Cannot write to metadata table when there are fewer than 5 species in the results

[apetkau]

The species abundance pipeline will read the species_abundance.tsv file and write metadata entries for the top 5 most abundance species under columns species-abundance/taxon_name, species-abundance/taxon_name_2, and so on.

When there are fewer than 5 species in the species_abundance.tsv file, the pipeline will fail to write any metadata and result in the following exception:

2023-06-26 15:10:06.969 ERROR 42416 --- [pool-4-thread-3] .e.g.AnalysisExecutionServiceGalaxyAsync : Error updating corresponding samples with analysis results for
AnalysisSubmission = [x]. Skipping this step.

java.lang.NullPointerException: null                                                                                                                      
        at org.publichealthbioinformatics.irida.plugin.speciesabundance.SpeciesAbundancePluginUpdater.parseSpeciesAbundanceFile(SpeciesAbundancePluginUpdater.java:1
97) ~[na:na]
        at org.publichealthbioinformatics.irida.plugin.speciesabundance.SpeciesAbundancePluginUpdater.update(SpeciesAbundancePluginUpdater.java:91) ~[na:na]
        at ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl.updateSamples(AnalysisSubmissionSampleProcessorImpl.java
:88) ~[classes/:na]
        at ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl$$FastClassBySpringCGLIB$$41d9a648.invoke(<generated>) ~[
classes/:na]
        at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) ~[spring-core-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:793) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:763) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:61) ~[spring-security-core-5.7.
5.jar:5.7.5]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:763) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) ~[spring-tx-5.3.24.jar:5.3.24
]
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) ~[spring-tx-5.3.24.jar:5.
3.24]
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:763) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:708) ~[spring-aop-5.3.24.jar:5.3.24]
        at ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl$$EnhancerBySpringCGLIB$$23e51d98.updateSamples(<generate
d>) ~[classes/:na]
        at ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync.postProcessResults(AnalysisExecutionServiceGal
axyAsync.java:227) ~[classes/:na]
        at ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync$$FastClassBySpringCGLIB$$fc2d896.invoke(<gener
ated>) ~[classes/:na]
        at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) ~[spring-core-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:793) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:763) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) ~[spring-tx-5.3.24.jar:5.3.24
]
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) ~[spring-tx-5.3.24.jar:5.
3.24]
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:763) ~[spring-aop-5.3.24.jar:5.3.24]
        at org.springframework.aop.aspectj.MethodInvocationProceedingJoinPoint.proceed(MethodInvocationProceedingJoinPoint.java:89) ~[spring-aop-5.3.24.jar:5.3.24]
        at ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUserAspect.setSecurityContextFromAnalysisSubmission(RunAsUserAspect.java:100) ~[cl
asses/:na]
        at jdk.internal.reflect.GeneratedMethodAccessor634.invoke(Unknown Source) ~[na:na]
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
...

The final output results will be available, but nothing ends up being written to the metadata table.

I have attached example files where this issue occurs:

• 08-5578-small
  • 08-5578-small_S1_L001_R1_001.fastq.gz
  • 08-5578-small_S1_L001_R2_001.fastq.gz