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neo4j-contrib / spatial

Neo4j Spatial is a library of utilities for Neo4j that faciliates the enabling of spatial operations on data. In particular you can add spatial indexes to already located data, and perform spatial operations on the data like searching for data within specified regions or within a specified distance of a point of interest. In addition classes are provided to expose the data to geotools and thereby to geotools enabled applications like geoserver and uDig.
http://neo4j-contrib.github.io/spatial
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Can't create neo4j data store: NotInTransactionException #149

Open noisyboiler opened 10 years ago

noisyboiler commented 10 years ago

I've seen some chatter about this but no solution. Mac OS, Neo 2.1.2, Geoserver 2.5, Neo4j Spatial master. But I've tried many combinations of these tools.

27883 [btpool0-4] INFO org.apache.wicket.resource.PropertiesFactory - Loading properties files from org.geoserver.web.GeoServerResourceStreamLocator$1@6faf7242
35448 [btpool0-4] INFO org.apache.wicket.resource.PropertiesFactory - Loading properties files from jar:file:/usr/local/Cellar/geoserver/2.5/libexec/webapps/geoserver/WEB-INF/lib/wicket-1.4.12.jar!/org/apache/wicket/Application.properties
40503 [btpool0-4] INFO org.apache.wicket.RequestListenerInterface - registered listener interface [RequestListenerInterface name=INewBrowserWindowListener, method=public abstract void org.apache.wicket.markup.html.INewBrowserWindowListener.onNewBrowserWindow()]
65637 [btpool0-3] WARN  org.geoserver.web.data.store  - Error obtaining new data store
java.io.IOException
    at org.geoserver.catalog.ResourcePool.getDataStore(ResourcePool.java:586)
    at org.geoserver.catalog.impl.DataStoreInfoImpl.getDataStore(DataStoreInfoImpl.java:37)
    at org.geoserver.web.data.store.DataAccessNewPage.onSaveDataStore(DataAccessNewPage.java:91)
    at org.geoserver.web.data.store.AbstractDataAccessPage$1.onSubmit(AbstractDataAccessPage.java:162)
    at org.apache.wicket.ajax.markup.html.form.AjaxSubmitLink$1.onSubmit(AjaxSubmitLink.java:68)
    at org.apache.wicket.ajax.form.AjaxFormSubmitBehavior.onEvent(AjaxFormSubmitBehavior.java:143)
    at org.apache.wicket.ajax.AjaxEventBehavior.respond(AjaxEventBehavior.java:177)
    at org.apache.wicket.ajax.AbstractDefaultAjaxBehavior.onRequest(AbstractDefaultAjaxBehavior.java:300)
    at org.apache.wicket.request.target.component.listener.BehaviorRequestTarget.processEvents(BehaviorRequestTarget.java:119)
    at org.apache.wicket.request.AbstractRequestCycleProcessor.processEvents(AbstractRequestCycleProcessor.java:92)
    at org.apache.wicket.RequestCycle.processEventsAndRespond(RequestCycle.java:1250)
    at org.apache.wicket.RequestCycle.step(RequestCycle.java:1329)
    at org.apache.wicket.RequestCycle.steps(RequestCycle.java:1436)
    at org.apache.wicket.RequestCycle.request(RequestCycle.java:545)
    at org.apache.wicket.protocol.http.WicketFilter.doGet(WicketFilter.java:484)
    at org.apache.wicket.protocol.http.WicketServlet.doPost(WicketServlet.java:160)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
    at org.springframework.web.servlet.mvc.ServletWrappingController.handleRequestInternal(ServletWrappingController.java:159)
    at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
    at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:923)
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:789)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
    at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:487)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1093)
    at org.geoserver.filters.ThreadLocalsCleanupFilter.doFilter(ThreadLocalsCleanupFilter.java:27)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(SpringDelegatingFilter.java:74)
    at org.geoserver.wms.animate.AnimatorFilter.doFilter(AnimatorFilter.java:70)
    at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(SpringDelegatingFilter.java:70)
    at org.geoserver.filters.SpringDelegatingFilter.doFilter(SpringDelegatingFilter.java:45)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.geoserver.platform.AdvancedDispatchFilter.doFilter(AdvancedDispatchFilter.java:49)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:311)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:68)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:116)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:83)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:72)
    at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:323)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:68)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:72)
    at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:323)
    at org.geoserver.security.filter.GeoServerAnonymousAuthenticationFilter.doFilter(GeoServerAnonymousAuthenticationFilter.java:53)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:323)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:68)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:182)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:72)
    at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91)
    at org.geoserver.security.filter.GeoServerUserNamePasswordAuthenticationFilter.doFilter(GeoServerUserNamePasswordAuthenticationFilter.java:115)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:323)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:68)
    at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:146)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:72)
    at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:323)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:68)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    at org.geoserver.security.filter.GeoServerSecurityContextPersistenceFilter$1.doFilter(GeoServerSecurityContextPersistenceFilter.java:52)
    at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:72)
    at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:323)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:173)
    at org.geoserver.security.GeoServerSecurityFilterChainProxy.doFilter(GeoServerSecurityFilterChainProxy.java:134)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:259)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.geoserver.filters.LoggingFilter.doFilter(LoggingFilter.java:75)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.geoserver.filters.GZIPFilter.doFilter(GZIPFilter.java:42)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.geoserver.filters.SessionDebugFilter.doFilter(SessionDebugFilter.java:47)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.geoserver.filters.FlushSafeFilter.doFilter(FlushSafeFilter.java:43)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.vfny.geoserver.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:109)
    at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1084)
    at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:360)
    at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
    at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:181)
    at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:726)
    at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:405)
    at org.mortbay.jetty.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:206)
    at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
    at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
    at org.mortbay.jetty.Server.handle(Server.java:324)
    at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:505)
    at org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java:842)
    at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:648)
    at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:211)
    at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:380)
    at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:395)
    at org.mortbay.thread.BoundedThreadPool$PoolThread.run(BoundedThreadPool.java:450)
Caused by: org.neo4j.graphdb.NotInTransactionException
    at org.neo4j.kernel.impl.persistence.PersistenceManager.getCurrentTransaction(PersistenceManager.java:297)
    at org.neo4j.kernel.impl.persistence.PersistenceManager.getResource(PersistenceManager.java:249)
    at org.neo4j.kernel.impl.persistence.PersistenceManager.currentKernelTransactionForReading(PersistenceManager.java:235)
    at org.neo4j.kernel.impl.core.ThreadToStatementContextBridge.instance(ThreadToStatementContextBridge.java:55)
    at org.neo4j.kernel.impl.core.NodeProxy.getRelationships(NodeProxy.java:167)
    at org.neo4j.kernel.impl.core.NodeProxy.getRelationships(NodeProxy.java:161)
    at org.neo4j.kernel.impl.core.NodeProxy.getRelationships(NodeProxy.java:76)
    at org.neo4j.gis.spatial.SpatialDatabaseService.getLayerNames(SpatialDatabaseService.java:94)
    at org.geotools.data.neo4j.Neo4jSpatialDataStore.getTypeNames(Neo4jSpatialDataStore.java:102)
    at org.vfny.geoserver.util.DataStoreUtils.getDataAccess(DataStoreUtils.java:114)
    at org.geoserver.catalog.ResourcePool.getDataStore(ResourcePool.java:546)
    ... 99 more

There is a failing test that may indicate the case of this error.

<?xml version="1.0" encoding="UTF-8" ?>
<testsuite failures="0" time="0.312" errors="2" skipped="0" tests="2" name="org.neo4j.gis.spatial.SpatialPluginFunctionalTest">
  <properties>
    <property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/>
    <property name="sun.boot.library.path" value="/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib"/>
    <property name="java.vm.version" value="24.0-b56"/>
    <property name="user.country.format" value="GB"/>
    <property name="gopherProxySet" value="false"/>
    <property name="java.vm.vendor" value="Oracle Corporation"/>
    <property name="java.vendor.url" value="http://java.oracle.com/"/>
    <property name="path.separator" value=":"/>
    <property name="guice.disable.misplaced.annotation.check" value="true"/>
    <property name="java.vm.name" value="Java HotSpot(TM) 64-Bit Server VM"/>
    <property name="file.encoding.pkg" value="sun.io"/>
    <property name="user.country" value="US"/>
    <property name="sun.java.launcher" value="SUN_STANDARD"/>
    <property name="sun.os.patch.level" value="unknown"/>
    <property name="java.vm.specification.name" value="Java Virtual Machine Specification"/>
    <property name="user.dir" value="/Users/simon/src/spatial"/>
    <property name="java.runtime.version" value="1.7.0_40-b43"/>
    <property name="java.awt.graphicsenv" value="sun.awt.CGraphicsEnvironment"/>
    <property name="java.endorsed.dirs" value="/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/endorsed"/>
    <property name="os.arch" value="x86_64"/>
    <property name="java.io.tmpdir" value="/var/folders/b3/tp9ljrf50ts982cg99qd19dm0000gn/T/"/>
    <property name="line.separator" value="
"/>
    <property name="java.vm.specification.vendor" value="Oracle Corporation"/>
    <property name="os.name" value="Mac OS X"/>
    <property name="classworlds.conf" value="/usr/local/Cellar/maven/3.2.1/libexec/bin/m2.conf"/>
    <property name="sun.jnu.encoding" value="UTF-8"/>
    <property name="java.library.path" value="/Users/simon/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:."/>
    <property name="java.specification.name" value="Java Platform API Specification"/>
    <property name="java.class.version" value="51.0"/>
    <property name="sun.management.compiler" value="HotSpot 64-Bit Tiered Compilers"/>
    <property name="os.version" value="10.9.2"/>
    <property name="http.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
    <property name="user.home" value="/Users/simon"/>
    <property name="user.timezone" value="Europe/London"/>
    <property name="java.awt.printerjob" value="sun.lwawt.macosx.CPrinterJob"/>
    <property name="java.specification.version" value="1.7"/>
    <property name="file.encoding" value="UTF-8"/>
    <property name="user.name" value="simon"/>
    <property name="java.class.path" value="/usr/local/Cellar/maven/3.2.1/libexec/boot/plexus-classworlds-2.5.1.jar"/>
    <property name="org.slf4j.simpleLogger.defaultLogLevel" value="debug"/>
    <property name="java.vm.specification.version" value="1.7"/>
    <property name="sun.arch.data.model" value="64"/>
    <property name="java.home" value="/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre"/>
    <property name="sun.java.command" value="org.codehaus.plexus.classworlds.launcher.Launcher test -e -X"/>
    <property name="java.specification.vendor" value="Oracle Corporation"/>
    <property name="user.language" value="en"/>
    <property name="awt.toolkit" value="sun.lwawt.macosx.LWCToolkit"/>
    <property name="java.vm.info" value="mixed mode"/>
    <property name="java.version" value="1.7.0_40"/>
    <property name="java.ext.dirs" value="/Users/simon/Library/Java/Extensions:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/ext:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java"/>
    <property name="sun.boot.class.path" value="/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/resources.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/rt.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/sunrsasign.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/jsse.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/jce.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/charsets.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/jfr.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/JObjC.jar:/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/classes"/>
    <property name="java.vendor" value="Oracle Corporation"/>
    <property name="maven.home" value="/usr/local/Cellar/maven/3.2.1/libexec"/>
    <property name="file.separator" value="/"/>
    <property name="java.vendor.url.bug" value="http://bugreport.sun.com/bugreport/"/>
    <property name="sun.cpu.endian" value="little"/>
    <property name="sun.io.unicode.encoding" value="UnicodeBig"/>
    <property name="socksNonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
    <property name="ftp.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
    <property name="sun.cpu.isalist" value=""/>
  </properties>
  <testcase time="0.156" classname="org.neo4j.gis.spatial.SpatialPluginFunctionalTest" name="org.neo4j.gis.spatial.SpatialPluginFunctionalTest">
    <error message="javax/servlet/Filter" type="java.lang.NoClassDefFoundError">java.lang.NoClassDefFoundError: javax/servlet/Filter
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    at org.neo4j.server.helpers.CommunityServerBuilder.build(CommunityServerBuilder.java:134)
    at org.neo4j.server.helpers.CommunityServerBuilder.build(CommunityServerBuilder.java:129)
    at org.neo4j.gis.spatial.SpatialPluginFunctionalTest.allocateServer(SpatialPluginFunctionalTest.java:71)
</error>
  </testcase>
  <testcase time="0.156" classname="org.neo4j.gis.spatial.SpatialPluginFunctionalTest" name="org.neo4j.gis.spatial.SpatialPluginFunctionalTest">
    <error type="java.lang.NullPointerException:">java.lang.NullPointerException: null
    at org.neo4j.gis.spatial.SpatialPluginFunctionalTest.releaseAltServer(SpatialPluginFunctionalTest.java:78)
</error>
  </testcase>
</testsuite>
jexp commented 10 years ago

Probably a overseen issue due to missing tests in this area. Since Neo4j 2.0 all graph operations require a transaction also for reading. So the GeoServer integration might have this issue in many more places. Not sure how to test the implementation of the GeoServer APIs (know too little about them).

Would you mind taking a look?

In most cases just putting a transactional block around the call is good enough. Like this:

try (Transaction tx = graphDb.beginTx()) {
    access code
    tx.success(); // mostly needed for write operations but also doesn't hurt for read ops
}

The transaction is automatically closed when the try-block is closed.

noisyboiler commented 10 years ago

That has worked a charm, thanks. Happy to raise a PR with any such fixes I need to add?

noisyboiler commented 10 years ago

Hi Michael

I did manage to mostly achieve what i wanted. I had to wrap a LOT of calls with the try pattern. Surely there is a DRYer way to achieve this? Maybe at a lower level nearer the connection?

Have you got any plans to update the transaction handling? Every time I try something new on GeoServer with Neo4j something goes bang, so there is little point in submitting my PR. It's also too much repeated code!!

Happy to help if I can.

Simon

On 17 July 2014 18:19, Michael Hunger notifications@github.com wrote:

Probably a overseen issue due to missing tests in this area. Since Neo4j 2.0 all graph operations require a transaction also for reading. So the GeoServer integration might have this issue in many more places. Not sure how to test the implementation of the GeoServer APIs (know too little about them).

Would you mind taking a look?

In most cases just putting a transactional block around the call is good enough. Like this:

try (Transaction tx = graphDb.beginTx()) { access code tx.success(); // mostly needed for write operations but also doesn't hurt for read ops }

The transaction is automatically closed when the try-block is closed.

— Reply to this email directly or view it on GitHub https://github.com/neo4j-contrib/spatial/issues/149#issuecomment-49336769 .

Simon Harrison Application Developer onefinestay

e. simon.harrison@onefinestay.com

5 St Johns Lane London EC1M 4BH

http://onefinestay.com

craigtaverner commented 10 years ago

Perhaps the PR is a good opportunity for us to take a look, and get started with fixing this. Either by accepting the request and taking it from there, or by investigating a better way. Not sure when Michael, or I, or someone else will have time to look, but hopefully soon.