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IHTSDO / snowstorm

Scalable SNOMED CT Terminology Server using Elasticsearch
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Import is getting rollbacked with 8.2.2 jar file #608

Closed TechAspirant closed 2 months ago

TechAspirant commented 3 months ago

I am trying to make snowstorm 8.2.2 jar up and running with open JDK version 11 and Elastic search version 7.7 and 7.10.0 where swagger gets up where I can see my branch as MAIN but concepts, relationships are rollbacked after saving batch. Below is the error or log I am getting. Please help.

java.lang.IllegalStateException: Failed to update concept definition status.org.springframework.data.elasticsearch.UncategorizedElasticsearchException: Elasticsearch exception [type=x_content_parse_exception, reason=[1:955] [bool] failed to parse field [must]]; nested exception is ElasticsearchStatusException[Elasticsearch exception [type=x_content_parse_exception, reason=[1:955] [bool] failed to parse field [must]]]; nested: ElasticsearchException[Elasticsearch exception [type=parsing_exception, reason=[match_phrase_prefix] query does not support [zero_terms_query]]]; at org.snomed.snowstorm.core.data.services.ConceptDefinitionStatusUpdateService.preCommitCompletion(ConceptDefinitionStatusUpdateService.java:62) at io.kaicode.elasticvc.api.BranchService.completeCommit(BranchService.java:409) at io.kaicode.elasticvc.domain.Commit.close(Commit.java:61) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.completeImportCommit(ImportComponentFactoryImpl.java:229) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.loadingComponentsCompleted(ImportComponentFactoryImpl.java:218) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:251) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:203) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.access$100(ReleaseImporter.java:186) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:46) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:80) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.snapshotImport(ImportService.java:216) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importFiles(ImportService.java:161) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importArchive(ImportService.java:114) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$FastClassBySpringCGLIB$$3479d1da.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy.invokeMethod(CglibAopProxy.java:386) at org.springframework.aop.framework.CglibAopProxy.access$000(CglibAopProxy.java:85) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:704) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$EnhancerBySpringCGLIB$$3e523e4d.importArchive() at org.snomed.snowstorm.SnowstormApplication.importEditionRF2FromDisk(SnowstormApplication.java:141) at org.snomed.snowstorm.SnowstormApplication.run(SnowstormApplication.java:101) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:759) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:749) at org.springframework.boot.SpringApplication.run(SpringApplication.java:314) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292) at org.snomed.snowstorm.SnowstormApplication.main(SnowstormApplication.java:61) 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:108) at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65) Caused by: org.springframework.data.elasticsearch.UncategorizedElasticsearchException: Elasticsearch exception [type=x_content_parse_exception, reason=[1:955] [bool] failed to parse field [must]]; nested exception is ElasticsearchStatusException[Elasticsearch exception [type=x_content_parse_exception, reason=[1:955] [bool] failed to parse field [must]]]; nested: ElasticsearchException[Elasticsearch exception [type=parsing_exception, reason=[match_phrase_prefix] query does not support [zero_terms_query]]]; at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:66) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:367) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:350) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.searchScrollStart(ElasticsearchRestTemplate.java:276) at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.searchForStream(AbstractElasticsearchTemplate.java:339) at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.searchForStream(AbstractElasticsearchTemplate.java:326) at org.snomed.snowstorm.core.data.services.ConceptDefinitionStatusUpdateService.getConceptsWithDefinedAxiomStatus(ConceptDefinitionStatusUpdateService.java:122) at org.snomed.snowstorm.core.data.services.ConceptDefinitionStatusUpdateService.performUpdate(ConceptDefinitionStatusUpdateService.java:83) at org.snomed.snowstorm.core.data.services.ConceptDefinitionStatusUpdateService.preCommitCompletion(ConceptDefinitionStatusUpdateService.java:59) ... 34 common frames omitted Caused by: org.elasticsearch.ElasticsearchStatusException: Elasticsearch exception [type=x_content_parse_exception, reason=[1:955] [bool] failed to parse field [must]] at org.elasticsearch.rest.BytesRestResponse.errorFromXContent(BytesRestResponse.java:187) at org.elasticsearch.client.RestHighLevelClient.parseEntity(RestHighLevelClient.java:1911) at org.elasticsearch.client.RestHighLevelClient.parseResponseException(RestHighLevelClient.java:1888) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1645) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1602) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1572) at org.elasticsearch.client.RestHighLevelClient.search(RestHighLevelClient.java:1088) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$searchScrollStart$11(ElasticsearchRestTemplate.java:276) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:348) ... 40 common frames omitted Suppressed: org.elasticsearch.client.ResponseException: method [POST], host [http://localhost:9200], URI [/member/_search?typed_keys=true&max_concurrent_shard_requests=5&ignore_unavailable=false&expand_wildcards=open&allow_no_indices=true&ignore_throttled=true&scroll=60000ms&search_type=dfs_query_then_fetch&batched_reduce_size=512&ccs_minimize_roundtrips=true], status line [HTTP/1.1 400 Bad Request] {"error":{"root_cause":[{"type":"parsing_exception","reason":"[match_phrase_prefix] query does not support [zero_terms_query]","line":1,"col":955}],"type":"x_content_parse_exception","reason":"[1:955] [bool] failed to parse field [must]","caused_by":{"type":"parsing_exception","reason":"[match_phrase_prefix] query does not support [zero_terms_query]","line":1,"col":955}},"status":400} at org.elasticsearch.client.RestClient.convertResponse(RestClient.java:326) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:296) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:270) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1632) ... 45 common frames omitted Caused by: org.elasticsearch.ElasticsearchException: Elasticsearch exception [type=parsing_exception, reason=[match_phrase_prefix] query does not support [zero_terms_query]] at org.elasticsearch.ElasticsearchException.innerFromXContent(ElasticsearchException.java:496) at org.elasticsearch.ElasticsearchException.fromXContent(ElasticsearchException.java:407) at org.elasticsearch.ElasticsearchException.innerFromXContent(ElasticsearchException.java:437) at org.elasticsearch.ElasticsearchException.failureFromXContent(ElasticsearchException.java:603) at org.elasticsearch.rest.BytesRestResponse.errorFromXContent(BytesRestResponse.java:179) ... 48 common frames omitted

2024-07-05 20:36:53.916 INFO 43828 --- [ main] io.kaicode.elasticvc.api.BranchService : Rolling back commit on MAIN started at 1720190455145 2024-07-05 20:36:53.923 INFO 43828 --- [ main] io.kaicode.elasticvc.api.BranchService : Deleting documents on MAIN started at 1720190455145. 2024-07-05 20:37:24.165 ERROR 43828 --- [ main] o.s.s.core.rf2.rf2import.ImportService : Failed RF2 SNAPSHOT import on branch MAIN. ID 59baaf81-edb9-41d0-a66b-ab941f300dee

org.springframework.dao.DataAccessResourceFailureException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE]; nested exception is java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:75) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:367) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:350) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.delete(ElasticsearchRestTemplate.java:208) at io.kaicode.elasticvc.api.BranchService.doContentRollback(BranchService.java:556) at io.kaicode.elasticvc.api.BranchService.rollbackCommit(BranchService.java:499) at io.kaicode.elasticvc.api.BranchService.completeCommit(BranchService.java:415) at io.kaicode.elasticvc.domain.Commit.close(Commit.java:61) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.completeImportCommit(ImportComponentFactoryImpl.java:229) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.loadingComponentsCompleted(ImportComponentFactoryImpl.java:218) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:251) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:203) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.access$100(ReleaseImporter.java:186) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:46) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:80) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.snapshotImport(ImportService.java:216) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importFiles(ImportService.java:161) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importArchive(ImportService.java:114) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$FastClassBySpringCGLIB$$3479d1da.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy.invokeMethod(CglibAopProxy.java:386) at org.springframework.aop.framework.CglibAopProxy.access$000(CglibAopProxy.java:85) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:704) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$EnhancerBySpringCGLIB$$3e523e4d.importArchive() at org.snomed.snowstorm.SnowstormApplication.importEditionRF2FromDisk(SnowstormApplication.java:141) at org.snomed.snowstorm.SnowstormApplication.run(SnowstormApplication.java:101) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:759) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:749) at org.springframework.boot.SpringApplication.run(SpringApplication.java:314) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292) at org.snomed.snowstorm.SnowstormApplication.main(SnowstormApplication.java:61) 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:108) at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65) Caused by: java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:365) ... 38 common frames omitted Caused by: java.net.SocketTimeoutException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:864) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:283) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:270) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1632) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1602) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1572) at org.elasticsearch.client.RestHighLevelClient.deleteByQuery(RestHighLevelClient.java:648) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$delete$5(ElasticsearchRestTemplate.java:208) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:348) ... 37 common frames omitted Caused by: java.net.SocketTimeoutException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.apache.http.nio.protocol.HttpAsyncRequestExecutor.timeout(HttpAsyncRequestExecutor.java:387) at org.apache.http.impl.nio.client.InternalIODispatch.onTimeout(InternalIODispatch.java:98) at org.apache.http.impl.nio.client.InternalIODispatch.onTimeout(InternalIODispatch.java:40) at org.apache.http.impl.nio.reactor.AbstractIODispatch.timeout(AbstractIODispatch.java:175) at org.apache.http.impl.nio.reactor.BaseIOReactor.sessionTimedOut(BaseIOReactor.java:261) at org.apache.http.impl.nio.reactor.AbstractIOReactor.timeoutCheck(AbstractIOReactor.java:506) at org.apache.http.impl.nio.reactor.BaseIOReactor.validate(BaseIOReactor.java:211) at org.apache.http.impl.nio.reactor.AbstractIOReactor.execute(AbstractIOReactor.java:280) at org.apache.http.impl.nio.reactor.BaseIOReactor.execute(BaseIOReactor.java:104) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor$Worker.run(AbstractMultiworkerIOReactor.java:591) at java.base/java.lang.Thread.run(Thread.java:829)

2024-07-05 20:37:24.507 ERROR 43828 --- [ main] o.snomed.snowstorm.SnowstormApplication : 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE]; nested exception is java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE]

org.springframework.dao.DataAccessResourceFailureException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE]; nested exception is java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:75) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:367) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:350) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.delete(ElasticsearchRestTemplate.java:208) at io.kaicode.elasticvc.api.BranchService.doContentRollback(BranchService.java:556) at io.kaicode.elasticvc.api.BranchService.rollbackCommit(BranchService.java:499) at io.kaicode.elasticvc.api.BranchService.completeCommit(BranchService.java:415) at io.kaicode.elasticvc.domain.Commit.close(Commit.java:61) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.completeImportCommit(ImportComponentFactoryImpl.java:229) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.loadingComponentsCompleted(ImportComponentFactoryImpl.java:218) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:251) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:203) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.access$100(ReleaseImporter.java:186) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:46) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:80) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.snapshotImport(ImportService.java:216) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importFiles(ImportService.java:161) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importArchive(ImportService.java:114) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$FastClassBySpringCGLIB$$3479d1da.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy.invokeMethod(CglibAopProxy.java:386) at org.springframework.aop.framework.CglibAopProxy.access$000(CglibAopProxy.java:85) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:704) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$EnhancerBySpringCGLIB$$3e523e4d.importArchive() at org.snomed.snowstorm.SnowstormApplication.importEditionRF2FromDisk(SnowstormApplication.java:141) at org.snomed.snowstorm.SnowstormApplication.run(SnowstormApplication.java:101) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:759) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:749) at org.springframework.boot.SpringApplication.run(SpringApplication.java:314) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292) at org.snomed.snowstorm.SnowstormApplication.main(SnowstormApplication.java:61) 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:108) at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65) Caused by: java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:365) ... 38 common frames omitted Caused by: java.net.SocketTimeoutException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:864) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:283) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:270) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1632) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1602) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1572) at org.elasticsearch.client.RestHighLevelClient.deleteByQuery(RestHighLevelClient.java:648) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$delete$5(ElasticsearchRestTemplate.java:208) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:348) ... 37 common frames omitted Caused by: java.net.SocketTimeoutException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.apache.http.nio.protocol.HttpAsyncRequestExecutor.timeout(HttpAsyncRequestExecutor.java:387) at org.apache.http.impl.nio.client.InternalIODispatch.onTimeout(InternalIODispatch.java:98) at org.apache.http.impl.nio.client.InternalIODispatch.onTimeout(InternalIODispatch.java:40) at org.apache.http.impl.nio.reactor.AbstractIODispatch.timeout(AbstractIODispatch.java:175) at org.apache.http.impl.nio.reactor.BaseIOReactor.sessionTimedOut(BaseIOReactor.java:261) at org.apache.http.impl.nio.reactor.AbstractIOReactor.timeoutCheck(AbstractIOReactor.java:506) at org.apache.http.impl.nio.reactor.BaseIOReactor.validate(BaseIOReactor.java:211) at org.apache.http.impl.nio.reactor.AbstractIOReactor.execute(AbstractIOReactor.java:280) at org.apache.http.impl.nio.reactor.BaseIOReactor.execute(BaseIOReactor.java:104) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor$Worker.run(AbstractMultiworkerIOReactor.java:591) at java.base/java.lang.Thread.run(Thread.java:829)

2024-07-05 20:37:24.512 INFO 43828 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2024-07-05 20:37:24.546 ERROR 43828 --- [ main] o.s.boot.SpringApplication : Application run failed

java.lang.IllegalStateException: Failed to execute ApplicationRunner at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:762) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:749) at org.springframework.boot.SpringApplication.run(SpringApplication.java:314) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292) at org.snomed.snowstorm.SnowstormApplication.main(SnowstormApplication.java:61) 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:108) at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65) Caused by: org.springframework.dao.DataAccessResourceFailureException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE]; nested exception is java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.springframework.data.elasticsearch.core.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:75) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:367) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:350) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.delete(ElasticsearchRestTemplate.java:208) at io.kaicode.elasticvc.api.BranchService.doContentRollback(BranchService.java:556) at io.kaicode.elasticvc.api.BranchService.rollbackCommit(BranchService.java:499) at io.kaicode.elasticvc.api.BranchService.completeCommit(BranchService.java:415) at io.kaicode.elasticvc.domain.Commit.close(Commit.java:61) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.completeImportCommit(ImportComponentFactoryImpl.java:229) at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.loadingComponentsCompleted(ImportComponentFactoryImpl.java:218) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:251) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.doLoadReleaseFiles(ReleaseImporter.java:203) at org.ihtsdo.otf.snomedboot.ReleaseImporter$ImportRun.access$100(ReleaseImporter.java:186) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:46) at org.ihtsdo.otf.snomedboot.ReleaseImporter.loadSnapshotReleaseFiles(ReleaseImporter.java:80) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.snapshotImport(ImportService.java:216) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importFiles(ImportService.java:161) at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importArchive(ImportService.java:114) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$FastClassBySpringCGLIB$$3479d1da.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy.invokeMethod(CglibAopProxy.java:386) at org.springframework.aop.framework.CglibAopProxy.access$000(CglibAopProxy.java:85) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:704) at org.snomed.snowstorm.core.rf2.rf2import.ImportService$$EnhancerBySpringCGLIB$$3e523e4d.importArchive() at org.snomed.snowstorm.SnowstormApplication.importEditionRF2FromDisk(SnowstormApplication.java:141) at org.snomed.snowstorm.SnowstormApplication.run(SnowstormApplication.java:101) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:759) ... 13 common frames omitted Caused by: java.lang.RuntimeException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.translateException(ElasticsearchRestTemplate.java:365) ... 38 common frames omitted Caused by: java.net.SocketTimeoutException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:864) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:283) at org.elasticsearch.client.RestClient.performRequest(RestClient.java:270) at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1632) at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1602) at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1572) at org.elasticsearch.client.RestHighLevelClient.deleteByQuery(RestHighLevelClient.java:648) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.lambda$delete$5(ElasticsearchRestTemplate.java:208) at org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate.execute(ElasticsearchRestTemplate.java:348) ... 37 common frames omitted Caused by: java.net.SocketTimeoutException: 30,000 milliseconds timeout on connection http-outgoing-6 [ACTIVE] at org.apache.http.nio.protocol.HttpAsyncRequestExecutor.timeout(HttpAsyncRequestExecutor.java:387) at org.apache.http.impl.nio.client.InternalIODispatch.onTimeout(InternalIODispatch.java:98) at org.apache.http.impl.nio.client.InternalIODispatch.onTimeout(InternalIODispatch.java:40) at org.apache.http.impl.nio.reactor.AbstractIODispatch.timeout(AbstractIODispatch.java:175) at org.apache.http.impl.nio.reactor.BaseIOReactor.sessionTimedOut(BaseIOReactor.java:261) at org.apache.http.impl.nio.reactor.AbstractIOReactor.timeoutCheck(AbstractIOReactor.java:506) at org.apache.http.impl.nio.reactor.BaseIOReactor.validate(BaseIOReactor.java:211) at org.apache.http.impl.nio.reactor.AbstractIOReactor.execute(AbstractIOReactor.java:280) at org.apache.http.impl.nio.reactor.BaseIOReactor.execute(BaseIOReactor.java:104) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor$Worker.run(AbstractMultiworkerIOReactor.java:591) at java.base/java.lang.Thread.run(Thread.java:829)

kaicode commented 3 months ago

The underlying error here is an Elasticsearch query timeout.

(After import a search is run automatically to check concepts definition status. If this takes longer than 30 seconds it times out and the commit fails).

Please see this answer for the solution: https://github.com/IHTSDO/snowstorm/issues/158#issuecomment-1600910490

TechAspirant commented 3 months ago

I imported this zip file 'SnomedCT_InternationalRF2_PRODUCTION_20240701T120000Z.zip'. How can I get the Diagnosis Procedure and Drug information from API ? How can I import drug extension zip along with the 'SnomedCT_InternationalRF2_PRODUCTION_20240701T120000Z.zip'

kaicode commented 3 months ago

Which drug extension would you like to use? There are a couple of different ones for different countries but no International drug extension. There are some base drug concepts in the International Edition.

TechAspirant commented 3 months ago

I imported this one 'SnomedCT_IndiaDrugExtensionRF2_PRODUCTION_IN1000189_20240415T120000Z.zip' and I want to find out a way to query or filter drugs by name.

kaicode commented 3 months ago

Snowstorm has two APIs. One is a custom API for SNOMED CT and the other is a standardised FHIR Terminology API. I suggest using the FHIR API.

I have not seen how the India drug extension is authored. Is there a browser available for this?

Assuming the drugs are in the SNOMED CT hierarchy under the 763158003 |Medicinal product (product)| concept they can be searched using the following FHIR implicit value set: https://snowstorm.ihtsdotools.org/fhir/ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=isa/763158003&filter=paracetamol This example uses the demo Snowstorm instance and should not be used in production. This example searches within the International Edition of SNOMED CT. We do not host the India drug extension on that server.

It's possible to search a specific code system using the FHIR API. Have you imported the drug extension using a new code system or did you just import the second package into the existing codesystem (on the MAIN branch).

TechAspirant commented 3 months ago

Yes, first I imported the Production zip then without deleting the indices I imported the drug extension zip. I can access the api via localhost at port 8080 and I want to know how can I query or filter the drug information at the server running locally.

kaicode commented 3 months ago

You can. Try this: http://localhost:8080/fhir/ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=isa/763158003&filter=paracetamol The filter parameter can be used to support text search over this set of all medicinal products.

TechAspirant commented 3 months ago

Also is there any API to get the diagnosis procedure. Means can I get the diagnosis procedure using the local API server. I am now importing IPS Terminology server. I want to test the use cases specially third one via local API server. https://confluence.ihtsdotools.org/display/DOCIPSTUG/4.+Use+cases @kaicode Any Help on this?

TechAspirant commented 3 months ago

I tried using GET /fhir/ValueSet/$expand?url=http%3A%2F%2Fsnomed.info%2Fsct%3Ffhir_vs%3Decl%2F%3C%20404684003&count=20&includeDesignations=true&filter=Identify%20all%20diabetic%20patients%20with%20a%20history%20of%20cardiovascular%20disease%20for%20inclusion%20in%20a%20clinical%20trial%20for%20a%20new%20drug HTTP/1.1

But not getting expected results.

kaicode commented 3 months ago

I don't think there is a concept in SNOMED CT that groups together all types of diagnosis procedure. There is 5880005 |Physical examination procedure (procedure)|, that might be useful to fetch all types patient examination? For example: GET /fhir/ValueSet/$expand?url=http%3A%2F%2Fsnomed.info%2Fsct%3Ffhir_vs%3Decl%2F%3C5880005 Does that hep?