Closed justaddcoffee closed 4 years ago
I think that this is an "old" phenopacket schema version--there were a few backwards -incompatible changes. HPO Case annotator stores data in an internal format that can be exported to the current version, so probably just re-export. Where does this phenopacket come from?
Ah okay, thanks. This phenopacket came from Daniel. It's easy enough to fix, just trying to find and eliminate some pain points that users might encounter.
We possibly could incorporate Jules' phenopacket validator to alert users about these formatting issues
I do not think the phenopacket validator is up and running yet. There is this: https://github.com/pnrobinson/phenotools but it is also rough around the edges...
Okay, duly noted. Maybe for now we could emit an error message that alerts the user that the phenopacket might be malformed? Glad to do a quick PR for this
I am cleaning up and added a simpler error message for this! This should not happen out in the wild since nobody but our group will have any old format packets.
Getting a parse error when processing a phenopacket from the wild: Willoughby-2018-WDR45-proband.txt
Possibly the problem field
datasetId
is illegal, but we should possibly still recover gracefully if possible.