prelude-parser 0.5.0__cp38-none-win_amd64.whl

prelude_parser/__init__.py

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+from prelude_parser._prelude_parser import parse_subject_native_file
+from prelude_parser.parser import parse_to_classes, parse_to_dict
+
+__all__ = ["parse_subject_native_file", "parse_to_classes", "parse_to_dict"]

prelude_parser/_prelude_parser.pyi

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+from __future__ import annotations
+
+from pathlib import Path
+
+from prelude_parser._prelude_parser import SubjectNative  # type: ignore[attr-defined]
+from prelude_parser.types import FlatFormInfo
+
+def _parse_flat_file_to_dict(
+    xml_file: str | Path, short_names: bool
+) -> dict[str, FlatFormInfo]: ...
+def _parse_flat_file_to_pandas_dict(
+    xml_file: str | Path, short_names: bool
+) -> dict[str, FlatFormInfo]: ...
+def parse_subject_native_file(xml_file: str | Path) -> SubjectNative: ...
+
+class FileNotFoundError(Exception):
+    pass
+
+class InvalidFileTypeError(Exception):
+    pass
+
+class ParsingError(Exception):
+    pass

prelude_parser/pandas.py

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+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+from prelude_parser._prelude_parser import _parse_flat_file_to_pandas_dict
+
+
+class UnsupportedPythonVersionError(Exception):
+    pass
+
+
+try:
+    import pandas as pd
+except ImportError as e:  # pragma: no cover
+    if sys.version_info < (3, 9):  # pargma: no cover
+        raise UnsupportedPythonVersionError("Pandas only supports Python 3.9+") from e
+
+    raise ImportError(
+        "prelude-parser must be installed with the pandas or all extra to use pandas"
+    ) from e
+
+
+def to_dataframe(xml_file: str | Path, *, short_names: bool = False) -> pd.DataFrame:
+    """Parse a Prelude flat XML file into a Pandas DataFrame.
+
+    This works for Prelude flat XML files that were exported with the "write tables to seperate
+    files" option.
+
+    Args:
+        xml_file: The path to the XML file to parser.
+        short_names: Set to True if short names were used in the export.
+
+    Returns:
+        A Pandas DataFrame the data from the XML file.
+
+    Examples:
+        >>> from prelude_parser.pandas import to_dataframe
+        >>> df = to_dataframe("physical_examination.xml")
+    """
+    data = _parse_flat_file_to_pandas_dict(xml_file, short_names)
+    return pd.DataFrame.from_dict(data)

prelude_parser/parser.py

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+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+from camel_converter import to_pascal
+
+from prelude_parser._prelude_parser import _parse_flat_file_to_dict
+from prelude_parser.types import FieldInfo, FlatFormInfo
+
+
+class _MetaCls(type):
+    def __new__(
+        cls, clsname: str, superclasses: tuple[type, ...], attributedict: dict[str, FieldInfo]
+    ) -> _MetaCls:
+        return super().__new__(cls, clsname, superclasses, attributedict)
+
+
+def parse_to_dict(xml_file: str | Path, *, short_names: bool = False) -> dict[str, FlatFormInfo]:
+    """Parse a Prelude flat XML file into a dict.
+
+    Args:
+        xml_file: The path to the XML file to parser.
+        short_names: Set to True if short names were used in the export.
+
+    Returns:
+        A Python dictionary containing the data from the XML file.
+
+    Examples:
+        >>> from prelude_parser import parse_to_dict
+        >>> data = parse_to_dict("physical_examination.xml")
+    """
+    return _parse_flat_file_to_dict(xml_file, short_names)
+
+
+def parse_to_classes(xml_file: str | Path, short_names: bool = False) -> list[Any]:
+    """Parse a Prelude flat XML file into a list of Python class.
+
+    The name of the class is taken from the form name node in the XML file converted to pascal case.
+    For example a <physical_examination> node will result in a PhysicalExamination class being
+    created.
+
+    Args:
+        xml_file: The path to the XML file to parser.
+        short_names: Set to True if short names were used in the export.
+
+    Returns:
+        A list of Python classes containing the data from the XML file.
+
+    Examples:
+        >>> from prelude_parser import parse_to_classes
+        >>> data = parse_to_classes("physical_examination.xml")
+    """
+    parsed = parse_to_dict(xml_file, short_names=short_names)
+    formatted: list[Any] = []
+    for form, data in parsed.items():
+        class_name = to_pascal(form)
+        for d in data:
+            formatted.append(_MetaCls(class_name, (object,), d))
+
+    return formatted

prelude_parser/polars.py

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+from __future__ import annotations
+
+from pathlib import Path
+
+from prelude_parser._prelude_parser import _parse_flat_file_to_pandas_dict
+
+try:
+    import polars as pl
+except ImportError as e:  # pragma: no cover
+    raise ImportError(
+        "prelude-parser must be installed with the polars or all extra to use pandas"
+    ) from e
+
+
+def to_dataframe(xml_file: str | Path, *, short_names: bool = False) -> pl.DataFrame:
+    """Parse a Prelude flat XML file into a Polars DataFrame.
+
+    This works for Prelude flat XML files that were exported with the "write tables to seperate
+    files" option.
+
+    Args:
+        xml_file: The path to the XML file to parser.
+        short_names: Set to True if short names were used in the export.
+
+    Returns:
+        A Polars DataFrame the data from the XML file.
+
+    Examples:
+        >>> from prelude_parser.polars import to_dataframe
+        >>> df = to_dataframe("physical_examination.xml")
+    """
+    data = _parse_flat_file_to_pandas_dict(xml_file, short_names)
+    return pl.from_dict(data)

prelude_parser/types.py

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+from datetime import date, datetime
+from typing import Dict, List, Union
+
+FieldInfo = Union[str, int, float, date, datetime, None]
+FlatFormInfo = List[Dict[str, FieldInfo]]

prelude_parser-0.5.0.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: prelude-parser
+Version: 0.5.0
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Typing :: Typed
+Requires-Dist: camel-converter >=3.0.0
+Requires-Dist: pandas >=2.1.0 ; python_version > '3.8' and extra == 'pandas'
+Requires-Dist: polars >=0.17.14 ; extra == 'polars'
+Requires-Dist: pandas >=2.1.0 ; python_version > '3.8' and extra == 'all'
+Requires-Dist: polars >=0.17.14 ; extra == 'all'
+Provides-Extra: pandas
+Provides-Extra: polars
+Provides-Extra: all
+License-File: LICENSE
+Summary: Parses XML files exported from Prelude EDC into formats usable by Python.
+Keywords: parser,prelude-edc,xml,pandas,polars
+Home-Page: https://github.com/pbs-data-solutions/prelude-parser
+Author-email: Paul Sanders <paul@pbsdatasolutions.com>
+License: MIT
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Source Code, https://github.com/pbs-data-solutions/prelude-parser
+
+# Prelude Parser
+
+[![Tests Status](https://github.com/pbs-data-solutions/prelude-parser/workflows/Testing/badge.svg?branch=main&event=push)](https://github.com/pbs-data-solutions/prelude-parser/actions?query=workflow%3ATesting+branch%3Amain+event%3Apush)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pbs-data-solutions/prelude-parser/main.svg)](https://results.pre-commit.ci/latest/github/pbs-data-solutions/prelude-parser/main)
+[![Coverage](https://codecov.io/github/pbs-data-solutions/prelude-parser/coverage.svg?branch=main)](https://codecov.io/gh/pbs-data-solutions/prelude-parser)
+[![PyPI version](https://badge.fury.io/py/prelude-parser.svg)](https://badge.fury.io/py/prelude-parser)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/prelude-parser?color=5cc141)](https://github.com/pbs-data-solutions/prelude-parser)
+
+Parses XML files exported from [Prelude EDC](https://preludeedc.com/) into formats Python can use.
+
+## Installation
+
+```sh
+pip install prelude-parser
+```
+
+Optionally the `pandas` extra can be installed to parse to a Pandas `DataFrame`
+
+Note: Pandas only supports Python 3.9+ so this is not available in Python 3.8.
+
+```sh
+pip install prelude-parser[pandas]
+```
+
+Optionally the `polars` extra can be installed to parse to a Polars `DataFrame`
+
+```sh
+pip install prelude-parser[polars]
+```
+
+All extras can be install with
+
+```sh
+pip install prelude-parser[all]
+```
+
+## Usage
+
+Parse a Prelude flat XML file to a Python dictionary.
+
+```py
+from prelude_parser import parse_to_dict
+data = parse_to_dict("physical_examination.xml")
+```
+
+Parse a Prelude flat XML file into a list of Python class. The name of the class is taken from the
+form name node in the XML file converted to pascal case. For example a <physical_examination> node
+will result in a PhysicalExamination class being created.
+
+```py
+from prelude_parser import parse_to_classes
+data = parse_to_classes("physical_examination.xml")
+```
+
+Parse a Prelude flat XML file into a Pandas DataFrame. This works for Prelude flat XML files that
+were exported with the "write tables to seperate files" option. In order to use this option
+`prelude-parser` either needs to be installed with the `pandas` extra or the `all` extras.
+
+```py
+from prelude_parser.pandas import to_dataframe
+df = to_dataframe("physical_examination.xml")
+```
+
+Parse a Prelude flat XML file into a Polars DataFrame. This works for Prelude flat XML files that
+were exported with the "write tables to seperate files" option. In order to use this option
+`prelude-parser` either needs to be installed with the `polars` extra or the `all` extras.
+
+```py
+from prelude_parser.polars import to_dataframe
+df = to_dataframe("physical_examination.xml")
+```
+
+## Contributing
+
+Contributions to this project are welcome. If you are interesting in contributing please see our [contributing guide](CONTRIBUTING.md)
+

prelude_parser-0.5.0.dist-info/RECORD

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prelude_parser-0.5.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.5.1)
+Root-Is-Purelib: false
+Tag: cp38-none-win_amd64

prelude_parser-0.5.0.dist-info/license_files/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 PBS Data Solutions, LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.