v1.0.0-RC3

The pre-production release 3.

What's Changed

• Improve format and element sniffing by @ielis in #171
• Add showcase of apps that use phenopacket-tools by @ielis in #172
• Add latest and stable documentation branches by @ielis in #173
• Fix bug in handling of the default elements when converting from v1 to v2 by @ielis in #178

Full Changelog: v1.0.0-RC2...v1.0.0-RC3

v1.0.0-RC2

The pre-production release 2.

What's Changed

• Improve documentation by @ielis in #157 #165
• Add unspecified zygosity into AllelicState constants by @ielis in #158
• Fix varargs CLI options by @ielis in #164
• Update dependency versions by @ielis in #166
• Fix issues in example phenopackets by @ielis in #167 and @cmungall in #163
• Add an example cohort. by @ielis in #168

Full Changelog: v1.0.0-RC1...v1.0.0-RC2

v1.0.0-RC1

The pre-production release 1.

What's Changed

• Setup Javadoc hosting by @ielis in #141
• Update predefined constants, convenience functions and builders
• Remove the concept of syntax and semantic validators. by @ielis in #143
• Improve the tutorial, documetation, and the user guide by @ielis in #144
• Run MetaDataValidator in the base validation step. by @ielis in #149
• Removing space from CURIE by @cmungall in #146
• Fix example phenopackets #150

Full Changelog: v0.4.7...v1.0.0-RC1

v0.4.7

What's Changed

• Let the user adjust the output verbosity at runtime by @ielis in #101
• Implement ancestry validation of HPO terms. by @ielis in #105
• revising our examples by @pnrobinson in #106
• Adding HGNC Resource builder by @pnrobinson in #107
• Update constants by @ielis in #108
• More constants by @pnrobinson in #112
• Separate code for phenopacket I/O and format sniffing by @ielis in #110
• Update VRS and VERSATILE validation by @ielis in #103
• Fixing typo in isoISO8601onset method by @pnrobinson in #116
• Implement organ systems validator by @ielis in #117
• Implement YAML I/O by @ielis in #119
• Disease stage by @pnrobinson in #121
• Dedicated CLI package by @ielis in #122
• Point out generated code in the source files. by @ielis in #123
• Setup the distribution process. by @ielis in #125
• Severity constant by @pnrobinson in #118
• Change miligram per day to milligram per liter by @cmungall in #130
• Validate Variation object embedded in the the Phenopacket Schema by @ielis in #133
• Add organ system validator and validation examples by @ielis in #127
• Improve UCUM resources by @ielis in #136

Full Changelog: v0.4.6...v0.4.7

v0.4.6

What's Changed

• Validate metadata by @pnrobinson in #93
• Convert v1 variants by @pnrobinson in #95
• Extend phenopacket examples by @pnrobinson in #97
• Update documentation by @hrshdhgd in #98
• Improve CLI and extend CLI documentation by @ielis in #96

New Contributors

• @hrshdhgd made their first contribution in #98

Full Changelog: v0.4.5...v0.4.6

v0.4.5

First release of the phenopacket-tools cli.

Phenopacket tools CLI

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

alias pfx-tools='java -jar phenopacket-tools-cli-0.4.5.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