Re: [Dspace-tech] Dspace-cris invalid db.name
Ok, I did not experienced an OutOfMemoryException during the test phase before the tag, usually I run DSpace-CRIS less than 2GB. Maybe you are running all the webapps under the same Tomcat (in particular you can remove xmlui because is not fully integrated in DSpace-CRIS, is just a starting point to allow other to jump in) Please send a pull request on github with all your modifications. Thank you. Andrea Il 17/06/2015 13:51, alastair.dun...@stfc.ac.uk ha scritto: I’ve checked out the 5.x.x branch and added the maven dependency but found that this then led on to a further missing dependency which was for the dspace-cris-jsp-api. The dspace-services is also required but this leads to a conflict with the ehcache dependency so it requires the exclusion of ehcache-core for the dspace-services. dependency groupIdorg.dspace/groupId artifactIddspace-services/artifactId exclusions exclusion groupIdnet.sf.ehcache/groupId artifactIdehcache-core/artifactId /exclusion /exclusions /dependency The services that now start in this order are, swordv2, rdf, solr, sword and xmlui Jspui fails with an out of memory exception. I’ve given tomcat 10G of memory and its still failing. I’ll do a bit more investigation. Alastair *From:*Pascarelli Luigi Andrea [mailto:l.pascare...@cineca.it] *Sent:* 16 June 2015 16:24 *To:* Duncan, Alastair (STFC,RAL,SC) *Cc:* dspace-tech@lists.sourceforge.net *Subject:* Re: [Dspace-tech] Dspace-cris invalid db.name Hi, I’ve had a further dig into this and it seems that the db.name has been removed on dspace v 5.x.x but is still referenced in the cris version and so causes the problem. If I set the db.name = postgres in the build.properties file it is not propagated to the dspace.cfg file. If I set it directly in the dspace.cfg file then the exception goes away and it has a further exception: ERROR: column metadatavalue.item_id does not exist this problems has been resolved with https://github.com/Cineca/DSpace/commit/6578145e547db9f1468142e548ab1ce6c183102b Please use the dspace-5_x_x-cris branch, we will make a fix release in the next few days. The class not found exception occurs in the sword, sword2, rdf, rest and oai web applications if I remove these from the webapps directory then the errors go away. The classes in the dspace-api-CRIS-5.3.0.SNAPSHOT.jar files for these apps do not contain the CrisSearchService class but they do contain the SearchService class. Seems that there are a missing resources on classpath. You can found the CrisSearchService.class into dspace-cris-api-CRIS-5.3.0.SNAPSHOT.jar but perhaps the maven dependencies missed him. Try to add the dependency to webapps pom files and rebuild the application. e.g. dspace/modules/oai/pom.xml dependency groupIdorg.dspace/groupId artifactIddspace-cris-api/artifactId /dependency Thanks for your patience. Please keep us up-to-date with your progress, we hope to achieve a better release together. Best, Andrea Il 16/06/2015 15:20, alastair.dun...@stfc.ac.uk mailto:alastair.dun...@stfc.ac.uk ha scritto: I’ve had a further dig into this and it seems that the db.name has been removed on dspace v 5.x.x but is still referenced in the cris version and so causes the problem. If I set the db.name = postgres in the build.properties file it is not propagated to the dspace.cfg file. If I set it directly in the dspace.cfg file then the exception goes away and it has a further exception: ERROR: column metadatavalue.item_id does not exist I’ve had a look in the database and it is correct it does not exist. The class not found exception occurs in the sword, sword2, rdf, rest and oai web applications if I remove these from the webapps directory then the errors go away. The classes in the dspace-api-CRIS-5.3.0.SNAPSHOT.jar files for these apps do not contain the CrisSearchService class but they do contain the SearchService class. I’ll move back to the 4.3.0 version for the present. Alastair *From:*alastair.dun...@stfc.ac.uk mailto:alastair.dun...@stfc.ac.uk [mailto:alastair.dun...@stfc.ac.uk] *Sent:* 02 June 2015 11:10 *To:* dspace-tech@lists.sourceforge.net mailto:dspace-tech@lists.sourceforge.net *Subject:* [Dspace-tech] Dspace-cris invalid db.name Hi, I’ve setup dspace-cris v 5.2.0 and this starts up and I can login ok. I’ve added in the default CRIS objects and can browse to these ok. This suggests that the db.name is valid. When I try and create a researcher page and save this an Internal exception is thrown which states that there is an invalid db.name: java.lang.IllegalStateException: The configuration for db.name is either invalid, or contains an unrecognised database at org.dspace.content.authority.AuthorityDAOFactory.getInstance(AuthorityDAOFactory.java:42
Re: [Dspace-tech] So the CRIS module only works with JSPUI?
Yes, DSpace-CRIS is fully integrated only with DSpace JSPUI but in my opinion with a bit of work (a bit and hard work) could be run also in XMLUI (need to have both jspui than xmlui up and running). To try, only the brave can perform this todo list: - use SSO (single sign on) to share login from DSPACE-CRIS and DSPACE XMLUI - setup URL redirect/rewrite in Apache to perform redirect for links from DSpace-CRIS to DSpace pages and viceversa - improve browse/search section to show anchor in result page that link to DSpace-CRIS entities Best Andrea Il 17/06/2015 15:36, Tim Donohue ha scritto: Hi David, Correct, CRIS is only for the JSPUI at this time. Currently DSpace-CRIS is essentially a separate application, based on the DSpace JSPUI and supported primarily by CINECA (who developed DSpace-CRIS). While you can migrate to DSpace-CRIS from an existing DSpace, it changes the underlying data model (so you are no longer running the out-of-the-box DSpace). More info here: http://cineca.github.io/dspace-cris/ While migration of DSpace-CRIS into core DSpace is not yet on the RoadMap, there have been informal discussions with CINECA on trying to find a way to make CRIS easier to enable or install for those who want that type of functionality (so it isn't an entirely different application with a different data model). But, this idea is dependent on coming up with a better definition/structure for DSpace third-party modules (which is on the RoadMap), so that we can better enable/support this sort of plugability in DSpace. More info on the Roadmap in general is at: https://wiki.duraspace.org/display/DSPACE/RoadMap - Tim On 6/17/2015 8:06 AM, Schuster, David wrote: Just wanting to be sure. We have been running the XMLUI interface as that was what seemed the best option 2 years ago. Are there plans for porting it to XMLUI or what advice would people give if we were interested in the CRIS module. David Schuster Texas Woman's University Director of Library Information Technology Technical Support Phone: 940-898-3909 dschus...@twu.edu mailto:dschus...@twu.edu emailsignature -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Dspace-cris invalid db.name
Hi, I’ve had a further dig into this and it seems that the db.name has been removed on dspace v 5.x.x but is still referenced in the cris version and so causes the problem. If I set the db.name = postgres in the build.properties file it is not propagated to the dspace.cfg file. If I set it directly in the dspace.cfg file then the exception goes away and it has a further exception: ERROR: column metadatavalue.item_id does not exist this problems has been resolved with https://github.com/Cineca/DSpace/commit/6578145e547db9f1468142e548ab1ce6c183102b Please use the dspace-5_x_x-cris branch, we will make a fix release in the next few days. The class not found exception occurs in the sword, sword2, rdf, rest and oai web applications if I remove these from the webapps directory then the errors go away. The classes in the dspace-api-CRIS-5.3.0.SNAPSHOT.jar files for these apps do not contain the CrisSearchService class but they do contain the SearchService class. Seems that there are a missing resources on classpath. You can found the CrisSearchService.class into dspace-cris-api-CRIS-5.3.0.SNAPSHOT.jar but perhaps the maven dependencies missed him. Try to add the dependency to webapps pom files and rebuild the application. e.g. dspace/modules/oai/pom.xml dependency groupIdorg.dspace/groupId artifactIddspace-cris-api/artifactId /dependency Thanks for your patience. Please keep us up-to-date with your progress, we hope to achieve a better release together. Best, Andrea Il 16/06/2015 15:20, alastair.dun...@stfc.ac.uk ha scritto: I’ve had a further dig into this and it seems that the db.name has been removed on dspace v 5.x.x but is still referenced in the cris version and so causes the problem. If I set the db.name = postgres in the build.properties file it is not propagated to the dspace.cfg file. If I set it directly in the dspace.cfg file then the exception goes away and it has a further exception: ERROR: column metadatavalue.item_id does not exist I’ve had a look in the database and it is correct it does not exist. The class not found exception occurs in the sword, sword2, rdf, rest and oai web applications if I remove these from the webapps directory then the errors go away. The classes in the dspace-api-CRIS-5.3.0.SNAPSHOT.jar files for these apps do not contain the CrisSearchService class but they do contain the SearchService class. I’ll move back to the 4.3.0 version for the present. Alastair *From:*alastair.dun...@stfc.ac.uk [mailto:alastair.dun...@stfc.ac.uk] *Sent:* 02 June 2015 11:10 *To:* dspace-tech@lists.sourceforge.net *Subject:* [Dspace-tech] Dspace-cris invalid db.name Hi, I’ve setup dspace-cris v 5.2.0 and this starts up and I can login ok. I’ve added in the default CRIS objects and can browse to these ok. This suggests that the db.name is valid. When I try and create a researcher page and save this an Internal exception is thrown which states that there is an invalid db.name: java.lang.IllegalStateException: The configuration for db.name is either invalid, or contains an unrecognised database at org.dspace.content.authority.AuthorityDAOFactory.getInstance(AuthorityDAOFactory.java:42) at org.dspace.app.webui.cris.controller.ResearcherPageDetailsController.handleDetails(ResearcherPageDetailsController.java:134) at it.cilea.osd.jdyna.web.controller.SimpleDynaController.handleRequestInternal(SimpleDynaController.java:116) I don’t get this problem with v 4.3.0 Any ideas? There are a few other problems when the system starts but these do not seem to be a problem yet as I’ve not done any searching: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'org.dspace.servicemanager.spring.DSpaceBeanPostProcessor#0' defined in class path resource [spring/spring-dspace-applicationContext.xml]: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.dspace.servicemanager.config.DSpaceConfigurationService]: : Cannot find class [org.dspace.app.cris.discovery.CrisSearchService] nested exception is java.lang.ClassNotFoundException: org.dspace.app.cris.discovery.CrisSearchService at org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener.contextInitialized(DSpaceKernelServletContextListener.java:92) This is the final problem which eventually results in a null pointer in the DspaceContextListener. Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dspace.eventService' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanDefinitionStoreException: Factory method
Re: [Dspace-tech] DSpace-cris
Hi Alastair, *Server:Jetty(9.2.9.v20150224)* Sorry, but Jetty is not fully supported by DSpace-CRIS (see http://cineca.github.io/dspace-cris/installation-stepbystep.html we suggest use of Tomcat). DSpace support Jetty but DSpace-CRIS uses an advanced configuration of the spring mvc framework and surely there is a little issue with the resolution of the path that match an url (see https://github.com/Cineca/DSpace/blob/dspace-4_x_x-cris/dspace-cris/jspui-webapp/src/main/webapp/WEB-INF/springmvc-rp-servlet.xml). If you have time to work for fully compliance with Jetty in DSpace-CRIS you are welcome! Best, Luigi Andrea Il 29/05/2015 09:50, alastair.dun...@stfc.ac.uk ha scritto: Hi Luigi, On both of the urls I get document not found. I’ve logged in as administrator and from the chrome developer tools you can see I’ve navigated from http://hostname /jspui/cris/administrator/rp/index.htm I’ve removed the hostname and ip address. *Remote Address:ipaddress:80* *Request URL:http:// hostname /jspui/cris/administrator/rp/listTabs.htm* *Request Method:GET* *Status Code:404 /jspui/dspace-cris//tabs/tabList.jsp* ** *Response Headers* *view source* *Content-Language:en-GB* *Content-Type:text/html; charset=UTF-8* *Server:Jetty(9.2.9.v20150224)* *Transfer-Encoding:chunked* ** *Request Headers* *view source* *Accept:text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8* *Accept-Encoding:gzip, deflate, sdch* *Accept-Language:en-GB,en-US;q=0.8,en;q=0.6* *Connection:keep-alive* *Cookie:JSESSIONID=15ns92zschful14giohx8r3seg* *Host: hostname* *Referer:http:// hostname /jspui/cris/administrator/rp/index.htm* ** I suspect the internal server error may have been a cut paste error by me :-/ but the document not found error can’t be as I’m navigating via the user interface. Thanks Alastair *From:*Pascarelli Luigi Andrea [mailto:l.pascare...@cineca.it] *Sent:* 28 May 2015 17:05 *To:* Duncan, Alastair (STFC,RAL,SC) *Cc:* dspace-tech@lists.sourceforge.net *Subject:* Re: [Dspace-tech] DSpace-cris Hi Alastair, from the stacktrace I see that you have a strange call to the controller that manages the metadata configuration of DSpace-CRIS entities. I try to explain better. First, I think you trying to reach createTabs.htm page directly and the logs error show this: at org.dspace.app.webui.cris.controller.DynamicObjectDetailsController.extractDynamicObject(DynamicObjectDetailsController.java:238) at org.dspace.app.webui.cris.controller.DynamicObjectDetailsController.handleDetails(DynamicObjectDetailsController.java:79) Whoops, this controller manages the details of dynamic entities but there is another controller that does the createTabs work under the scene. Try to log in with an administrator user and hit from the browser this url (please change host:port with your and remove jspui if you have another context settings for the jspui webapp): http://host:port/jspui/cris/administrator/rp/listTabs.htm http://host:port/jspui/cris/administrator/rp/createTabs.htm This should be the correct url to list or create the tabs for Researcher Profile. I'm assuming that you writing the url directly but this issue happens also if you reach the page using administration links? (Administer- Cris Module- Researchers Pages - Layout configuration (Public view)) Note that the error that you are reporting will be shown also if you remove the code of the entity (rp, pj, ou, journals, etc..) from url e.g /jspui/cris/administrator//listTabs.htm (missing rp should be shown Document not found and the error reported in your stacktrace). Let me know. Luigi Andrea Il 28/05/2015 15:37, alastair.dun...@stfc.ac.uk mailto:alastair.dun...@stfc.ac.uk ha scritto: Sending again as I was not registered on the mailing list :-O Alastair *From:*Duncan, Alastair (STFC,RAL,SC) *Sent:* 28 May 2015 09:54 *To:* 'Andrea Bollini' *Cc:* 'dspace-tech' *Subject:* RE: DSpace-cris Hi Andrea, Sorry this is an installation behind a firewall, I’m looking at it to see if it is suitable for our needs. The listTabs.htm causes a document not found error to be displayed in the browser with nothing in the log files : Error: Document Not Found The createTabs.htm causes an InternalSystemError to be displayed in the browser with this exception in the log files snipped to show the cause : Caused by: java.lang.IllegalArgumentException: id to load is required for loading at org.hibernate.event.spi.LoadEvent.init(LoadEvent.java:87) at org.hibernate.event.spi.LoadEvent.init(LoadEvent.java:59) at org.hibernate.internal.SessionImpl$IdentifierLoadAccessImpl.load(SessionImpl.java:2421) at org.hibernate.internal.SessionImpl.get(SessionImpl.java:974) at it.cilea.osd.common.dao.impl.GenericDaoHibernateImpl.read(GenericDaoHibernateImpl.java:85
Re: [Dspace-tech] DSpace-cris
Hi Alastair, from the stacktrace I see that you have a strange call to the controller that manages the metadata configuration of DSpace-CRIS entities. I try to explain better. First, I think you trying to reach createTabs.htm page directly and the logs error show this: at org.dspace.app.webui.cris.controller.DynamicObjectDetailsController.extractDynamicObject(DynamicObjectDetailsController.java:238) at org.dspace.app.webui.cris.controller.DynamicObjectDetailsController.handleDetails(DynamicObjectDetailsController.java:79) Whoops, this controller manages the details of dynamic entities but there is another controller that does the createTabs work under the scene. Try to log in with an administrator user and hit from the browser this url (please change host:port with your and remove jspui if you have another context settings for the jspui webapp): http://host:port/jspui/cris/administrator/rp/listTabs.htm http://host:port/jspui/cris/administrator/rp/createTabs.htm This should be the correct url to list or create the tabs for Researcher Profile. I'm assuming that you writing the url directly but this issue happens also if you reach the page using administration links? (Administer- Cris Module- Researchers Pages - Layout configuration (Public view)) Note that the error that you are reporting will be shown also if you remove the code of the entity (rp, pj, ou, journals, etc..) from url e.g /jspui/cris/administrator//listTabs.htm (missing rp should be shown Document not found and the error reported in your stacktrace). Let me know. Luigi Andrea Il 28/05/2015 15:37, alastair.dun...@stfc.ac.uk ha scritto: Sending again as I was not registered on the mailing list :-O Alastair *From:*Duncan, Alastair (STFC,RAL,SC) *Sent:* 28 May 2015 09:54 *To:* 'Andrea Bollini' *Cc:* 'dspace-tech' *Subject:* RE: DSpace-cris Hi Andrea, Sorry this is an installation behind a firewall, I’m looking at it to see if it is suitable for our needs. The listTabs.htm causes a document not found error to be displayed in the browser with nothing in the log files : Error: Document Not Found The createTabs.htm causes an InternalSystemError to be displayed in the browser with this exception in the log files snipped to show the cause : Caused by: java.lang.IllegalArgumentException: id to load is required for loading at org.hibernate.event.spi.LoadEvent.init(LoadEvent.java:87) at org.hibernate.event.spi.LoadEvent.init(LoadEvent.java:59) at org.hibernate.internal.SessionImpl$IdentifierLoadAccessImpl.load(SessionImpl.java:2421) at org.hibernate.internal.SessionImpl.get(SessionImpl.java:974) at it.cilea.osd.common.dao.impl.GenericDaoHibernateImpl.read(GenericDaoHibernateImpl.java:85) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:318) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at it.cilea.osd.common.dao.impl.NamedQueryIntroductionAdvisor$1.invoke(NamedQueryIntroductionAdvisor.java:94) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at com.sun.proxy.$Proxy234.read(Unknown Source) at it.cilea.osd.common.service.PersistenceService.get(PersistenceService.java:163) at it.cilea.osd.common.service.PersistenceService$$FastClassByCGLIB$$b40d0435.invoke(generated) at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191) at org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:689) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:622) at org.dspace.app.cris.service.ApplicationService$$EnhancerByCGLIB$$63de70c9.get(generated) at org.dspace.app.webui.cris.controller.DynamicObjectDetailsController.extractDynamicObject(DynamicObjectDetailsController.java:238) at org.dspace.app.webui.cris.controller.DynamicObjectDetailsController.handleDetails(DynamicObjectDetailsController.java:79) at
Re: [Dspace-tech] difference in index-discovery
I think that the help is wrong but the code says: -b reindex all items without destroy the index (https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/IndexClient.java#L117) -f destroy the index and after that reindex all items (https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/IndexClient.java#L126) Il 07/11/2014 08:27, Adan Roman ha scritto: Hi Jose -b destroy the index and rebuild. You will see 0 results if you look at dspace at this moment, and items will be agregated to a 0 lenght index -f keep the index but reindex all items, so you never see the 0 results, and data will be overwriten regards What is the diff between these two: /dspace index-discovery -f /dspace index-discovery -b I just made a change in the discovery.xml file and the instructions say to run /dspace index-discovery -b in looking at the launcher these two commands apper to be very similiar. I wonder how running -b will affect production. I have 85K items. Thank you! Jose -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette:https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- http://www.avast.com/ El software de antivirus Avast ha analizado este correo electrónico en busca de virus. www.avast.com http://www.avast.com/ -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] difference in index-discovery
Hi Ivan, If you call IndexClient with -f the behaviour is force the clean (see the row that destroy the index, force parameters in this case is set to true - https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java#L455) and after that updateIndex index all items as you said before. p.s. we are linking to different branches but i think that the code is not different Regards, Andrea Il 07/11/2014 11:28, helix84 ha scritto: On Fri, Nov 7, 2014 at 10:53 AM, Pascarelli Luigi Andrea l.pascare...@cineca.it wrote: I think that the help is wrong but the code says: -b reindex all items without destroy the index (https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/IndexClient.java#L117) -f destroy the index and after that reindex all items (https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/IndexClient.java#L126) Hi Andrea, your description of -f seems incorrect. cleanIndex() first removes from index all items which no longer exist in the database [1]. updateIndex() then iterates over all items in the DB and updates them in the index. In my test, as expected, -b was about 10% faster than -f, but I'd say it's still within the error margin. [1] https://github.com/DSpace/DSpace/blob/dspace-4_x/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java#L424-L425 [2] https://github.com/DSpace/DSpace/blob/dspace-4_x/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java#L424-L425 Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] R: Release DSpace-CRIS v-4.1.1
In regards to PMC, you have to build solr core for pmc (check if into your solr instance there is pmc core configurations). Download the csv file from pubmed ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz After that try to run this script (you need a basic experience with the shell script and the curl tool): split -d -l 5 file.pmc.csv split_files. for file in `ls split_files.*` do curl 'http://host:port/solr/pmc/update?update.contentType=text/csvfieldnames=,,,DOI,PMCID,PMID,,' -H 'Content-type:text/csv; charset=utf-8' --data-binary @$file; done The script split the csv file in n files to avoid problem due to the max upload limit on your server and send it to your solr to ingest it. Tune it with your need. Good luck :-) After that launch the main script at org.dspace.app.cris.pmc.script.RetrieveCitationInPMC with -x 0 parameter, this query pmc to retrieve the actual count and citation informations. After all launch org.dspace.app.cris.pmc.script.RetrievePubMedID (with no params) to retrieve pmc/pmid identifier for items that have a doi. Hope this help. Let me know. Luigi Andrea Pascarelli Il 07/07/2014 11:50, Andrea Bollini ha scritto: Hi Alexander, I'm out-of-office these days I'm sure that Luigi will reply with information about the script need to update the pmc count. There are two script one is able to retrieve pmc/pmid identifier for items that have a doi, the other query pmc to retrieve the actual count and citation information. About the statistics you need to look to the solr log files. When you hit a researcher page do you see an insert on solr (call to the /update handler?). What if you hit an item page? Andrea -- Cineca - Sede di Roma via dei Tizii 6 - 00185 Roma ph. +39 06 44486626 email: l.pascare...@cineca.it -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] DSpace-CRIS 4.1 Installation Issue
Dear Alexander, SOLR Stats not logged properly. == I found that none of the stats were written to solr statistics core correctly. Even if I remove all the files in index and start everything from scratch, the numDocs in solr statistics core is 0. (I have tried to do all kind of activities on DSpace-CRIS) The DSpace Solr core I am using is bundled in the DSpace-CRIS - which is version 4.4. Please, can you write something more about this issue? INDEX-DISCOVERY ISSUE = If a certain orgunit or rp does not carry names, issuing an index-discovery command will generate nullpointer error. This is a known issue, there are cases (via insert direct on database, build CRIS entities and close browser or exit the creation flow...etc etc) which the required metadata for the entities are missing (fullName for RP, name for orgunit, title for projects and researchentitityshortnamename for all other entities). In the next version i try to fix this issue. Sorry but now the only suggest to fix this issues is an update on database or via administration tool order all entities by name and edit manually each entities that have no name/title. RP rebind Seems a bug. I'll look into the problems and i will let you know. Luigi Andrea Pascarelli -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] CRIS module installation
Hi Keir, DSpace-CRIS support only 1.8.2 and 3.2, the support for 4.1 is in progress and it is expected soon. A clarification: the DSpace-CRIS is connected to DSpace via maven, infact the DSpace-CRIS module is installed in a customizable version of DSpace for the DSpace-CRIS module, see the branch called dspace-cris-master on github available at https://github.com/Cineca/DSpace contains a early upgrade to DSpace 4 but is not guaranteed. I think you'll find a lot of issues. If you want take a look for a stable version (the current line of development 3.x.x) follow the instruction at http://cineca.github.io/dspace-cris/installation-stepbystep.html The technical documentation is here http://cineca.github.io/dspace-cris/doc/technical-documentation.pdf and for your case i think that you can read page 18, the chapter called Upgrade an existent DSpace installation. I hope this help. Let me know. Best Andrea Il 03/06/2014 23:53, Keir Vaughan-Taylor ha scritto: The CRIS install instructions assume the install is done during a full DSpace install although I want install into an existing instance of DSpace 4.1. CRIS install instructions say to create an independent directory, in my ase, /home/dspace/crisinstallation into which git adds the CRIS module source files into the directory dspace-parent. Then run mvn package and this all works for me. I can run the CRIS postgres sql to update postgres database. then recompiling DSpace cd src-release mvn clean package cd ./dspace/target/dspace-version-build ant update Restart httpd and tomcat but no sign of CRIS on the GUI. How the CRIS material makes its way into the DSpace compile is unclear to me. I tried copying /home/dspace/crisinstallation/dspace-parent cris modules to the DSpace source directory - nope no good. I tried editing the build.properties in /home/dspace/crisinstallation/dspace-parent and recompiling CRIS (No good) What am I missing? -- CINECA *Luigi Andrea Pascarelli* /Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca/ Via dei Tizii, 6 00185 Roma, Italy /ph. +39 06 44486626/ http://www.cineca.it -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Upgrade Solr 3.5 to 4.1
Hi Ruben, you have to deploy a fresh Solr webapp into your tomcat. So, unzip the package and find the solr.war (usually is under dist folder). Deploy war in context solr/ (via tomcat manager or copy war under tomcat webapps directory) and set environment variable in tomcat context.xml file like: Parameter name="log4j.configuration" value="[dspace-config]/log4j-solr.properties" override="false"/ Parameter name="LocalhostRestrictionFilter.localhost" value="false" override="false"/ Environment name="solr/home" value="[dspace.dir]/solr" type="java.lang.String" override="false"/ Startup tomcat and check the correct installation in your browser at http://localhost:8080/solr/search I assert that you have done a default cris installation and the url of solr server is http://localhost:8080/solr and the context container is the same of your DSpace webapp, to deploy a war google knows more that me :-) Hope this help. Luigi Andrea Il 28/11/2013 12:51, Ruben ha scritto: Hi, Now I have 3.5 version of Solr installed with DSpace 3.2 + CRIS module and I want to upgrade to 4.1 version, because it's a pre-requisit of DSpace + CRIS module. I downloaded Solr from: http://archive.apache.org/dist/lucene/solr/4.1.0/solr-4.1.0.zip I don't know which files of Solr modify or copy into DSpace, so I need your help to upgrade Solr succesfully. Thanks in advance -- __ / / Rubn Boada Navarrete C E / S / C A Tcnic de Portals i Repositoris /_/ Centre de Serveis Cientfics i Acadmics de Catalunya Gran Capit, 2-4 (Edifici Nexus) 08034 Barcelona T. 93 205 6464 (ext. 302) F. 93 551 62 13 rbo...@cesca.cat Subscriu-te al butllet (www.cesca.cat/butlleti) -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] How to install dpsace-CRIS in existing DSpace 3.x
Hi, i try to answer but first to start i recommended to understand the official DSpace installation documentation at https://wiki.duraspace.org/display/DSDOC3x/Installation and read the standard DSpace-CRIS installation documentation (http://cineca.github.io/dspace-cris/installation.html and http://cineca.github.io/dspace-cris/installation-stepbystep.html) Let's get start. So in the past few day the project have change the home and the suggestion is to download the source from the new git page: DSpace customizations based on official 3.2 for DSpace-CRIS module: https://github.com/Cineca/DSpace/archive/dspace-3_x_x-cris.zip DSpace-CRIS module: https://github.com/Cineca/dspace-cris/archive/3.x.x.zip Unzip the DSpace parent project and copy the unzipped content of the DSpace-CRIS module into dspace-cris folder under the root of the parent project. For example: unzip custom DSpace into folder [path-for-dspace-unzipped]\DSpace-dspace-3_x_x-cris (from here dspace-src) the content of the DSpace-CRIS zip must be copied into folder [dspace-src]\dspace-cris Now dspace-cris directory looks like with the follow contents: - api - jspui-api - jspui-webapp - webservices - other files ... After that you have to apply all your changes make in the past from your DSpace 3.2 to new DSpace 3.x for DSpace-CRIS So now you have to build the application from [dspace-src] run the follow command: mvn -U clean package After mvn say build success, you can run "ant update" from [dspace-src]/dspace/target/dspace-[version]-build.dir . The last step is apply all custom folders/files to the [dspace.dir] - refers to the install directory for your existing DSpace installation - and create database table for DSpace-CRIS. To update your database run: psql -h [db-host] -d [db.name] -U [db.user] -f [dspace-src]/etc/postgres/addon-crismodule.sql psql -h [db-host] -d [db.name] -U [db.user] -f [dspace-src]/etc/postgres/addon-crispubmed.sql psql -h [db-host] -d [db.name] -U [db.user] -f [dspace-src]/etc/postgres/addon-subscription.sql Now go to [dspace.dir] and run: mkdir rp-files mkdir rg-files mkdir ou-files mkdir do-files mkdir ws-xsd cp [dspace-src]/dspace/etc/webservice/* [dspace.dir]/ws-xsd If all the steps described are right you can deploy your webapps (see step 7 from http://cineca.github.io/dspace-cris/installation-stepbystep.html) Hope this helps. Luigi Andrea Il 26/11/2013 15:45, LifeH2O ha scritto: I can do the remaining installation steps. I only need to know that how to combine or use those .zip pakages on existing DSpace 3.2 -- View this message in context: http://dspace.2283337.n4.nabble.com/How-to-install-dpsace-CRIS-in-existing-DSpace-3-x-tp4668527p4669169.html Sent from the DSpace - Tech mailing list archive at Nabble.com. -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Can't add project in DSpace with module CRIS
Dear Daniel,
Can you tell us which tomcat version do you use and which parameters
do you have in the tomcat startup script?
Thank you
Luigi Andrea
Il 25/11/2013 11:31, Daniel Garcia ha
scritto:
Hi,
I install the last version of DSpace+CRIS Module following the
steps (http://cineca.github.io/dspace-cris/installation.html)
All is OK, DSpace works correctly but when I want to 'Add a
project' in Administration panel I get a 'Internal Error'. I check
logs and I see:
2013-11-25 11:23:45,007 INFO
org.dspace.app.cris.discovery.CrisSearchService @ Wrote cris:
14bd5ce5-8a4d-433e-bbc8-9d862257db41 to Index
2013-11-25 11:23:45,249 WARN
org.dspace.app.webui.servlet.InternalErrorServlet @
:session_id=D3AE81A2DD7447ECEE8ABCA8039AED14.projecte1:internal_error:--
URL Was: http://portalrecerca-dev.cesca.cat/internal-error?id=8
-- Method: GET
-- Parameters were:
-- id: "8"
javax.servlet.ServletException:
org.apache.jasper.JasperException:
/dspace-cris/jdyna/projectDataEditForm.jsp (line: 511, column:
4) "${researcher:isThereMetadataNoEditable(holder.shortName,
holder.class)}" contains invalid _expression_(s):
javax.el.ELException: Failed to parse the _expression_
[${researcher:isThereMetadataNoEditable(holder.shortName,
holder.class)}]
at
org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:85)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:749)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:487)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:412)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:339)
at
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:238)
at
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:262)
at
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
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.doGet(FrameworkServlet.java:778)
at
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.dspace.app.webui.cris.filter.DSpaceContextCleanupFilter.doFilter(DSpaceContextCleanupFilter.java:54)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.dspace.app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilter.java:66)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at
Re: [Dspace-tech] Can't add project in DSpace with module CRIS
Yes, using Tomcat 7 you have to add the follow parameter to the JAVA_OPTS: -Dorg.apache.el.parser.SKIP_IDENTIFIER_CHECK=true At http://cineca.github.io/dspace-cris/installation-stepbystep.html we report this configuration for Tomcat 7 but perhaps is better point out it and create a isolate paragraph with this options that depend to the underlying used tool. Sorry for that, we upgrade the documentation asap. Luigi Andrea Il 25/11/2013 16:12, Daniel Garcia ha scritto: I try with this values in JAVA_OPTS: -Xmx950M -Xms512M -XX:PermSize=128M -XX:MaxPermSize=256M -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:+UseAdaptiveSizePolicy -XX:-UseConcMarkSweepGC -Dfile.encoding=UTF-8 I need some more parameter? Thanks in advance, Daniel El 25/11/13 15:48, helix84 ha escrit: Hi Daniel, what is your value of the JAVA_OPTS (and any other optional Java environment variables, see comments in bin/catalina.sh) in the environment where you run startup.sh? Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Can't add project in DSpace with module CRIS
Dear Daniel, to use DSpace-CRIS is mandatory migrate to Solr 4.1.0. To rebuild solr data index in the right format for the 4.1.0, you can call the optimize command directly to the solr server: http://[hostname:port]/solr/[solrcore]/update?optimize=true DSpace-CRIS have 5 solr core (3 derived from DSpace - 1 core for network feature - 1 for pubmed feature) so for example you can call via http (open your browser or use wget or curl tool) the follow link: http://localhost:8080/solr/search/update?optimize=true http://localhost:8080/solr/statistics/update?optimize=true http://localhost:8080/solr/oai/update?optimize=true http://localhost:8080/solr/network/update?optimize=true http://localhost:8080/solr/pmc/update?optimize=true If your installation of DSpace-CRIS is derived from an old DSpace installation (1.8) then before to migrate data index to 4.1.0 you need to optimize index with the optimize implemented on solr server 3.5.0(after that you can turn off this and migrate to 4.1.0 optimize core again). For other details see https://jira.duraspace.org/browse/DS-1776 BTW for the solr search core you can remove manually the index data directory [dspace]/solr/search/data and run from [dspace]/bin the "dspace update-discovery-index" command (recall that solr server must be up and running before launch indexer). After this you can rebuild also index data for network feature running "dspace dsrun org.dspace.app.cris.batch.ScriptIndexNetwork -a" or if you have interest only to create the network for coauthored publications launch "dspace dsrun org.dspace.app.cris.batch.ScriptIndexNetwork -s coauthors" Hope this helps. Luigi Andrea Il 25/11/2013 17:03, Daniel Garcia ha scritto: Hi Luigi, Thanks it works! I see that I have Solr Specification Version: 3.5.0. In documentation I see that prerequisite software is Solr 4.1.0. You recommend to me to upgrade? I'm afraid to stop working, at now it works. Thanks in advance, Daniel El 25/11/13 16:21, Pascarelli Luigi Andrea ha escrit: Yes, using Tomcat 7 you have to add the follow parameter to the JAVA_OPTS: -Dorg.apache.el.parser.SKIP_IDENTIFIER_CHECK=true At http://cineca.github.io/dspace-cris/installation-stepbystep.html we report this configuration for Tomcat 7 but perhaps is better point out it and create a isolate paragraph with this options that depend to the underlying used tool. Sorry for that, we upgrade the documentation asap. Luigi Andrea Il 25/11/2013 16:12, Daniel Garcia ha scritto: I try with this values in JAVA_OPTS: -Xmx950M -Xms512M -XX:PermSize=128M -XX:MaxPermSize=256M -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:+UseAdaptiveSizePolicy -XX:-UseConcMarkSweepGC -Dfile.encoding=UTF-8 I need some more parameter? Thanks in advance, Daniel El 25/11/13 15:48, helix84 ha escrit: Hi Daniel, what is your value of the JAVA_OPTS (and any other optional Java environment variables, see comments in bin/catalina.sh) in the environment where you run startup.sh? Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l
Re: [Dspace-tech] DSpace + CRIS module problem in edit researcher page
Dear Daniel,
if you run tomcat7 please add the following environment variable to
the startup script -Dorg.apache.el.parser.SKIP_IDENTIFIER_CHECK=true
Sorry if this workaround is not well documented on website but we
working to release DSpace 4.0.
By the way if the issue is not related to that then send us your
environment configuration info (Oracle JDK vs OpenJDK, tomcat
version, OS platform and so on) and the step followed to the
DSpace-CRIS installation (if you using the last beta tag or the
current dspace-3_x_x-cris branch, if you using a pre-existent DSpace
upgraded installation and so on)
Thanks in advance
Luigi Andrea
Il 04/11/2013 11:23, Daniel Garcia ha
scritto:
Hi,
I followed the steps to
install DSpace + CRIS but when I want to edit my 'Researcher
Page' I obtain an internal error.
Reviewing the logs I see these error:
2013-11-04 10:52:11,036 WARN
org.dspace.app.webui.servlet.InternalErrorServlet @
:session_id=5B3B8C4AFDCB724D2E4F66E2A45655FB.projecte1:internal_error:--
URL Was:
http://portalrecerca-dev.cesca.cat/internal-error?id=3anagraficaId=3
-- Method: GET
-- Parameters were:
-- id: "3"
-- anagraficaId: "3"
javax.servlet.ServletException:
org.apache.jasper.JasperException:
/dspace-cris/jdyna/rpDataEditForm.jsp (line: 635, column:
4)
"${researcher:isThereMetadataNoEditable(holder.shortName,
holder.class)}" contains invalid _expression_(s):
javax.el.ELException: Failed to parse the _expression_
[${researcher:isThereMetadataNoEditable(holder.shortName,
holder.class)}]
at
org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:85)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:749)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:487)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:412)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:339)
at
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:238)
at
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:262)
at
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
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.doGet(FrameworkServlet.java:778)
at
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.dspace.app.webui.cris.filter.DSpaceContextCleanupFilter.doFilter(DSpaceContextCleanupFilter.java:54)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.dspace.app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilter.java:66)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
Re: [Dspace-tech] Solr config parameter interpolation
To be thorough, autoCommit works doing commit every 15sec but do that not cause a new searcher to be opened to make changes visible (because openSearcher is set to false). The parameter autoSoftCommit is setted by default to -1 meaning that no action to do. So having openSearcher=false is not the best choice, maybe try to change that setting could be not need to do a soft commit either the change proposed by me in the previous email. Surely have sense to change the configuration to obtain an autoCommit every 10sec or maxDocs reach the 1 documents (like the old DSpace solrconfig.xml says). Note that this changes would to apply to all Solr core used by DSpace (search/statistics/oai). For more informations see: https://cwiki.apache.org/confluence/display/solr/UpdateHandlers+in+SolrConfig https://cwiki.apache.org/confluence/display/solr/Near+Real+Time+Searching Regards, Luigi Andrea Il 29/10/2013 01:37, Pascarelli Luigi Andrea ha scritto: Hi all, solr supports system property substitution as you can see at http://wiki.apache.org/solr/SolrConfigXml#System_property_substitution So the two mentioned parameters can be tuned as you like using autoCommit and autoSoftCommit features. The strange behaviour noticed by Robin is because the discovery consumer call an index method that do not call the programmatically solr commit, which the update-discovery do well (as noticed by helix). Imho the https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/IndexEventConsumer.java#L170 could be modified with calling the "void indexContent(Context context, DSpaceObject dso, boolean force, boolean commit)" method and force commit to true (or get this information from configuration to left the user to use autoSoftCommit in case the commit property is false) Hope this helps. Regards, Luigi Andrea Il 18/10/2013 15:57, TAYLOR Robin ha scritto: Hi, I suspect, but I am definitely not sure, that no automatic commits will be done with the config as it is. If I run an 'optimize' using the Solr Admin client, or restart Tomcat, then the indices get updated. Not a big issue, I think we maybe just need to set some default values. I'll do a wee bit more investigation. Cheers. On 18/10/2013 14:43, "helix84" heli...@centrum.sk wrote: I can confirm I'm seeing the same thing in DSpace 4 and that DSpace 3 had actual numbers there. I join you in your confusion. Can you observe any ill effects? I didn't notice anything wrong and I ran "update-discovery-index -f" on ~20k items yesterday. Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware
Re: [Dspace-tech] Solr config parameter interpolation
Hi all, solr supports system property substitution as you can see at http://wiki.apache.org/solr/SolrConfigXml#System_property_substitution So the two mentioned parameters can be tuned as you like using autoCommit and autoSoftCommit features. The strange behaviour noticed by Robin is because the discovery consumer call an index method that do not call the programmatically solr commit, which the update-discovery do well (as noticed by helix). Imho the https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/discovery/IndexEventConsumer.java#L170 could be modified with calling the "void indexContent(Context context, DSpaceObject dso, boolean force, boolean commit)" method and force commit to true (or get this information from configuration to left the user to use autoSoftCommit in case the commit property is false) Hope this helps. Regards, Luigi Andrea Il 18/10/2013 15:57, TAYLOR Robin ha scritto: Hi, I suspect, but I am definitely not sure, that no automatic commits will be done with the config as it is. If I run an 'optimize' using the Solr Admin client, or restart Tomcat, then the indices get updated. Not a big issue, I think we maybe just need to set some default values. I'll do a wee bit more investigation. Cheers. On 18/10/2013 14:43, "helix84" heli...@centrum.sk wrote: I can confirm I'm seeing the same thing in DSpace 4 and that DSpace 3 had actual numbers there. I join you in your confusion. Can you observe any ill effects? I didn't notice anything wrong and I ran "update-discovery-index -f" on ~20k items yesterday. Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Luigi Andrea Pascarelli Dipartimento Servizi e Soluzioni per l'Amministrazione Universitaria Divisione Ricerca Via dei Tizii, 6 00185 Roma, Italy ph. +39 06 59292895 http://www.cineca.it -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951iu=/4140/ostg.clktrk___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] CRIS Installation not clear
Dear Keir, have you published under tomcat the new webapp builded with mvn package? I have the suspect that the code in your tomcat is out-of-update. You have mentioned tomcat5, please upgrade tomcat at least to the 6 version, DSpace-CRIS is not tested for tomcat5 Luigi Andrea Il 17/10/2013 01:32, Keir Vaughan-Taylor ha scritto: Thank you for you help. I recompiled doing a fresh_install The postgres sql updates ran without error and also the sql base-configuration-crismodule.sql ran without error. Restored the original database After restarting httpd and tomcat5 the CRIS module in the administration section reference in the installation guide doesn't appear. Must be close to working but can't see where the module is initiated. On Wed, 2013-10-16 at 09:07 +0200, Andrea Bollini wrote: Hi Keir, you are right the installation instructions are not so clear as need and don't include information for upgrading an existent installation. We will try to update this documentation as soon as possible, please note that, in these last weeks, much developer resources from my company has been devolved to the next DSpace 4.0 release so we are slight late with the dspace-cris upgrade. 1) mvn package from the dspace-src directory is the right way to build DSpace-CRIS 2) to install dspace-cris on top of an existent dspace installation, you need to follow the steps required for a normal dspace update (like you have done) plus execute the following sql scripts: addon-crismodule.sql, addon-crispubmed.sql, addon-subscription.sql all located in https://github.com/CILEA/DSpace/tree/dspace-cris-1.8.2.1-beta/dspace/etc/postgres These sql will create the extra tables and sequences need by the DSpace-CRIS entities. Finally, if you want to start with a preconfigured, very basic, datamodel you can proceed with the post installation instructions, i.e. load /etc/postgres/base-configuration-crismodule.sql Hope this help, Andrea Il 16/10/2013 04.00, Keir Vaughan-Taylor ha scritto: I want to install CRIS on DSpace 1.82. In academia the package is all the rage. I have been using install instructions from Github http://cilea.github.io/dspace-cris/installation.html The install instructions refer to unpacking the CRIS module in [dspace-parent] The mvn package command only works for me in the [dspace-src] directory. I can go with that but possibly that is wrong also. The GIT instructions are for a fresh install with no existing database rather than adding the module to an existing setup. At first I tried leaving the database intact and compiling using ant update instead of ant fresh_install. After which the post-install script base-configuration-crismodule.sql fails (using psql) and also the CRIS module doesn't appear in the DSpace administration. I tried deleting the existing database and using ant fresh_install but still running base-configuration-crismodule.sql with psql fails. (It tries to do inserts into non existant tables.) Again CRIS module doesn't appear in administration tab Anyone know what I'm doing wrong? Any hints and tips? -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135031iu=/4140/ostg.clktrk ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
