-Python: >=3.10
+Provides-Extra: opa
+Description-Content-Type: text/markdown
+
+# jsonprofile Python
+
+Python implementation of jsonprofile.
+
+Requires Python 3.10 or later. CI tests Python 3.10 through 3.14.
+
+From this directory, run `uv sync --locked` to install dependencies and
+`uv run pytest` to run the tests. The default development interpreter is
+Python 3.10; use `uv run --python 3.14 pytest` to test another version.
+
+Local OPA policy evaluation is optional. Install it with `pip install "jsonprofile[opa]"`
+or use `uv sync --extra opa` when working from this directory. The validator
+automatically uses the local OPA engine when the optional dependency is installed.

jsonprofile-0.1.1/README.md

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+# jsonprofile Python
+
+Python implementation of jsonprofile.
+
+Requires Python 3.10 or later. CI tests Python 3.10 through 3.14.
+
+From this directory, run `uv sync --locked` to install dependencies and
+`uv run pytest` to run the tests. The default development interpreter is
+Python 3.10; use `uv run --python 3.14 pytest` to test another version.
+
+Local OPA policy evaluation is optional. Install it with `pip install "jsonprofile[opa]"`
+or use `uv sync --extra opa` when working from this directory. The validator
+automatically uses the local OPA engine when the optional dependency is installed.

jsonprofile-0.1.1/pyproject.toml

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+[project]
+name = "jsonprofile"
+version = "0.1.1"
+description = "Dynamic profile management for json files share same schema"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "bioregistry>=0.13.64",
+    "cachetools>=7.1.4",
+    "email-validator>=2.3.0",
+    "httpx2>=0.28.1",
+    "jsonpath-ng>=1.8.0",
+    "jsonschema-rs>=0.46.9",
+    "ontology-lookup>=0.1.1",
+    "orjson>=3.11.9",
+    "pydantic>=2.12.4",
+    "pyyaml>=6.0.3",
+    "rfc3986>=2.0.0",
+]
+
+[project.optional-dependencies]
+opa = ["opa-wasmtime>=0.1.1"]
+
+[dependency-groups]
+dev = [
+    "pre-commit>=3.10.1",
+    "commitizen>=4.13.9",
+    "pytest>=9.0.3",
+    "ruff>=0.17.00",
+    "uv-build>=0.9.8",
+    "mkdocs-material>=9.7.0",
+]
+
+[tool.ruff]
+target-version = "py310"
+cache-dir = "../.cache/python/ruff"
+src = ["src"]
+
+[tool.ruff.lint]
+select = [
+    "E",
+    "F",
+    "C",
+    "I",
+    "G",
+    "SLF",
+    "PTH",
+    "Q",
+    "T",
+]
+ignore = ["C901"]
+fixable = ["ALL"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["jsonprofile"]
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+version_provider = "uv"
+tag_format = "v$major.$minor.$patch"
+version_files = [
+    "pyproject.toml:version",
+    "src/jsonprofile/__init__.py:__version__",
+]
+bump_message = "bump: version $current_version -> $new_version"
+update_changelog_on_bump = true
+
+[tool.pytest.ini_options]
+addopts = "-v"
+cache_dir = "../.cache/python/pytest"
+testpaths = ["tests"]
+log_cli = true
+log_cli_level = "INFO"
+log_cli_date_format = "%Y-%m-%d %H:%M:%S"
+log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
+
+[tool.uv.build-backend]
+module-name = "jsonprofile"
+
+[build-system]
+requires = ["uv_build>=0.9.8,<0.12.0"]
+build-backend = "uv_build"

jsonprofile-0.1.1/pyproject.toml.orig

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+[project]
+name = "jsonprofile"
+version = "0.1.1"
+description = "Dynamic profile management for json files share same schema"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "bioregistry>=0.13.64",
+    "cachetools>=7.1.4",
+    "email-validator>=2.3.0",
+    "httpx2>=0.28.1",
+    "jsonpath-ng>=1.8.0",
+    # "jsonschema>=4.26.0",
+    "jsonschema-rs>=0.46.9",
+    "ontology-lookup>=0.1.1",
+    "orjson>=3.11.9",
+    "pydantic>=2.12.4",
+    "pyyaml>=6.0.3",
+    "rfc3986>=2.0.0",
+]
+[project.optional-dependencies]
+opa = ["opa-wasmtime>=0.1.1"]
+
+[dependency-groups]
+dev = [
+    "pre-commit>=3.10.1",
+    "commitizen>=4.13.9",
+    "pytest>=9.0.3",
+    "ruff>=0.17.00",
+    "uv-build>=0.9.8",
+    "mkdocs-material>=9.7.0",
+]
+
+[tool.ruff]
+target-version = "py310"
+cache-dir = "../.cache/python/ruff"
+src = ["src"]
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+version_provider = "uv"
+tag_format = "v$major.$minor.$patch"
+version_files = [
+    "pyproject.toml:version",
+    "src/jsonprofile/__init__.py:__version__",
+]
+bump_message = "bump: version $current_version -> $new_version"
+update_changelog_on_bump = true
+
+[tool.ruff.lint]
+select = ["E", "F", "C", "I", "G", "SLF", "PTH", "Q", "T"]
+ignore = [ "C901"]
+
+fixable = ["ALL"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["jsonprofile"]
+
+[tool.pytest.ini_options]
+addopts = "-v"
+cache_dir = "../.cache/python/pytest"
+testpaths = ["tests"]
+log_cli = true
+log_cli_level = "INFO"
+log_cli_date_format = "%Y-%m-%d %H:%M:%S"
+log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
+
+[build-system]
+requires = ["uv_build>=0.9.8,<0.12.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "jsonprofile"

jsonprofile-0.1.1/src/jsonprofile/__init__.py

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+from jsonprofile import profile, utils, validator
+
+__version__ = "v0.1.1"
+
+
+__all__ = ["profile", "validator", "utils", "cv_term_search"]

jsonprofile-0.1.1/src/jsonprofile/cv_term_search.py

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+import logging
+
+from ontology_lookup import OntologyLookupService
+from ontology_lookup.models import (
+    CurieResolutionResponse,
+    IriResolutionResponse,
+    SearchTermSummary,
+    TermResponse,
+)
+
+from jsonprofile.profile.base import CvTerm as ProfileCvTerm
+from jsonprofile.validator.base import (
+    CvTermSearch,
+)
+
+logger = logging.getLogger(__name__)
+
+
+class OntologyLookupCvTermSearch(CvTermSearch):
+    def __init__(self, db_path: str, *args, **kwargs):
+        self.svc = OntologyLookupService(db_path=db_path)
+
+    def get_iri(self, cv_term: ProfileCvTerm) -> str | None:
+        if cv_term.cv_accession.startswith(("http://", "https://")):
+            return cv_term.cv_accession
+        result: None | IriResolutionResponse = self.svc.find_iri(
+            curie=cv_term.cv_accession, ontology=cv_term.cv_label
+        )
+
+        if not result:
+            return None
+        return result.iri or None
+
+    def get_curie(self, cv_term: ProfileCvTerm) -> str | None:
+        if not cv_term.cv_accession.startswith(("http://", "https://")):
+            return cv_term.cv_accession
+        result: CurieResolutionResponse = self.svc.find_curie(
+            iri=cv_term.cv_accession, ontology=cv_term.cv_label
+        )
+
+        if not result:
+            return None
+        return result.curie or None
+
+    def find_cv_term(
+        self,
+        source: str,
+        accession_or_label: str,
+        matched_accession: None | str = None,
+        allow_synonym_search: bool = False,
+    ) -> None | ProfileCvTerm:
+        if matched_accession:
+            result: TermResponse = self.svc.get_term_by_accession(
+                ontology=source, accession=matched_accession
+            )
+        if result:
+            return ProfileCvTerm(
+                cv_label=result.ontology, cv_accession=result.curie, name=result.label
+            )
+        result: TermResponse = self.svc.get_term_by_accession(
+            ontology=source, accession=accession_or_label
+        )
+        if result:
+            return ProfileCvTerm(
+                cv_label=result.ontology, cv_accession=result.curie, name=result.label
+            )
+        if allow_synonym_search:
+            result: list[SearchTermSummary] = self.svc.search_by_label(
+                ontology=source, label_or_synonym=accession_or_label
+            )
+            if result:
+                result = result[0]
+        else:
+            result: TermResponse = self.svc.get_term_by_exact_label(
+                ontology=source, label=accession_or_label
+            )
+        if result:
+            return ProfileCvTerm(
+                cv_label=result.ontology, cv_accession=result.curie, name=result.label
+            )
+        return None
+
+    def check_cv_term(
+        self,
+        cv_term: ProfileCvTerm,
+        parent_cv_term: None | ProfileCvTerm = None,
+        allow_synonym_search: bool = False,
+    ) -> tuple[bool, str]:
+        ontology = cv_term.cv_label
+        if not cv_term.cv_label:
+            if ":" in cv_term.cv_accession:
+                ontology = cv_term.cv_label.split(":", maxsplit=1)[0]
+            else:
+                return (
+                    False,
+                    f"Invalid ontology for {cv_term.name}",
+                )
+        if parent_cv_term:
+            result = self.svc.search_by_label(
+                ontology=ontology,
+                label_or_synonym=cv_term.name,
+                parent_curie=parent_cv_term.cv_accession,
+                search_in_synonyms=allow_synonym_search,
+            )
+            if result:
+                result_item = result[0]
+                if result_item.curie == cv_term.cv_accession:
+                    return (
+                        True,
+                        f"{cv_term.cv_accession} is "
+                        f"child of {parent_cv_term.cv_accession}",
+                    )
+                else:
+                    return (
+                        False,
+                        f"{cv_term.cv_accession} {cv_term.name} does not match.",
+                    )
+            return (
+                False,
+                f"{cv_term.cv_accession} is not child of {parent_cv_term.cv_accession}",
+            )
+        result: list[SearchTermSummary] = self.svc.search_by_label(
+            ontology=ontology,
+            label_or_synonym=cv_term.name,
+            search_in_synonyms=allow_synonym_search,
+            limit=1,
+        )
+        if result:
+            return (
+                True,
+                f"{cv_term.cv_accession} is found result with label {result[0].label} ",
+            )
+        return (
+            False,
+            f"{cv_term.cv_accession} '{cv_term.name}' "
+            f"is not found in ontology {cv_term.cv_label}",
+        )
+
+    def find_cv_term_with_accession(
+        self, source: str, accession: str
+    ) -> tuple[ProfileCvTerm | None, list[str] | None]:
+        ontology = source
+        if not ontology:
+            if ":" in accession:
+                ontology = accession.split(":", maxsplit=1)[0]
+            else:
+                return None, []
+
+        result: None | TermResponse = self.svc.get_term_by_accession(
+            ontology=ontology, accession=accession
+        )
+        if result:
+            profile_cv_term = ProfileCvTerm(
+                cv_label=result.ontology,
+                cv_accession=result.curie,
+                name=result.label,
+            )
+            return profile_cv_term, result.synonyms or []
+        return None, None