README.md

phenopacket-tools

Multimodule Java library/app that contains a "streamlined builder" module, a v1 to v2 converter app, a validator API and a JSON validator.

Phenopacket tools CLI

The cli application works in a standard UNIX-like manner.

mvn package
alias pfx-tools='java -jar phenotools-cli/target/phenotools-cli-0.0.2-SNAPSHOT.jar'

Example Phenopackets

The examples command in the CLI module writes a series of example Phenopackets to file.

# writes to the current directory by default
pfx-tools examples
# or write explicitly to the current directory
pfx-tools examples .
# or write to another directory
pfx-tools examples ~/phenopacket-examples

Convert Phenopacket versions

pfx-tools convert phenopacket.json

Validate Phenopacket JSON files

pfx-tools validate ~/phenopacket-examples/covid.json
# or all the json files in a directory
pfx-tools validate ~/phenopacket-examples/*.json