refscan 0.3.3__tar.gz → 0.4.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {refscan-0.3.3 → refscan-0.4.0}/PKG-INFO +2 -2
- {refscan-0.3.3 → refscan-0.4.0}/pyproject.toml +2 -5
- refscan-0.4.0/refscan/__init__.py +23 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/cli/scan.py +1 -3
- {refscan-0.3.3 → refscan-0.4.0}/refscan/cli/version.py +1 -3
- {refscan-0.3.3 → refscan-0.4.0}/refscan/grapher.py +2 -2
- refscan-0.3.3/refscan/__init__.py +0 -18
- {refscan-0.3.3 → refscan-0.4.0}/README.md +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/cli/cli.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/cli/graph.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/Finder.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/Reference.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/ReferenceList.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/Violation.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/ViolationList.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/constants.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/lib/helpers.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/scanner.py +0 -0
- {refscan-0.3.3 → refscan-0.4.0}/refscan/templates/graph.template.html +0 -0
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Metadata-Version: 2.3
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Name: refscan
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Version: 0.
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Version: 0.4.0
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Summary: Command-line program that scans the NMDC MongoDB database for referential integrity violations
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Keywords: mongodb,mongo,relationships,reference,database,data,referential integrity,scan
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Requires-Dist: linkml-runtime>=1.7.5,<2
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Requires-Dist: pymongo>=4.7.1,<5
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Requires-Dist: rich>=13.7.1,<14
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Requires-Dist: typer>=0.15.1,<0.16
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Requires-Python: >=3.9, <
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Requires-Python: >=3.9, <4.0
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Project-URL: Documentation, https://github.com/microbiomedata/refscan
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Project-URL: Homepage, https://github.com/microbiomedata/refscan
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Project-URL: Repository, https://github.com/microbiomedata/refscan
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@@ -1,12 +1,9 @@
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[project]
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name = "refscan"
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version = "0.
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version = "0.4.0"
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description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
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authors = []
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# package, is also constrained to Python 3.9.* (according to its `pyproject.toml` file).
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# Reference: https://github.com/microbiomedata/nmdc-schema/blob/main/pyproject.toml#L34
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requires-python = ">= 3.9, < 3.10"
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requires-python = ">= 3.9, < 4.0"
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readme = "README.md"
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keywords = [
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"mongodb",
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from importlib.metadata import PackageNotFoundError, version
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from typing import Optional
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def get_package_version(package_name: str) -> Optional[str]:
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r"""
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Returns the version identifier (e.g., "1.2.3") of the package having the specified name.
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Args:
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package_name: The name of the package
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Returns:
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The version identifier of the package, or `None` if package not found
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"""
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try:
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return version(package_name)
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except PackageNotFoundError:
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return None
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# Make an `import`-able variable whose value is the version identifier of this package.
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app_name = "refscan"
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app_version = get_package_version(app_name)
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@@ -16,9 +16,7 @@ from refscan.lib.helpers import (
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)
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from refscan.lib.ViolationList import ViolationList
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from refscan.scanner import scan as refscan_scan
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from refscan import
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app_version = get_package_metadata("Version")
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from refscan import app_version
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def scan(
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@@ -6,7 +6,7 @@ from importlib import resources
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import linkml_runtime
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from refscan import
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from refscan import app_version
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from refscan.lib.constants import console
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from refscan.lib.helpers import (
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get_collection_name_to_class_names_map,
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@@ -161,7 +161,7 @@ def graph(
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graph_data_json_base64_str = encode_json_value_as_base64_str(elements)
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graph_metadata_json_base64_str = encode_json_value_as_base64_str(
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dict(
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app_version=
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app_version=app_version,
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schema_version=schema_view.schema.version,
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subject_singular="class" if subject == Subject.class_ else "collection",
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subject_plural="classes" if subject == Subject.class_ else "collections",
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from importlib.metadata import metadata, PackageNotFoundError
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def get_package_metadata(key: str) -> str:
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r"""
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Returns metadata about the installed package.
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References:
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- https://docs.python.org/3/library/importlib.metadata.html#distribution-metadata
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- https://github.com/python-poetry/poetry/issues/273#issuecomment-570999678
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"""
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metadata_value = ""
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try:
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package_metadata = metadata("refscan")
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metadata_value = package_metadata.get(key, "")
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except PackageNotFoundError:
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pass
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return metadata_value
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