de-workflow 0.2.2

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DE Workflow

This is a small wrapper program around the drug-extraction-cli program.

It is effectively a convenience wrapper for us and our typical use-case.

Benefits over the standard CLI:

• Multi-column support (it expects two columns -- a primary and a secondary)
• Wide form data created automatically
• Wide form data attached to source data ready for analysis
• Automated report generation
• Use of either our/your custom search template with tags!

It can generate a nice report using datapane for some quick eye-ball analysis.

It uses data/drug_info.json (link) as our template for custom search words with tags. This can be extended or edited where you can provide ANY custom search file you want as long as it matches our format. Alternatively you can enable --live mode and just use ours 🙂.

• DE Workflow
  • Requirements
  • Installation
  • Usage
  • Sample Output
  • Support
  • Contributing
  • MIT License

Requirements

• pipx
• drug-extraction-cli program

Installation

You can install this program with pipx:

pipx install de-workflow

You can then easily get help for the only command (execute) like so:

de-workflow execute --help

Which should look something like this:

Usage

To run this tool all you will need to know is:

• The name of your file
• Your ID column for linking
• Your Target column(s) to search in

You can then run the tool:

de-workflow execute ../cli/data/records.csv "Case Number" "Primary Cause" "Secondary Cause"

This will run the underlying drug extraction program so you MUST have the main CLI tool installed.

There are additional flags for reporting and custom file searching.

--report/--no-report identifies whether or not to produce a datapane report at the end. Suggested and default value is --report.

--live/no-live identifies whether or not you want you use our template.

If you do NOT want to use our template, you can disable live (--no-live) but you then MUST provide a custom --search-file for the program to use. This file should be in json format and match the structure of our template so that the tool can work correctly.

Sample Output

Support

If you encounter any issues or need support please either contact @nanthony007 or open an issue.

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

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

See CONTRIBUTING.md for more details.

MIT License

LICENSE