VEuPathDB / service-eda

Repo containing EDA web service
Apache License 2.0
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Look into subsetting failure related to binary files metadata #17

Open dmgaldi opened 4 months ago

dmgaldi commented 4 months ago
ESC[m org.gusdb.fgputil.db.runner.SQLRunnerException: Unable to process result of SQL <SELECT distinct stable_id, parent_stable_id, provider_label, display_name, definition, vocabulary, display_type, hidden, display_order, display_range_min, display_rang
e_max, range_min, range_max, bin_width_override, bin_width_computed, is_temporal, is_featured, is_merge_key, impute_zero, is_repeated, has_values, data_type, distinct_values_count, is_multi_valued, data_shape, unit, precision, scale, has_study_dependent_
vocabulary, variable_spec_to_impute_zeroes_for
FROM eda.attributegraph_2023_t0_poc_EventLinker
ORDER BY stable_id> with args [ ]
        at org.gusdb.fgputil.db.runner.SQLRunner.executeSql(SQLRunner.java:442) ~[service.jar:3.9.0]
        at org.gusdb.fgputil.db.runner.SQLRunner.executeQuery(SQLRunner.java:353) ~[service.jar:3.9.0]
        at org.gusdb.fgputil.db.runner.SQLRunner.executeQuery(SQLRunner.java:340) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.model.db.VariableFactory.loadVariables(VariableFactory.java:52) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.model.db.StudyFactory.getStudyById(StudyFactory.java:80) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.service.MetadataCache.lambda$getStudyById$1(MetadataCache.java:60) ~[service.jar:3.9.0]
        at java.util.HashMap.computeIfAbsent(HashMap.java:1224) ~[?:?]
        at org.veupathdb.service.eda.ss.service.MetadataCache.getStudyById(MetadataCache.java:59) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.model.db.StudyResolver.lambda$getStudyById$2(StudyResolver.java:44) ~[service.jar:3.9.0]
        at java.util.Optional.map(Optional.java:260) ~[?:?]
        at org.veupathdb.service.eda.ss.model.db.StudyResolver.getStudyById(StudyResolver.java:41) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.service.StudiesService.getStudiesByStudyId(StudiesService.java:109) ~[service.jar:3.9.0]
        at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) ~[?:?]
        at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
        at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:146) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:189) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:93) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81) ~[service.jar:3.9.0]
        at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261) [service.jar:3.9.0]
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) [service.jar:3.9.0]
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) [service.jar:3.9.0]
        at org.glassfish.jersey.internal.Errors.process(Errors.java:292) [service.jar:3.9.0]
        at org.glassfish.jersey.internal.Errors.process(Errors.java:274) [service.jar:3.9.0]
        at org.glassfish.jersey.internal.Errors.process(Errors.java:244) [service.jar:3.9.0]
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) [service.jar:3.9.0]
        at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240) [service.jar:3.9.0]
        at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697) [service.jar:3.9.0]
        at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.service(GrizzlyHttpContainer.java:367) [service.jar:3.9.0]
        at org.glassfish.grizzly.http.server.HttpHandler$1.run(HttpHandler.java:190) [service.jar:3.9.0]
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535) [service.jar:3.9.0]
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515) [service.jar:3.9.0]
        at java.lang.Thread.run(Thread.java:831) [?:?]
Caused by: java.lang.ClassCastException: class org.veupathdb.service.eda.ss.model.variable.binary.EmptyBinaryProperties cannot be cast to class org.veupathdb.service.eda.ss.model.variable.Utf8EncodingLengthProperties (org.veupathdb.service.eda.ss.model.variable.binary.EmptyBinaryProperties and org.veupathdb.service.eda.ss.model.variable.Utf8EncodingLengthProperties are in unnamed module of loader 'app')
        at org.veupathdb.service.eda.ss.model.db.VariableFactory.createValueVarFromResultSet(VariableFactory.java:130) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.model.db.VariableFactory.createVariableFromResultSet(VariableFactory.java:91) ~[service.jar:3.9.0]
        at org.veupathdb.service.eda.ss.model.db.VariableFactory.lambda$loadVariables$0(VariableFactory.java:55) ~[service.jar:3.9.0]
        at org.gusdb.fgputil.db.runner.SQLRunnerExecutors$QueryExecutor.handleResult(SQLRunnerExecutors.java:258) ~[service.jar:3.9.0]
        at org.gusdb.fgputil.db.runner.SQLRunner.executeSql(SQLRunner.java:419) ~[service.jar:3.9.0]
        ... 36 more