aehrc / aehrc/pathling

Command line interface to pathling encoders

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new feature
Dominant language
Java
Stars
134
Forks
24
Avg merge
1d 15h
Merged PRs (30d)
8

Description

Command line interface that would allow to

  • encode a single resource
  • encode a set of resources

Could be something like:

pathling encode INPUT OUTPUT --resource Patient --input-type json --write-mode 'overwrite'

pathling encode-db INPUT_DIR OUTPUT-DIR --include '*.ndjson' 

This could be based on the current python API and should include support for writing both parquet and delta files.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the current Python API that the proposed CLI would build on, along with how single resources and sets of resources are currently encoded. Define the command behavior for the shown encode and encode-db examples, including JSON input, resource selection, overwrite mode, and parquet or delta output; the work is done when both workflows are supported.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, data-engineering
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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