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CatalogueOfLife / backend

Complete backend of COL ChecklistBank
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ERROR: column "max_classification_depth" of relation "dataset_import" does not exist Position: 1031 #1271

Closed gdower closed 10 months ago

gdower commented 10 months ago

Logs&_a=(columns:!(level,logger_name,message),filters:!())):

org.postgresql.util.PSQLException: ERROR: column "max_classification_depth" of relation "dataset_import" does not exist
  Position: 1031
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356)
    at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496)
    at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413)
    at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
    at org.postgresql.jdbc.PgPreparedStatement.execute(PgPreparedStatement.java:177)
    at com.zaxxer.hikari.pool.ProxyPreparedStatement.execute(ProxyPreparedStatement.java:44)
    at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.execute(HikariProxyPreparedStatement.java)
    at org.apache.ibatis.executor.statement.PreparedStatementHandler.update(PreparedStatementHandler.java:48)
    at org.apache.ibatis.executor.statement.RoutingStatementHandler.update(RoutingStatementHandler.java:75)
    at org.apache.ibatis.executor.SimpleExecutor.doUpdate(SimpleExecutor.java:50)
    at org.apache.ibatis.executor.BaseExecutor.update(BaseExecutor.java:117)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.update(DefaultSqlSession.java:197)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.insert(DefaultSqlSession.java:184)
    at org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:62)
    at org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:142)
    at org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
    at com.sun.proxy.$Proxy120.create(Unknown Source)
    at life.catalogue.dao.DatasetImportDao.createWaiting(DatasetImportDao.java:87)
    at life.catalogue.importer.ImportJob.importDataset(ImportJob.java:298)
    at life.catalogue.importer.ImportJob.run(ImportJob.java:156)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:834)
gdower commented 10 months ago

According to builds, the backed should be done deploying, so I think this is a bug. We also can't visit the syncs queue without getting a 400.

I think the above error was generated from the running queue of automated imports. Below is what I get when you visit the imports queue:

org.apache.ibatis.exceptions.PersistenceException: 
### Error querying database.  Cause: org.postgresql.util.PSQLException: ERROR: column "max_classification_depth" does not exist
  Position: 1023
### The error may exist in life/catalogue/db/mapper/DatasetImportMapper.xml
### The error may involve defaultParameterMap
### The error occurred while setting parameters
### SQL: SELECT       dataset_key,     attempt,     state,           job,     error,     started,     finished,     created_by,     applied_decision_count,     bare_name_count,     distribution_count,     estimate_count,     media_count,     name_count,     reference_count,     synonym_count,     taxon_count,     treatment_count,     type_material_count,     vernacular_count,     distributions_by_gazetteer_count,     extinct_taxa_by_rank_count,     ignored_by_reason_count,     issues_by_issue_count,     media_by_type_count,     name_relations_by_type_count,     names_by_code_count,     names_by_rank_count,     names_by_status_count,     names_by_type_count,     names_by_match_type_count,     species_interactions_by_type_count,     synonyms_by_rank_count,     taxa_by_rank_count,     taxon_concept_relations_by_type_count,     type_material_by_status_count,     usages_by_origin_count,     usages_by_status_count,     vernaculars_by_language_count    ,     md5,     download_uri,     download,     format,     origin,     max_classification_depth,     verbatim_count,     verbatim_by_term_count,     verbatim_by_row_type_count         FROM       dataset_import di                WHERE  di.state IN           (             ?::IMPORTSTATE           ,             ?::IMPORTSTATE           ,             ?::IMPORTSTATE           ,             ?::IMPORTSTATE           )          ORDER BY coalesce(di.started, di.finished) DESC NULLS LAST, di.attempt DESC, di.dataset_key                       LIMIT ? OFFSET ?
### Cause: org.postgresql.util.PSQLException: ERROR: column "max_classification_depth" does not exist
  Position: 1023
    at org.apache.ibatis.exceptions.ExceptionFactory.wrapException(ExceptionFactory.java:30)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:156)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:147)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:142)
    at org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:147)
    at org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:80)
    at org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:142)
    at org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
    at com.sun.proxy.$Proxy120.list(Unknown Source)
    at life.catalogue.dao.DatasetImportDao.list(DatasetImportDao.java:68)
    at life.catalogue.importer.ImportManager.listImports(ImportManager.java:165)
    at life.catalogue.resources.ImporterResource.list(ImporterResource.java:76)
    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.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:134)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:177)
    at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:219)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:81)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81)
    at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:256)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:235)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:684)
    at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:358)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799)
    at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1656)
    at io.dropwizard.servlets.ThreadNameFilter.doFilter(ThreadNameFilter.java:35)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1626)
    at io.dropwizard.jersey.filter.AllowedMethodsFilter.handle(AllowedMethodsFilter.java:47)
    at io.dropwizard.jersey.filter.AllowedMethodsFilter.doFilter(AllowedMethodsFilter.java:41)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1626)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:552)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1440)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:505)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1355)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
    at com.codahale.metrics.jetty9.InstrumentedHandler.handle(InstrumentedHandler.java:315)
    at io.dropwizard.jetty.RoutingHandler.handle(RoutingHandler.java:52)
    at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:772)
    at io.dropwizard.jetty.ZipExceptionHandlingGzipHandler.handle(ZipExceptionHandlingGzipHandler.java:26)
    at org.eclipse.jetty.server.handler.RequestLogHandler.handle(RequestLogHandler.java:54)
    at org.eclipse.jetty.server.handler.StatisticsHandler.handle(StatisticsHandler.java:181)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
    at org.eclipse.jetty.server.Server.handle(Server.java:516)
    at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:487)
    at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:732)
    at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:479)
    at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
    at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
    at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
    at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
    at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
    at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.postgresql.util.PSQLException: ERROR: column "max_classification_depth" does not exist
  Position: 1023
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356)
    at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496)
    at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413)
    at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
    at org.postgresql.jdbc.PgPreparedStatement.execute(PgPreparedStatement.java:177)
    at com.zaxxer.hikari.pool.ProxyPreparedStatement.execute(ProxyPreparedStatement.java:44)
    at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.execute(HikariProxyPreparedStatement.java)
    at org.apache.ibatis.executor.statement.PreparedStatementHandler.query(PreparedStatementHandler.java:65)
    at org.apache.ibatis.executor.statement.RoutingStatementHandler.query(RoutingStatementHandler.java:80)
    at org.apache.ibatis.executor.SimpleExecutor.doQuery(SimpleExecutor.java:65)
    at org.apache.ibatis.executor.BaseExecutor.queryFromDatabase(BaseExecutor.java:333)
    at org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:158)
    at org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:137)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:154)
    ... 77 common frames omitted
mdoering commented 10 months ago

forgot to add the column to the db, its there now