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INCATools / dosdp-tools

Utility for working with DOSDP design patterns and OWL ontologies
MIT License
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Missing column warnings should include pattern names #389

Closed matentzn closed 2 years ago

matentzn commented 2 years ago

When running a huge process like:

dosdp-tools generate --catalog=catalog-v001.xml --infile=../patterns/data/default/ --template=../patterns/dosdp-patterns --batch-patterns="abnormalSizeOfAnatomicalEntity abnormalAbsenceOfMolecularFunction abnormallyDelayedBiologicalProcessInLocation abnormallyIncreasedWidthOfAnatomicalEntity abnormalStabilityOfAnatomicalEntity abnormallyIncreasedLengthOfAnatomicalEntity abnormalMorphologyOfAnatomicalEntity abnormallyDecreasedLengthOfAnatomicalEntity abnormallyPrematureBiologicalProcess abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation abnormalBiologicalProcessInLocation abnormallyIncreasedNumberOfCellularComponent abnormallyDecreasedWidthOfAnatomicalEntity abnormalAnatomicalEntity abnormallyDelayedBiologicalProcess abnormallyIncreasedSizeOfAnatomicalEntity abnormallyDecreasedSizeOfCellularComponent abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation abnormallyIncreasedRateOfBiologicalProcess abnormallyIncreasedSizeOfCellularComponent abnormallyDecreasedNumberOfCellularComponent abnormalAbsenceOfBiologicalProcessInLocation abnormalColorOfAnatomicalEntity abnormallyArrestedBiologicalProcess abnormallyIncreasedRateOfMolecularFunction abnormalCellularComponentProcess abnormallyIncreasedOccurrenceOfBiologicalProcess abnormalBiologicalProcess abnormalAbsenceOfProteinLocalizationInCellularComponent abnormalMorphologyOfCellularComponent abnormallyIncreasedEfficacyOfProteinLocalizationInCellularComponent abnormallyDecreasedRateOfBiologicalProcess abnormalEfficacyOfProteinLocalizationInCellularComponent abnormallyIncreasedNumberOfAnatomicalEntity abnormallyDecreasedSizeOfAnatomicalEntity abnormalMolecularFunction abnormallyDecreasedRateOfMolecularFunction abnormallyDecreasedOccurrenceOfBiologicalProcess abnormalAbsenceOfBiologicalProcess abnormallyDecreasedNumberOfAnatomicalEntity abnormallyDecreasedEfficacyOfProteinLocalizationInCellularComponent abnormallyDecreasedMassOfAnatomicalEntity abnormallyPrematureBiologicalProcessInLocation" --ontology=ddpheno-edit.obo --obo-prefixes=true --restrict-axioms-to=logical --outfile=../patterns/data/default

The following is not very helpful:

2022.01.19 15:06:47:000 [zio-def...] [WARN ] org.monarchinitiative.dosdp.cli.Generate.run:40 - Input is missing column for pattern variable <anatomical_entity>
2022.01.19 15:06:48:000 [zio-def...] [WARN ] org.monarchinitiative.dosdp.cli.Generate.run:40 - Input is missing column for pattern variable <location>
2022.01.19 15:06:48:000 [zio-def...] [WARN ] org.monarchinitiative.dosdp.cli.Generate.run:40 - Input is missing column for pattern variable <location>
2022.01.19 15:06:48:000 [zio-def...] [WARN ] org.monarchinitiative.dosdp.cli.Generate.run:40 - Input is missing column for pattern variable <location>
2022.01.19 15:06:49:000 [zio-def...] [WARN ] org.monarchinitiative.dosdp.cli.Generate.run:40 - Input is missing column for pattern variable <location>

It will take a long time figuring out which input tables have wrong column names.. I also feel like something as severe as as missing column should result in a total failure..

dosumis commented 2 years ago

Might be a general issue with warnings and filenames - see #387

balhoff commented 2 years ago

Fixed by #400.