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Cannot import knowledge graph from a file when the file contains additional columns. #5

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yjcyxky opened this issue Jul 1, 2024 · 0 comments
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yjcyxky commented Jul 1, 2024

Describe the bug

Cannot import knowledge graph from a file when the file contains additional columns.

To Reproduce

Prepare a knowledge graph file formatted_primekg.tsv following the BioMedGPS format, but add additional columns. For example, add a column called "extra" with the value "extra_value" in the first row. Then run the following command:

export NEO4J_URL=neo4j://neo4j:xxx@localhost:7687 && export DATABASE_URL=postgres://postgres:xxx@localhost:5432/biomedgps && bin/biomedgps-cli --debug importdb --annotation-file ./relation_types.tsv --dataset PrimeKG -f ./formatted_primekg.tsv -t relation --drop

Expected behavior

The import should fail with an error message indicating that the file is not formatted correctly or just ignore the additional columns.

Additional context
Using biomedgps-cli version 0.3.0

@yjcyxky yjcyxky self-assigned this Jul 1, 2024
@yjcyxky yjcyxky added the bug Something isn't working label Jul 1, 2024
@yjcyxky yjcyxky changed the title Assignees: @yjcyxky Labels: Milestone: Projects: Cannot import knowledge graph from a file when the file contains additional columns. Jul 1, 2024
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