Re: [base] can't export data to Mev
Dear Jari We checked the directory we assigned for experiment (template/raw data). No Mev files appears here, neither in home directory. Yesterday I sent Tomcat's log file with error that perhaps explain why the Mev files are not saved. Any help will be highly appreciated Regards Daniel Nicklas Nordborg wrote: > Daniel Octavio Palenzuela Gardon wrote: >> By other side, when we try to launch Mev in the "Tools" column when >> viewing bioassay sets of an experiment, there is a file with extension >> ...TDMS.TXT that it`s suppose to be save in raw data, but when we do >> browse, there isn't any file with this extension in raw data folder. > > Again... check your filters. And remember, the MeV generated file ends up in the directory you assigned for your experiment when the experiment was created. If you did not set a directory for your experiment, the files end up in your hone directory. Cheers, Jari -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Can't export data to Tmev
Dear Niklas The filters were checked in both case and nor Mev plugin is created neither file TDMS.TXT is saved. Do you have any other suggestion to solve this problem?? Regards Daniel Daniel Octavio Palenzuela Gardon wrote: > During the installation of Tmev there is a step to create a plugin by > clicking the 'New' button on the 'Administrate -> Plugins -> > Definitions' page. After this step we cannot see any new Mev plugin in > Definition page. Where we can find TDMS exporter plugin to verify its > permissions options?. Please make sure that you remove all filters from the list page. Search for 'MeV%' in the name column. > By other side, when we try to launch Mev in the "Tools" column when > viewing bioassay sets of an experiment, there is a file with extension > ...TDMS.TXT that it`s suppose to be save in raw data, but when we do > browse, there isn't any file with this extension in raw data folder. Again... check your filters -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Can't export data to Tmev
During the installation of Tmev there is a step to create a plugin by clicking the 'New' button on the 'Administrate -> Plugins -> Definitions' page. After this step we cannot see any new Mev plugin in Definition page. Where we can find TDMS exporter plugin to verify its permissions options?. By other side, when we try to launch Mev in the "Tools" column when viewing bioassay sets of an experiment, there is a file with extension ...TDMS.TXT that it`s suppose to be save in raw data, but when we do browse, there isn't any file with this extension in raw data folder. Regards Daniel Daniel Octavio Palenzuela Gardon wrote: > I have logged as postgres the default administrator of BASE, which > suppose to have full access. Do I have to create a new user?? > No, you don't need another user. The root user should have full access. Are you sure that you are using the correct account? Have you modified the permissions for the TDMS exporter plug-in? It should be using the 'no permissions' option. From: Daniel Octavio Palenzuela Gardon Sent: Thursday, September 24, 2009 4:59 PM To: 'basedb-users@lists.sourceforge.net' Subject: RE: Can't export data to Tmev I have logged as postgres the default administrator of BASE, which suppose to have full access. Do I have to create a new user?? Regards Daniel Daniel Octavio Palenzuela Gardon wrote: > Hi all, > > > > We installed Tmev pluging in BASE and we are trying to export data to > Mev but we receive below error. Could someone give us a help to solve > this problem.?? It seems like the logged in user doesn't have permission to access the "raw data" directory. /Nicklas From: Daniel Octavio Palenzuela Gardon Sent: Wednesday, September 23, 2009 12:33 PM To: 'basedb-users@lists.sourceforge.net' Subject: Can't export data to Tmev Hi all, We installed Tmev pluging in BASE and we are trying to export data to Mev but we receive below error. Could someone give us a help to solve this problem.?? Regards Daniel Error: Permission denied: Not allowed to read Directory[id=501; name=raw data] Show Permission denied: Not allowed to read Directory[id=501; name=raw data] net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed to read Directory[id=501; name=raw data] ...at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110) ...at net.sf.basedb.core.DbControl.getItem(DbControl.java:824) ...at net.sf.basedb.core.DbControl.loadItem(DbControl.java:709) ...at net.sf.basedb.core.Directory.getById(Directory.java:197) ...at net.sf.basedb.core.Directory.getByPath(Directory.java:217) ...at net.sf.basedb.core.File.getByPath(File.java:180) ...at net.sf.basedb.core.plugin.AbstractExporterPlugin.pathCanBeUsed(AbstractExporterPlugin.java:363) ...at net.sf.basedb.mev.plugin.TdmsExporterPlugin.configure(TdmsExporterPlugin.java:163) ...at net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:114) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:493) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:70) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849) ...at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583) ...at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454) ...at java.lang.Thread.run(Unknown Source) -
Re: [base] Can't export data to Tmev
I have logged as postgres the default administrator of BASE, which suppose to have full access. Do I have to create a new user?? Regards Daniel Daniel Octavio Palenzuela Gardon wrote: > Hi all, > > > > We installed Tmev pluging in BASE and we are trying to export data to > Mev but we receive below error. Could someone give us a help to solve > this problem.?? It seems like the logged in user doesn't have permission to access the "raw data" directory. /Nicklas From: Daniel Octavio Palenzuela Gardon Sent: Wednesday, September 23, 2009 12:33 PM To: 'basedb-users@lists.sourceforge.net' Subject: Can't export data to Tmev Hi all, We installed Tmev pluging in BASE and we are trying to export data to Mev but we receive below error. Could someone give us a help to solve this problem.?? Regards Daniel Error: Permission denied: Not allowed to read Directory[id=501; name=raw data] Show Permission denied: Not allowed to read Directory[id=501; name=raw data] net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed to read Directory[id=501; name=raw data] ...at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110) ...at net.sf.basedb.core.DbControl.getItem(DbControl.java:824) ...at net.sf.basedb.core.DbControl.loadItem(DbControl.java:709) ...at net.sf.basedb.core.Directory.getById(Directory.java:197) ...at net.sf.basedb.core.Directory.getByPath(Directory.java:217) ...at net.sf.basedb.core.File.getByPath(File.java:180) ...at net.sf.basedb.core.plugin.AbstractExporterPlugin.pathCanBeUsed(AbstractExporterPlugin.java:363) ...at net.sf.basedb.mev.plugin.TdmsExporterPlugin.configure(TdmsExporterPlugin.java:163) ...at net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:114) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:493) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:70) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849) ...at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583) ...at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454) ...at java.lang.Thread.run(Unknown Source) -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Can't export data to Tmev
Hi all, We installed Tmev pluging in BASE and we are trying to export data to Mev but we receive below error. Could someone give us a help to solve this problem.?? Regards Daniel Error: Permission denied: Not allowed to read Directory[id=501; name=raw data] Show Permission denied: Not allowed to read Directory[id=501; name=raw data] net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed to read Directory[id=501; name=raw data] ...at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110) ...at net.sf.basedb.core.DbControl.getItem(DbControl.java:824) ...at net.sf.basedb.core.DbControl.loadItem(DbControl.java:709) ...at net.sf.basedb.core.Directory.getById(Directory.java:197) ...at net.sf.basedb.core.Directory.getByPath(Directory.java:217) ...at net.sf.basedb.core.File.getByPath(File.java:180) ...at net.sf.basedb.core.plugin.AbstractExporterPlugin.pathCanBeUsed(AbstractExporterPlugin.java:363) ...at net.sf.basedb.mev.plugin.TdmsExporterPlugin.configure(TdmsExporterPlugin.java:163) ...at net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:114) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:493) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:70) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849) ...at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583) ...at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454) ...at java.lang.Thread.run(Unknown Source) -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Can't find getting started guide
Hi, Iam new in BASE and I wanted to start from getting_started guide that outlines the first steps with BASE 2. I tried next link http://base.thep.lu.se/chrome/site/doc/user/getting_started.html but unfortunately, this page is not found in the web. Can someone help me to find started guide for BASE2?. Many thanks Daniel -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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