https://github.com/sri-csl/datum

A parser for biological experiment shorthand.
https://github.com/sri-csl/datum

Last synced: 15 days ago
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A parser for biological experiment shorthand.

• Host: GitHub
• URL: https://github.com/sri-csl/datum
• Owner: SRI-CSL
• License: mit
• Created: 2017-05-15T20:34:11.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2020-10-07T22:39:43.000Z (over 4 years ago)
• Last Synced: 2024-11-06T04:37:17.147Z (2 months ago)
• Language: Clojure
• Size: 732 KB
• Stars: 2
• Watchers: 17
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# datum

A parser for the [Human Readable Datum Format](http://pl.csl.sri.com/datumkb.html) used by [Pathway Logic](http://pl.csl.sri.com/index.html). Takes in a file or directory of datums, does some basic sanity checking, and emits JSON.

## Usage

    $ java -jar datum-0.1.0-standalone.jar [args] [files/directories]

## Options

    Options:

      -e, --errors         Print errors

      -o, --ops-file FILE  Provide an external ops json file

      -j, --json           Print parsed datums as JSON

      -J, --pretty-json    Pretty-print parsed datums as JSON

      -D, --duplicates     Print a list of duplicate datums

      -m, --merge          Merge datums that only differ in extras.

## Ops

For sanity and type checking, you will need an `ops file`, which is a JSON file containing a Maude type hierarchy of relevant sorts and ops. The parser is bundled with some default ops. Instructions for generating your own TBD.

## License

Released under the MIT license. See LICENSE for the full license.