Can't load YAGO taxonomy into Protege - parsing

I've downloaded Protege 5.2.0 and I tried to open the YAGO taxonomy ontology( YAGOTaxonomy.ttl,YAGOTaxonomy.tsv).Every time i tried to open an ontology I got alot of errors, such that i won't be able to show all of them here.
turle syntax
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <FULLIRI> "<wikicat_Companies_operating_former_Chicago,_Milwaukee,_St._Paul_and_Pacific_Railroad_lines<!--on_the_CC&P--> "" at line 5044, column 1.
Was expecting:
<EOF>
Full Stack Trace
-----------------------------------------------------------------------------------------
org.semanticweb.owlapi.rdf.turtle.parser.TurtleParserException: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <FULLIRI> "<wikicat_Companies_operating_former_Chicago,_Milwaukee,_St._Paul_and_Pacific_Railroad_lines<!--on_the_CC&P--> "" at line 5044, column 1.
Was expecting:
<EOF>
at org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1011)
at org.protege.editor.owl.model.io.OntologyLoader.loadOntologyInternal(OntologyLoader.java:101)
at org.protege.editor.owl.model.io.OntologyLoader.lambda$loadOntologyInOtherThread$210(OntologyLoader.java:60)
at org.protege.editor.owl.model.io.OntologyLoader$$Lambda$106/2002289766.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <FULLIRI> "<wikicat_Companies_operating_former_Chicago,_Milwaukee,_St._Paul_and_Pacific_Railroad_lines<!--on_the_CC&P--> "" at line 5044, column 1.
Was expecting:
<EOF>
at org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1960)
at org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1829)
at org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:122)
at org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:82)
... 11 more
OBO format
LINENO: 11 - Could not find tag separator ':' in line.
LINE: ## <id_AEcHoUuL2G_owS_ZJzFuvXiv2>
Full Stack Trace
-----------------------------------------------------------------------------------------
org.semanticweb.owlapi.io.OWLParserException: LINENO: 11 - Could not find tag separator ':' in line.
LINE: ## <id_AEcHoUuL2G_owS_ZJzFuvXiv2>
at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1011)
at org.protege.editor.owl.model.io.OntologyLoader.loadOntologyInternal(OntologyLoader.java:101)
at org.protege.editor.owl.model.io.OntologyLoader.lambda$loadOntologyInOtherThread$210(OntologyLoader.java:60)
at org.protege.editor.owl.model.io.OntologyLoader$$Lambda$106/2002289766.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: LINENO: 11 - Could not find tag separator ':' in line.
LINE: ## <id_AEcHoUuL2G_owS_ZJzFuvXiv2>
at org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501)
at org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897)
at org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528)
at org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521)
at org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderFrame(OBOFormatParser.java:504)
at org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:377)
at org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:335)
at org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281)
at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76)
at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83)
at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58)
... 11 more
I've attached an image that shows the group of errors protege has generated
protege error image. Any help to fix this problem would be greatly appreciated.

Related

How to deal with CoderException: cannot encode a null String with scio

I just started using scio and dataflow. Trying my code to one input file, worked fine. But when I add more files to the input, got the following exception:
java.lang.RuntimeException: org.apache.beam.sdk.coders.CoderException: cannot encode a null String
at org.apache.beam.runners.dataflow.worker.SimpleParDoFn$1.output(SimpleParDoFn.java:280)
at org.apache.beam.runners.core.SimpleDoFnRunner.outputWindowedValue(SimpleDoFnRunner.java:309)
at org.apache.beam.runners.core.SimpleDoFnRunner.access$700(SimpleDoFnRunner.java:77)
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:621)
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:609)
at com.spotify.scio.util.Functions$$anon$3.processElement(Functions.scala:158)
Caused by: org.apache.beam.sdk.coders.CoderException: cannot encode a null String
at org.apache.beam.sdk.coders.StringUtf8Coder.getEncodedElementByteSize(StringUtf8Coder.java:136)
at org.apache.beam.sdk.coders.StringUtf8Coder.getEncodedElementByteSize(StringUtf8Coder.java:37)
at org.apache.beam.sdk.coders.Coder.registerByteSizeObserver(Coder.java:291)
at com.spotify.scio.coders.RecordCoder.registerByteSizeObserver(Coder.scala:279)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.registerByteSizeObserver(WindowedValue.java:564)
at org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.registerByteSizeObserver(WindowedValue.java:480)
at org.apache.beam.runners.dataflow.worker.IntrinsicMapTaskExecutorFactory$ElementByteSizeObservableCoder.registerByteSizeObserver(IntrinsicMapTaskExecutorFactory.java:399)
at org.apache.beam.runners.dataflow.worker.util.common.worker.OutputObjectAndByteCounter.update(OutputObjectAndByteCounter.java:125)
at org.apache.beam.runners.dataflow.worker.DataflowOutputCounter.update(DataflowOutputCounter.java:64)
at org.apache.beam.runners.dataflow.worker.util.common.worker.OutputReceiver.process(OutputReceiver.java:43)
at org.apache.beam.runners.dataflow.worker.SimpleParDoFn$1.output(SimpleParDoFn.java:272)
at org.apache.beam.runners.core.SimpleDoFnRunner.outputWindowedValue(SimpleDoFnRunner.java:309)
at org.apache.beam.runners.core.SimpleDoFnRunner.access$700(SimpleDoFnRunner.java:77)
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:621)
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:609)
at com.spotify.scio.util.Functions$$anon$3.processElement(Functions.scala:158)
at com.spotify.scio.util.Functions$$anon$3$DoFnInvoker.invokeProcessElement(Unknown Source)
at org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:275)
at org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:240)
at org.apache.beam.runners.dataflow.worker.SimpleParDoFn.processElement(SimpleParDoFn.java:325)
at org.apache.beam.runners.dataflow.worker.util.common.worker.ParDoOperation.process(ParDoOperation.java:44)
at org.apache.beam.runners.dataflow.worker.util.common.worker.OutputReceiver.process(OutputReceiver.java:49)
at org.apache.beam.runners.dataflow.worker.util.common.worker.ReadOperation.runReadLoop(ReadOperation.java:201)
at org.apache.beam.runners.dataflow.worker.util.common.worker.ReadOperation.start(ReadOperation.java:159)
at org.apache.beam.runners.dataflow.worker.util.common.worker.MapTaskExecutor.execute(MapTaskExecutor.java:76)
at org.apache.beam.runners.dataflow.worker.BatchDataflowWorker.executeWork(BatchDataflowWorker.java:394)
at org.apache.beam.runners.dataflow.worker.BatchDataflowWorker.doWork(BatchDataflowWorker.java:363)
at org.apache.beam.runners.dataflow.worker.BatchDataflowWorker.getAndPerformWork(BatchDataflowWorker.java:291)
at org.apache.beam.runners.dataflow.worker.DataflowBatchWorkerHarness$WorkerThread.doWork(DataflowBatchWorkerHarness.java:135)
at org.apache.beam.runners.dataflow.worker.DataflowBatchWorkerHarness$WorkerThread.call(DataflowBatchWorkerHarness.java:115)
at org.apache.beam.runners.dataflow.worker.DataflowBatchWorkerHarness$WorkerThread.call(DataflowBatchWorkerHarness.java:102)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
I guess one of my input files may include some malformed data. But how to bypass the bad data? There is a similar question with Java Beam com.google.cloud.dataflow.sdk.coders.CoderException: cannot encode a null String
So I tried this:
val scText = sc.textFile(input)
scText.setCoder(NullableCoder.of(StringUtf8Coder.of()))
It didn't help. Can someone help me on this? Thanks.
The scio team provided a solution to this problem. Basically add --nullableCoders=true in command line argument.

Sonarqube 6.7 - Fail to read ISSUES.LOCATIONS, com.google.protobuf.InvalidProtocolBufferException

Having the below issue after upgrading to SonarQube 6.7. I'm using docker image for sonarqube, I just ran the migrations scripts just like suggested by Sonarquibe UI.
Can someone suggest ?
Thank you
2018.05.15 06:58:42 INFO ce[AWNimASHSOFQrk0D-LC8][o.s.c.t.CeWorkerImpl] Execute task | project=myproject:develop | type=REPORT | id=AWNimASHSOFQrk0D-LC8 | submitter=jenkins
2018.05.15 06:59:52 ERROR ce[AWNimASHSOFQrk0D-LC8][o.s.c.t.CeWorkerImpl] Failed to execute task AWNimASHSOFQrk0D-LC8
org.sonar.server.computation.task.projectanalysis.component.VisitException: Visit of Component {key=myproject:develop,type=PROJECT} failed
at org.sonar.server.computation.task.projectanalysis.component.VisitException.rethrowOrWrap(VisitException.java:44)
at org.sonar.server.computation.task.projectanalysis.component.VisitorsCrawler.visit(VisitorsCrawler.java:74)
at org.sonar.server.computation.task.projectanalysis.step.ExecuteVisitorsStep.execute(ExecuteVisitorsStep.java:51)
at org.sonar.server.computation.task.step.ComputationStepExecutor.executeSteps(ComputationStepExecutor.java:64)
at org.sonar.server.computation.task.step.ComputationStepExecutor.execute(ComputationStepExecutor.java:52)
at org.sonar.server.computation.task.projectanalysis.taskprocessor.ReportTaskProcessor.process(ReportTaskProcessor.java:73)
at org.sonar.ce.taskprocessor.CeWorkerImpl.executeTask(CeWorkerImpl.java:134)
at org.sonar.ce.taskprocessor.CeWorkerImpl.findAndProcessTask(CeWorkerImpl.java:97)
at org.sonar.ce.taskprocessor.CeWorkerImpl.withCustomizedThreadName(CeWorkerImpl.java:81)
at org.sonar.ce.taskprocessor.CeWorkerImpl.call(CeWorkerImpl.java:73)
at org.sonar.ce.taskprocessor.CeWorkerImpl.call(CeWorkerImpl.java:43)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.ibatis.exceptions.PersistenceException:
Error querying database. Cause: java.lang.IllegalStateException: Fail to read ISSUES.LOCATIONS [KEE=AV9aIkjMZ-jmCeoEg-IR]
The error may exist in org.sonar.db.issue.IssueMapper
The error may involve org.sonar.db.issue.IssueMapper.scrollNonClosedByComponentUuid
The error occurred while handling results
SQL: select i.id, i.kee as kee, i.rule_id as ruleId, i.severity as severity, i.manual_severity as manualSeverity, i.message as message, i.line as line, i.locations as locations, i.gap as gap, i.effort as effort, i.status as status, i.resolution as resolution, i.checksum as checksum, i.assignee as assignee, i.author_login as authorLogin, i.tags as tagsString, i.issue_attributes as issueAttributes, i.issue_creation_date as issueCreationTime, i.issue_update_date as issueUpdateTime, i.issue_close_date as issueCloseTime, i.created_at as createdAt, i.updated_at as updatedAt, r.plugin_rule_key as ruleKey, r.plugin_name as ruleRepo, r.language as language, p.kee as componentKey, i.component_uuid as componentUuid, p.module_uuid as moduleUuid, p.module_uuid_path as moduleUuidPath, p.path as filePath, root.kee as projectKey, i.project_uuid as projectUuid, i.issue_type as type from issues i inner join rules r on r.id=i.rule_id inner join projects p on p.uuid=i.component_uuid inner join projects root on root.uuid=i.project_uuid where i.component_uuid = ? and i.status <> 'CLOSED'
Cause: java.lang.IllegalStateException: Fail to read ISSUES.LOCATIONS [KEE=AV9aIkjMZ-jmCeoEg-IR]
at org.apache.ibatis.exceptions.ExceptionFactory.wrapException(ExceptionFactory.java:30)
at org.apache.ibatis.session.defaults.DefaultSqlSession.select(DefaultSqlSession.java:172)
at org.apache.ibatis.session.defaults.DefaultSqlSession.select(DefaultSqlSession.java:158)
at org.apache.ibatis.binding.MapperMethod.executeWithResultHandler(MapperMethod.java:126)
at org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:72)
at org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:59)
at com.sun.proxy.$Proxy42.scrollNonClosedByComponentUuid(Unknown Source)
at org.sonar.server.computation.task.projectanalysis.issue.ComponentIssuesLoader.loadForComponentUuid(ComponentIssuesLoader.java:73)
at org.sonar.server.computation.task.projectanalysis.issue.ComponentIssuesLoader.loadForComponentUuid(ComponentIssuesLoader.java:51)
at org.sonar.server.computation.task.projectanalysis.issue.CloseIssuesOnRemovedComponentsVisitor.closeIssuesForDeletedComponentUuids(CloseIssuesOnRemovedComponentsVisitor.java:60)
at org.sonar.server.computation.task.projectanalysis.issue.CloseIssuesOnRemovedComponentsVisitor.visitProject(CloseIssuesOnRemovedComponentsVisitor.java:53)
at org.sonar.server.computation.task.projectanalysis.component.TypeAwareVisitorWrapper.visitProject(TypeAwareVisitorWrapper.java:47)
at org.sonar.server.computation.task.projectanalysis.component.VisitorsCrawler.visitNode(VisitorsCrawler.java:120)
at org.sonar.server.computation.task.projectanalysis.component.VisitorsCrawler.visitImpl(VisitorsCrawler.java:100)
at org.sonar.server.computation.task.projectanalysis.component.VisitorsCrawler.visit(VisitorsCrawler.java:72)
... 17 common frames omitted
Caused by: java.lang.IllegalStateException: Fail to read ISSUES.LOCATIONS [KEE=AV9aIkjMZ-jmCeoEg-IR]
at org.sonar.db.issue.IssueDto.parseLocations(IssueDto.java:652)
at org.sonar.db.issue.IssueDto.toDefaultIssue(IssueDto.java:721)
at org.sonar.server.computation.task.projectanalysis.issue.ComponentIssuesLoader.lambda$loadForComponentUuid$1(ComponentIssuesLoader.java:74)
at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.callResultHandler(DefaultResultSetHandler.java:363)
at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.storeObject(DefaultResultSetHandler.java:356)
at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.handleRowValuesForSimpleResultMap(DefaultResultSetHandler.java:348)
at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.handleRowValues(DefaultResultSetHandler.java:322)
at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.handleResultSet(DefaultResultSetHandler.java:298)
at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.handleResultSets(DefaultResultSetHandler.java:192)
at org.apache.ibatis.executor.statement.PreparedStatementHandler.query(PreparedStatementHandler.java:64)
at org.apache.ibatis.executor.statement.RoutingStatementHandler.query(RoutingStatementHandler.java:79)
at org.apache.ibatis.executor.ReuseExecutor.doQuery(ReuseExecutor.java:60)
at org.apache.ibatis.executor.BaseExecutor.queryFromDatabase(BaseExecutor.java:324)
at org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:156)
at org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:109)
at org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:83)
at org.apache.ibatis.session.defaults.DefaultSqlSession.select(DefaultSqlSession.java:170)
... 30 common frames omitted
Caused by: com.google.protobuf.InvalidProtocolBufferException: While parsing a protocol message, the input ended unexpectedly in the middle of a field. This could mean either that the input has been truncated or that an embedded message misreported its own length.
at com.google.protobuf.InvalidProtocolBufferException.truncatedMessage(InvalidProtocolBufferException.java:70)
at com.google.protobuf.CodedInputStream.refillBuffer(CodedInputStream.java:1068)
at com.google.protobuf.CodedInputStream.readRawByte(CodedInputStream.java:1135)
at com.google.protobuf.CodedInputStream.readRawVarint64SlowPath(CodedInputStream.java:778)
at com.google.protobuf.CodedInputStream.readRawVarint32(CodedInputStream.java:637)
at com.google.protobuf.CodedInputStream.readInt32(CodedInputStream.java:348)
at org.sonar.db.protobuf.DbCommons$TextRange.<init>(DbCommons.java:149)
at org.sonar.db.protobuf.DbCommons$TextRange.<init>(DbCommons.java:90)
at org.sonar.db.protobuf.DbCommons$TextRange$1.parsePartialFrom(DbCommons.java:750)
at org.sonar.db.protobuf.DbCommons$TextRange$1.parsePartialFrom(DbCommons.java:744)
at com.google.protobuf.CodedInputStream.readMessage(CodedInputStream.java:495)
at org.sonar.db.protobuf.DbIssues$Locations.<init>(DbIssues.java:99)
at org.sonar.db.protobuf.DbIssues$Locations.<init>(DbIssues.java:55)
at org.sonar.db.protobuf.DbIssues$Locations$1.parsePartialFrom(DbIssues.java:852)
at org.sonar.db.protobuf.DbIssues$Locations$1.parsePartialFrom(DbIssues.java:846)
at com.google.protobuf.AbstractParser.parsePartialFrom(AbstractParser.java:137)
at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:169)
at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:180)
at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:185)
at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:49)
at org.sonar.db.protobuf.DbIssues$Locations.parseFrom(DbIssues.java:253)
at org.sonar.db.issue.IssueDto.parseLocations(IssueDto.java:650)
... 46 common frames omitted
2018.05.15 06:59:52 ERROR ce[AWNimASHSOFQrk0D-LC8][o.s.c.t.CeWorkerImpl] Executed task | project=myproject:develop | type=REPORT | id=AWNimASHSOFQrk0D-LC8 | submitter=jenkins | time=70255ms
Actually I solved my problem executing this query on sonar schema. I guess that was definitely related to version upgrade... not a clean solution but still ok to me as I didn't need to have historical data
delete from issues where STATUS != "CLOSED"

Neo4j 3.1.2 Database has encountered some p*oblem, please perform necessary action (tx recovery/restart)

I have moved to Neo4j 3.1.2 and already a few times I have encountered the following database issue with no any changes in my application:
Caused by: java.lang.RuntimeException: org.neo4j.ogm.exception.TransactionException: Database has encountered some problem, please perform necessary action (tx recovery/restart)
at org.neo4j.ogm.drivers.bolt.request.BoltRequest.executeRequest(BoltRequest.java:175)
at org.neo4j.ogm.drivers.bolt.request.BoltRequest.execute(BoltRequest.java:89)
at org.neo4j.ogm.autoindex.AutoIndexManager.assertIndexes(AutoIndexManager.java:170)
at org.neo4j.ogm.autoindex.AutoIndexManager.build(AutoIndexManager.java:92)
at org.neo4j.ogm.session.SessionFactory.<init>(SessionFactory.java:45)
at org.neo4j.ogm.session.SessionFactory.<init>(SessionFactory.java:62)
at com.example.domain.api.configuration.Neo4jConfig.sessionFactory(Neo4jConfig.java:26)
at com.example.domain.api.configuration.Neo4jConfig$$EnhancerBySpringCGLIB$$93871c91.CGLIB$sessionFactory$0(<generated>)
at com.example.domain.api.configuration.Neo4jConfig$$EnhancerBySpringCGLIB$$93871c91$$FastClassBySpringCGLIB$$8bc180c.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228)
at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:358)
at com.example.domain.api.configuration.Neo4jConfig$$EnhancerBySpringCGLIB$$93871c91.sessionFactory(<generated>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
... 131 common frames omitted
What can be a reason of this ?
UPDATED
This is my Neo4j database logs
Oh, this time this was caused by a known (although considered very rare) issue:
org.neo4j.graphdb.TransactionFailureException: Database has encountered some problem, please perform necessary action (tx recovery/restart)
at org.neo4j.kernel.impl.factory.ClassicCoreSPI.beginTransaction(ClassicCoreSPI.java:181)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransactionInternal(GraphDatabaseFacade.java:578)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:383)
at org.neo4j.bolt.v1.runtime.TransactionStateMachineSPI.beginTransaction(TransactionStateMachineSPI.java:95)
at org.neo4j.bolt.v1.runtime.TransactionStateMachine$State$1.run(TransactionStateMachine.java:184)
at org.neo4j.bolt.v1.runtime.TransactionStateMachine.run(TransactionStateMachine.java:77)
at org.neo4j.bolt.v1.runtime.BoltStateMachine$State$2.run(BoltStateMachine.java:396)
at org.neo4j.bolt.v1.runtime.BoltStateMachine.run(BoltStateMachine.java:196)
at org.neo4j.bolt.v1.messaging.BoltMessageRouter.lambda$onRun$3(BoltMessageRouter.java:80)
at org.neo4j.bolt.v1.runtime.concurrent.RunnableBoltWorker.execute(RunnableBoltWorker.java:135)
at org.neo4j.bolt.v1.runtime.concurrent.RunnableBoltWorker.run(RunnableBoltWorker.java:89)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.neo4j.kernel.api.exceptions.TransactionFailureException: Database has encountered some problem, please perform necessary action (tx recovery/restart)
at sun.reflect.GeneratedConstructorAccessor46.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.neo4j.kernel.internal.DatabaseHealth.assertHealthy(DatabaseHealth.java:62)
at org.neo4j.kernel.impl.api.Kernel.newTransaction(Kernel.java:99)
at org.neo4j.kernel.impl.factory.ClassicCoreSPI.beginTransaction(ClassicCoreSPI.java:173)
... 11 more
Caused by: java.lang.IllegalStateException: Concurrent drop() while updates have not completed
at org.neo4j.kernel.impl.api.index.ContractCheckingIndexProxy.ensureNoOpenCalls(ContractCheckingIndexProxy.java:187)
at org.neo4j.kernel.impl.api.index.ContractCheckingIndexProxy.drop(ContractCheckingIndexProxy.java:144)
at org.neo4j.kernel.impl.api.index.IndexingService.dropIndex(IndexingService.java:611)
at org.neo4j.kernel.impl.transaction.command.IndexBatchTransactionApplier$SingleTransactionApplier.visitSchemaRuleCommand(IndexBatchTransactionApplier.java:248)
at org.neo4j.kernel.impl.transaction.command.Command$SchemaRuleCommand.handle(Command.java:645)
at org.neo4j.kernel.impl.api.TransactionApplierFacade.visit(TransactionApplierFacade.java:61)
at org.neo4j.kernel.impl.api.TransactionApplierFacade.visit(TransactionApplierFacade.java:35)
at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69)
at org.neo4j.kernel.impl.api.TransactionToApply.accept(TransactionToApply.java:111)
at org.neo4j.kernel.impl.storageengine.impl.recordstorage.RecordStorageEngine.apply(RecordStorageEngine.java:349)
at org.neo4j.kernel.impl.api.TransactionRepresentationCommitProcess.applyToStore(TransactionRepresentationCommitProcess.java:78)
at org.neo4j.kernel.impl.api.TransactionRepresentationCommitProcess.commit(TransactionRepresentationCommitProcess.java:51)
at org.neo4j.kernel.impl.api.KernelTransactionImplementation.commit(KernelTransactionImplementation.java:608)
at org.neo4j.kernel.impl.api.KernelTransactionImplementation.closeTransaction(KernelTransactionImplementation.java:484)
at org.neo4j.kernel.api.KernelTransaction.close(KernelTransaction.java:135)
at org.neo4j.bolt.v1.runtime.TransactionStateMachine$State.closeTransaction(TransactionStateMachine.java:325)
at org.neo4j.bolt.v1.runtime.TransactionStateMachine$State$2.run(TransactionStateMachine.java:229)
... 7 more
Ideally it will be fixed soon. And I'm not sure how to get out of it w/o restarting server.

org.apache.flume.ChannelException: Unable to put batch on required channel: FileChannel ch_file Caused by: java.util.ConcurrentModificationException

there is an error in my flume system, why and how to fix it ??????
org.apache.flume.ChannelException: Unable to put batch on required channel: FileChannel ch_file Caused by: java.util.ConcurrentModificationException!
2016-02-24 17:42:54,715 ERROR org.apache.flume.source.AvroSource: Avro source src_avro_c1: Unable to process event batch. Exception follows.
org.apache.flume.ChannelException: Unable to put batch on required channel: FileChannel ch_file { dataDirs: [/data01/flume/data] }
at org.apache.flume.channel.ChannelProcessor.processEventBatch(ChannelProcessor.java:200)
at org.apache.flume.source.AvroSource.appendBatch(AvroSource.java:386)
at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.apache.avro.ipc.specific.SpecificResponder.respond(SpecificResponder.java:91)
at org.apache.avro.ipc.Responder.respond(Responder.java:151)
at org.apache.avro.ipc.NettyServer$NettyServerAvroHandler.messageReceived(NettyServer.java:188)
at org.jboss.netty.channel.SimpleChannelUpstreamHandler.handleUpstream(SimpleChannelUpstreamHandler.java:70)
at org.apache.avro.ipc.NettyServer$NettyServerAvroHandler.handleUpstream(NettyServer.java:173)
at org.jboss.netty.channel.DefaultChannelPipeline.sendUpstream(DefaultChannelPipeline.java:560)
at org.jboss.netty.channel.DefaultChannelPipeline$DefaultChannelHandlerContext.sendUpstream(DefaultChannelPipeline.java:787)
at org.jboss.netty.channel.Channels.fireMessageReceived(Channels.java:296)
at org.jboss.netty.handler.codec.frame.FrameDecoder.unfoldAndFireMessageReceived(FrameDecoder.java:462)
at org.jboss.netty.handler.codec.frame.FrameDecoder.callDecode(FrameDecoder.java:443)
at org.jboss.netty.handler.codec.frame.FrameDecoder.messageReceived(FrameDecoder.java:303)
at org.jboss.netty.channel.SimpleChannelUpstreamHandler.handleUpstream(SimpleChannelUpstreamHandler.java:70)
at org.jboss.netty.channel.DefaultChannelPipeline.sendUpstream(DefaultChannelPipeline.java:560)
at org.jboss.netty.channel.DefaultChannelPipeline.sendUpstream(DefaultChannelPipeline.java:555)
at org.jboss.netty.channel.Channels.fireMessageReceived(Channels.java:268)
at org.jboss.netty.channel.Channels.fireMessageReceived(Channels.java:255)
at org.jboss.netty.channel.socket.nio.NioWorker.read(NioWorker.java:88)
at org.jboss.netty.channel.socket.nio.AbstractNioWorker.process(AbstractNioWorker.java:107)
at org.jboss.netty.channel.socket.nio.AbstractNioSelector.run(AbstractNioSelector.java:312)
at org.jboss.netty.channel.socket.nio.AbstractNioWorker.run(AbstractNioWorker.java:88)
at org.jboss.netty.channel.socket.nio.NioWorker.run(NioWorker.java:178)
at org.jboss.netty.util.ThreadRenamingRunnable.run(ThreadRenamingRunnable.java:108)
at org.jboss.netty.util.internal.DeadLockProofWorker$1.run(DeadLockProofWorker.java:42)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextNode(HashMap.java:1429)
at java.util.HashMap$KeyIterator.next(HashMap.java:1453)
at org.apache.flume.channel.file.Put.writeProtos(Put.java:82)
at org.apache.flume.channel.file.TransactionEventRecord.toByteBuffer(TransactionEventRecord.java:174)
at org.apache.flume.channel.file.Log.put(Log.java:622)
at org.apache.flume.channel.file.FileChannel$FileBackedTransaction.doPut(FileChannel.java:469)
at org.apache.flume.channel.BasicTransactionSemantics.put(BasicTransactionSemantics.java:93)
at org.apache.flume.channel.BasicChannelSemantics.put(BasicChannelSemantics.java:80)
at org.apache.flume.channel.ChannelProcessor.processEventBatch(ChannelProcessor.java:189)
... 30 more
yes, i fixed the problem, first i set 3 replcating channels like below, but unfortunately, i changed the kafka sink event header that from channel:ch_mem_kafka, it caused this problem, but i also cann't understant, why cause the event from channel:ch_file to be modified?
# The channel can be defined as follows.
collector1.sources.src_avro_c1.channels = ch_file ch_mem ch_mem_kafka
collector1.sources.src_avro_c1.selector.type = replicating

Unable to import neo4j database with blueprints

i'm trying to open a neo4j database by using blueprints implementation, but i got the following exceptions:
Neo4jGraph graph = new Neo4jGraph("/Users/pipe/Dev/neo4j-community-2.1.0-M01/data/graph.db");
this cause
Caused by: javax.faces.el.EvaluationException: java.lang.RuntimeException: Bad value '-192M' for setting 'neostore.propertystore.db.strings.mapped_memory': value does not match expression:\d+[kmgKMG]?
at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:102)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:101)
... 32 more
Caused by: java.lang.RuntimeException: Bad value '-192M' for setting 'neostore.propertystore.db.strings.mapped_memory': value does not match expression:\d+[kmgKMG]?
at com.tinkerpop.blueprints.impls.neo4j.Neo4jGraph.<init>(Neo4jGraph.java:165)
at com.tinkerpop.blueprints.impls.neo4j.Neo4jGraph.<init>(Neo4jGraph.java:135)
at org.pipe.java.web.netnografica.persistenza.graphdb.DAONodo.toGraphml(DAONodo.java:204)
at org.pipe.java.web.netnografica.controllo.ControlloGenerale.esportaGraphml(ControlloGenerale.java:133)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.el.parser.AstValue.invoke(AstValue.java:278)
at org.apache.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:274)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:105)
at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:88)
... 33 more
Caused by: java.lang.IllegalArgumentException: Bad value '-192M' for setting 'neostore.propertystore.db.strings.mapped_memory': value does not match expression:\d+[kmgKMG]?
at org.neo4j.helpers.Settings$DefaultSetting.apply(Settings.java:782)
at org.neo4j.helpers.Settings$DefaultSetting.apply(Settings.java:702)
at org.neo4j.graphdb.factory.GraphDatabaseSetting$SettingWrapper.apply(GraphDatabaseSetting.java:215)
at org.neo4j.graphdb.factory.GraphDatabaseSetting$SettingWrapper.apply(GraphDatabaseSetting.java:189)
at org.neo4j.kernel.configuration.ConfigurationValidator.validate(ConfigurationValidator.java:50)
at org.neo4j.kernel.configuration.Config.applyChanges(Config.java:121)
at org.neo4j.kernel.InternalAbstractGraphDatabase.create(InternalAbstractGraphDatabase.java:339)
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:253)
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:106)
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:81)
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:63)
at com.tinkerpop.blueprints.impls.neo4j.Neo4jGraph.<init>(Neo4jGraph.java:155)
... 44 more
there seems to be a need to provide a properties file. Is correct?
*Edited to answer to Michael Hunger:
Well .. I changed the version of blueprints, now is 2.5.0-SNAPSHOT, but nothing changed. So i provided the configs using the map ask asked by the constructor
Map<String, String> configurazione = new HashMap<String, String>();
configurazione.put("neostore.propertystore.db.strings.mapped_memory", "250M");
configurazione.put("neostore.propertystore.db.arrays.mapped_memory", "100M");
configurazione.put("neostore.relationshipstore.db.mapped_memory", "3845M");
configurazione.put("neostore.nodestore.db.mapped_memory", "350M");
configurazione.put("neostore.propertystore.db.mapped_memory", "350M");
configurazione.put("neostore.nodestore.db.mapped_memory", "769M");
Neo4j2Graph grafo = new Neo4j2Graph("/Users/pipe/Dev/neo4j-community-2.1.0-M01/data/graph.db", configurazione);
Now the exception is changed, and i really don't know what is wrong.. I linked in paste bin to report the complete stack.
http://pastebin.com/XpipSysp
at last a NoSuchMethodError is thrown. What am I missing?
Thanks a lot.
Which blueprints version are you using?
Blueprints 2.5-SNAPSHOT is compatible with Neo4j 2.0.0.
Please note there is a separate module for Neo4j 2.0 called blueprints-neo4j2
And the classes are called Neo4j2Graph Neo4j2Vertex etc.
You should also be able to provide config to the Neo4j2Graph.

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