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GMOD / Apollo3Server

Apollo 3 Server: Grails 4 + Neo4j 3.5 + JB2
BSD 3-Clause "New" or "Revised" License
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Fix exon service #88

Closed nathandunn closed 3 years ago

nathandunn commented 3 years ago

fixes https://github.com/GMOD/apollo-gmod-js/issues/41

nathandunn commented 3 years ago 
iro.authc.pam.UnsupportedTokenException: Realm [org.bbop.apollo.DbRealm@6d9eeecf] does not support authentication token [org.apache.shiro.authc.UsernamePasswordToken - test@test.com, rememberMe=false].  Please ensure that the appropriate Realm implementation is configured correctly or that the realm accepts AuthenticationTokens of this type.
location: null
2021-04-12 12:56:09.548 ERROR --- [nio-8080-exec-1] o.g.web.errors.GrailsExceptionResolver   : NullPointerException occurred when processing request: [POST] /annotationEditor/deleteExon
Cannot get property 'to' on null object. Stacktrace follows:

java.lang.reflect.InvocationTargetException: null
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.grails.core.DefaultGrailsControllerClass$ReflectionInvoker.invoke(DefaultGrailsControllerClass.java:211)
        at org.grails.core.DefaultGrailsControllerClass.invoke(DefaultGrailsControllerClass.java:188)
        at org.grails.web.mapping.mvc.UrlMappingsInfoHandlerAdapter.handle(UrlMappingsInfoHandlerAdapter.groovy:90)
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1040)
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:943)
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)
        at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)
        at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
        at org.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:77)
        at org.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:67)
        at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
        at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
        at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
        at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
        at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
        at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
        at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.NullPointerException: Cannot get property 'to' on null object
        at org.bbop.apollo.FeatureService.$tt__getOverlappingFeatures(FeatureService.groovy:202)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at grails.gorm.transactions.GrailsTransactionTemplate$2.doInTransaction(GrailsTransactionTemplate.groovy:94)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
        at grails.gorm.transactions.GrailsTransactionTemplate.execute(GrailsTransactionTemplate.groovy:91)
        at org.bbop.apollo.FeatureService.$tt__getOverlappingTranscripts(FeatureService.groovy:84)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at grails.gorm.transactions.GrailsTransactionTemplate$2.doInTransaction(GrailsTransactionTemplate.groovy:94)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
        at grails.gorm.transactions.GrailsTransactionTemplate.execute(GrailsTransactionTemplate.groovy:91)
        at org.bbop.apollo.FeatureService.$tt__handleDynamicIsoformOverlap(FeatureService.groovy:3274)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at grails.gorm.transactions.GrailsTransactionTemplate$2.doInTransaction(GrailsTransactionTemplate.groovy:94)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
        at grails.gorm.transactions.GrailsTransactionTemplate.execute(GrailsTransactionTemplate.groovy:91)
        at org.bbop.apollo.RequestHandlingService.$tt__deleteExon(RequestHandlingService.groovy:1953)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at grails.gorm.transactions.GrailsTransactionTemplate$2.doInTransaction(GrailsTransactionTemplate.groovy:94)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
        at grails.gorm.transactions.GrailsTransactionTemplate.execute(GrailsTransactionTemplate.groovy:91)
        at org.bbop.apollo.AnnotationEditorController.deleteExon(AnnotationEditorController.groovy:973)
        ... 22 common frames omitted