Re: [dspace-tech] Recent-submissions homepage error in DSpace 6.3
Hi Jose, Thanks for the link, looks very helpful (the table should not be empty) and I'll pass onto our sysadmin. Carl On Tuesday, April 13, 2021 at 10:04:12 AM UTC-4 bla...@umich.edu wrote: > Look at this: > https://groups.google.com/g/dspace-tech/c/k33Thvse0LA/m/v2XEQeOfAQAJ > > Look at what Hernan did. I'm not sure how he created the UUID he inserted > in the tables. Perhaps you know how to create one. I googled a bit and > saw some documentation about it. > > Hope this helps. > -Jose > > On Mon, Apr 12, 2021 at 6:25 PM Carl Jones wrote: > >> >> It's been a while, but following up, what if the Site table is present >> but it's empty? >> >> Carl >> On Tuesday, December 8, 2020 at 9:49:07 AM UTC-5 Carl Jones wrote: >> >>> Hi Jose, >>> >>> Thanks, much, for the suggestions. We’ll check those out. >>> >>> Carl >>> >>> > On Dec 7, 2020, at 6:01 PM, Jose Blanco wrote: >>> > >>> > I remember having this issue, and I think it was a migration that had >>> not run. You can check your database to make sure you have a table named >>> site: >>> > >>> > => \d site >>> > Table "public.site" >>> > Column | Type | Modifiers >>> > +--+--- >>> > uuid | uuid | not null >>> > >>> > Indexes: >>> > "site_pkey" PRIMARY KEY, btree (uuid) >>> > Foreign-key constraints: >>> > "site_uuid_fkey" FOREIGN KEY (uuid) REFERENCES dspaceobject(uuid) >>> > >>> > And also, In the config area take a look at this file: >>> hibernate.cfg.xml >>> > >>> > You should have this in the file: >>> > >>> > >>> > Hope this helps! >>> > -Jose >>> > >>> > On Mon, Dec 7, 2020 at 5:11 PM Carl Jones wrote: >>> > Hi, >>> > >>> > We've upgraded from 1.8 to 6.3 a couple of months ago and are >>> experiencing a similar error with the 'Recently Added' list when we try to >>> hit the 'View more' link at the site homepage. Tim Donohue mentioned this >>> could be because of a missing virtual Site Object that represents our >>> system as a whole. We get the following Stack Trace (similar to what was >>> reported by Donna Barber back in February of this year): >>> > >>> > Java stacktrace: java.lang.NullPointerException at >>> org.dspace.app.xmlui.aspect.discovery.recentSubmissions.RecentSubmissionTransformer.setMainTitle(RecentSubmissionTransformer.java:154) >>> >>> at >>> org.dspace.app.xmlui.aspect.discovery.recentSubmissions.RecentSubmissionTransformer.addBody(RecentSubmissionTransformer.java:124) >>> >>> at >>> org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:234) >>> >>> at sun.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) at >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >>> >>> at java.lang.reflect.Method.invoke(Method.java:607) at >>> org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71) >>> >>> at com.sun.proxy.$Proxy493.startElement(Unknown Source) at >>> org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87) >>> >>> at >>> org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94) >>> at >>> org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251) >>> >>> at sun.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) at >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >>> >>> at java.lang.reflect.Method.invoke(Method.java:607) >>> > >>> > >>> > I followed the suggestion to run 'bin/database info' but as far as I >>> can tell the database update checks all come back as Successful. >>> > >>> > I'm attaching the stack trace and database info output. >>> > >>> > I was curious if there were any other things I might check before >>> passing this onto our sysadmin for further investigation into what might >>> cause a missing virtual Site object problem? >>> > >>> > Thanks, >>> > >>> > Carl >>> > On Wednesday, February 19, 2020 at 6:50:34 PM UTC-5 >>> donna@canterbury.ac.nz wrote: >>> > Hi Tim, >>> > >>> > >>> > >>> > Thanks very much for pointing us in the right direction. We think >>> we’ve now resolved the issue by following the instructions for a post you >>> responded to in 2015. >>> > >>> > >>> > >>> > The registry update was being ignored, and when I tried to run it >>> separately, we were getting the error: >>> > >>> > >>> > >>> > Caused by: java.sql.BatchUpdateException: Batch entry 0 update >>> public.bitstreamformatregistry set description=NULL, internal='FALSE', >>> mimetype='application/vnd.openxmlformats-officedocument.wordprocessingml.document', >>> >>> short_description=NULL, support_level=-1 where bitstream_format_id=52 was >>> aborted: ERROR: value too long for type character varying(48) >>> > >>> > >>> > >>> > Which led me to your 2015 reply to a post about the change of the >>> bitstreamformatregistry table’s mimetype column
[dspace-tech] DSpace 6.3 another Hibernate LazyInitialzationException
Hi all, we have run in an Hibernate LazyInitialization issue not yet listed (or not found by me) in JIRA (there are a couple of similar issues, most of which seemed to have been fixed in 6.3 or earlier). Env (DSpace 6.3 with bug fixes, JSPUI, Postgres 10.16, Tomcat 8.5.51, Java 1.7.0_281). VersionedIdentifier Provider enabled but not used yet. After editing the bitstreams of an item and the bitstream description, the item is not accessible via the link anymore (though accessible for admin via edit item). From the logs first there is a warning (Comparison method violates its general contract!) and later the hibernate exception see below. The item is still in the browse index and searchable, but not accessible. Has anyone run into a similar issue? Sunny Greetings Claudia 2021-04-12 20:19:51,630 WARN org.dspace.app.webui.servlet.DSpaceServlet @ anonymous:session_id=62F86E01B179D7BC16B03EF27629:ip_addr=94.220.0.0:general_jspui_error:java.lang.IllegalArgumentException\colon; Comparison method violates its general contract! java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.util.TimSort.mergeLo(TimSort.java:777) at java.util.TimSort.mergeAt(TimSort.java:514) at java.util.TimSort.mergeForceCollapse(TimSort.java:457) at java.util.TimSort.sort(TimSort.java:254) at java.util.Arrays.sort(Arrays.java:1438) at java.util.List.sort(List.java:478) at java.util.Collections.sort(Collections.java:177) at org.dspace.app.util.GoogleMetadata.findLinkableFulltext(GoogleMetadata.java:1054) at org.dspace.app.util.GoogleMetadata.getPDFSimpleUrl(GoogleMetadata.java:1008) at org.dspace.app.util.GoogleMetadata.addSingleField(GoogleMetadata.java:259) at org.dspace.app.util.GoogleMetadata.parseItem(GoogleMetadata.java:704) at org.dspace.app.util.GoogleMetadata.(GoogleMetadata.java:219) at org.dspace.app.webui.servlet.HandleServlet.displayItem(HandleServlet.java:461) at org.dspace.app.webui.servlet.HandleServlet.doDSGet(HandleServlet.java:263) at org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:126) at org.dspace.app.webui.servlet.DSpaceServlet.doGet(DSpaceServlet.java:73) at javax.servlet.http.HttpServlet.service(HttpServlet.java:634) at javax.servlet.http.HttpServlet.service(HttpServlet.java:741) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.dspace.rdf.negotiation.NegotiationFilter.doFilter(NegotiationFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:543) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:688) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) at org.apache.coyote.ajp.AjpProcessor.service(AjpProcessor.java:508) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:818) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1623) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at
Re: [dspace-tech] Recent-submissions homepage error in DSpace 6.3
Look at this: https://groups.google.com/g/dspace-tech/c/k33Thvse0LA/m/v2XEQeOfAQAJ Look at what Hernan did. I'm not sure how he created the UUID he inserted in the tables. Perhaps you know how to create one. I googled a bit and saw some documentation about it. Hope this helps. -Jose On Mon, Apr 12, 2021 at 6:25 PM Carl Jones wrote: > > It's been a while, but following up, what if the Site table is present > but it's empty? > > Carl > On Tuesday, December 8, 2020 at 9:49:07 AM UTC-5 Carl Jones wrote: > >> Hi Jose, >> >> Thanks, much, for the suggestions. We’ll check those out. >> >> Carl >> >> > On Dec 7, 2020, at 6:01 PM, Jose Blanco wrote: >> > >> > I remember having this issue, and I think it was a migration that had >> not run. You can check your database to make sure you have a table named >> site: >> > >> > => \d site >> > Table "public.site" >> > Column | Type | Modifiers >> > +--+--- >> > uuid | uuid | not null >> > >> > Indexes: >> > "site_pkey" PRIMARY KEY, btree (uuid) >> > Foreign-key constraints: >> > "site_uuid_fkey" FOREIGN KEY (uuid) REFERENCES dspaceobject(uuid) >> > >> > And also, In the config area take a look at this file: >> hibernate.cfg.xml >> > >> > You should have this in the file: >> > >> > >> > Hope this helps! >> > -Jose >> > >> > On Mon, Dec 7, 2020 at 5:11 PM Carl Jones wrote: >> > Hi, >> > >> > We've upgraded from 1.8 to 6.3 a couple of months ago and are >> experiencing a similar error with the 'Recently Added' list when we try to >> hit the 'View more' link at the site homepage. Tim Donohue mentioned this >> could be because of a missing virtual Site Object that represents our >> system as a whole. We get the following Stack Trace (similar to what was >> reported by Donna Barber back in February of this year): >> > >> > Java stacktrace: java.lang.NullPointerException at >> org.dspace.app.xmlui.aspect.discovery.recentSubmissions.RecentSubmissionTransformer.setMainTitle(RecentSubmissionTransformer.java:154) >> at >> org.dspace.app.xmlui.aspect.discovery.recentSubmissions.RecentSubmissionTransformer.addBody(RecentSubmissionTransformer.java:124) >> at >> org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:234) >> at sun.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> at java.lang.reflect.Method.invoke(Method.java:607) at >> org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71) >> at com.sun.proxy.$Proxy493.startElement(Unknown Source) at >> org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87) >> at >> org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94) >> at >> org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251) >> at sun.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> at java.lang.reflect.Method.invoke(Method.java:607) >> > >> > >> > I followed the suggestion to run 'bin/database info' but as far as I >> can tell the database update checks all come back as Successful. >> > >> > I'm attaching the stack trace and database info output. >> > >> > I was curious if there were any other things I might check before >> passing this onto our sysadmin for further investigation into what might >> cause a missing virtual Site object problem? >> > >> > Thanks, >> > >> > Carl >> > On Wednesday, February 19, 2020 at 6:50:34 PM UTC-5 >> donna@canterbury.ac.nz wrote: >> > Hi Tim, >> > >> > >> > >> > Thanks very much for pointing us in the right direction. We think we’ve >> now resolved the issue by following the instructions for a post you >> responded to in 2015. >> > >> > >> > >> > The registry update was being ignored, and when I tried to run it >> separately, we were getting the error: >> > >> > >> > >> > Caused by: java.sql.BatchUpdateException: Batch entry 0 update >> public.bitstreamformatregistry set description=NULL, internal='FALSE', >> mimetype='application/vnd.openxmlformats-officedocument.wordprocessingml.document', >> short_description=NULL, support_level=-1 where bitstream_format_id=52 was >> aborted: ERROR: value too long for type character varying(48) >> > >> > >> > >> > Which led me to your 2015 reply to a post about the change of the >> bitstreamformatregistry table’s mimetype column switching from 48 to 256 >> characters in DSpace 1.5. We’ve been on DSpace since 1.4, so we’ve >> obviously been hauling this problem along for a while! >> > >> > >> > >> > After altering the column character length on the 5.6 database the >> registry update task was initially ignored, but this time when we ran >> [dspace]/bin/dspace database migrate ignored, it completed successfully. We >> now have an entry in the site table, and the recent submissions are working >>
[dspace-tech] unable to edit an item in dspace6 jspui
hello every body, i have dspace 6.2 with jspui on debian 9.1 , with : tomcat8, java8, maven3.5, ant1.10 whene i try to modify one item it indicates : Internal System Error The system has experienced an internal error. Please try to do what you were doing again, and if the problem persists, please contact us so we can fix the problem. and that is what says dspace.log file : - 2021-04-12 10:49:34,399 INFO org.dspace.app.webui.servlet.HandleServlet @ informatique.e...@gmail.com:session_id=E24EBEC10834299F3A3B874D96172F5C:ip_addr=172.20.17.135:view_item:handle=123456789/734 2021-04-12 10:49:35,322 WARN org.dspace.app.webui.servlet.DSpaceServlet @ informatique.e...@gmail.com:session_id=E24EBEC10834299F3A3B874D96172F5C:ip_addr=172.20.17.135:general_jspui_error:java.lang.ArrayIndexOutOfBoundsException\colon; 0 java.lang.ArrayIndexOutOfBoundsException: 0 at java.util.Arrays$ArrayList.get(Arrays.java:3841) at org.dspace.app.webui.servlet.HandleServlet.displayItem(HandleServlet.java:409) at org.dspace.app.webui.servlet.HandleServlet.doDSGet(HandleServlet.java:268) at org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:126) at org.dspace.app.webui.servlet.DSpaceServlet.doGet(DSpaceServlet.java:73) at javax.servlet.http.HttpServlet.service(HttpServlet.java:635) at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.dspace.rdf.negotiation.NegotiationFilter.doFilter(NegotiationFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:748) all other items, communities and collections are normaly editable . what can i do to correct this problem ? thank you. -- All messages to this mailing list should adhere to the 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. To view this discussion on the web visit https://groups.google.com/d/msgid/dspace-tech/0003a670-a125-416f-a088-72fadae52aeen%40googlegroups.com.
