adjust logger message #581
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niekdejonge
reviewed
Nov 24, 2023
| "this shows that these repair functions were not yet run.") | ||
| logger.warning("Please first run derive_inchi_from_smiles, derive_smiles_from_inchi and derive_inchikey. " | ||
| "The spectrum has partly valid annotations, " | ||
| "either these repair functions were not yet run or conversions between the formats failed.") |
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Can the conversion between the formats fail? That would also explain the removal of some spectra after repairing. I would expect that every annotation that has at least one valid form of annotation, should be able to derive the inchi and inchikey.
niekdejonge
reviewed
Nov 24, 2023
| @@ -84,9 +84,9 @@ def _check_repairing_is_possible(smiles, inchi, inchikey) -> bool: | |||
| elif valid_smiles or valid_inchi or valid_inchikey: | |||
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Now I see this, the valid_inchikey is not enough, since we cannot derive smiles and inchi from inchikey alone. So I would only check elif valid_smiles or valid_inchi:
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And above we should also do the same. Instead of if not valid_smiles and not valid_inchi and not valid_inchikey: we should just check if not valid_smiles and not valid_inchi:
niekdejonge
reviewed
Nov 24, 2023
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