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A parser for biological experiment shorthand.

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datum

A parser for the Human Readable Datum Format used by Pathway Logic. 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.

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A parser for biological experiment shorthand.

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