search

pantherdb / fullgo_paint_update

Update of Panther and PAINT DBs with monthly GO release data
0 stars 0 forks source link

"using with evidence (an annotation id) #### is invalid, since there is no information about annotation id ####" #21

Open dustine32 opened 6 years ago

dustine32 commented 6 years ago

A type of warning from PAINT validation service:

PTN000218930 annotated to term GO:0000981 for annotation id 313863640 using with evidence (an annotation id) 385055487 is invalid, since there is no information about annotation id 385055487

I'm wondering if it's simply caused by an aggregate view switcheroo in the warning query. It looks like this should be valid. I can find annotation_id 313863640 in the paint_aggregate view and evidence (as annotation_id) 385055487 in go_aggregate view. None of these records or their "_evidence" records are obsoleted.

The warning query may be checking these two annotation_ids (one for paint, the other for go) against only one of the views? Otherwise, I can't find anything in the DB that would indicate this to be invalid. We'd need to double-check the service code.

dustine32 commented 6 years ago

Likely caused by not factoring in experimental confidence codes in determining when to obsolete paint_evidence records during the update. Fix will be committed soon.

pgaudet commented 6 years ago

@dustine32 This is very cryptic. Let me know if there anything that needs testing or just looking at.

Thanks, Pascale

dustine32 commented 6 years ago

@pgaudet Agreed. @mugitty and I are just going through a list of warnings produced by her service for certain books. The example here is for PTHR11849. I think I've already found where in the update pipeline this can be fixed.

dustine32 commented 6 years ago

We can test that this book is fixed with this URL: http://panthercuratest.usc.edu/webservices/family.jsp?searchValue=PTHR11849&searchType=SEARCH_TYPE_AGG_FAMILY_ANNOTATION_INFO

It shouldn't return any warnings.