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obiba / mica2

Mica is a web portal for epidemiological study consortia.
http://www.obiba.org/pages/products/mica/
GNU General Public License v3.0
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Alternative sources of taxonomies #4381

Open ymarcon opened 1 year ago

ymarcon commented 1 year ago

Just like #4376 for the value tables, this feature proposes to bypass usage of an Opal server for providing the taxonomies. The taxonomies could be read from a local configuration file, or an external server source. The latter implies that a plugin, of type mica-taxonomies, is defined so that one can extend the Mica with custom taxonomies.

johannes-darms commented 11 months ago

I believe there is some kind of loop. The following lines indicated that the indexing fails, which triggers a reindex. Sadly, the process never stops.

mica-mica-1   | 2023-09-13 08:34:11.556 DEBUG 22 --- [         task-1] org.obiba.es.mica.ESIndexer              : Indexing all indexables for indexName [term] persistableObjectNumber [2]
mica-mica-1   | 2023-09-13 08:34:12.332  INFO 22 --- [        task-10] org.obiba.mica.taxonomy.TaxonomyIndexer  : All taxonomies were updated
mica-mica-1   | 2023-09-13 08:34:12.333 DEBUG 22 --- [        task-13] org.obiba.es.mica.ESIndexer              : Indexing for indexName [taxonomy] indexableObject [org.obiba.mica.taxonomy.TaxonomyIndexable@1ce983d0]
mica-mica-1   | 2023-09-13 08:34:12.354 ERROR 22 --- [        task-11] .a.i.SimpleAsyncUncaughtExceptionHandler : Unexpected exception occurred invoking async method: public void org.obiba.mica.taxonomy.TaxonomyIndexer.taxonomiesUpdated(org.obiba.mica.micaConfig.event.TaxonomiesUpdatedEvent)
mica-mica-1   | 
mica-mica-1   | org.elasticsearch.index.IndexNotFoundException: no such index
mica-mica-1   |     at org.elasticsearch.cluster.metadata.IndexNameExpressionResolver$WildcardExpressionResolver.resolve(IndexNameExpressionResolver.java:581)
mica-mica-1   |     at org.elasticsearch.cluster.metadata.IndexNameExpressionResolver.concreteIndices(IndexNameExpressionResolver.java:133)
mica-mica-1   |     at org.elasticsearch.cluster.metadata.IndexNameExpressionResolver.concreteIndices(IndexNameExpressionResolver.java:77)
mica-mica-1   |     at org.elasticsearch.action.admin.indices.mapping.put.TransportPutMappingAction.checkBlock(TransportPutMappingAction.java:66)
mica-mica-1   |     at org.elasticsearch.action.admin.indices.mapping.put.TransportPutMappingAction.checkBlock(TransportPutMappingAction.java:41)
mica-mica-1   |     at org.elasticsearch.action.support.master.TransportMasterNodeAction$AsyncSingleAction.doStart(TransportMasterNodeAction.java:156)
mica-mica-1   |     at org.elasticsearch.action.support.master.TransportMasterNodeAction$AsyncSingleAction.start(TransportMasterNodeAction.java:148)
mica-mica-1   |     at org.elasticsearch.action.support.master.TransportMasterNodeAction.doExecute(TransportMasterNodeAction.java:115)
mica-mica-1   |     at org.elasticsearch.action.support.master.TransportMasterNodeAction.doExecute(TransportMasterNodeAction.java:50)
mica-mica-1   |     at org.elasticsearch.action.support.TransportAction.execute(TransportAction.java:137)
mica-mica-1   |     at org.elasticsearch.action.support.TransportAction.execute(TransportAction.java:85)
mica-mica-1   |     at org.elasticsearch.client.node.NodeClient.doExecute(NodeClient.java:58)
mica-mica-1   |     at org.elasticsearch.client.support.AbstractClient.execute(AbstractClient.java:359)
mica-mica-1   |     at org.elasticsearch.client.support.AbstractClient$IndicesAdmin.execute(AbstractClient.java:1226)
mica-mica-1   |     at org.elasticsearch.action.ActionRequestBuilder.execute(ActionRequestBuilder.java:86)
mica-mica-1   |     at org.elasticsearch.action.ActionRequestBuilder.execute(ActionRequestBuilder.java:56)
mica-mica-1   |     at org.obiba.es.mica.mapping.TaxonomyIndexConfiguration.onIndexCreated(TaxonomyIndexConfiguration.java:57)
mica-mica-1   |     at org.obiba.es.mica.ESIndexer.lambda$createIndexIfNeeded$2(ESIndexer.java:250)
mica-mica-1   |     at java.lang.Iterable.forEach(Iterable.java:75)
mica-mica-1   |     at org.obiba.es.mica.ESIndexer.createIndexIfNeeded(ESIndexer.java:250)
mica-mica-1   |     at org.obiba.es.mica.ESIndexer.index(ESIndexer.java:79)
mica-mica-1   |     at org.obiba.es.mica.ESIndexer.index(ESIndexer.java:73)
mica-mica-1   |     at org.obiba.mica.search.SearchEngineIndexer.index(SearchEngineIndexer.java:46)
mica-mica-1   |     at org.obiba.mica.taxonomy.TaxonomyIndexer.lambda$index$5(TaxonomyIndexer.java:119)
mica-mica-1   |     at java.lang.Iterable.forEach(Iterable.java:75)
mica-mica-1   |     at org.obiba.mica.taxonomy.TaxonomyIndexer.index(TaxonomyIndexer.java:118)
mica-mica-1   |     at org.obiba.mica.taxonomy.TaxonomyIndexer.taxonomiesUpdated(TaxonomyIndexer.java:75)
mica-mica-1   |     at org.obiba.mica.taxonomy.TaxonomyIndexer$$FastClassBySpringCGLIB$$1c4955a2.invoke(<generated>)
mica-mica-1   |     at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
mica-mica-1   |     at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:793)
mica-mica-1   |     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
mica-mica-1   |     at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:763)
mica-mica-1   |     at org.springframework.aop.interceptor.AsyncExecutionInterceptor.lambda$invoke$0(AsyncExecutionInterceptor.java:115)
mica-mica-1   |     at java.util.concurrent.FutureTask.run(FutureTask.java:266)
mica-mica-1   |     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
mica-mica-1   |     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
mica-mica-1   |     at java.lang.Thread.run(Thread.java:750)
mica-mica-1   | 
mica-mica-1   | 2023-09-13 08:34:12.354  INFO 22 --- [         task-9] org.obiba.es.mica.ESIndexer              : Creating index taxonomy
mica-mica-1   | 
mica-mica-1   | 2023-09-13 08:34:12.362 DEBUG 22 --- [        task-10] org.obiba.es.mica.ESIndexer              : Indexing for indexName [taxonomy] indexableObject [org.obiba.mica.taxonomy.TaxonomyIndexable@3abf1694]
mica-mica-1   | 2023-09-13 08:34:12.362  INF