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biocypher / clinical-knowledge-graph

GNU General Public License v3.0
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Neo4j Input Exception #2

Closed nilskre closed 1 year ago

nilskre commented 1 year ago

First of all thanks a lot for this project!

When trying to import the generated CSV files into Neo4j, the process fails with org.neo4j.internal.batchimport.input.InputException: ERROR in input ... there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Carrion's'

Proposed solution: remove ' from the input.

slobentanzer commented 1 year ago

Hi @nilskre, thanks for the report! Did you try setting the quote character to double quotes instead of single ones? I.e. biocypher_config.yaml (the one you are using in the script):

neo4j:
  quote_character: '"'

Maybe I forgot adding that after the last update. For me, using the double quote works.

nilskre commented 1 year ago

Hi @slobentanzer, thanks for the fast and helpful response! I did not know, that this config option exists. With this config, it works without any problems. Thanks for fixing it by the commit. One final question here: Was it intended to only add this to one of the three config files? Maybe this can cause confusion because this option is still missing in the subset and embedding config. Or am I missing something? Thanks in advance!

slobentanzer commented 1 year ago

No, you're completely right. I updated the code recently for a new version of BioCypher, and did not add the config option. Thanks for the report. :)