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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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Trouble converting interpretations #198

Closed gsfk closed 2 months ago

gsfk commented 2 months ago

Phenopackets v1 has four top-level elements: Phenopacket, Family, Cohort and Interpretation. But the -e | --element flag in the v1->v2 converter only accepts the first three as options. It's unclear how I'm supposed to convert an interpretation. I get this or similar errors when attempting:

input element (-e | --element) was not provided and element sniffing failed

Looking through the docs and the code I see interpretations generated using --convert-variants but I have no variants or diseases to convert, neither is required for an interpretation. So it's not clear to me that my use case is covered (and adding --convert-variants doesn't help).

ielis commented 2 months ago

Hi @gsfk

Phenopacket tools does not support conversion of v1 interpretation at the moment. I could, however, add it and it sounds like you would have some use for it, right?

Is this something you need? Would you be willing to test a patch version if it works OK on your end? Please let me know, thank you!

gsfk commented 2 months ago

Hi, sorry, this was only a one-time use for us, we started using interpretations only when they became a "building block" component so it's unlikely to come up again. So I won't be able to find the time to write a patch anytime soon.

I came across this when trying to convert phenopackets in this test dataset to PXF v2.

ielis commented 2 months ago

... So I won't be able to find the time to write a patch anytime soon.

Actually, I was proposing to write the patch and I wanted you to test it

... we started using interpretations only when they became a "building block" so it's unlikely to come up again ...

however, yes, this is why I am not "all in" regarding writing a patch unless you really really need it

... this was only a one-time use for us

and it seems like you do not really really need it.. :)

So, unless this simplifies your life a lot, I will refrain myself from writing the patch for converting v1 interpretation into a v2 phenopacket or family, and I will close the issue.

Please feel free to reopen/comment should there be a need for converting interpretations.