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molgenis-app-palga's Introduction

molgenis-palga

Molgenis app for PALGA

molgenis-app-palga's People

Contributors

chaopang avatar dennishendriksen avatar erwinwinder avatar fdlk avatar georgebyelas avatar jjettenn avatar mark-de-haan avatar molgenis-jenkins avatar tommydeboer avatar

Watchers

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Forkers

bartcharbon erwinwinder mdijkstra chaopang fdlk tommydeboer mark-de-haan roankanninga marieke-bijlsma

molgenis-app-palga's Issues

Palga build warning that threatens build stability

See Jenkins build logs:

[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.molgenis:molgenis-palga:war:1.4.2
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.molgenis:molgenis-das:jar -> duplicate declaration of version ${project.parent.version} @ line 180, column 21
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]

Palga server sometimes fails to boot.

How to Reproduce

Check palga boot logs on molgenis68.

Expected behavior

Boot succeeds every time

Observed behavior

INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
16:04:00.127 [localhost-startStop-1] INFO  o.m.d.e.f.EmbeddedElasticSearchServiceFactory - Embedded elasticsearch server started, data path=[/data/.molgenis/palga/data]
16:04:32.148 [localhost-startStop-1] WARN  o.m.data.mysql.MysqlRepository - Table for entity tags already exists. Skipping creation
16:04:33.650 [localhost-startStop-1] WARN  o.m.data.mysql.MysqlRepository - Table for entity packages already exists. Skipping creation
16:04:33.744 [localhost-startStop-1] WARN  o.s.w.c.s.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'elasticSearchRepositoryRegistrator' defined in file [/srv/molgenis/apache-tomcat-7.0.78/webapps/ROOT/WEB-INF/classes/org/molgenis/palga/elasticsearch/ElasticSearchRepositoryRegistrator.class]: Unsatisfied dependency expressed through constructor argument with index 7 of type [org.molgenis.data.mysql.MysqlRepositoryCollection]: : Error creating bean with name 'mysqlRepositoryCollection' defined in class path resource [org/molgenis/data/mysql/MySqlConfiguration.class]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mysqlRepositoryCollection' defined in class path resource [org/molgenis/data/mysql/MySqlConfiguration.class]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:747) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:185) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1115) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1018) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:475) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:706) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:762) ~[spring-context-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482) ~[spring-context-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403) [spring-web-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306) [spring-web-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106) [spring-web-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5116) [catalina.jar:7.0.78]
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634) [catalina.jar:7.0.78]
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145) [catalina.jar:7.0.78]
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899) [catalina.jar:7.0.78]
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875) [catalina.jar:7.0.78]
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652) [catalina.jar:7.0.78]
	at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092) [catalina.jar:7.0.78]
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984) [catalina.jar:7.0.78]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_131]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_131]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_131]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_131]
	at java.lang.Thread.run(Thread.java:748) [na:1.8.0_131]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mysqlRepositoryCollection' defined in class path resource [org/molgenis/data/mysql/MySqlConfiguration.class]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:597) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1095) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:990) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:475) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1021) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:964) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:862) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:811) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:739) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	... 28 common frames omitted
Caused by: org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:188) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:586) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	... 41 common frames omitted
Caused by: org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.elasticsearch.action.search.type.TransportSearchTypeAction$BaseAsyncAction.onFirstPhaseResult(TransportSearchTypeAction.java:233) ~[elasticsearch-1.4.4.jar:na]
	at org.elasticsearch.action.search.type.TransportSearchTypeAction$BaseAsyncAction$1.onFailure(TransportSearchTypeAction.java:179) ~[elasticsearch-1.4.4.jar:na]
	at org.elasticsearch.search.action.SearchServiceTransportAction$23.run(SearchServiceTransportAction.java:565) ~[elasticsearch-1.4.4.jar:na]
	... 3 common frames omitted
16:04:34.561 [localhost-startStop-1] INFO  o.m.d.e.f.EmbeddedElasticSearchServiceFactory - Elastic search server stopped
16:04:34.569 [localhost-startStop-1] ERROR o.s.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'elasticSearchRepositoryRegistrator' defined in file [/srv/molgenis/apache-tomcat-7.0.78/webapps/ROOT/WEB-INF/classes/org/molgenis/palga/elasticsearch/ElasticSearchRepositoryRegistrator.class]: Unsatisfied dependency expressed through constructor argument with index 7 of type [org.molgenis.data.mysql.MysqlRepositoryCollection]: : Error creating bean with name 'mysqlRepositoryCollection' defined in class path resource [org/molgenis/data/mysql/MySqlConfiguration.class]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mysqlRepositoryCollection' defined in class path resource [org/molgenis/data/mysql/MySqlConfiguration.class]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:747) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:185) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1115) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1018) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:475) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:706) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:762) ~[spring-context-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482) ~[spring-context-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403) ~[spring-web-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306) ~[spring-web-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106) [spring-web-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5116) [catalina.jar:7.0.78]
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634) [catalina.jar:7.0.78]
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145) [catalina.jar:7.0.78]
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899) [catalina.jar:7.0.78]
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875) [catalina.jar:7.0.78]
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652) [catalina.jar:7.0.78]
	at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092) [catalina.jar:7.0.78]
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984) [catalina.jar:7.0.78]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_131]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_131]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_131]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_131]
	at java.lang.Thread.run(Thread.java:748) [na:1.8.0_131]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'mysqlRepositoryCollection' defined in class path resource [org/molgenis/data/mysql/MySqlConfiguration.class]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:597) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1095) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:990) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:475) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1021) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:964) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:862) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:811) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:739) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	... 28 common frames omitted
Caused by: org.springframework.beans.factory.BeanDefinitionStoreException: Factory method [public org.molgenis.data.mysql.MysqlRepositoryCollection org.molgenis.data.mysql.MySqlConfiguration.mysqlRepositoryCollection()] threw exception; nested exception is org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:188) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:586) ~[spring-beans-4.0.8.RELEASE.jar:4.0.8.RELEASE]
	... 41 common frames omitted
Caused by: org.elasticsearch.action.search.SearchPhaseExecutionException: Failed to execute phase [query_fetch], all shards failed
	at org.elasticsearch.action.search.type.TransportSearchTypeAction$BaseAsyncAction.onFirstPhaseResult(TransportSearchTypeAction.java:233) ~[elasticsearch-1.4.4.jar:na]
	at org.elasticsearch.action.search.type.TransportSearchTypeAction$BaseAsyncAction$1.onFailure(TransportSearchTypeAction.java:179) ~[elasticsearch-1.4.4.jar:na]
	at org.elasticsearch.search.action.SearchServiceTransportAction$23.run(SearchServiceTransportAction.java:565) ~[elasticsearch-1.4.4.jar:na]
	... 3 common frames omitted
Nov 27, 2017 4:04:34 PM org.apache.catalina.core.StandardContext startInternal

File upload cannot exceed 1GB

WebAppInitializer defines MAX_FILE_SIZE=1024 and therefore files greater than 1GB cannot be uploaded using the importer.

The palga file currently is a bit over 2GB.

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