Hi Sudeep,

The project default setting for X!Tandem search is written to <pipeline root>/default_input.xml and for Mascot search is written to <pipeline>/mascot_default_input.xml

So, if the writing fail, (e.g. due to permission settings or out of storage, ) this error message will appear.

*Chee-Hong.

Yes, i got what you are trying to say. But the problem is not getting solved.
When a project is created,tomcat and cpas should have write permissions to that folder.
Since system admin can only create a project, so i am the owner of the project, tomcat and CPAS is been given all the permissions. SO why this error is occurring?

I "tail" the cpas-error.log and permission denied error is shown, please see the attached file.
OK for some reason i am NOT able to upload any file.
So have to do copy paste

ERROR PipelineProvider 2007-02-23 13:44:44,125 TP-Processor7 : Error writing default input file.
java.io.FileNotFoundException: /home/cpaspipeline/datasets/data3/default_input.xml (Permission denied)
        at java.io.FileOutputStream.open(Native Method)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:179)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:131)
        at java.io.FileWriter.<init>(FileWriter.java:73)
        at org.fhcrc.cpas.ms2.pipeline.MS2PipelineManager.setDefaultInputXML(MS2PipelineManager.java:465)
        at MS2.Pipeline.PipelineController.setTandemDefaults(PipelineController.java:660)
        at sun.reflect.GeneratedMethodAccessor118.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.apache.beehive.netui.pageflow.FlowController.invokeActionMethod(FlowController.java:815)
        at org.apache.beehive.netui.pageflow.FlowController.getActionMethodForward(FlowController.java:754)
        at org.apache.beehive.netui.pageflow.FlowController.internalExecute(FlowController.java:428)
        at org.apache.beehive.netui.pageflow.PageFlowController.internalExecute(PageFlowController.java:285)
        at org.apache.beehive.netui.pageflow.FlowController.execute(FlowController.java:308)
        at org.apache.beehive.netui.pageflow.internal.FlowControllerAction.execute(FlowControllerAction.java:48)
        at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
        at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.access$201(PageFlowRequestProcessor.java:106)
        at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor$ActionRunner.execute(PageFlowRequestProcessor.java:2049)
        at org.apache.beehive.netui.pageflow.interceptor.action.internal.ActionInterceptors.wrapAction(ActionInterceptors.java:90)
        at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processActionPerform(PageFlowRequestProcessor.java:2120)
        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
        at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processInternal(PageFlowRequestProcessor.java:601)
        at org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.process(PageFlowRequestProcessor.java:887)
        at org.apache.beehive.netui.pageflow.AutoRegisterActionServlet.process(AutoRegisterActionServlet.java:611)
        at org.apache.beehive.netui.pageflow.PageFlowActionServlet.process(PageFlowActionServlet.java:157)
        at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:432)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
        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.fhcrc.cpas.view.ViewServlet.service(ViewServlet.java:128)
        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.fhcrc.cpas.data.TransactionFilter.doFilter(TransactionFilter.java:36)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
        at filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
        at org.fhcrc.cpas.module.ModuleLoader.doFilter(ModuleLoader.java:833)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
        at org.fhcrc.cpas.security.AuthFilter.doFilter(AuthFilter.java:82)
        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.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:199)
        at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:282)
        at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
        at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:697)
        at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:889)
        at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
        at java.lang.Thread.run(Thread.java:595)

I would suggest giving everyone write permission to the file specified in the error. At this point, you really should not get a permissions error changing it. Assuming that succeeds, then you need to figure out why the user under which tomcat is getting run does not own the file, or is not part of a group that has write permission to it.

Hi Brendan, Chee Hong,
We already have given all the permissions to TOMCAT and CPAS.

This is what i found out.

Sudeep,TOMCAT and CPAS are in the same group. When i am creating a directory to put the data files, i am the owner of the file. I narrowed down the problem is with write permissions. Each time i create a directory i have to give write permissions to the group i.e TOMCAT and CPAS, as soon as this is done, there is no problem.
It would be really handy if using CPAS we can upload the files and then take care of the permissions. When is version 2.0 is being released? I think you are planning to provide this feature.

Further it would be helpful to have a "delete" feature in MS2. There is a "delete" and "complete" feature in data pipeline. So far as i understood, "delete" deletes the run and "complete" forces it to stops the process, more sort of "force quit" however, in MS2 the files remains and there is no way to remove the file(s) created in MS2 if either of the options(delete, complete) are used in data pipeline during the run.

Hi Sudeep,

Most Unix system setting will not have group write permission turn on by default. You can use "umask" and "newgrp" commands in your shell default set up or in a separate shell script that you can "source" when you need too to create file with the right permission settings. Please consult your system &/ security administrator on your site policy.

Yes, there are plans to address this usability issues.

*Chee-Hong.

Thanks Brendan and Chee Hong for the suggestions, i will follow them.