ODV to DwC does not work with all Bio-ODV files?

EMODnet / EMODnetBiocheck

Checks if IPT resources meet the OBIS guidelines

http://rshiny.lifewatch.be/BioCheck/

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ODV to DwC does not work with all Bio-ODV files? #24

Closed LennertSchepers closed 3 years ago

LennertSchepers commented 3 years ago

The conversion from ODV to DwC (ODVtoDwC function in https://github.com/EMODnet/EMODnetBiocheck/blob/master/R/ODVtoDwC.R) seems to have some problems with specific Bio-ODV files, such as the ones from https://www.seadatanet.org/Standards/Data-Transport-Formats.

meliezer commented 3 years ago

I confirm that the HTTP 500 error in the BioQC in https://vre.seadatanet.org/ doesn't happen with the original test file. I looked inside this file and it seems obvious. This service is NOT accepting SeaDataNet ODV spreadsheet format as used by SeaDataNet, but ODV spreadsheet format! SDN format does not have DataVariable. I converted one of the examples above to SeaDataNet ODV spreadsheet, but unfortunately I still get an error as a VRE user. I'll send the file by email.

LennertSchepers commented 3 years ago

Thanks @meliezer, file attached for further reference. BioODV_BiotaPol_converted.txt

Compare these files: example Bio-ODV that works with ODVtoDwC example Bio-ODV from https://www.seadatanet.org/Standards/Data-Transport-Formats (does not work with ODVtoDwC)

bart-v commented 3 years ago

The SDN VRE development has stopped, so this will not be fixed. Closing