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NCBI Export fails when handled by IRIDA background task #1449

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apetkau opened this issue Jan 20, 2023 · 0 comments
Closed

NCBI Export fails when handled by IRIDA background task #1449

apetkau opened this issue Jan 20, 2023 · 0 comments
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back-end Issues relating to the service layer, repository, model, configuration, or database bug critical Urgently required bugfixes or issues

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@apetkau
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apetkau commented Jan 20, 2023

Describe the bug

Uploading data to NCBI crashes with the following exception:

2023-01-20 09:42:26.299 DEBUG 25707 --- [pool-2-thread-2] c.c.b.i.s.export.ExportUploadService     : Creating export xml for submission 1
2023-01-20 09:42:26.361 ERROR 25707 --- [pool-2-thread-2] org.thymeleaf.TemplateEngine             : [THYMELEAF][pool-2-thread-2] Exception processing template "ncb
i": Exception evaluating SpringEL expression: "sample.instrumentModel.value" (template: "ncbi" - line 75, col 39)

org.thymeleaf.exceptions.TemplateProcessingException: Exception evaluating SpringEL expression: "sample.instrumentModel.value" (template: "ncbi" - line 75, col 39)
        at org.thymeleaf.spring5.expression.SPELVariableExpressionEvaluator.evaluate(SPELVariableExpressionEvaluator.java:292) ~[thymeleaf-spring5-3.0.15.RELEASE.ja
r:3.0.15.RELEASE]
        at org.thymeleaf.standard.expression.VariableExpression.executeVariableExpression(VariableExpression.java:166) ~[thymeleaf-3.0.15.RELEASE.jar:3.0.15.RELEASE
]
        at org.thymeleaf.standard.expression.SimpleExpression.executeSimple(SimpleExpression.java:66) ~[thymeleaf-3.0.15.RELEASE.jar:3.0.15.RELEASE]
...
Caused by: org.springframework.expression.spel.SpelEvaluationException: EL1008E: Property or field 'value' cannot be found on object of type 'ca.corefacility.bioinf
ormatics.irida.model.export.NcbiInstrumentModel' - maybe not public or not valid?
        at org.springframework.expression.spel.ast.PropertyOrFieldReference.readProperty(PropertyOrFieldReference.java:217) ~[spring-expression-5.3.23.jar:5.3.23]
...
2023-01-20 09:42:26.362 ERROR 25707 --- [pool-2-thread-2] c.c.b.i.s.export.ExportUploadService     : Upload failed

This occurs in the latest stable version (22.09.6).

Steps to reproduce the problem

What were you doing when you encountered the problem?

  1. Select samples and create new NCBI Export. Submit the NCBI Export.
  2. The export will appear to be submitted successfully.
  3. Wait until the NCBI Export is picked up by the IRIDA background task (this means IRIDA must be run in prod mode or with the NCBI profile enabled).
  4. When the NCBI Export is picked up by the background task, it will fail with the above exception.

Expected behaviour

I expected the NCBI Export to succeed.

Additional context

None.

@apetkau apetkau added bug back-end Issues relating to the service layer, repository, model, configuration, or database critical Urgently required bugfixes or issues labels Jan 20, 2023
@apetkau apetkau mentioned this issue Jan 20, 2023
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Labels
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