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IHTSDO / snowstorm

Scalable SNOMED CT Terminology Server using Elasticsearch
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Snowstorm is not working with docker: nested exception is java.lang.RuntimeException: Connection refused #355

Open anilskalyane opened 2 years ago

anilskalyane commented 2 years ago

Getting the error while running the snowstorm in docker, here are the output,

Stack details: Snowstorm version: 7.5.4

____ _ __/\__ / ___| _ __ _____ _____| |_ ___ _ __ _ __ ___ \_\/_/ \___ \| '_ \ / _ \ \ /\ / / __| __/ _ \| '__| '_ \ //_\ ) | | | | () \ V V /_ \ || () | | | | | | | | \/ |__/|| ||_/ _/_/ |/\\/|| || || ||

:: Snowstorm, SNOMED CT Terminology Server :: (v7.5.4)

2021-12-23 05:44:20.290 INFO 1 --- [ main] o.snomed.snowstorm.SnowstormApplication : Starting SnowstormApplication v7.5.4 on 5360075c35f9 with PID 1 (/app/snowstorm.jar started by snowstorm in /app) 2021-12-23 05:44:20.380 INFO 1 --- [ main] o.snomed.snowstorm.SnowstormApplication : No active profile set, falling back to default profiles: default 2021-12-23 05:44:41.836 INFO 1 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data Elasticsearch repositories in DEFAULT mode. 2021-12-23 05:44:42.139 INFO 1 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 291ms. Found 21 Elasticsearch repository interfaces. 2021-12-23 05:44:43.716 INFO 1 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data Reactive Elasticsearch repositories in DEFAULT mode. 2021-12-23 05:44:43.812 INFO 1 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 95ms. Found 0 Reactive Elasticsearch repository interfaces. 2021-12-23 05:44:51.779 INFO 1 --- [ main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.security.access.expression.method.DefaultMethodSecurityExpressionHandler@57adfab0' of type [org.springframework.security.access.expression.method.DefaultMethodSecurityExpressionHandler] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying) 2021-12-23 05:44:51.888 INFO 1 --- [ main] trationDelegate$BeanPostProcessorChecker : Bean 'permissionEvaluator' of type [org.snomed.snowstorm.config.MethodSecurityConfig$1] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying) 2021-12-23 05:44:51.891 INFO 1 --- [ main] trationDelegate$BeanPostProcessorChecker : Bean 'methodSecurityConfig' of type [org.snomed.snowstorm.config.MethodSecurityConfig$$EnhancerBySpringCGLIB$$ea8bdf74] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying) 2021-12-23 05:44:51.927 INFO 1 --- [ main] trationDelegate$BeanPostProcessorChecker : Bean 'methodSecurityMetadataSource' of type [org.springframework.security.access.method.DelegatingMethodSecurityMetadataSource] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying) 2021-12-23 05:44:53.969 INFO 1 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat initialized with port(s): 8080 (http) 2021-12-23 05:44:54.028 INFO 1 --- [ main] o.apache.catalina.core.StandardService : Starting service [Tomcat] 2021-12-23 05:44:54.029 INFO 1 --- [ main] org.apache.catalina.core.StandardEngine : Starting Servlet engine: [Apache Tomcat/9.0.37] 2021-12-23 05:44:54.390 INFO 1 --- [ main] o.a.c.c.C.[Tomcat].[localhost].[/] : Initializing Spring embedded WebApplicationContext 2021-12-23 05:44:54.392 INFO 1 --- [ main] w.s.c.ServletWebServerApplicationContext : Root WebApplicationContext: initialization completed in 32344 ms 2021-12-23 05:44:54.563 INFO 1 --- [ main] ca.uhn.fhir.util.VersionUtil : HAPI FHIR version 4.2.0 - Rev 8491707942 2021-12-23 05:44:56.890 INFO 1 --- [ main] ication$$EnhancerBySpringCGLIB$$75663c57 : Elasticsearch host: http://localhost:9200 2021-12-23 05:44:56.892 INFO 1 --- [ main] ication$$EnhancerBySpringCGLIB$$75663c57 : Elasticsearch index prefix: 2021-12-23 05:44:58.057 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from class org.springframework.data.geo.Point to interface java.util.Map as writing converter although it doesn't convert to a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.058 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from interface java.util.Map to class org.springframework.data.geo.Point as reading converter although it doesn't convert from a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.059 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from class org.springframework.data.elasticsearch.core.geo.GeoPoint to interface java.util.Map as writing converter although it doesn't convert to a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.060 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from interface java.util.Map to class org.springframework.data.elasticsearch.core.geo.GeoPoint as reading converter although it doesn't convert from a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.082 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from class org.springframework.data.geo.Point to interface java.util.Map as writing converter although it doesn't convert to a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.083 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from interface java.util.Map to class org.springframework.data.geo.Point as reading converter although it doesn't convert from a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.084 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from class org.springframework.data.elasticsearch.core.geo.GeoPoint to interface java.util.Map as writing converter although it doesn't convert to a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.085 WARN 1 --- [ main] o.s.data.convert.CustomConversions : Registering converter from interface java.util.Map to class org.springframework.data.elasticsearch.core.geo.GeoPoint as reading converter although it doesn't convert from a store-supported type! You might want to check your annotation setup at the converter implementation. 2021-12-23 05:44:58.975 INFO 1 --- [ main] o.s.d.elasticsearch.support.VersionInfo : Version Spring Data Elasticsearch: 4.0.4 2021-12-23 05:44:58.977 INFO 1 --- [ main] o.s.d.elasticsearch.support.VersionInfo : Version Elasticsearch Client in build: 7.6.2 2021-12-23 05:44:58.978 INFO 1 --- [ main] o.s.d.elasticsearch.support.VersionInfo : Version Elasticsearch Client used: 7.7.0 2021-12-23 05:44:58.979 WARN 1 --- [ main] o.s.d.elasticsearch.support.VersionInfo : Version mismatch in between Elasticsearch Clients build/use: 7.6.2 - 7.7.0 2021-12-23 05:44:59.745 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:00.071 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:00.253 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:00.391 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:00.535 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:00.670 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:01.088 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$2 (jar:file:/app/snowstorm.jar!/BOOT-INF/lib/guice-4.0.jar!/) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$2 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 2021-12-23 05:45:08.580 INFO 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Identifier cache manager polling commencing with 10 second period. 2021-12-23 05:45:08.587 INFO 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Topping up IdCache(0 - 00) by 1000 2021-12-23 05:45:08.635 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:09.196 ERROR 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Failed to top-up IdCache(0 - 00) with 1000 identifiers

org.springframework.dao.DataAccessResourceFailureException: Connection refused; nested exception is java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:76) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:398) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:381) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.search(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.search(AbstractElasticsearchTemplate.java:331) at org.snomed.snowstorm.core.data.services.identifier.LocalRandomIdentifierSource.findExistingIdentifiersInAnyBranch(LocalRandomIdentifierSource.java:86) at org.snomed.snowstorm.core.data.services.identifier.LocalRandomIdentifierSource.reserveIds(LocalRandomIdentifierSource.java:55) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.topUp(IdentifierCacheManager.java:119) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.checkTopUpRequired(IdentifierCacheManager.java:102) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.run(IdentifierCacheManager.java:67) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:396) ... 9 common frames omitted Caused by: java.net.ConnectException: Connection refused at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:823) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:248) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:235) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1609) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1579) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1549) at org.elasticsearch.client.RestHighLevelClient.search(RestHighLevelClient.java:1065) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$search$11(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:379) ... 8 common frames omitted Caused by: java.net.ConnectException: Connection refused at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method) at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:777) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvent(DefaultConnectingIOReactor.java:174) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvents(DefaultConnectingIOReactor.java:148) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor.execute(AbstractMultiworkerIOReactor.java:351) at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager.execute(PoolingNHttpClientConnectionManager.java:221) at org.apache.http.impl.nio.client.CloseableHttpAsyncClientBase$1.run(CloseableHttpAsyncClientBase.java:64) ... 1 common frames omitted

2021-12-23 05:45:09.199 INFO 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Topping up IdCache(0 - 01) by 2000 2021-12-23 05:45:09.242 ERROR 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Failed to top-up IdCache(0 - 01) with 2000 identifiers

org.springframework.dao.DataAccessResourceFailureException: Connection refused; nested exception is java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:76) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:398) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:381) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.search(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.search(AbstractElasticsearchTemplate.java:331) at org.snomed.snowstorm.core.data.services.identifier.LocalRandomIdentifierSource.findExistingIdentifiersInAnyBranch(LocalRandomIdentifierSource.java:86) at org.snomed.snowstorm.core.data.services.identifier.LocalRandomIdentifierSource.reserveIds(LocalRandomIdentifierSource.java:60) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.topUp(IdentifierCacheManager.java:119) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.checkTopUpRequired(IdentifierCacheManager.java:102) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.run(IdentifierCacheManager.java:67) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:396) ... 9 common frames omitted Caused by: java.net.ConnectException: Connection refused at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:823) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:248) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:235) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1609) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1579) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1549) at org.elasticsearch.client.RestHighLevelClient.search(RestHighLevelClient.java:1065) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$search$11(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:379) ... 8 common frames omitted Caused by: java.net.ConnectException: Connection refused at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method) at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:777) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvent(DefaultConnectingIOReactor.java:174) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvents(DefaultConnectingIOReactor.java:148) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor.execute(AbstractMultiworkerIOReactor.java:351) at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager.execute(PoolingNHttpClientConnectionManager.java:221) at org.apache.http.impl.nio.client.CloseableHttpAsyncClientBase$1.run(CloseableHttpAsyncClientBase.java:64) ... 1 common frames omitted

2021-12-23 05:45:09.245 INFO 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Topping up IdCache(0 - 02) by 4000 2021-12-23 05:45:09.306 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:09.328 ERROR 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Failed to top-up IdCache(0 - 02) with 4000 identifiers

org.springframework.dao.DataAccessResourceFailureException: Connection refused; nested exception is java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:76) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:398) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:381) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.search(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.search(AbstractElasticsearchTemplate.java:331) at org.snomed.snowstorm.core.data.services.identifier.LocalRandomIdentifierSource.findExistingIdentifiersInAnyBranch(LocalRandomIdentifierSource.java:86) at org.snomed.snowstorm.core.data.services.identifier.LocalRandomIdentifierSource.reserveIds(LocalRandomIdentifierSource.java:65) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.topUp(IdentifierCacheManager.java:119) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.checkTopUpRequired(IdentifierCacheManager.java:102) at org.snomed.snowstorm.core.data.services.identifier.IdentifierCacheManager.run(IdentifierCacheManager.java:67) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:396) ... 9 common frames omitted Caused by: java.net.ConnectException: Connection refused at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:823) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:248) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:235) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1609) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1579) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1549) at org.elasticsearch.client.RestHighLevelClient.search(RestHighLevelClient.java:1065) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$search$11(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:379) ... 8 common frames omitted Caused by: java.net.ConnectException: Connection refused at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method) at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:777) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvent(DefaultConnectingIOReactor.java:174) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvents(DefaultConnectingIOReactor.java:148) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor.execute(AbstractMultiworkerIOReactor.java:351) at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager.execute(PoolingNHttpClientConnectionManager.java:221) at org.apache.http.impl.nio.client.CloseableHttpAsyncClientBase$1.run(CloseableHttpAsyncClientBase.java:64) ... 1 common frames omitted

2021-12-23 05:45:09.496 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:09.566 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:10.009 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:10.136 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:10.210 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:10.979 INFO 1 --- [ main] o.s.s.c.d.s.s.CommitServiceHookClient : CommitServiceHookClient is muted as service url not configured. 2021-12-23 05:45:11.157 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:11.680 INFO 1 --- [ main] o.i.drools.service.TestResourceProvider : 0 semantic tags loaded 2021-12-23 05:45:11.682 INFO 1 --- [ main] o.i.drools.service.TestResourceProvider : 0 case significant words loaded 2021-12-23 05:45:11.684 INFO 1 --- [ main] o.i.drools.service.TestResourceProvider : 0 US to GB term map entries loaded 2021-12-23 05:45:11.717 INFO 1 --- [ main] .s.s.c.d.s.WebRouterConfigurationService : Fall-back route set for use with unconfigured namespaces 2021-12-23 05:45:11.768 INFO 1 --- [ main] .s.s.c.d.s.WebRouterConfigurationService : WebRoute fhir application/fhir+json -> /fhir/CodeSystem/$lookup?code={SCTID}&version={VERSION_URI}&property=normalForm configured for namespace: default 2021-12-23 05:45:11.769 INFO 1 --- [ main] .s.s.c.d.s.WebRouterConfigurationService : WebRoute all application/json -> /browser/{BRANCH}/concepts/{SCTID} configured for namespace: default 2021-12-23 05:45:11.846 WARN 1 --- [ main] .d.e.r.s.AbstractElasticsearchRepository : Cannot create index: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:12.070 WARN 1 --- [ main] ConfigServletWebServerApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'permissionService': Invocation of init method failed; nested exception is org.springframework.dao.DataAccessResourceFailureException: Connection refused; nested exception is java.lang.RuntimeException: Connection refused 2021-12-23 05:45:12.087 INFO 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Identifier cache manager sleep interrupted. 2021-12-23 05:45:12.088 INFO 1 --- [heManagerDaemon] o.s.s.c.d.s.i.IdentifierCacheManager : Identifier cache manager polling stopped. 2021-12-23 05:45:12.157 INFO 1 --- [ main] o.apache.catalina.core.StandardService : Stopping service [Tomcat] 2021-12-23 05:45:12.257 INFO 1 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-12-23 05:45:12.269 ERROR 1 --- [ main] o.s.boot.SpringApplication : Application run failed

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'permissionService': Invocation of init method failed; nested exception is org.springframework.dao.DataAccessResourceFailureException: Connection refused; nested exception is java.lang.RuntimeException: Connection refused at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:160) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:415) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1786) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:594) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:897) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:879) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:551) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226) at org.snomed.snowstorm.SnowstormApplication.main(SnowstormApplication.java:63) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 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/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49) at org.springframework.boot.loader.Launcher.launch(Launcher.java:109) at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88) Caused by: org.springframework.dao.DataAccessResourceFailureException: Connection refused; nested exception is java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:76) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:398) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:381) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.search(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.SearchOperations.searchOne(SearchOperations.java:276) at org.springframework.data.elasticsearch.repository.query.ElasticsearchPartQuery.execute(ElasticsearchPartQuery.java:115) at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor$QueryMethodInvoker.invoke(QueryExecutorMethodInterceptor.java:195) at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.doInvoke(QueryExecutorMethodInterceptor.java:152) at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.invoke(QueryExecutorMethodInterceptor.java:130) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.data.projection.DefaultMethodInvokingMethodInterceptor.invoke(DefaultMethodInvokingMethodInterceptor.java:80) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:95) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy165.findByGlobalAndPathAndRole(Unknown Source) at org.snomed.snowstorm.core.data.services.PermissionService.findByGlobalPathAndRole(PermissionService.java:167) at org.snomed.snowstorm.core.data.services.PermissionService.setGlobalOrBranchRoleGroups(PermissionService.java:155) at org.snomed.snowstorm.core.data.services.PermissionService.setGlobalRoleGroups(PermissionService.java:134) at org.snomed.snowstorm.core.data.services.PermissionService.setGlobalRoleGroups(PermissionService.java:129) at org.snomed.snowstorm.core.data.services.PermissionService.init(PermissionService.java:49) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:389) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:333) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:157) ... 27 common frames omitted Caused by: java.lang.RuntimeException: Connection refused at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:396) ... 53 common frames omitted Caused by: java.net.ConnectException: Connection refused at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:823) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:248) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:235) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1609) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1579) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1549) at org.elasticsearch.client.RestHighLevelClient.search(RestHighLevelClient.java:1065) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$search$11(ElasticsearchRestTemplate.java:289) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:379) ... 52 common frames omitted Caused by: java.net.ConnectException: Connection refused at java.base/sun.nio.ch.SocketChannelImpl.checkConnect(Native Method) at java.base/sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:777) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvent(DefaultConnectingIOReactor.java:174) at org.apache.http.impl.nio.reactor.DefaultConnectingIOReactor.processEvents(DefaultConnectingIOReactor.java:148) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor.execute(AbstractMultiworkerIOReactor.java:351) at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager.execute(PoolingNHttpClientConnectionManager.java:221) at org.apache.http.impl.nio.client.CloseableHttpAsyncClientBase$1.run(CloseableHttpAsyncClientBase.java:64) at java.base/java.lang.Thread.run(Thread.java:829) `

Thanks in advance for the support!

rorydavidson commented 2 years ago

Hi @anilskalyane, are you running using the docker-compose in the repo or as a container on its own?

anilskalyane commented 2 years ago

@rorydavidson As a container. Here is the cmd - docker run -d -p 8080:8080 snowstorm

rorydavidson commented 2 years ago

Are you running any elasticsearch instance anywhere?

anilskalyane commented 2 years ago

No, I have created a new EC2 machine and set up the docker.

rorydavidson commented 2 years ago

That sounds like the issue. Snowstorm uses elasticsearch to store the data so you will need access to that. If you use the docker-compose in this report (as detailed on https://github.com/IHTSDO/snowstorm/blob/master/docs/using-docker.md) then that creates the necessary elasticsearch instance.

anilskalyane commented 2 years ago

Got it @rorydavidson. thanks for the information.