koza 0.5.2

Data transformation framework for LinkML data models

Koza - a data transformation framework

Documentation

Disclaimer: Koza is in beta - we are looking for testers!

Overview

• Transform csv, json, yaml, jsonl, and xml and converting them to a target csv, json, or jsonl format based on your dataclass model.
• Koza also can output data in the KGX format
• Write data transforms in semi-declarative Python
• Configure source files, expected columns/json properties and path filters, field filters, and metadata in yaml
• Create or import mapping files to be used in ingests (eg id mapping, type mappings)
• Create and use translation tables to map between source and target vocabularies

Installation

Koza is available on PyPi and can be installed via pip/pipx:

[pip|pipx] install koza

Usage

NOTE: As of version 0.2.0, there is a new method for getting your ingest's KozaApp instance. Please see the updated documentation for details.

See the Koza documentation for usage information

Try the Examples

Validate

Give Koza a local or remote csv file, and get some basic information (headers, number of rows)

koza validate \
  --file https://raw.githubusercontent.com/monarch-initiative/koza/main/examples/data/string.tsv \
  --delimiter ' '

Sending a json or jsonl formatted file will confirm if the file is valid json or jsonl

koza validate \
  --file ./examples/data/ZFIN_PHENOTYPE_0.jsonl.gz \
  --format jsonl

koza validate \
  --file ./examples/data/ddpheno.json.gz \
  --format json

Transform

Run the example ingest, "string/protein-links-detailed"

koza transform \
  --source examples/string/protein-links-detailed.yaml \
  --global-table examples/translation_table.yaml

koza transform \
  --source examples/string-declarative/protein-links-detailed.yaml \
  --global-table examples/translation_table.yaml

Note: Koza expects a directory structure as described in the above example
with the source config file and transform code in the same directory:

.
├── ...
│   ├── your_source
│   │   ├── your_ingest.yaml
│   │   └── your_ingest.py
│   └── some_translation_table.yaml
└── ...