%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]
Runrex
Library to aid in organizing, running, and debugging regular expressions against large bodies of text.
## 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
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
See the [open issues](https://github.com/kpwhri/runrex/issues) for a list of proposed features (and known issues).
## 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
Distributed under the MIT License.
See `LICENSE` or https://kpwhri.mit-license.org for more information.
## Contact
Please use the [issue tracker](https://github.com/kpwhri/runrex/issues).
## Acknowledgements
[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
%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]
Runrex
Library to aid in organizing, running, and debugging regular expressions against large bodies of text.
## 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
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
See the [open issues](https://github.com/kpwhri/runrex/issues) for a list of proposed features (and known issues).
## 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
Distributed under the MIT License.
See `LICENSE` or https://kpwhri.mit-license.org for more information.
## Contact
Please use the [issue tracker](https://github.com/kpwhri/runrex/issues).
## Acknowledgements
[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
%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]
Runrex
Library to aid in organizing, running, and debugging regular expressions against large bodies of text.
## 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
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
See the [open issues](https://github.com/kpwhri/runrex/issues) for a list of proposed features (and known issues).
## 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
Distributed under the MIT License.
See `LICENSE` or https://kpwhri.mit-license.org for more information.
## Contact
Please use the [issue tracker](https://github.com/kpwhri/runrex/issues).
## Acknowledgements
[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
%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 - 0.5.0-1
- Package Spec generated