Re: [base] Error on Biomaterials LIMS
It works fine now, thanks for the help. I guess I missed that spot on the second install I performed. Thanks a lot Paulo On 2012-11-22, at 2:19 PM, Nicklas Nordborg wrote: > On 2012-11-22 19:40, Paulo Nuin wrote: >> Hi >> >> We have a couple of instances of BASE installed in our systems. We are >> getting a problem whenever we are accessing entities created in the >> Biomaterial LIMS, either samples or biosources: > > This is a Tomcat configuration problem and is described in the > installation documentation: > > http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html > > Check the section about STRICT_QUOTE_ESCAPING and make sure that this is > set to 'false'. > > Hope this helps. > > /Nicklas > > -- > Monitor your physical, virtual and cloud infrastructure from a single > web console. Get in-depth insight into apps, servers, databases, vmware, > SAP, cloud infrastructure, etc. Download 30-day Free Trial. > Pricing starts from $795 for 25 servers or applications! > http://p.sf.net/sfu/zoho_dev2dev_nov > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] Error on Biomaterials LIMS
Hi We have a couple of instances of BASE installed in our systems. We are getting a problem whenever we are accessing entities created in the Biomaterial LIMS, either samples or biosources: type Exception report message description The server encountered an internal error () that prevented it from fulfilling this request. exception org.apache.jasper.JasperException: /biomaterials/samples/view_sample.jsp(191,28) Attribute value "index.jsp?ID="+ID is quoted with " which must be escaped when used within the value org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:40) org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:407) org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:88) org.apache.jasper.compiler.Parser.parseAttributeValue(Parser.java:256) org.apache.jasper.compiler.Parser.parseAttribute(Parser.java:205) org.apache.jasper.compiler.Parser.parseAttributes(Parser.java:148) org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1208) org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422) org.apache.jasper.compiler.Parser.parseBody(Parser.java:1634) org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:978) org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1246) org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422) org.apache.jasper.compiler.Parser.parseBody(Parser.java:1634) org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:978) org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1246) org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422) org.apache.jasper.compiler.Parser.parseBody(Parser.java:1634) org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:978) org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1246) org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422) org.apache.jasper.compiler.Parser.parse(Parser.java:130) org.apache.jasper.compiler.ParserController.doParse(ParserController.java:255) org.apache.jasper.compiler.ParserController.parse(ParserController.java:103) org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:185) org.apache.jasper.compiler.Compiler.compile(Compiler.java:354) org.apache.jasper.compiler.Compiler.compile(Compiler.java:334) org.apache.jasper.compiler.Compiler.compile(Compiler.java:321) org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:592) org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313) org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:709) org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:680) org.apache.jsp.biomaterials.samples.index_jsp._jspService(index_jsp.java:522) org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:388) org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313) org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69) note The full stack trace of the root cause is available in the Apache Tomcat/6.0.33 logs. Any help is appreciated. Thanks Paulo-- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] Schema
Hi Is there any available image/diagram of the current schema? Thanks in advance Paulo -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
Re: [base] Change BASE's HTML title
Noticed that domain and hostname were identical, don't know why, and reset it, but it still shows me the same thing. Paulo On 2012-08-20, at 3:01 PM, Paulo Nuin wrote: > Indeed there's some error getting localhost > > 13:40:29,172 ERROR Cache:202 - Unable to set localhost. This prevents > creation of a GUID. Cause was: braincode-linux: braincode-linux > java.net.UnknownHostException: braincode-linux: braincode-linux > at java.net.InetAddress.getLocalHost(InetAddress.java:1426) > at net.sf.ehcache.Cache.(Cache.java:200) > at > net.sf.ehcache.config.ConfigurationHelper.createCache(ConfigurationHelper.java:302) > at > net.sf.ehcache.config.ConfigurationHelper.createDefaultCache(ConfigurationHelper.java:218) > at net.sf.ehcache.CacheManager.configure(CacheManager.java:618) > at net.sf.ehcache.CacheManager.init(CacheManager.java:361) > at net.sf.ehcache.CacheManager.(CacheManager.java:302) > at org.hibernate.cache.EhCacheProvider.start(EhCacheProvider.java:131) > at > org.hibernate.cache.impl.bridge.RegionFactoryCacheProviderBridge.start(RegionFactoryCacheProviderBridge.java:72) > at > org.hibernate.impl.SessionFactoryImpl.(SessionFactoryImpl.java:238) > at > org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1872) > at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:210) > at net.sf.basedb.core.Application.start(Application.java:507) > at net.sf.basedb.core.Application.start(Application.java:399) > at > net.sf.basedb.clients.web.servlet.StartStopServlet.init(StartStopServlet.java:58) > at javax.servlet.GenericServlet.init(GenericServlet.java:212) > at > org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173) > at > org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993) > at > org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java:4734) > at > org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799) > at > org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779) > at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601) > at > org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1079) > at > org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1002) > at > org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:506) > at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1385) > at > org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:306) > at > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142) > at > org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1389) > at > org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653) > at > org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662) > at > org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642) > at java.lang.Thread.run(Thread.java:679) > > > How can this be solved? > > Thanks > Paulo > > > On 2012-08-20, at 1:57 PM, Nicklas Nordborg wrote: > >> On 2012-08-20 18:56, Paulo Nuin wrote: >>> Hi >>> >>> The computer has a name under /etc/HOSTNAME running SuSE, and network is >>> fine. >> >> Check Tomcat's log file if there are any error messages. The name is set >> to 'unknown' if the name can't be retrieved from the system. >> >> /Nicklas >> >> >> -- >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> ___ >> The BASE general discussion mailing list >> basedb-users@lists.sourceforge.net >> unsubscribe: send a mail with subject "unsubscribe" to >> basedb-users-requ...@lists.sourceforge.net > > > -- > Live Security Virtual Conference >
Re: [base] Change BASE's HTML title
Indeed there's some error getting localhost 13:40:29,172 ERROR Cache:202 - Unable to set localhost. This prevents creation of a GUID. Cause was: braincode-linux: braincode-linux java.net.UnknownHostException: braincode-linux: braincode-linux at java.net.InetAddress.getLocalHost(InetAddress.java:1426) at net.sf.ehcache.Cache.(Cache.java:200) at net.sf.ehcache.config.ConfigurationHelper.createCache(ConfigurationHelper.java:302) at net.sf.ehcache.config.ConfigurationHelper.createDefaultCache(ConfigurationHelper.java:218) at net.sf.ehcache.CacheManager.configure(CacheManager.java:618) at net.sf.ehcache.CacheManager.init(CacheManager.java:361) at net.sf.ehcache.CacheManager.(CacheManager.java:302) at org.hibernate.cache.EhCacheProvider.start(EhCacheProvider.java:131) at org.hibernate.cache.impl.bridge.RegionFactoryCacheProviderBridge.start(RegionFactoryCacheProviderBridge.java:72) at org.hibernate.impl.SessionFactoryImpl.(SessionFactoryImpl.java:238) at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1872) at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:210) at net.sf.basedb.core.Application.start(Application.java:507) at net.sf.basedb.core.Application.start(Application.java:399) at net.sf.basedb.clients.web.servlet.StartStopServlet.init(StartStopServlet.java:58) at javax.servlet.GenericServlet.init(GenericServlet.java:212) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173) at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993) at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4734) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601) at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1079) at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1002) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:506) at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1385) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:306) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142) at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1389) at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653) at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662) at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642) at java.lang.Thread.run(Thread.java:679) How can this be solved? Thanks Paulo On 2012-08-20, at 1:57 PM, Nicklas Nordborg wrote: > On 2012-08-20 18:56, Paulo Nuin wrote: >> Hi >> >> The computer has a name under /etc/HOSTNAME running SuSE, and network is >> fine. > > Check Tomcat's log file if there are any error messages. The name is set > to 'unknown' if the name can't be retrieved from the system. > > /Nicklas > > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
Re: [base] Change BASE's HTML title
Hi The computer has a name under /etc/HOSTNAME running SuSE, and network is fine. Thanks Paulo On 2012-08-20, at 12:32 PM, Nicklas Nordborg wrote: > On 2012-08-20 17:09, Paulo Nuin wrote: >> Hi >> >> I have a quick question on configuring BASE's HTML page title. In the >> server we have installed now it appears >> >> BASE 3.1.1 @ unknown >> >> I found the jsp pages in the www directory but it is not clear to me >> where this title is coming from. I was able to add a value to the >> title variable in the jsp, but the unknown still appears. > > The title is generated from the current BASE version and the name of the > computer it is installed on. I have never seen the string 'unknown' > there. Usually, if the computer doesn't have a name the title will be > something like: 'BASE x.y.z @ 127.0.0.1' or 'BASE x.y.z @ localhost' > > Maybe it is an indication that there is no network connection... > > Or maybe the computer's name is 'unknown'? > > /Nicklas > > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] Change BASE's HTML title
Hi I have a quick question on configuring BASE's HTML page title. In the server we have installed now it appears BASE 3.1.1 @ unknown I found the jsp pages in the www directory but it is not clear to me where this title is coming from. I was able to add a value to the title variable in the jsp, but the unknown still appears. Any help is appreciated. Thanks in advance Paulo -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
