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koza

Details
GitHub monarch-initiative/koza
Language Python
Description Data transformation framework for LinkML data models

Dependencies

External Dependencies

Package Version
python ^3.9
linkml >=1.6.3
pydantic ^2.4
pyyaml >=5.0.0
requests ^2.24.0
ordered-set >=4.1.0
typer ^0.7.0
typer-cli ^0.0.13
loguru *
sssom >=0.4

Documentation

Koza - a data transformation framework

Pyversions PyPi Github Action

pupa

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
└── ...