Taxonomy not harvesting - harvester warning

BioKIC / NEON-Biorepository

Development base for the NEON Biorepository Data Portal host by BioKIC - Arizona State University (https://biorepo.neonscience.org)

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Taxonomy not harvesting - harvester warning #48

Closed mandrewj closed 2 years ago

mandrewj commented 2 years ago

When harvesting herp bycatch, such as bet_sorting_in.subsampleID.herp, there is a long list of warning messages about illegal offset in the scientific name field:

This seems to result in the taxon name not making it into the occurrence record and no harvesting issue is recorded (just a warning).

Working with Tera right now, it looks like the data are correct in the NEON system so likely an issue with the harvester

mandrewj commented 2 years ago

See https://biorepo.neonscience.org/portal/neon/shipment/manifestviewer.php?shipmentPK=2745

lsteger commented 2 years ago

This is happening across many collections. "Illegal string offset " warning is popping up for most samples harvested

egbot commented 2 years ago

Bug fixed during Oct 26 & 28 code submits: https://github.com/BioKIC/NEON-Biorepository/commit/73ab59c70f6ec029df313780fcfc2be2268ce41c https://github.com/BioKIC/NEON-Biorepository/commit/64ce85a70f9b15d62ccbeca23609d44363e3d6c4

kyule commented 2 years ago

@egbot Should this be working now? I'm still seeing the same errors eg. TREE.20200730.R6493.B.DNA

....many more lines....

egbot commented 2 years ago

Added extra data checks to ensure identifications are complete. Within some of the NEON tables, identification dates were being reported without another information for the identification. Also added new collections to the taxon groups defined to ensure proper translations of taxon codes. https://github.com/BioKIC/NEON-Biorepository/commit/0d0e54fe364d6e82bb5e92fcebfb41863056a786