Hi Tim, that's how I did it :) However, the release tar ball does not contain the modules sources, thats why I needed to check out from git directly and apply the fix. My question was regarding how to apply this fix in the release tarballs where the files do not exist.
I acknowledge this solved the issue and will add a comment to the PR. Is there a plan when the next version (5.11?) with this fix will be released? thx & greetings Stefan On 11/28/18 7:07 PM, Tim Donohue wrote: > Hi Stefan, > > Luckily, this PR is literally a one line change. > > So, you could simply open up the [dspace-src]/dspace-swordv2/pom.xml > file, search for the "abdera-client", and then manually change the > version from 1.1.1 to 1.1.3. > > After doing so, you should do a full rebuild of DSpace... from > [dspace-src], run "mvn -U clean package", and then redeploy (e.g. "ant > update"). > > Does that make sense? > > Tim > > On Wed, Nov 28, 2018 at 11:29 AM Stefan Kombrink > <stefan.kombr...@uni-ulm.de <mailto:stefan.kombr...@uni-ulm.de>> wrote: > > Hmm, I am using the official src release 5.10 and can't simply merge > the PR. > I found a > > ./dspace/modules/swordv2/target/war/work/org.swordapp/sword2-server/META-INF/maven/org.swordapp/sword2-server/pom.xml > where I changes the abdera version to 1.1.3 but when I rebuilt the > version is again 1.1.1 and the error will occur. > Is there a way to force abdera version 1.1.3 using the official src > tarball? > > > On 11/28/18 5:47 PM, Stefan Kombrink wrote: > > Thanks Tim, > > > > that seems to be it! Going to test it and reporting back whether it > > worked! Btw I am running DSpace 5.10 > > > > greets > > Stefan > > > > On 11/28/18 3:41 PM, Tim Donohue wrote: > >> Hi Stefan, > >> > >> What specific version of DSpace are you testing with. You mentioned > >> DSpace 5, but didn't say which version. > >> > >> The error that you sent almost seems like a dependency conflict (or a > >> missing dependency). It reminded me of a similar error that someone > >> else recently reported with SWORDv2 on DSpace v5.9 and v5.10 > specifically: > >> > >> https://jira.duraspace.org/browse/DS-4085 > >> > >> That particular bug was caused by a dependency upgrade in v5.9 that > >> seemed to conflict with the version of Apache Abdera we are using. > >> There's a possible fix in the works in this Pull Request (which > simply > >> upgrades Apache Abdera to a compatible > >> version): https://github.com/DSpace/DSpace/pull/2271 > >> > >> The error stack you sent along also references "org.apache.abdera" > >> (Apache Abdera), which makes me wonder if this is a similar error you > >> are encountering. > >> > >> If you are running version 5.9 or 5.10, you might try upgrading > Apache > >> Abdera (i.e. applying the changes in that PR) to see if that > fixes the > >> bug. If so, please do let us know -- as we are still > reviewing/testing > >> this change to ensure it works properly (and if so, it likely will be > >> released in a future version of DSpace). > >> > >> - Tim > >> > >> On Wed, Nov 28, 2018 at 8:18 AM Stefan Kombrink > >> <stefan.kombr...@uni-ulm.de <mailto:stefan.kombr...@uni-ulm.de> > <mailto:stefan.kombr...@uni-ulm.de > <mailto:stefan.kombr...@uni-ulm.de>>> wrote: > >> > >> Okay, I've watched the wrong logs -here we go: > >> > >> tail -f /opt/tomcat/logs/localhost.2018-11-28.log > >> > >> SEVERE: Servlet.service() for servlet [servicedocument] in > context with > >> path [/swordv2] threw exception [Servlet execution threw an > exception] > >> with root cause java.lang.NoSuchMethodError: > >> > > org.apache.axiom.om.impl.llom.OMElementImpl.<init>(Ljava/lang/String;Lorg/apache/axiom/om/OMNamespace;Lorg/apache/axiom/om/OMContainer;Lorg/apache/axiom/om/OMFactory;)V > >> at > org.apache.abdera.parser.stax.FOMElement.<init>(FOMElement.java:88) > >> at > >> > > org.apache.abdera.parser.stax.FOMExtensibleElement.<init>(FOMExtensibleElement.java:52) > >> at > org.apache.abdera.parser.stax.FOMService.<init>(FOMService.java:63) > >> at > >> > org.apache.abdera.parser.stax.FOMFactory.newService(FOMFactory.java:113) > >> at > >> > org.apache.abdera.parser.stax.FOMFactory.newService(FOMFactory.java:156) > >> at org.apache.abdera.Abdera.newService(Abdera.java:110) at > >> > org.swordapp.server.ServiceDocument.<init>(ServiceDocument.java:17) at > >> > > org.dspace.sword2.ServiceDocumentManagerDSpace.getServiceDocument(ServiceDocumentManagerDSpace.java:101) > >> at > >> > > org.dspace.sword2.ServiceDocumentManagerDSpace.getServiceDocument(ServiceDocumentManagerDSpace.java:60) > >> at > >> > org.swordapp.server.ServiceDocumentAPI.get(ServiceDocumentAPI.java:56) > >> at > >> > > org.swordapp.server.servlets.ServiceDocumentServletDefault.doGet(ServiceDocumentServletDefault.java:32) > >> at > javax.servlet.http.HttpServlet.service(HttpServlet.java:624) at > >> javax.servlet.http.HttpServlet.service(HttpServlet.java:731) at > >> > > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) > >> at > >> > > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) > >> at > >> > org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) > >> at > >> > > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) > >> at > >> > > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) > >> at > >> > > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) > >> at > >> > > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110) > >> at > >> > > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) > >> at > >> > > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) > >> at > >> > > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) > >> at > >> > org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962) > >> at > >> > > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) > >> at > >> > > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445) > >> at > >> > > org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115) > >> at > >> > > org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637) > >> at > >> org.apache.tomcat.util.net <http://org.apache.tomcat.util.net> > >> > > <http://org.apache.tomcat.util.net>.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) > >> at > >> > > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) > >> at > >> > > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) > >> at > >> > > org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) > >> at java.lang.Thread.run(Thread.java:745) > >> > >> > >> java -version > >> java version "1.7.0_95" > >> OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-3) > >> OpenJDK 64-Bit Server VM (build 24.95-b01, mixed mode) > >> > >> I've purged java 1.8 and JDK8 which had been installed as > well, ran > >> mvn clean package and made an > >> ant fresh install > >> > >> But to no avail... > >> > >> How can this happen? > >> > >> regards Stefan > >> > >> > >> On 11/28/18 10:09 AM, Stefan Kombrink wrote: > >> > Thanks Tim, > >> > > >> > you will find the log excerpts attached (DEBUG enabled for > DSpace). > >> > The mentioned requests were around 1:28PM > >> > > >> > regards Stefan > >> > > >> > On 11/26/18 4:52 PM, Tim Deonohue wrote: > >> >> Hi Stefan, > >> >> > >> >> I'd recommend checking your log files closely (both DSpace and > >> Tomcat) > >> >> when the error occurs. My suspicion is there may be an error > >> reported > >> >> there that could help diagnose the problem. Let us know > on this list > >> >> what you find. > >> >> > >> >> Tim > >> >> > >> >> On Mon, Nov 26, 2018 at 7:49 AM Stefan Kombrink > >> >> <stefan.kombr...@uni-ulm.de > <mailto:stefan.kombr...@uni-ulm.de> > <mailto:stefan.kombr...@uni-ulm.de <mailto:stefan.kombr...@uni-ulm.de>> > >> <mailto:stefan.kombr...@uni-ulm.de > <mailto:stefan.kombr...@uni-ulm.de> > >> <mailto:stefan.kombr...@uni-ulm.de > <mailto:stefan.kombr...@uni-ulm.de>>>> wrote: > >> >> > >> >> Hi there, > >> >> > >> >> we are struggling for a long time already with this issue > >> that under > >> >> unidentified circumstances our DSpace Instances stop > >> delivering service > >> >> documents via SwordV2. > >> >> > >> >> I do multiple setups where I follow identical installation > >> instructions > >> >> line by line, and yet I am able to obtain this behavior on > >> one machine > >> >> and not on another. However, the issue is not deliberately > >> reproducible. > >> >> Basically we have no idea when it happens nor what may > be the > >> cause. > >> >> > >> >> Here it can be observed: > >> >> > >> >> Working machine: > >> >> > >> >> curl -i > >> https://vm-152-118.bwcloud.uni-ulm.de/swordv2/servicedocument > >> >> --user > >> >> > >> > <https://vm-152-118.bwcloud.uni-ulm.de/swordv2/servicedocument--user> > >> 'katako...@gmail.com:iamthebest' > >> >> > >> >> <service xmlns="http://www.w3.org/2007/app"; > >> >> > xmlns:atom="http://www.w3.org/2005/Atom";><workspace><atom:title > >> >> type="text">bwFDM test DSpace</atom:title><collection > >> >> > >> > > href="https://vm-152-118.bwcloud.uni-ulm.de/xmlui/handle/123456789/1";><atom:title > >> >> type="text">Faculty of Education</atom:title><mediation > >> >> > xmlns="http://purl.org/net/sword/terms/";>true</mediation><service > >> >> > >> > > xmlns="http://purl.org/net/sword/terms/";>https://vm-152-118.bwcloud.uni-ulm.de/swordv2/servicedocument/123456789/1</service></collection><collection > >> >> > >> > > href="https://vm-152-118.bwcloud.uni-ulm.de/xmlui/handle/123456789/2";><atom:title > >> >> type="text">Faculty of Science and > >> Technology</atom:title><mediation > >> >> > xmlns="http://purl.org/net/sword/terms/";>true</mediation><service > >> >> > >> > > xmlns="http://purl.org/net/sword/terms/";>https://vm-152-118.bwcloud.uni-ulm.de/swordv2/servicedocument/123456789/2</service></collection><collection > >> >> > >> > > href="https://vm-152-118.bwcloud.uni-ulm.de/xmlui/handle/123456789/12";><atom:title > >> >> type="text">Oparu Bibliography</atom:title><mediation > >> >> > xmlns="http://purl.org/net/sword/terms/";>true</mediation><service > >> >> > >> > > xmlns="http://purl.org/net/sword/terms/";>https://vm-152-118.bwcloud.uni-ulm.de/swordv2/servicedocument/123456789/12</service><abstract > >> >> xmlns="http://purl.org/dc/terms/";>for performance > >> >> testing...</abstract></collection></workspace><generator > >> >> xmlns="http://www.w3.org/2005/Atom"; > >> >> uri="http://www.dspace.org/ns/sword/2.0/"; > >> >> version="2.0">bwfdm.dspacet...@gmail.com > <mailto:bwfdm.dspacet...@gmail.com> > >> <mailto:bwfdm.dspacet...@gmail.com > <mailto:bwfdm.dspacet...@gmail.com>> > >> >> <mailto:bwfdm.dspacet...@gmail.com > <mailto:bwfdm.dspacet...@gmail.com> > >> <mailto:bwfdm.dspacet...@gmail.com > <mailto:bwfdm.dspacet...@gmail.com>>></generator><version > >> >> > xmlns="http://purl.org/net/sword/terms/";>2.0</version></service> > >> >> > >> >> Non-Working machine: > >> >> > >> >> curl -i > >> >> > >> > http://dspace5-test.sara-service.org:8080/swordv2/servicedocument > >> --user > >> >> 'katako...@gmail.com:iamthebest' > >> >> > >> >> HTTP/1.1 200 OK > >> >> Server: Apache-Coyote/1.1 > >> >> Transfer-Encoding: chunked > >> >> Date: Mon, 26 Nov 2018 13:42:41 GMT > >> >> > >> >> curl: (18) transfer closed with outstanding read data > remaining > >> >> > >> >> What is strange is that I can obtain a sword service > document > >> whereas I > >> >> can't on the okay-working machine: > >> >> > >> >> curl -i > >> http://dspace5-test.sara-service.org:8080/sword/servicedocument > >> >> --user > >> >> > >> > <http://dspace5-test.sara-service.org:8080/sword/servicedocument--user> > >> >> 'katako...@gmail.com:iamthebest' > >> >> > >> >> HTTP/1.1 200 OK > >> >> Server: Apache-Coyote/1.1 > >> >> Content-Type: application/atomsvc+xml;charset=UTF-8 > >> >> Transfer-Encoding: chunked > >> >> Date: Mon, 26 Nov 2018 13:44:11 GMT > >> >> > >> >> <?xml version="1.0" encoding="UTF-8"?> > >> >> <app:service xmlns:app="http://www.w3.org/2007/app"; > >> >> xmlns:sword="http://purl.org/net/sword/"; > >> >> xmlns:dcterms="http://purl.org/dc/terms/"; > >> >> xmlns:atom="http://www.w3.org/2005/Atom";> > >> >> <sword:version>1.3</sword:version> > >> >> <sword:verbose>true</sword:verbose> > >> >> <sword:noOp>true</sword:noOp> > >> >> <sword:maxUploadSize>-1</sword:maxUploadSize> > >> >> <atom:generator > uri="http://www.dspace.org/ns/sword/1.3.1"; > >> >> version="1.3"/> > >> >> <app:workspace> > >> >> <atom:title type="text">SARA DSpace 5 Test > >> Instance</atom:title> > >> >> </app:workspace> > >> >> </app:service> > >> >> > >> >> We find this an issue for both DSpace5 and DSpace6, in > >> DSpace5 however > >> >> it seems to happen much more frequently. > >> >> > >> >> Clues & suggestions are highly welcome! > >> >> > >> >> With best regards > >> >> Stefan > >> >> > >> >> -- > >> >> Stefan Kombrink > >> >> Universität Ulm > >> >> Kommunikations- und Informationszentrum (kiz) > >> >> Abteilung Informationsmedien > >> >> +49-731-50-31482 <tel:+49%20731%205031482> > <tel:+49%20731%205031482> > >> <tel:+49%20731%205031482> > >> >> > >> >> -- > >> >> All messages to this mailing list should adhere to the > DuraSpace > >> >> Code of Conduct: > >> https://duraspace.org/about/policies/code-of-conduct/ > >> >> --- > >> >> You received this message because you are subscribed > to the > >> Google > >> >> Groups "DSpace Technical Support" group. > >> >> To unsubscribe from this group and stop receiving > emails from it, > >> >> send an email to > dspace-tech+unsubscr...@googlegroups.com > <mailto:dspace-tech%2bunsubscr...@googlegroups.com> > >> <mailto:dspace-tech%2bunsubscr...@googlegroups.com > <mailto:dspace-tech%252bunsubscr...@googlegroups.com>> > >> >> <mailto:dspace-tech%2bunsubscr...@googlegroups.com > <mailto:dspace-tech%252bunsubscr...@googlegroups.com> > >> <mailto:dspace-tech%252bunsubscr...@googlegroups.com > <mailto:dspace-tech%25252bunsubscr...@googlegroups.com>>>. > >> >> To post to this group, send email to > >> dspace-tech@googlegroups.com > <mailto:dspace-tech@googlegroups.com> > <mailto:dspace-tech@googlegroups.com > <mailto:dspace-tech@googlegroups.com>> > >> >> <mailto:dspace-tech@googlegroups.com > <mailto:dspace-tech@googlegroups.com> > >> <mailto:dspace-tech@googlegroups.com > <mailto:dspace-tech@googlegroups.com>>>. > >> >> Visit this group at > https://groups.google.com/group/dspace-tech. > >> >> For more options, visit > https://groups.google.com/d/optout. > >> >> > >> >> -- > >> >> Tim Donohue > >> >> Technical Lead for DSpace & DSpaceDirect > >> >> DuraSpace.org | DSpace.org | DSpaceDirect.org > >> > > >> > >> -- > >> Stefan Kombrink > >> Universität Ulm > >> Kommunikations- und Informationszentrum (kiz) > >> Abteilung Informationsmedien > >> +49-731-50-31482 <tel:+49%20731%205031482> > <tel:+49%20731%205031482> > >> > >> -- > >> All messages to this mailing list should adhere to the DuraSpace > >> Code of Conduct: > https://duraspace.org/about/policies/code-of-conduct/ > >> --- > >> You received this message because you are subscribed to the > Google > >> Groups "DSpace Technical Support" group. > >> To unsubscribe from this group and stop receiving emails from it, > >> send an email to dspace-tech+unsubscr...@googlegroups.com > <mailto:dspace-tech%2bunsubscr...@googlegroups.com> > >> <mailto:dspace-tech%2bunsubscr...@googlegroups.com > <mailto:dspace-tech%252bunsubscr...@googlegroups.com>>. > >> To post to this group, send email to > dspace-tech@googlegroups.com <mailto:dspace-tech@googlegroups.com> > >> <mailto:dspace-tech@googlegroups.com > <mailto:dspace-tech@googlegroups.com>>. > >> Visit this group at https://groups.google.com/group/dspace-tech. > >> For more options, visit https://groups.google.com/d/optout. > >> > >> -- > >> Tim Donohue > >> Technical Lead for DSpace & DSpaceDirect > >> DuraSpace.org | DSpace.org | DSpaceDirect.org > > > > -- > Stefan Kombrink > Universität Ulm > Kommunikations- und Informationszentrum (kiz) > Abteilung Informationsmedien > +49-731-50-31482 <tel:+49%20731%205031482> > > -- > All messages to this mailing list should adhere to the DuraSpace > Code of Conduct: https://duraspace.org/about/policies/code-of-conduct/ > --- > You received this message because you are subscribed to the Google > Groups "DSpace Technical Support" group. > To unsubscribe from this group and stop receiving emails from it, > send an email to dspace-tech+unsubscr...@googlegroups.com > <mailto:dspace-tech%2bunsubscr...@googlegroups.com>. > To post to this group, send email to dspace-tech@googlegroups.com > <mailto:dspace-tech@googlegroups.com>. > Visit this group at https://groups.google.com/group/dspace-tech. > For more options, visit https://groups.google.com/d/optout. > > -- > Tim Donohue > Technical Lead for DSpace & DSpaceDirect > DuraSpace.org | DSpace.org | DSpaceDirect.org -- Stefan Kombrink Universität Ulm Kommunikations- und Informationszentrum (kiz) Abteilung Informationsmedien +49-731-50-31482 -- All messages to this mailing list should adhere to the DuraSpace Code of Conduct: https://duraspace.org/about/policies/code-of-conduct/ --- You received this message because you are subscribed to the Google Groups "DSpace Technical Support" group. 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