/Johan
On 06-04-10 15.27, "Ana Conesa" <[EMAIL PROTECTED]> wrote:
Thanks Johan, I hope you do not mind another question...
I did find the plugins (were there but I did not have the permissions...)
I have been trying to create a configuration following the steps you give in your mail. It´s OK to create it (I think, although while creating I could only select the plugin, give a name and write a Definition in plain text), but when I have to do the actual configuration, I get the following error message...
..at
org.apache.jsp.common.plugin.configure_jsp._jspService(configure_jsp.java:244)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)
...at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
...at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463)
...at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
...at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
...at
org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:703)
...at
org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:670)
...at
org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:389)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)
...at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:595)
What am I doing wrong now?
Ana
At 03:18 PM 4/6/2006, you wrote:
The plugins that you need are located in the package net.sf.basedb.plugins and they are added to the base2 installation during the installation. If you click Administrate -> Plugins -> Definitions you will see them. To be able to run a plugin in base you have to create a configuration. In the case of these importer plugins this means that you have to describe the layout of your flatfile.
To create a Configuration click Administrate -> Plugins -> Configurations. There you will find a link called “new”, click it. Here you add some values to the configuration and most important you choose a Definition. When you are done, click save. You will see that your new configuration is added to the table. Now you have to configure your configuration, click configure and you will be redirected to the parameter list. Now add the regular expressions that defines your file and specify which column that should be associated with what value.
Ex
Configuration for a small reporter file.
---
Name ID
Homo sapiens clone HQ0670 H200018394
V-akt murine thymoma viral oncogene homolog 2 H200019178
G protein-coupled receptor 10 H200016066
---
Data header = Name\tID
Data splitter = \t
Name = \0\
Id = \1\
/Johan
On 06-04-03 14.33, "Ana Conesa" <[EMAIL PROTECTED]> wrote:
Hi,
I am a new BASE user, getting started with BASE2 . I am trying to import reporters, printmaps and rawdata and it seems that I would need the corresponding plugins to do so. I have not been able to find them within the Base2 installation or at the project site, and I do not get very far with the available documentation for BASE v1.3. Can anybody help me out in this?.
Cheers
Ana
O @@@@@ Ana Conesa, PhD.
@@@ O @@ O @ Centro de Genómica
@ O @@@@ O @ Instituto Valenciano de Investigaciones Agrarias (IVIA)
@@@ O @@@@ Carretera Moncada - Naquera, Km. 4,5
@@@@ O @ 46113 Moncada (Valencia) SPAIN
|| Tel. +34 963424000 ext.70161; Fax. +34 963424001
|| email: [EMAIL PROTECTED]
------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk0944$17201642 <http://sel.as-us.falkag.net/sel?cmd=lnk0944$17201642> _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
O @@@@@ Ana Conesa, PhD.
@@@ O @@ O @ Centro de Genómica
@ O @@@@ O @ Instituto Valenciano de Investigaciones Agrarias (IVIA)
@@@ O @@@@ Carretera Moncada - Naquera, Km. 4,5
@@@@ O @ 46113 Moncada (Valencia) SPAIN
|| Tel. +34 963424000 ext.70161; Fax. +34 963424001
|| email: [EMAIL PROTECTED]
------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk0944$17201642 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
