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phenopackets / phenopacket-tools

An app and library for building, conversion, and validation of GA4GH Phenopackets.
http://phenopackets.org/phenopacket-tools/stable/
GNU General Public License v3.0
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`dateOfBirth` field filled in phenopacket conversion #177

Closed yaseminbridges closed 1 year ago

yaseminbridges commented 1 year ago

Hi,

When converting a v1.0 phenopacket to a v2.0 phenopacket the dateOfBirth field is filled with 1970-01-01T00:00:00Z, even when there is no reference to a dateOfBirth in the v1 phenopacket. I am using the latest release (RC1).

Thanks,

Yasemin

ielis commented 1 year ago

HI Yasemin, thanks for the bug report. There is an issue with how the converter is handling default protobuf instances. I'll let you know when I fix it.

ielis commented 1 year ago

Hi @yaseminbridges I posted a fix to the latest phenopacket-tools version. Can you please test that it works OK on your data?

Note that you'll have to build the latest code from source, which requires git and JDK 17 or better on your system:

git clone git@github.com:phenopackets/phenopacket-tools.git
cd phenopacket-tools
./mvnw -Prelease clean package

This will create a distribution ZIP file in phenopacket-tools-cli/target folder. You can use the distribution file to install the bleeding edge phenopacket-tools as described in the manual (unpack the ZIP, set up alias, etc.).

The latest code should provide correct output.

Thanks & cheers, Daniel

ielis commented 1 year ago

Hi @yaseminbridges I posted a fix to the latest phenopacket-tools version. Can you please test that it works OK on your data?

Note that you'll have to build the latest code from source, which requires git and JDK 17 or better on your system:

git clone git@github.com:phenopackets/phenopacket-tools.git
cd phenopacket-tools
./mvnw -Prelease clean package

This will create a distribution ZIP file in phenopacket-tools-cli/target folder. You can use the distribution file to install the bleeding edge phenopacket-tools as described in the manual (unpack the ZIP, set up alias, etc.).

The latest code should provide correct output.

Thanks & cheers, Daniel

yaseminbridges commented 1 year ago

Hi @ielis, I just tested the latest code (RC3) and it all worked great! The dateOfBirth is no longer automatically filled.

Thanks, Yasemin

ielis commented 1 year ago

Thanks a lot for letting me know about the bug, it was very helpful. Please let me know if you find any other odd things.