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diff --git a/python-runrex.spec b/python-runrex.spec new file mode 100644 index 0000000..0957a3e --- /dev/null +++ b/python-runrex.spec @@ -0,0 +1,663 @@ +%global _empty_manifest_terminate_build 0 +Name: python-runrex +Version: 0.5.0 +Release: 1 +Summary: Library to aid in organizing, running, and debugging regular expressions against large bodies of text. +License: MIT License +URL: https://pypi.org/project/runrex/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/a4/c7/309a1e180ba0a7d5090a7e36b58023ced8372df8635cee67b9ff230e9c01/runrex-0.5.0.tar.gz +BuildArch: noarch + +Requires: python3-pyodbc +Requires: python3-pytest +Requires: python3-pandas +Requires: python3-psycopg2 +Requires: python3-sas7bdat +Requires: python3-syntok + +%description +[![Contributors][contributors-shield]][contributors-url] +[![Forks][forks-shield]][forks-url] +[![Stargazers][stars-shield]][stars-url] +[![Issues][issues-shield]][issues-url] +[![MIT License][license-shield]][license-url] +[![LinkedIn][linkedin-shield]][linkedin-url] + + + +<!-- PROJECT LOGO --> +<br /> +<div> + <p> + <a href="https://github.com/kpwhri/runrex"> + <img src="images/logo.png" alt="Logo"> + </a> + </p> + + <h3 align="center">Runrex</h3> + + <p> + Library to aid in organizing, running, and debugging regular expressions against large bodies of text. + </p> +</div> + + +<!-- TABLE OF CONTENTS --> +## Table of Contents + +* [About the Project](#about-the-project) +* [Getting Started](#getting-started) + * [Prerequisites](#prerequisites) + * [Installation](#installation) +* [Usage](#usage) +* [Roadmap](#roadmap) +* [Contributing](#contributing) +* [License](#license) +* [Contact](#contact) +* [Acknowledgements](#acknowledgements) + + + +## About the Project +The goal of this library is to simplify the deployment of regular expression on large bodies of text, in a variety of input formats. + + +<!-- GETTING STARTED --> +## Getting Started + +To get a local copy up and running follow these simple steps. + +### Prerequisites + +* Python 3.8+ +* runrex package: https://github.com/kpwhri/runrex + +### Installation + +1. Clone the repo + ```sh + git clone https://github.com/kpwhri/runrex.git + ``` +2. Install requirements (`requirements-dev` is for test packages) + ```sh + pip install -r requirements.txt -r requirements-dev.txt + ``` +3. If you wish to read text from SAS or SQL, you will need to install additional requirements. These additional requirements files may be of use: + - ODBC-connection: `requirements-db.txt` + - Postgres: `requirements-psql.txt` + - SAS: `requirements-sas.txt` +4. Run tests. + ```sh + set/export PYTHONPATH=src + pytest tests + ``` + +## Usage + +### Example Implementations +* [Social Isolation](https://github.com/kpwhri/social-isolation-runrex) +* [Acute Pancreatitis](https://github.com/kpwhri/apanc-runrex) +* [Anaphylaxis](https://github.com/kpwhri/anaphylaxis-runrex) +* [PCOS](https://github.com/kpwhri/pcos-runrex) + +### Build Customized Algorithm + +* Create 4 files: + * `patterns.py`: defines regular expressions of interest + * See `examples/example_patterns.py` for some examples + * `test_patterns.py`: tests for those regular expressions + * Why? Make sure the patterns do what you think they do + * `algorithm.py`: defines algorithm (how to use regular expressions); returns a Result + * See `examples/example_algorithm.py` for guidance + * `config.(py|json|yaml)`: various configurations defined in `schema.py` + * See example in `examples/example_config.py` for basic config + +## Input Data + +Accepts a variety of input formats, but will need to at least specify a `document_id` and `document_text`. The names are configurable. + +### Sentence Splitting + +By default, the input document text is expected to have each sentence on a separate line. If a sentence splitting scheme is desired, it will need to be supplied to the application. + +### Schema/Examples +For more details, see the [example config](https://github.com/kpwhri/runrex/blob/master/examples/example_config.py) +or consult the [schema](https://github.com/kpwhri/runrex/blob/master/src/runrex/schema.py) + +## Output Format + +* Recommended output format is `jsonl` + - The data can be extracted using python: +```python +import json +with open('output.jsonl') as fh: + for line in fh: + data = json.loads(line) # data is dict +``` + +* Output variables are configurable and can include: + - **id**: unique id for line + - **name**: document name + - **algorithm**: name of algorithm with finding + - **value** + - **category**: name of category (usually the pattern; multiple categories contribute to an algorithm) + - **date** + - **extras** + - **matches**: pattern matches + - **text**: captured text + - **start**: start index/offset of match + - **end**: end index/offset of match + +* Scripts to accomplish useful tasks with the output are included in the `scripts` directory. + +## Versions + +Uses [SEMVER](https://semver.org/). + +See https://github.com/kpwhri/runrex/releases. + +<!-- ROADMAP --> +## Roadmap + +See the [open issues](https://github.com/kpwhri/runrex/issues) for a list of proposed features (and known issues). + + + +<!-- CONTRIBUTING --> +## Contributing + +Any contributions you make are **greatly appreciated**. + +1. Fork the Project +2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`) +3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`) +4. Push to the Branch (`git push origin feature/AmazingFeature`) +5. Open a Pull Request + + +<!-- LICENSE --> +## License + +Distributed under the MIT License. + +See `LICENSE` or https://kpwhri.mit-license.org for more information. + + + +<!-- CONTACT --> +## Contact + +Please use the [issue tracker](https://github.com/kpwhri/runrex/issues). + + +<!-- ACKNOWLEDGEMENTS --> +## Acknowledgements + + + +<!-- MARKDOWN LINKS & IMAGES --> +<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links --> +[contributors-shield]: https://img.shields.io/github/contributors/kpwhri/runrex.svg?style=flat-square +[contributors-url]: https://github.com/kpwhri/runrex/graphs/contributors +[forks-shield]: https://img.shields.io/github/forks/kpwhri/runrex.svg?style=flat-square +[forks-url]: https://github.com/kpwhri/runrex/network/members +[stars-shield]: https://img.shields.io/github/stars/kpwhri/runrex.svg?style=flat-square +[stars-url]: https://github.com/kpwhri/runrex/stargazers +[issues-shield]: https://img.shields.io/github/issues/kpwhri/runrex.svg?style=flat-square +[issues-url]: https://github.com/kpwhri/runrex/issues +[license-shield]: https://img.shields.io/github/license/kpwhri/runrex.svg?style=flat-square +[license-url]: https://kpwhri.mit-license.org/ +[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=flat-square&logo=linkedin&colorB=555 +[linkedin-url]: https://www.linkedin.com/company/kaiserpermanentewashingtonresearch +<!-- [product-screenshot]: images/screenshot.png --> + + + +%package -n python3-runrex +Summary: Library to aid in organizing, running, and debugging regular expressions against large bodies of text. +Provides: python-runrex +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-runrex +[![Contributors][contributors-shield]][contributors-url] +[![Forks][forks-shield]][forks-url] +[![Stargazers][stars-shield]][stars-url] +[![Issues][issues-shield]][issues-url] +[![MIT License][license-shield]][license-url] +[![LinkedIn][linkedin-shield]][linkedin-url] + + + +<!-- PROJECT LOGO --> +<br /> +<div> + <p> + <a href="https://github.com/kpwhri/runrex"> + <img src="images/logo.png" alt="Logo"> + </a> + </p> + + <h3 align="center">Runrex</h3> + + <p> + Library to aid in organizing, running, and debugging regular expressions against large bodies of text. + </p> +</div> + + +<!-- TABLE OF CONTENTS --> +## Table of Contents + +* [About the Project](#about-the-project) +* [Getting Started](#getting-started) + * [Prerequisites](#prerequisites) + * [Installation](#installation) +* [Usage](#usage) +* [Roadmap](#roadmap) +* [Contributing](#contributing) +* [License](#license) +* [Contact](#contact) +* [Acknowledgements](#acknowledgements) + + + +## About the Project +The goal of this library is to simplify the deployment of regular expression on large bodies of text, in a variety of input formats. + + +<!-- GETTING STARTED --> +## Getting Started + +To get a local copy up and running follow these simple steps. + +### Prerequisites + +* Python 3.8+ +* runrex package: https://github.com/kpwhri/runrex + +### Installation + +1. Clone the repo + ```sh + git clone https://github.com/kpwhri/runrex.git + ``` +2. Install requirements (`requirements-dev` is for test packages) + ```sh + pip install -r requirements.txt -r requirements-dev.txt + ``` +3. If you wish to read text from SAS or SQL, you will need to install additional requirements. These additional requirements files may be of use: + - ODBC-connection: `requirements-db.txt` + - Postgres: `requirements-psql.txt` + - SAS: `requirements-sas.txt` +4. Run tests. + ```sh + set/export PYTHONPATH=src + pytest tests + ``` + +## Usage + +### Example Implementations +* [Social Isolation](https://github.com/kpwhri/social-isolation-runrex) +* [Acute Pancreatitis](https://github.com/kpwhri/apanc-runrex) +* [Anaphylaxis](https://github.com/kpwhri/anaphylaxis-runrex) +* [PCOS](https://github.com/kpwhri/pcos-runrex) + +### Build Customized Algorithm + +* Create 4 files: + * `patterns.py`: defines regular expressions of interest + * See `examples/example_patterns.py` for some examples + * `test_patterns.py`: tests for those regular expressions + * Why? Make sure the patterns do what you think they do + * `algorithm.py`: defines algorithm (how to use regular expressions); returns a Result + * See `examples/example_algorithm.py` for guidance + * `config.(py|json|yaml)`: various configurations defined in `schema.py` + * See example in `examples/example_config.py` for basic config + +## Input Data + +Accepts a variety of input formats, but will need to at least specify a `document_id` and `document_text`. The names are configurable. + +### Sentence Splitting + +By default, the input document text is expected to have each sentence on a separate line. If a sentence splitting scheme is desired, it will need to be supplied to the application. + +### Schema/Examples +For more details, see the [example config](https://github.com/kpwhri/runrex/blob/master/examples/example_config.py) +or consult the [schema](https://github.com/kpwhri/runrex/blob/master/src/runrex/schema.py) + +## Output Format + +* Recommended output format is `jsonl` + - The data can be extracted using python: +```python +import json +with open('output.jsonl') as fh: + for line in fh: + data = json.loads(line) # data is dict +``` + +* Output variables are configurable and can include: + - **id**: unique id for line + - **name**: document name + - **algorithm**: name of algorithm with finding + - **value** + - **category**: name of category (usually the pattern; multiple categories contribute to an algorithm) + - **date** + - **extras** + - **matches**: pattern matches + - **text**: captured text + - **start**: start index/offset of match + - **end**: end index/offset of match + +* Scripts to accomplish useful tasks with the output are included in the `scripts` directory. + +## Versions + +Uses [SEMVER](https://semver.org/). + +See https://github.com/kpwhri/runrex/releases. + +<!-- ROADMAP --> +## Roadmap + +See the [open issues](https://github.com/kpwhri/runrex/issues) for a list of proposed features (and known issues). + + + +<!-- CONTRIBUTING --> +## Contributing + +Any contributions you make are **greatly appreciated**. + +1. Fork the Project +2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`) +3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`) +4. Push to the Branch (`git push origin feature/AmazingFeature`) +5. Open a Pull Request + + +<!-- LICENSE --> +## License + +Distributed under the MIT License. + +See `LICENSE` or https://kpwhri.mit-license.org for more information. + + + +<!-- CONTACT --> +## Contact + +Please use the [issue tracker](https://github.com/kpwhri/runrex/issues). + + +<!-- ACKNOWLEDGEMENTS --> +## Acknowledgements + + + +<!-- MARKDOWN LINKS & IMAGES --> +<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links --> +[contributors-shield]: https://img.shields.io/github/contributors/kpwhri/runrex.svg?style=flat-square +[contributors-url]: https://github.com/kpwhri/runrex/graphs/contributors +[forks-shield]: https://img.shields.io/github/forks/kpwhri/runrex.svg?style=flat-square +[forks-url]: https://github.com/kpwhri/runrex/network/members +[stars-shield]: https://img.shields.io/github/stars/kpwhri/runrex.svg?style=flat-square +[stars-url]: https://github.com/kpwhri/runrex/stargazers +[issues-shield]: https://img.shields.io/github/issues/kpwhri/runrex.svg?style=flat-square +[issues-url]: https://github.com/kpwhri/runrex/issues +[license-shield]: https://img.shields.io/github/license/kpwhri/runrex.svg?style=flat-square +[license-url]: https://kpwhri.mit-license.org/ +[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=flat-square&logo=linkedin&colorB=555 +[linkedin-url]: https://www.linkedin.com/company/kaiserpermanentewashingtonresearch +<!-- [product-screenshot]: images/screenshot.png --> + + + +%package help +Summary: Development documents and examples for runrex +Provides: python3-runrex-doc +%description help +[![Contributors][contributors-shield]][contributors-url] +[![Forks][forks-shield]][forks-url] +[![Stargazers][stars-shield]][stars-url] +[![Issues][issues-shield]][issues-url] +[![MIT License][license-shield]][license-url] +[![LinkedIn][linkedin-shield]][linkedin-url] + + + +<!-- PROJECT LOGO --> +<br /> +<div> + <p> + <a href="https://github.com/kpwhri/runrex"> + <img src="images/logo.png" alt="Logo"> + </a> + </p> + + <h3 align="center">Runrex</h3> + + <p> + Library to aid in organizing, running, and debugging regular expressions against large bodies of text. + </p> +</div> + + +<!-- TABLE OF CONTENTS --> +## Table of Contents + +* [About the Project](#about-the-project) +* [Getting Started](#getting-started) + * [Prerequisites](#prerequisites) + * [Installation](#installation) +* [Usage](#usage) +* [Roadmap](#roadmap) +* [Contributing](#contributing) +* [License](#license) +* [Contact](#contact) +* [Acknowledgements](#acknowledgements) + + + +## About the Project +The goal of this library is to simplify the deployment of regular expression on large bodies of text, in a variety of input formats. + + +<!-- GETTING STARTED --> +## Getting Started + +To get a local copy up and running follow these simple steps. + +### Prerequisites + +* Python 3.8+ +* runrex package: https://github.com/kpwhri/runrex + +### Installation + +1. Clone the repo + ```sh + git clone https://github.com/kpwhri/runrex.git + ``` +2. Install requirements (`requirements-dev` is for test packages) + ```sh + pip install -r requirements.txt -r requirements-dev.txt + ``` +3. If you wish to read text from SAS or SQL, you will need to install additional requirements. These additional requirements files may be of use: + - ODBC-connection: `requirements-db.txt` + - Postgres: `requirements-psql.txt` + - SAS: `requirements-sas.txt` +4. Run tests. + ```sh + set/export PYTHONPATH=src + pytest tests + ``` + +## Usage + +### Example Implementations +* [Social Isolation](https://github.com/kpwhri/social-isolation-runrex) +* [Acute Pancreatitis](https://github.com/kpwhri/apanc-runrex) +* [Anaphylaxis](https://github.com/kpwhri/anaphylaxis-runrex) +* [PCOS](https://github.com/kpwhri/pcos-runrex) + +### Build Customized Algorithm + +* Create 4 files: + * `patterns.py`: defines regular expressions of interest + * See `examples/example_patterns.py` for some examples + * `test_patterns.py`: tests for those regular expressions + * Why? Make sure the patterns do what you think they do + * `algorithm.py`: defines algorithm (how to use regular expressions); returns a Result + * See `examples/example_algorithm.py` for guidance + * `config.(py|json|yaml)`: various configurations defined in `schema.py` + * See example in `examples/example_config.py` for basic config + +## Input Data + +Accepts a variety of input formats, but will need to at least specify a `document_id` and `document_text`. The names are configurable. + +### Sentence Splitting + +By default, the input document text is expected to have each sentence on a separate line. If a sentence splitting scheme is desired, it will need to be supplied to the application. + +### Schema/Examples +For more details, see the [example config](https://github.com/kpwhri/runrex/blob/master/examples/example_config.py) +or consult the [schema](https://github.com/kpwhri/runrex/blob/master/src/runrex/schema.py) + +## Output Format + +* Recommended output format is `jsonl` + - The data can be extracted using python: +```python +import json +with open('output.jsonl') as fh: + for line in fh: + data = json.loads(line) # data is dict +``` + +* Output variables are configurable and can include: + - **id**: unique id for line + - **name**: document name + - **algorithm**: name of algorithm with finding + - **value** + - **category**: name of category (usually the pattern; multiple categories contribute to an algorithm) + - **date** + - **extras** + - **matches**: pattern matches + - **text**: captured text + - **start**: start index/offset of match + - **end**: end index/offset of match + +* Scripts to accomplish useful tasks with the output are included in the `scripts` directory. + +## Versions + +Uses [SEMVER](https://semver.org/). + +See https://github.com/kpwhri/runrex/releases. + +<!-- ROADMAP --> +## Roadmap + +See the [open issues](https://github.com/kpwhri/runrex/issues) for a list of proposed features (and known issues). + + + +<!-- CONTRIBUTING --> +## Contributing + +Any contributions you make are **greatly appreciated**. + +1. Fork the Project +2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`) +3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`) +4. Push to the Branch (`git push origin feature/AmazingFeature`) +5. Open a Pull Request + + +<!-- LICENSE --> +## License + +Distributed under the MIT License. + +See `LICENSE` or https://kpwhri.mit-license.org for more information. + + + +<!-- CONTACT --> +## Contact + +Please use the [issue tracker](https://github.com/kpwhri/runrex/issues). + + +<!-- ACKNOWLEDGEMENTS --> +## Acknowledgements + + + +<!-- MARKDOWN LINKS & IMAGES --> +<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links --> +[contributors-shield]: https://img.shields.io/github/contributors/kpwhri/runrex.svg?style=flat-square +[contributors-url]: https://github.com/kpwhri/runrex/graphs/contributors +[forks-shield]: https://img.shields.io/github/forks/kpwhri/runrex.svg?style=flat-square +[forks-url]: https://github.com/kpwhri/runrex/network/members +[stars-shield]: https://img.shields.io/github/stars/kpwhri/runrex.svg?style=flat-square +[stars-url]: https://github.com/kpwhri/runrex/stargazers +[issues-shield]: https://img.shields.io/github/issues/kpwhri/runrex.svg?style=flat-square +[issues-url]: https://github.com/kpwhri/runrex/issues +[license-shield]: https://img.shields.io/github/license/kpwhri/runrex.svg?style=flat-square +[license-url]: https://kpwhri.mit-license.org/ +[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=flat-square&logo=linkedin&colorB=555 +[linkedin-url]: https://www.linkedin.com/company/kaiserpermanentewashingtonresearch +<!-- [product-screenshot]: images/screenshot.png --> + + + +%prep +%autosetup -n runrex-0.5.0 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-runrex -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 0.5.0-1 +- Package Spec generated |