5.4.2 and 5.4.1 releases highlighting validation errors for host age and host gender (SARS-CoV-2)

[taranewman]

Hello,

We've been encountering validation errors with the CanCOGeNCovid19 template in versions 5.4.2 and 5.4.1 where the host age is being highlighted if the value is "Missing" and the host gender is being highlighted in all the rows. The validation errors are not occurring with the 5.3.0 release.

Thanks!

[KirstenPalmier]

In the MPOX template (pathogen-genomics-package - 5.4.2
When I upload the data, the date collected precision value is entered as day but still comes up as an error. If I pick it from the picklist, the error goes away after validating again:
Before validating:

After validating:

When I pick the dropdown item day for one sample:

The rest are validated without errors:

The collection dates do not allow for null values, is that correct?

^ after validation
Not replicating the same issue with gender as above for Tara except for the following fields are producing errors (however different template):

[GLTOhorsman]

Experiencing similar issues in the Cancogen template for host age and diagnostic pcr Ct value 1 when using existing restricted access statement

[GLTOhorsman]

A note here that https://github.com/cidgoh/pathogen-genomics-package/releases/tag/PGPv5.5.0 carries the same issues noted here for 5.4.2 in the test i ran

[cbarcl01]

Hi @GLTOhorsman thanks for the message!

We have not resolved this in 5.5.0 as we still need to do some further testing and wanted to make sure there was no hold up with releasing the new organisation terms for 'sample collected by' and 'sequence submitted by'.

It looks like this is related to case sensitivity (capitalised D instead of lower case for day). We will keep working to resolve this our side, but in the mean time hopefully this provides a bit of a work around.

Thanks for the patience, we are hoping to get this resolved soon and then we can do a patch release.

[GLTOhorsman]

unfortunately since it doesn't roll back to the 5.3 version it doesn't give a "clean" output. However, using 5.5 in combination with 5.3 as a pair of tools can give a user to highlight errors that are are only present in both

[cbarcl01]

Great, glad there is a temporary work around. We will keep working to resolve the issue with 'sample collection date precision' (if users make sure in any data they open in DH is lowercase for now that should prevent an issue).

Can you confirm if you are still getting the issue with 'host gender'? I can replicate the issue seen for 'host age' but not for the former. Thanks for all your help!

[GLTOhorsman]

Seeing it in host age "Restricted Access" and diagnostic pcr Ct value 1 "Not Collected"

[GLTOhorsman]

Gender issue reported by @KirstenPalmier
KirstenPalmier testing 5.4.2 on a different dataset

[cbarcl01]

OK great so not 'host gender' for now. Will work on a resolution. Thanks for the extra testing team! Have a great weekend.

[ddooley]

Capitalization normalization is fixed now in a DataHarmonizer draft version so we hope to have that in a PGP release in the coming week. Fix for menus that have both date or number + Null Value List still on the way. The datepicker app may block ability to select a null value for that field, so that one may take more time to resolve.