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graph-genome / SPARQL_PLAYGROUND

This repository should host preconstructed SPARQL endpoints serving graphs of the variation graph toolkit via virtuoso backend.
Apache License 2.0
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virtuoso yeast does not work #1

Open subwaystation opened 5 years ago

subwaystation commented 5 years ago

Apparently the data is malformed:

org.xml.sax.SAXParseException; lineNumber: 7; columnNumber: 2; schema_reference.4: Failed to read schema document 'WEB-INF/spring-beans-2.5.xsd', because 1) could not find the document; 2) the document could not be read; 3) the root element of the document is not <xsd:schema>.
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.warning(ErrorHandlerWrapper.java:99)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:392)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:306)
    at com.sun.org.apache.xerces.internal.impl.xs.traversers.XSDHandler.reportSchemaErr(XSDHandler.java:4158)
    at com.sun.org.apache.xerces.internal.impl.xs.traversers.XSDHandler.reportSchemaWarning(XSDHandler.java:4149)
    at com.sun.org.apache.xerces.internal.impl.xs.traversers.XSDHandler.getSchemaDocument1(XSDHandler.java:2491)
    at com.sun.org.apache.xerces.internal.impl.xs.traversers.XSDHandler.getSchemaDocument(XSDHandler.java:2193)
    at com.sun.org.apache.xerces.internal.impl.xs.traversers.XSDHandler.parseSchema(XSDHandler.java:578)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaLoader.loadSchema(XMLSchemaLoader.java:610)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.findSchemaGrammar(XMLSchemaValidator.java:2447)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1768)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:741)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl$NSContentDriver.scanRootElementHook(XMLNSDocumentScannerImpl.java:613)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3132)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:852)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
    at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
    at org.springframework.beans.factory.xml.DefaultDocumentLoader.loadDocument(DefaultDocumentLoader.java:75)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:388)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:334)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:302)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:174)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:209)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:180)
    at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:125)
    at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:94)
    at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:130)
    at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:537)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:451)
    at org.springframework.web.struts.ContextLoaderPlugIn.createWebApplicationContext(ContextLoaderPlugIn.java:355)
    at org.springframework.web.struts.ContextLoaderPlugIn.initWebApplicationContext(ContextLoaderPlugIn.java:296)
    at org.springframework.web.struts.ContextLoaderPlugIn.init(ContextLoaderPlugIn.java:226)
    at org.apache.struts.action.ActionServlet.initModulePlugIns(ActionServlet.java:871)
    at org.apache.struts.action.ActionServlet.init(ActionServlet.java:359)
    at javax.servlet.GenericServlet.init(GenericServlet.java:158)
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1142)
    at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1089)
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:983)
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4956)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5270)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:744)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:624)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1833)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.FileNotFoundException: /home/heumos/Downloads/WEB-INF/spring-beans-2.5.xsd (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at java.io.FileInputStream.<init>(FileInputStream.java:93)
    at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)
    at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)
    at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:623)
    at com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:148)
    at com.sun.org.apache.xerces.internal.impl.xs.opti.SchemaParsingConfig.parse(SchemaParsingConfig.java:583)
    at com.sun.org.apache.xerces.internal.impl.xs.opti.SchemaParsingConfig.parse(SchemaParsingConfig.java:686)
    at com.sun.org.apache.xerces.internal.impl.xs.opti.SchemaDOMParser.parse(SchemaDOMParser.java:530)
    at com.sun.org.apache.xerces.internal.impl.xs.traversers.XSDHandler.getSchemaDocument(XSDHandler.java:2181)
    ... 51 more
2019-09-25 13:46:20 +0200 org.springframework.web.struts.ContextLoaderPlugIn
  ERROR: Context initialization failed
org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 7 in XML document from ServletContext resource [/WEB-INF/spring-config-web.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 7; columnNumber: 2; cvc-elt.1: Cannot find the declaration of element 'beans'.
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:396)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:334)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:302)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:174)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:209)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:180)
    at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:125)
    at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:94)
    at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:130)
    at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:537)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:451)
    at org.springframework.web.struts.ContextLoaderPlugIn.createWebApplicationContext(ContextLoaderPlugIn.java:355)
    at org.springframework.web.struts.ContextLoaderPlugIn.initWebApplicationContext(ContextLoaderPlugIn.java:296)
    at org.springframework.web.struts.ContextLoaderPlugIn.init(ContextLoaderPlugIn.java:226)
    at org.apache.struts.action.ActionServlet.initModulePlugIns(ActionServlet.java:871)
    at org.apache.struts.action.ActionServlet.init(ActionServlet.java:359)
    at javax.servlet.GenericServlet.init(GenericServlet.java:158)
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1142)
    at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1089)
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:983)
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4956)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5270)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:744)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:624)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1833)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.xml.sax.SAXParseException; lineNumber: 7; columnNumber: 2; cvc-elt.1: Cannot find the declaration of element 'beans'.
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:134)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:396)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:284)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1901)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:741)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl$NSContentDriver.scanRootElementHook(XMLNSDocumentScannerImpl.java:613)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3132)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:852)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
    at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
    at org.springframework.beans.factory.xml.DefaultDocumentLoader.loadDocument(DefaultDocumentLoader.java:75)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:388)
    ... 32 more
2019-09-25 13:46:20 +0200 org.apache.struts.util.PropertyMessageResources
  WARN:   Resource org/apache/struts/action/ActionResources_en_US.properties Not Found.
2019-09-25 13:46:20 +0200 org.apache.struts.util.PropertyMessageResources
  WARN:   Resource org/apache/struts/action/ActionResources_en.properties Not Found.
Sep 25, 2019 11:46:20 AM org.apache.catalina.core.ApplicationContext log
SEVERE: Action: null
org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException: Line 7 in XML document from ServletContext resource [/WEB-INF/spring-config-web.xml] is invalid; nested exception is org.xml.sax.SAXParseException; lineNumber: 7; columnNumber: 2; cvc-elt.1: Cannot find the declaration of element 'beans'.
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:396)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:334)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:302)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:174)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:209)
    at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:180)
    at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:125)
    at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:94)
    at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:130)
    at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:537)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:451)
    at org.springframework.web.struts.ContextLoaderPlugIn.createWebApplicationContext(ContextLoaderPlugIn.java:355)
    at org.springframework.web.struts.ContextLoaderPlugIn.initWebApplicationContext(ContextLoaderPlugIn.java:296)
    at org.springframework.web.struts.ContextLoaderPlugIn.init(ContextLoaderPlugIn.java:226)
    at org.apache.struts.action.ActionServlet.initModulePlugIns(ActionServlet.java:871)
    at org.apache.struts.action.ActionServlet.init(ActionServlet.java:359)
    at javax.servlet.GenericServlet.init(GenericServlet.java:158)
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1142)
    at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1089)
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:983)
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4956)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5270)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:744)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:624)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1833)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.xml.sax.SAXParseException; lineNumber: 7; columnNumber: 2; cvc-elt.1: Cannot find the declaration of element 'beans'.
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:134)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:396)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:284)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1901)
    at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:741)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl$NSContentDriver.scanRootElementHook(XMLNSDocumentScannerImpl.java:613)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3132)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:852)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
    at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
    at org.springframework.beans.factory.xml.DefaultDocumentLoader.loadDocument(DefaultDocumentLoader.java:75)
    at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:388)
    ... 32 more

I will delete the data for now. Waiting for @JervenBollemann to give me some working SPARQL endpoint.

JervenBolleman commented 5 years ago

This is not a broken data. This is broken setup. I wonder what jvm you use.

subwaystation commented 5 years ago

I have the following JVM:

[heumos@wave ~]$ java -version
openjdk version "1.8.0_222"
OpenJDK Runtime Environment (build 1.8.0_222-b05)
OpenJDK 64-Bit Server VM (build 25.222-b05, mixed mode)

And your p53 SPARQL endpoint works.