tabulator.exceptions.SourceError: field larger than field limit #335
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I am getting this error when I validate my package. It seems to be related with the number of synonyms for a compound. I tried tweaking the preparation script and getting only a subset of synonyms fixed the issue. For reference, copper has more than 2000 synonyms: https://pubchem.ncbi.nlm.nih.gov/compound/23978#section=Depositor-Supplied-Synonyms&fullscreen=true |
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Replies: 2 comments
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I am looking into a systematic workaround for this issue: for now, stick with your stated workaround to get through validation. I may also wind up doing a (possibly brutal) truncation if the first few more palatable solutions don't work out. Leaving issue open; stand by |
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I have truncated the synonym lists and hope this fixes your issue -- am marking "answered," but please reopen and report if you find otherwise. Ontology files and the submission prep script have all been updated and published here: please overwrite local copies and try again. Note: the master C2M2 JSON schema has also updated (to match previous development schema): it is here and an up-to-date copy needs to be included with submissions during prep with the script. |
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I have truncated the synonym lists and hope this fixes your issue -- am marking "answered," but please reopen and report if you find otherwise.
Ontology files and the submission prep script have all been updated and published here: please overwrite local copies and try again.
Note: the master C2M2 JSON schema has also updated (to match previous development schema): it is here and an up-to-date copy needs to be included with submissions during prep with the script.