[21.09] Skip non JSON-encodable values in params_to_strings()
#13826
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Fix the error reported in galaxyproject#13455 , which was due to BioMart sending some binary empty strings as values, e.g. for the `hsapiens_gene_ensembl__filter.chromosomal_region__file` key. N.B.: the BioMart tool still doesn't work after this fix (probably BioMart's fault), but at least Galaxy doesn't fail with the mysterious: "Error executing tool id 'biomart': Object of type bytes is not JSON serializable"
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Co-authored-by: Nicola Soranzo <[email protected]>
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The failing Selenium tests are unrelated. |
mvdbeek
reviewed
May 5, 2022
| value = dumps(value, sort_keys=True) | ||
| except Exception as e: | ||
| log.warning(f"Error while serializing value {value} for key {key}: {e}") | ||
| continue |
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Seems risky, don't you want to raise here ?
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I think the issue is that we're not properly receiving the multi-part request from biomart in the legacy routes. The error message is of course a little unfortunate, but that's better than running a tool with incomplete data. If we want to special case something for biomart we should probably do that in , but I don't really understand the form data and what we're supposed to do with it. |
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Fix the error reported in #13455 , which was due to BioMart sending some binary empty strings as values, e.g. for the
hsapiens_gene_ensembl__filter.chromosomal_region__filekey.N.B.: the BioMart tool still doesn't work after this fix (probably BioMart's fault), but at least Galaxy doesn't fail with the mysterious: "Error executing tool id 'biomart': Object of type bytes is not JSON serializable"
Also, cherry-pick commits from dev to fix test failures.
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