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graphdb-free's Introduction

👋 Hi, I am Kevin

I am a software developer at deepsearch, and I am passionate about knowledge graphs.

🔭 Hobby Projects

KG-based recommendations

Together with Eleni Ilkou, I am working on a KG-based recommendation engine for an e-learning platform, on which students collaborate in groups for a project. Using named entity recognition on the search queries of students and their group members, we aim to infer their current interests and provide good query suggestions. Related repositories are:

Repositories will be published later after the paper gets accepted.

Exploratory Search System (inactive)

I was working on an exploratory search system which can be applied to any RDF-based knowledge graph that is aligned to a rich ontology. This system provides an adaptive user interface with different search paradigms such as full-text search, tree views and faceted navigation. You can see my workshop paper for details: Enabling Exploratory Search on Manufacturing Knowledge Graphs | (Slides).

  • khaller93/es-middleware - Middleware offering exploratory search services for a general knowledge graph over a HTTP+JSON API.
  • khaller93/es-web-app - Single-page web application providing an user interface for exploring knowledge graphs in a human-friendly manner.

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graphdb-free's Issues

Java Compiler Not Found Exception on Rule Insert

When trying to submit any falid rule via GraphDB-Sparql-Editor, e.g.

prefix sys: <http://www.ontotext.com/owlim/system#>
INSERT DATA {
    <_:custom> sys:addRuleset
        '''Prefices {
				rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
			}
           Axioms {}
           Rules
           {
           	Id: firstRule
           		e	a	c
            	-------------------------------
				e <rdf:type> c
           }'''
}

GraphDB throws a Compiler not found exception.

The below stack trace from the graphdb error logs suggests that this Exception is thrown when committing a rule via rdf4j SAIL.

This does not happen in on the GraphDB-Free version 10.0.0 when run without docker, but only using this docker image (tested with image versions 9.11.0 and 10.0.0).
Any idea why this happens?

[ERROR] 2022-08-18 13:32:16,447 [repositories/repo | c.o.t.SailConnectionImpl] Transaction failed. Commit will be rolled back.
java.lang.RuntimeException: java.lang.RuntimeException: Java compiler not found!
        at com.ontotext.trree.SwitchableInferencer.addRuleset(SwitchableInferencer.java:216)
        at com.ontotext.trree.SwitchableInferencerTransactionState.addRuleset(SwitchableInferencerTransactionState.java:327)
        at com.ontotext.trree.SwitchableInferencerTransactionState.manipulateRuleset(SwitchableInferencerTransactionState.java:98)
        at com.ontotext.trree.SwitchableInferencerTransactionState.onCommitStart(SwitchableInferencerTransactionState.java:81)
        at com.ontotext.trree.SailConnectionImpl.doActualCommit(SailConnectionImpl.java:817)
        at com.ontotext.trree.SailConnectionImpl.flushInternal(SailConnectionImpl.java:1006)
        at com.ontotext.trree.SailConnectionImpl.flush(SailConnectionImpl.java:2880)
        at org.eclipse.rdf4j.repository.sail.SailRepositoryConnection.commit(SailRepositoryConnection.java:213)
        at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection.commit(MonitorRepositoryConnection.java:302)
        at org.eclipse.rdf4j.repository.base.AbstractRepositoryConnection.conditionalCommit(AbstractRepositoryConnection.java:326)
        at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection.access$100(MonitorRepositoryConnection.java:76)
        at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection$1.execute(MonitorRepositoryConnection.java:466)
        at org.eclipse.rdf4j.http.server.repository.statements.StatementsController.getSparqlUpdateResult(StatementsController.java:257)
        at org.eclipse.rdf4j.http.server.repository.statements.StatementsController.handleRequestInternal(StatementsController.java:115)
        at com.ontotext.graphdb.sesame.StatementsController.handleRequestInternal(StatementsController.java:67)
        at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:177)
        at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:51)
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1067)
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:963)
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)
        at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:681)
        at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)

...skipping 1 line
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.github.ziplet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:263)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.ontotext.forest.security.AdminDelegatingFilterProxy.doFilter(AdminDelegatingFilterProxy.java:84)
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:354)
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:267)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.ontotext.forest.clusterproxy.ClusterFilterBean.doFilter(ClusterFilterBean.java:70)
        at com.ontotext.forest.clusterproxy.ClusterLoadBalancerFilter.doFilterInternal(ClusterLoadBalancerFilter.java:28)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:360)
        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:399)

...skipping 1 line
        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:890)
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1743)
        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
        at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
        at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.RuntimeException: Java compiler not found!
        at com.ontotext.trree.rules.RuntimeInferencerCompilerBase.compileSource(RuntimeInferencerCompilerBase.java:56)
        at com.ontotext.trree.SwitchableInferencer.addRuleset(SwitchableInferencer.java:214)
        ... 62 common frames omitted
[ERROR] 2022-08-18 13:32:16,552 [repositories/repo | c.o.f.s.GraphDBProtocolExceptionResolver] Error while handling request (500)
org.eclipse.rdf4j.http.server.ServerHTTPException: org.eclipse.rdf4j.repository.RepositoryException: org.eclipse.rdf4j.sail.SailException: java.lang.RuntimeException: java.lang.RuntimeException: Java compiler not found!
        at org.eclipse.rdf4j.http.server.repository.statements.StatementsController.getSparqlUpdateResult(StatementsController.java:269)
        at org.eclipse.rdf4j.http.server.repository.statements.StatementsController.handleRequestInternal(StatementsController.java:115)
        at com.ontotext.graphdb.sesame.StatementsController.handleRequestInternal(StatementsController.java:67)
        at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:177)
        at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:51)
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1067)
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:963)
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)
        at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:681)
        at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.ontotext.forest.core.request.RequestFilter.doFilterInternal(RequestFilter.java:47)

...skipping 1 line
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.github.ziplet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:263)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.ontotext.forest.security.AdminDelegatingFilterProxy.doFilter(AdminDelegatingFilterProxy.java:84)
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:354)
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:267)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at com.ontotext.forest.clusterproxy.ClusterFilterBean.doFilter(ClusterFilterBean.java:70)
        at com.ontotext.forest.clusterproxy.ClusterLoadBalancerFilter.doFilterInternal(ClusterLoadBalancerFilter.java:28)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:117)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:360)
        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:399)
        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)

...skipping 1 line
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1743)
        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
        at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
        at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.eclipse.rdf4j.repository.RepositoryException: org.eclipse.rdf4j.sail.SailException: java.lang.RuntimeException: java.lang.RuntimeException: Java compiler not found!
        at org.eclipse.rdf4j.repository.sail.SailRepositoryConnection.commit(SailRepositoryConnection.java:217)
        at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection.commit(MonitorRepositoryConnection.java:302)
        at org.eclipse.rdf4j.repository.base.AbstractRepositoryConnection.conditionalCommit(AbstractRepositoryConnection.java:326)
        at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection.access$100(MonitorRepositoryConnection.java:76)
        at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection$1.execute(MonitorRepositoryConnection.java:466)
        at org.eclipse.rdf4j.http.server.repository.statements.StatementsController.getSparqlUpdateResult(StatementsController.java:257)
        ... 50 common frames omitted
Caused by: org.eclipse.rdf4j.sail.SailException: java.lang.RuntimeException: java.lang.RuntimeException: Java compiler not found!
        at com.ontotext.trree.SailConnectionImpl.handleTransactionFailure(SailConnectionImpl.java:1479)
        at com.ontotext.trree.SailConnectionImpl$CommitContext.handleFailure(SailConnectionImpl.java:692)
        at com.ontotext.trree.SailConnectionImpl.flush(SailConnectionImpl.java:2883)
        at org.eclipse.rdf4j.repository.sail.SailRepositoryConnection.commit(SailRepositoryConnection.java:213)
        ... 55 common frames omitted
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: Java compiler not found!
        at com.ontotext.trree.SwitchableInferencer.addRuleset(SwitchableInferencer.java:216)
        at com.ontotext.trree.SwitchableInferencerTransactionState.addRuleset(SwitchableInferencerTransactionState.java:327)
        at com.ontotext.trree.SwitchableInferencerTransactionState.manipulateRuleset(SwitchableInferencerTransactionState.java:98)
        at com.ontotext.trree.SwitchableInferencerTransactionState.onCommitStart(SwitchableInferencerTransactionState.java:81)
        at com.ontotext.trree.SailConnectionImpl.doActualCommit(SailConnectionImpl.java:817)
        at com.ontotext.trree.SailConnectionImpl.flushInternal(SailConnectionImpl.java:1006)
        at com.ontotext.trree.SailConnectionImpl.flush(SailConnectionImpl.java:2880)

...skipping 1 line
Caused by: java.lang.RuntimeException: Java compiler not found!
        at com.ontotext.trree.rules.RuntimeInferencerCompilerBase.compileSource(RuntimeInferencerCompilerBase.java:56)
        at com.ontotext.trree.SwitchableInferencer.addRuleset(SwitchableInferencer.java:214)
        ... 62 common frames omitted

Java Compiler Not Found Exception with 9.11.2

Dear Author,

First of all, thank you for the nice work for providing all these docker files! :)

I am having issues with adding any data, even from the GraphDB UI, to the container 9.11.2. The issue again is the lack of Java Compiler, addressed somehow with the addition of a full JDK, but somehow this does not work with 9.11.2. It works fine with 9.10.3 though. Could you please help me? Probably it is fine on github, just not there on docker hub, or this is the assumption we have now.

Thank you!
Thomas

Rootless execution with non-existing toLoad folder fails

When executing the container with a different user (other than root), then the execution fails with a permission error.

db_1  | [REPO INIT] Warning: Couldn't find data to load for '/repository.init/pokemon'. 'toLoad' is missing.
db_1  | [REPO INIT] Warning: Couldn't create temporary folder '/tmp/graphdb/toLoad': mkdir /tmp/graphdb/toLoad: permission denied
db_1  | File: '/tmp/graphdb/toLoad' does not exist.
db_1  | Usage: importrdf load [-fhpsv] [-m <serial|parallel>] (-c <file> | -i
db_1  |                       <repository-id>) FILE...

Reproduce by:

  1. Creating a repository folder with a config file, but have no data to load. Hence, the toLoad directory is missing.
  2. Run the container with this setting as a non-root user. GDB_USER is not set too root.
  3. Get a permission error.

toLoad folder isn't optional anymore in v1.4.0

If a repository shall be initialized without having data to preload in toLoad, then an error will be thrown.

db_1  | [REPO INIT] ----- CHECK /repository.init/pokemon. -----
db_1  | [REPO INIT] Warning: Could not find data to load for '/repository.init/pokemon'. 'toLoad' is missing.
db_1  | WARNING: Unknown module: jdk.management.agent specified to --add-exports
db_1  | Missing required parameter: 'FILE'
db_1  | Usage: importrdf load [-fhpsv] [-m <serial|parallel>] (-c <file> | -i
db_1  |                       <repository-id>) FILE...
db_1  | Loads data using an algorithm very similar to the online data loading.
db_1  |       FILE...                Files to be loaded.
db_1  |   -c, --config-file <file>   Repository defining .ttl file.
db_1  |   -f, --force                Whether to overwrite the existing repository.
db_1  |   -h, --help                 Display this message and exit!
db_1  |   -i, --id <repository-id>   ID of an existing repository.
db_1  |   -m, --mode <serial|parallel>
db_1  |                              Singlethreaded (serial) or multithreaded
db_1  |                                (parallel) mode for parse/load/infer.
db_1  |   -p, --partial-load         Whether to allow partial load of file that
db_1  |                                contains corrupt line.
db_1  |   -s, --stop-on-error        Whether to stop process if the dataset contains a
db_1  |                                corrupt file.
db_1  |   -v, --verbose              Whether to print metrics during load.
db_1  | [REPO INIT] Error: Execution of preload command failed. exit status 2

The new tool importrdf for GraphDB version >=10 behaves slightly different then the old tool.

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