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CambridgeMolecularEngineering / chemdataextractor2

ChemDataExtractor Version 2.0
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Broken table parser #35

Closed OBrink closed 2 months ago

OBrink commented 1 year ago

When running, the notebook examples/automatic_parsing_for_tables.ipynb, there are a couple of issues:

1) One small thing: The path definition of the example table file is wrong. It should be path = "./data/table_example.csv" instead of path = "./example_tables/table_example_tkt_2.csv". 2) The more urgent issue: It does not work. After defining the model in cell 2, the records in cell 3 are still empty. Something is broken there.

I am running the dockerised version of ChemDataExtractor 2.1.2. A colleague (@ViktorWeissenborn) has the exact same issue on an M2 MacBook. Could you give me a hint on how to make the table parser work again?

Thanks a lot! Otto

OBrink commented 1 year ago

I have found the solution. The model needs to be specified when instantiating the Table object instead of adding it later. I have opened a PR (#37) so that the usage is properly described in the example notebook.