automatic import of python-runrex

3 files changed, 665 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..6b93230 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/runrex-0.5.0.tar.gz
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
diff --git a/sources b/sources
new file mode 100644
index 0000000..049f853
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+0091b3c7b9de974823908d19293f4cd1  runrex-0.5.0.tar.gz