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NIAID-Data-Ecosystem / nde-portal

Discovery platform to find NIAID-related datasets and tools
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corrupted CSV download of metadata #201

Closed andrewsu closed 11 months ago

andrewsu commented 12 months ago

From https://data-staging.niaid.nih.gov/search?q=plasmodium&from=1&filters=%28date%3A%5B%222022-08-01%22+TO+%222022-12-31%22%5D%29, I clicked the "Download metadata -> CSV" option and got this file:

nde-results.csv

When loading it in excel (which is how most people will probably view it), you'll see there are many cases where the column parsing isn't correct. I suspect that it has to do with unescaped quotes, newline characters in cell values, or possibly exceeding maximum string lengths in excel. Needs further investigation...

(But I'll note that the isBasedOn.additionalType.url looks funny to me -- an example value is shown below for NCBI_SRA_SRP387013)

`isBasedOn.additionalType.url` for `NCBI_SRA_SRP387013` `["http://purl.obolibrary.org/obo/NCIT_C45293","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","http://purl.obolibrary.org/obo/NCIT_C70699","http://purl.obolibrary.org/obo/NCIT_C47911","http://purl.obolibrary.org/obo/NCIT_C42790","ht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candicecz commented 11 months ago

Andrew found this dataset that specifically has the issue where the value in isBasedOn.additionalType exceeds the max cell count in excel and causes the corrupt csv.

As a solution, I've truncated the cell count of all cells that exceed that limit. We should also re-evaluate how we handle isBasedOn.additionalType