Missing CPIC version - Githubissues

PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool

Mozilla Public License 2.0

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Missing CPIC version #157

Closed krukanna closed 10 months ago

krukanna commented 11 months ago

Do you want to request a feature or report a bug? bug
What is the current behavior? In json file in version 2.8.0 and 2.8.1 is missing field for cpicVersion:
```
"pharmcatVersion": "2.8.1",
"cpicVersion": null
```
In any previous version for example:
```
"pharmcatVersion": "2.5.0",
"cpicVersion": "v1.26.0",
```
If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. java -jar /pharmcat/pharmcat.jar -vcf $vcf -del -reporterJson -o Pharmcat_output
Please tell us about your environment:
- PharmCAT Version: 2.8.0 and 2.8.1 docker version

Bioinf-usr commented 11 months ago

It is missing in version 2.8.2 as well.

BinglanLi commented 11 months ago

Thank you for reporting the issue. We are looking into it.

whaleyr commented 11 months ago

This will be fixed in the next release.

lacek commented 3 weeks ago

The issue reappears in v2.14.0 and v2.15.0

$ /opt/java/openjdk-17/bin/java -jar /opt/pharmcat/2.13.0/pharmcat.jar -vcf tmp/pharmcat/default.preprocessed.vcf.bgz -s "$SAMPLE" -rt "$SAMPLE" -o tmp/pharmcat -bf 2.13.0 -reporterJson
$ jq -r 'with_entries(select(.key | IN("pharmcatVersion","cpicVersion","dpwgVersion")))' tmp/pharmcat/2.13.0.report.json
{
  "pharmcatVersion": "2.13.0",
  "cpicVersion": "v1.39.0, 2024-05-23-09-04",
  "dpwgVersion": "2024-05-23-09-04"
}

$ /opt/java/openjdk-17/bin/java -jar /opt/pharmcat/2.14.0/pharmcat.jar -vcf tmp/pharmcat/default.preprocessed.vcf.bgz -s "$SAMPLE" -rt "$SAMPLE" -o tmp/pharmcat -bf 2.14.0 -reporterJson
$ q -r 'with_entries(select(.key | IN("pharmcatVersion","cpicVersion","dpwgVersion")))' tmp/pharmcat/2.14.0.report.json
{
  "pharmcatVersion": "2.14.0"
}

whaleyr commented 3 weeks ago

PharmCAT data has changed. CPIC and DPWG now both come from the same data source (plus, FDA data is now included) so they no longer have separate versions. There is a new dataVersion property which applies to all data in PharmCAT. You can see this in the example JSON report