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Scalable SNOMED CT Terminology Server using Elasticsearch
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Import error using docker setup for SnomedCT_InternationalRF2_PRODUCTION_20240701T12 #613

Closed jf29medma closed 1 month ago

jf29medma commented 1 month ago

Hello everybody, I wanted to set up a cloud instance (ubuntu 22.04, 16 GB memory, 100GB storage ) with snowstorm, elasticsearch and browser. Every service run in a docker container and the initial setup seems to work. After following the steps for importing the first release file "SnomedCT_InternationalRF2_PRODUCTION_20240701T120000Z.zip" it got stuck on the first commit (I do not have the error message anymore :/).

Now I want to try it again and it tells me that the MAIN branch is locked. By further investigation to unlock the MAIN branch, it tells me to use rollback-partial-commit to reset the commit from earlier, but I get a timeout error after 30 sec. 

2024-07-31T19:07:37.079Z  INFO 1 --- [nio-8080-exec-1] o.s.s.core.data.services.SBranchService  : Preparing to roll back commit 1722440063595 on MAIN.
2024-07-31T19:07:37.154Z  INFO 1 --- [nio-8080-exec-1] io.kaicode.elasticvc.api.BranchService   : Rolling back commit 1722440063595 on MAIN.
2024-07-31T19:07:37.326Z  INFO 1 --- [nio-8080-exec-1] io.kaicode.elasticvc.api.BranchService   : Deleting documents on MAIN started at 1722440063595.
2024-07-31T19:08:07.443Z ERROR 1 --- [nio-8080-exec-1] o.s.s.rest.config.RestControllerAdvice   : 30,000 milliseconds timeout on connection http-outgoing-3 [ACTIVE]

org.springframework.dao.DataAccessResourceFailureException: 30,000 milliseconds timeout on connection http-outgoing-3 [ACTIVE]
...

I could not find the configs to increase the timeout.

I also tried to remove all docker container, images, volumes, networks, cache but it somehow saves the partial commit somewhere.

I appreciate every help. If you need more information, feel free to ask.

jf29medma commented 1 month ago

I managed to rebuild the error mentioned above. Importing the "SnomedCT_InternationalRF2_PRODUCTION_20240701T120000Z.zip" following error appears.

I used this tutorial to load in the RF2: Loading SNOMED CT into Snowstorm

ubuntu: 22.04 Docker: 27.1.1 Docker-compose: 2.29.1

2024-08-01T07:25:42.405Z  INFO 1 --- [ool-7-thread-20] o.ihtsdo.otf.snomedboot.ReleaseImporter  : 3200679 reference set members read from der2_cRefset_LanguageSnapshot-en_INT_20240701.txt
2024-08-01T07:25:42.414Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.r.r.ImportComponentFactoryImpl   : 0 components of type Concept were not imported from RF2 because a newer version was found.
2024-08-01T07:25:42.415Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.r.r.ImportComponentFactoryImpl   : 0 components of type Description were not imported from RF2 because a newer version was found.
2024-08-01T07:25:42.415Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.r.r.ImportComponentFactoryImpl   : 0 components of type ReferenceSetMember were not imported from RF2 because a newer version was found.
2024-08-01T07:25:42.415Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.r.r.ImportComponentFactoryImpl   : 0 components of type Relationship were not imported from RF2 because a newer version was found.
2024-08-01T07:25:42.831Z  INFO 1 --- [pool-3-thread-1] i.k.elasticvc.api.ComponentService       : Saving batch of 142 ReferenceSetMembers
2024-08-01T07:26:06.728Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : Checking 394630 concepts.
2024-08-01T07:26:09.724Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 23623 concepts found with defined axioms.
2024-08-01T07:26:10.264Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:12.848Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 23714 concepts found with defined axioms.
2024-08-01T07:26:13.224Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:15.798Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 23639 concepts found with defined axioms.
2024-08-01T07:26:16.187Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:18.649Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 23426 concepts found with defined axioms.
2024-08-01T07:26:19.020Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:21.447Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 23709 concepts found with defined axioms.
2024-08-01T07:26:21.841Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:24.643Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 23633 concepts found with defined axioms.
2024-08-01T07:26:25.032Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:25.248Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 1700 concepts found with defined axioms.
2024-08-01T07:26:25.296Z  INFO 1 --- [pool-3-thread-1] d.s.ConceptDefinitionStatusUpdateService : 0 concepts need updating.
2024-08-01T07:26:48.438Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer TC index stated: Collect changed is-a relationships. took 23.12 seconds
2024-08-01T07:26:50.559Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   10,000 axioms...
2024-08-01T07:26:51.972Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   20,000 axioms...
2024-08-01T07:26:53.268Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   30,000 axioms...
2024-08-01T07:26:54.506Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   40,000 axioms...
2024-08-01T07:26:55.769Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   50,000 axioms...
2024-08-01T07:26:57.077Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   60,000 axioms...
2024-08-01T07:26:58.241Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   70,000 axioms...
2024-08-01T07:26:59.300Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   80,000 axioms...
2024-08-01T07:27:00.481Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised   90,000 axioms...
2024-08-01T07:27:01.444Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  100,000 axioms...
2024-08-01T07:27:02.451Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  110,000 axioms...
2024-08-01T07:27:03.453Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  120,000 axioms...
2024-08-01T07:27:04.474Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  130,000 axioms...
2024-08-01T07:27:05.446Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  140,000 axioms...
2024-08-01T07:27:06.473Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  150,000 axioms...
2024-08-01T07:27:07.431Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  160,000 axioms...
2024-08-01T07:27:08.382Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  170,000 axioms...
2024-08-01T07:27:09.292Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  180,000 axioms...
2024-08-01T07:27:10.291Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  190,000 axioms...
2024-08-01T07:27:11.450Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  200,000 axioms...
2024-08-01T07:27:12.590Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  210,000 axioms...
2024-08-01T07:27:13.685Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  220,000 axioms...
2024-08-01T07:27:14.480Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  230,000 axioms...
2024-08-01T07:27:15.343Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  240,000 axioms...
2024-08-01T07:27:16.200Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  250,000 axioms...
2024-08-01T07:27:17.056Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  260,000 axioms...
2024-08-01T07:27:17.930Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  270,000 axioms...
2024-08-01T07:27:18.919Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  280,000 axioms...
2024-08-01T07:27:19.909Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  290,000 axioms...
2024-08-01T07:27:20.779Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  300,000 axioms...
2024-08-01T07:27:21.731Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  310,000 axioms...
2024-08-01T07:27:22.637Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  320,000 axioms...
2024-08-01T07:27:23.628Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  330,000 axioms...
2024-08-01T07:27:24.670Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  340,000 axioms...
2024-08-01T07:27:25.579Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  350,000 axioms...
2024-08-01T07:27:26.523Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  360,000 axioms...
2024-08-01T07:27:27.357Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  370,000 axioms...
2024-08-01T07:27:28.228Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  380,000 axioms...
2024-08-01T07:27:29.108Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  390,000 axioms...
2024-08-01T07:27:29.882Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer TC index stated: Collect changed axiom is-a fragments. took 41.444 seconds
2024-08-01T07:27:35.699Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.d.s.SemanticIndexUpdateService   : Performing incremental update of stated semantic index
2024-08-01T07:27:36.667Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer TC index stated: Collect existingAncestors from QueryConcept. took 6.785 seconds
2024-08-01T07:27:38.056Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.d.s.SemanticIndexUpdateService   : 0 existing nodes loaded.
2024-08-01T07:27:38.608Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer MRCM: Load domains took 0.362 seconds
2024-08-01T07:27:38.643Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer MRCM: Load attribute domains took 0.035 seconds
2024-08-01T07:27:38.672Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer MRCM: Load attribute ranges took 0.029 seconds
2024-08-01T07:27:41.243Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer TC index stated: Update graph using relationships of concepts with changed modelling. took 3.187 seconds
2024-08-01T07:27:45.154Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  400,000 axioms...
2024-08-01T07:27:46.915Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  410,000 axioms...
2024-08-01T07:27:48.591Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  420,000 axioms...
2024-08-01T07:27:52.475Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  430,000 axioms...
2024-08-01T07:27:56.967Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  440,000 axioms...
2024-08-01T07:27:59.074Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  450,000 axioms...
2024-08-01T07:28:01.798Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  460,000 axioms...
2024-08-01T07:28:04.450Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  470,000 axioms...
2024-08-01T07:28:06.747Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  480,000 axioms...
2024-08-01T07:28:09.880Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  490,000 axioms...
2024-08-01T07:28:12.759Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  500,000 axioms...
2024-08-01T07:28:17.591Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  510,000 axioms...
2024-08-01T07:28:21.068Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  520,000 axioms...
2024-08-01T07:28:23.490Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  530,000 axioms...
2024-08-01T07:28:26.706Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  540,000 axioms...
2024-08-01T07:28:31.099Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  550,000 axioms...
2024-08-01T07:28:38.126Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  560,000 axioms...
2024-08-01T07:28:41.961Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  570,000 axioms...
2024-08-01T07:28:45.531Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  580,000 axioms...
2024-08-01T07:28:50.680Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  590,000 axioms...
2024-08-01T07:28:57.179Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  600,000 axioms...
2024-08-01T07:29:02.378Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  610,000 axioms...
2024-08-01T07:29:07.081Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  620,000 axioms...
2024-08-01T07:29:10.893Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  630,000 axioms...
2024-08-01T07:29:14.752Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  640,000 axioms...
2024-08-01T07:29:21.967Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  650,000 axioms...
2024-08-01T07:29:29.258Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  660,000 axioms...
2024-08-01T07:29:38.882Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  670,000 axioms...
2024-08-01T07:29:41.866Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  680,000 axioms...
2024-08-01T07:29:45.266Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  690,000 axioms...
2024-08-01T07:29:53.217Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  700,000 axioms...
2024-08-01T07:30:02.747Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  710,000 axioms...
2024-08-01T07:30:16.138Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  720,000 axioms...
2024-08-01T07:30:19.732Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  730,000 axioms...
2024-08-01T07:30:24.153Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  740,000 axioms...
2024-08-01T07:30:33.456Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  750,000 axioms...
2024-08-01T07:30:43.270Z  INFO 1 --- [pool-3-thread-1] o.s.o.o.taxonomy.AxiomDeserialiser       : Deserialised  760,000 axioms...
2024-08-01T07:30:45.349Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer TC index stated: Update graph using axioms of concepts with changed modelling. took 184.106 seconds
2024-08-01T07:30:48.609Z  INFO 1 --- [pool-3-thread-1] o.snomed.snowstorm.core.util.TimerUtil   : Timer TC index stated: Collect existingDescendants from QueryConcept. took 3.26 seconds
2024-08-01T07:31:00.065Z  INFO 1 --- [pool-3-thread-1] o.s.s.c.d.s.SemanticIndexUpdateService   : Semantic index change summary for stated form: 447753 concepts loaded into the graph. 368312 semantic concepts created including QueryConcept{conceptIdForm=225462008_s, parents=[365441007], ancestors=[365441007, 36456004, 138875005, 404684003], stated=true, attrMap=1:363714003=225464009}. No semantic concepts need updating. No semantic concepts need deleting.
2024-08-01T07:31:00.078Z  INFO 1 --- [pool-3-thread-1] i.k.elasticvc.api.ComponentService       : Saving batch of 5000 QueryConcepts
2024-08-01T07:31:00.184Z ERROR 1 --- [pool-3-thread-1] o.s.s.core.rf2.rf2import.ImportService   : Failed RF2 SNAPSHOT import on branch MAIN. ID ba9fd284-a4de-4443-b521-cbf9832e0147

org.springframework.dao.DataAccessResourceFailureException: es: Temporary failure in name resolution
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:110)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchExceptionTranslator.translateException(ElasticsearchExceptionTranslator.java:64)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.execute(ElasticsearchTemplate.java:635)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.searchScrollStart(ElasticsearchTemplate.java:395)
    at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.searchForStream(AbstractElasticsearchTemplate.java:426)
    at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.searchForStream(AbstractElasticsearchTemplate.java:413)
    at io.kaicode.elasticvc.api.VersionControlHelper.endOldVersionsOnThisBranch(VersionControlHelper.java:399)
    at io.kaicode.elasticvc.api.VersionControlHelper.endOldVersions(VersionControlHelper.java:313)
    at io.kaicode.elasticvc.api.ComponentService.doSaveBatchComponents(ComponentService.java:89)
    at org.snomed.snowstorm.core.data.services.SemanticIndexUpdateService.doSaveBatch(SemanticIndexUpdateService.java:727)
    at org.snomed.snowstorm.core.data.services.SemanticIndexUpdateService.updateSemanticIndex(SemanticIndexUpdateService.java:421)
    at org.snomed.snowstorm.core.data.services.SemanticIndexUpdateService.updateStatedAndInferredSemanticIndex(SemanticIndexUpdateService.java:130)
    at org.snomed.snowstorm.core.data.services.SemanticIndexUpdateService.preCommitCompletion(SemanticIndexUpdateService.java:95)
    at io.kaicode.elasticvc.api.BranchService.completeCommit(BranchService.java:419)
    at io.kaicode.elasticvc.domain.Commit.close(Commit.java:61)
    at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.completeImportCommit(ImportComponentFactoryImpl.java:231)
    at org.snomed.snowstorm.core.rf2.rf2import.ImportComponentFactoryImpl.loadingComponentsCompleted(ImportComponentFactoryImpl.java:220)
    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.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:232)
    at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importFiles(ImportService.java:179)
    at org.snomed.snowstorm.core.rf2.rf2import.ImportService.importArchive(ImportService.java:132)
    at org.snomed.snowstorm.core.rf2.rf2import.ImportService.lambda$importArchiveAsync$1(ImportService.java:280)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: java.lang.RuntimeException: es: Temporary failure in name resolution
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchExceptionTranslator.translateException(ElasticsearchExceptionTranslator.java:63)
    ... 28 common frames omitted
Caused by: java.io.IOException: es: Temporary failure in name resolution
    at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:935)
    at org.elasticsearch.client.RestClient.performRequest(RestClient.java:300)
    at org.elasticsearch.client.RestClient.performRequest(RestClient.java:288)
    at co.elastic.clients.transport.rest_client.RestClientHttpClient.performRequest(RestClientHttpClient.java:91)
    at co.elastic.clients.transport.ElasticsearchTransportBase.performRequest(ElasticsearchTransportBase.java:144)
    at co.elastic.clients.elasticsearch.ElasticsearchClient.search(ElasticsearchClient.java:1897)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.lambda$searchScrollStart$17(ElasticsearchTemplate.java:395)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.execute(ElasticsearchTemplate.java:633)
    ... 27 common frames omitted
Caused by: java.net.UnknownHostException: es: Temporary failure in name resolution
    at java.base/java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
    at java.base/java.net.InetAddress$PlatformNameService.lookupAllHostAddr(InetAddress.java:934)
    at java.base/java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1543)
    at java.base/java.net.InetAddress$NameServiceAddresses.get(InetAddress.java:852)
    at java.base/java.net.InetAddress.getAllByName0(InetAddress.java:1533)
    at java.base/java.net.InetAddress.getAllByName(InetAddress.java:1385)
    at java.base/java.net.InetAddress.getAllByName(InetAddress.java:1306)
    at org.apache.http.impl.conn.SystemDefaultDnsResolver.resolve(SystemDefaultDnsResolver.java:45)
    at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager$InternalAddressResolver.resolveRemoteAddress(PoolingNHttpClientConnectionManager.java:666)
    at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager$InternalAddressResolver.resolveRemoteAddress(PoolingNHttpClientConnectionManager.java:637)
    at org.apache.http.nio.pool.AbstractNIOConnPool.processPendingRequest(AbstractNIOConnPool.java:472)
    at org.apache.http.nio.pool.AbstractNIOConnPool.lease(AbstractNIOConnPool.java:280)
    at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager.requestConnection(PoolingNHttpClientConnectionManager.java:295)
    at org.apache.http.impl.nio.client.AbstractClientExchangeHandler.requestConnection(AbstractClientExchangeHandler.java:381)
    at org.apache.http.impl.nio.client.DefaultClientExchangeHandlerImpl.start(DefaultClientExchangeHandlerImpl.java:130)
    at org.apache.http.impl.nio.client.CloseableHttpAsyncClientBase.execute(CloseableHttpAsyncClientBase.java:116)
    at org.apache.http.impl.nio.client.InternalHttpAsyncClient.execute(InternalHttpAsyncClient.java:138)
    at org.elasticsearch.client.RestClient.performRequest(RestClient.java:296)
    ... 33 common frames omitted

2024-08-01T07:44:16.608Z ERROR 1 --- [   scheduling-1] o.s.s.s.TaskUtils$LoggingErrorHandler    : Unexpected error occurred in scheduled task

org.springframework.dao.DataAccessResourceFailureException: es: Temporary failure in name resolution
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchExceptionTranslator.translateExceptionIfPossible(ElasticsearchExceptionTranslator.java:110)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchExceptionTranslator.translateException(ElasticsearchExceptionTranslator.java:64)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.execute(ElasticsearchTemplate.java:635)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.doSearch(ElasticsearchTemplate.java:351)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.search(ElasticsearchTemplate.java:344)
    at org.springframework.data.elasticsearch.core.AbstractElasticsearchTemplate.search(AbstractElasticsearchTemplate.java:453)
    at io.kaicode.elasticvc.api.BranchService.findLatest(BranchService.java:145)
    at io.kaicode.elasticvc.api.BranchService.findBranchOrThrow(BranchService.java:198)
    at io.kaicode.elasticvc.api.BranchService.findBranchOrThrow(BranchService.java:194)
    at org.snomed.snowstorm.core.data.services.ModuleDependencyService.refreshCache(ModuleDependencyService.java:85)
    at jdk.internal.reflect.GeneratedMethodAccessor23.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:569)
    at org.springframework.scheduling.support.ScheduledMethodRunnable.runInternal(ScheduledMethodRunnable.java:130)
    at org.springframework.scheduling.support.ScheduledMethodRunnable.lambda$run$2(ScheduledMethodRunnable.java:124)
    at io.micrometer.observation.Observation.observe(Observation.java:499)
    at org.springframework.scheduling.support.ScheduledMethodRunnable.run(ScheduledMethodRunnable.java:124)
    at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:54)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305)
    at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: java.lang.RuntimeException: es: Temporary failure in name resolution
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchExceptionTranslator.translateException(ElasticsearchExceptionTranslator.java:63)
    ... 22 common frames omitted
Caused by: java.io.IOException: es: Temporary failure in name resolution
    at org.elasticsearch.client.RestClient.extractAndWrapCause(RestClient.java:935)
    at org.elasticsearch.client.RestClient.performRequest(RestClient.java:300)
    at org.elasticsearch.client.RestClient.performRequest(RestClient.java:288)
    at co.elastic.clients.transport.rest_client.RestClientHttpClient.performRequest(RestClientHttpClient.java:91)
    at co.elastic.clients.transport.ElasticsearchTransportBase.performRequest(ElasticsearchTransportBase.java:144)
    at co.elastic.clients.elasticsearch.ElasticsearchClient.search(ElasticsearchClient.java:1897)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.lambda$doSearch$14(ElasticsearchTemplate.java:351)
    at org.springframework.data.elasticsearch.client.elc.ElasticsearchTemplate.execute(ElasticsearchTemplate.java:633)
    ... 21 common frames omitted
Caused by: java.net.UnknownHostException: es: Temporary failure in name resolution
    at java.base/java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
    at java.base/java.net.InetAddress$PlatformNameService.lookupAllHostAddr(InetAddress.java:934)
    at java.base/java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1543)
    at java.base/java.net.InetAddress$NameServiceAddresses.get(InetAddress.java:852)
    at java.base/java.net.InetAddress.getAllByName0(InetAddress.java:1533)
    at java.base/java.net.InetAddress.getAllByName(InetAddress.java:1385)
    at java.base/java.net.InetAddress.getAllByName(InetAddress.java:1306)
    at org.apache.http.impl.conn.SystemDefaultDnsResolver.resolve(SystemDefaultDnsResolver.java:45)
    at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager$InternalAddressResolver.resolveRemoteAddress(PoolingNHttpClientConnectionManager.java:666)
    at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager$InternalAddressResolver.resolveRemoteAddress(PoolingNHttpClientConnectionManager.java:637)
    at org.apache.http.nio.pool.AbstractNIOConnPool.processPendingRequest(AbstractNIOConnPool.java:472)
    at org.apache.http.nio.pool.AbstractNIOConnPool.lease(AbstractNIOConnPool.java:280)
    at org.apache.http.impl.nio.conn.PoolingNHttpClientConnectionManager.requestConnection(PoolingNHttpClientConnectionManager.java:295)
    at org.apache.http.impl.nio.client.AbstractClientExchangeHandler.requestConnection(AbstractClientExchangeHandler.java:381)
    at org.apache.http.impl.nio.client.DefaultClientExchangeHandlerImpl.start(DefaultClientExchangeHandlerImpl.java:130)
    at org.apache.http.impl.nio.client.CloseableHttpAsyncClientBase.execute(CloseableHttpAsyncClientBase.java:116)
    at org.apache.http.impl.nio.client.InternalHttpAsyncClient.execute(InternalHttpAsyncClient.java:138)
    at org.elasticsearch.client.RestClient.performRequest(RestClient.java:296)
    ... 27 common frames omitted
kaicode commented 1 month ago

The Elasticsearch node has crashed. I would check the Elasticsearch logs for more information. Perhaps there is not enough memory or disk space.

jf29medma commented 1 month ago

The limited memory was the problem. I will close this issue with that comment. Thank you!