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NESCent / FossilCalibrations

Fossil calibrations database
http://fossilcalibrations.org
BSD 2-Clause "Simplified" License
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NCBI Browse no longer working as expected #68

Closed Ksepka closed 9 years ago

Ksepka commented 9 years ago

Our testers have noticed that the "Browse the NCBI taxonomy" feature is not working in almost all cases. For example, entering Amniota into the box yields this message:

Lineage: This node has no ancestors. root There are no calibrations directly attached to root.

Whereas we would expect the result to look as this page: http://fossilcalibrations.org/Browse.php?node=NCBI:32524&lineage=full&members=sparse&levels=2

Same issue arises with any higher taxon I try (Mammalia, Marsupialia, etc). It appears that only if a genus (e.g., Charadrius) is entered into the "Browse the NCBI taxonomy" box will the search complete.

The Bread Crumb Trail works fine, and the "Search for calibrations in the database" feature seems to be working correctly as well.

"Browse the NCBI taxonomy" was working fine in earlier testing and I am not sure if some recent modification had downstream effects.

jimallman commented 9 years ago

Found and fixed (will appear on fossilcalibrations.org when new code is applied).

This was due to recently added validation code that assumes an incoming multitree ID should be a positive integer. These are actually signed integers; as a result, negative numbers would bounce to the default (root) node of NCBI.

dleehr commented 9 years ago

Just pushed the latest code to fossilcalibrations.org