Running test data set

CPAS Forum (Inactive)
Running test data set sum732  2007-01-09 12:11
Status: Closed
Assigned To: adam
 
Hi,
I have been assigned a project which involves analysis and evaluation of CPAS in proteomics lab. I installed CPAS successfully and even ran the test dataset that came along with it. Today i tried to ran some different datasets, however, when i assign proper path to data file and to database file, and i return to pipeline module to upload and run, folders are shown, but when i click on the datafile nothing is shown there. What is the problem here.
The steps i followed:
1)Created a project, used custom to select, Experiment, MS2 and pipeline. Default was changed to experiment.
2)Clicked the pipeline tab, clicked "setup" gave the path to datafile (for example C:\Testdata1)
3)Path to the database (c:\Testdata1\databases).
4) Set X!Tandem parameters to default.
5) Now went back to upload and run, folders are shown but they are shown as empty.
I am not able to understand the reason.
I thought it might have to do some thing with the "root dir" of CPAS. So as shown in the example, i moved all my datafile and database to C:\cpaspipeline\Testdata1. But its the same problem (i should not have to do this, cause root can be any thing, am i correct??).
After repeatedly trying, i uninstalled CPAS and tried to install again. It is not accepting my user name and password.
It takes me to http://localhost:8080/cpas/admin/moduleStatus.view, where i click "express installation". Now when i enter my user name(email add) and password. It keeps looping back to the same pages with an error msg (The e-mail address and password you entered did not match any accounts on file). Also tried to reset the password but have no effect. I used the same user name and pswd to enter this page and posted this msg.

Any ideas as what is going wrong in both the case?

OS: Windows XP Profesional, SP2
CPAS ver: 1.7
Web Browser: IE 6.0
Thanks
Sudeep
 
 
sum732 responded:  2007-01-09 14:10
OK i was able to get CPAS accept my username and password. However, when i click "express installation", it is getting stuck at PORTAL, keeps looping back to the page (seem like refreshing the page many time). I had to kill the job. When i again ran it, got the following error msg

org.postgresql.util.PSQLException: ERROR: schema "comm" does not exist
       at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525)
       at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309)
       at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
       at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452)
       at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:354)
       at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:258)
       at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:92)
       at org.fhcrc.cpas.data.Table._executeQuery(Table.java:90)
       at org.fhcrc.cpas.data.Table.internalExecuteQueryArray(Table.java:280)
       at org.fhcrc.cpas.data.Table.select(Table.java:1205)
       at org.fhcrc.cpas.data.Table.select(Table.java:1197)
       at Wiki.model.WikiManager.getWikiByName(WikiManager.java:122)
       at Wiki.model.WikiManager.getLatestWikiAndVersion(WikiManager.java:630)
       at Wiki.model.WikiManager.getWiki(WikiManager.java:542)
       at Wiki.model.ServiceImpl.getHtml(ServiceImpl.java:38)
       at org.fhcrc.cpas.security.SecurityManager.getTermsOfUseHtml(SecurityManager.java:1378)
       at Login.LoginController.showLogin(LoginController.java:446)
       at Login.LoginController.showLogin(LoginController.java:412)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
       at java.lang.reflect.Method.invoke(Unknown Source)
       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.doGet(ActionServlet.java:414)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
       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:824)
       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.coyote.http11.Http11Processor.process(Http11Processor.java:869)
       at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:667)
       at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
       at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
       at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
       at java.lang.Thread.run(Unknown Source)


request attributes
javax.servlet.forward.request_uri = /cpas/Login/showLogin.view
javax.servlet.forward.context_path = /cpas
javax.servlet.forward.servlet_path = /Login/showLogin.view
javax.servlet.forward.query_string = URI=http%3A%2F%2Flocalhost%3A8080%2Fcpas%2FProject%2Fhome%2Fhome.view
_netui:sharedFlow:global.Global = global.Global@ecfaea
_netui:_actionURI = /cpas/Login/showLogin.do
org.apache.struts.action.ERROR = {java.lang.Throwable=[java.lang.Throwable[org.postgresql.util.PSQLException: ERROR: schema "comm" does not exist]]}
org.apache.struts.action.EXCEPTION = java.lang.RuntimeException: org.postgresql.util.PSQLException: ERROR: schema "comm" does not exist
sharedFlow = {}
_netui:changedAttrs = [_netui:sharedFlow:global.Global, _netui:facesBacking, _netui:curLongLivedModule, _netui:curPageFlow]
url_rewriters = [org.apache.beehive.netui.pageflow.internal.DefaultURLRewriter@0]
_defaultMsgs = org.apache.beehive.netui.pageflow.internal.ExpressionAwareMessageResources@4d37e5
_netui:failoverAttrs = {_netui:curPageFlow=Login.LoginController@190d1e8}
globalApp = global.Global@ecfaea
pageInput = {}
cpas.OriginalURL = http://localhost:8080/cpas/Login/showLogin.view?URI=http%3A%2F%2Flocalhost%3A8080%2Fcpas%2FProject%2Fhome%2Fhome.view
org.apache.struts.action.mapping.instance = ActionConfig[path=/showLogin,name=loginForm,parameter=Login.LoginController,scope=request,type=org.apache.beehive.netui.pageflow.internal.FlowControllerAction
loginForm = Login.LoginController$LoginForm@c5119e
bundle = {_defaultMsgs=StrutsBundleNode messageResource: org.apache.struts.util.PropertyMessageResources@5b84b locale: en_US}
pageFlow = Login.LoginController@190d1e8
_netui:curPageFlow = Login.LoginController@190d1e8
org.apache.beehive.controls.runtime.servlet.ServletBeanContext = org.apache.beehive.netui.pageflow.internal.PageFlowBeanContext@18662b6
_netui:servletContext = org.apache.catalina.core.ApplicationContextFacade@1baa8d8
org.apache.struts.action.MODULE = org.apache.struts.config.impl.ModuleConfigImpl@1a30706

core schema database configuration
Server URL jdbc:postgresql://localhost/cpas
Product Name PostgreSQL
Product Version 8.1.4
Driver Name PostgreSQL Native Driver
Driver Version PostgreSQL 8.1 JDBC3 with SSL (build 407)
 
adam responded:  2007-01-09 15:34
It appears that the initial bootstrapping process (the initial code that sets up the database schema) was interrupted before the schema could be created or the PostgreSQL database was modified directly after bootstrapping occurred.

The easiest thing to do at this point is simply uninstall CPAS and reinstall. You will choose a new CPAS id & password for the first adminstrator account; that's what you'll use to sign in and use your CPAS system. Once it's up and running do not uninstall it again; any issues you have using the MS2 module can probably be addressed with simple steps.

Note: the reset password feature will work only if you've configured CPAS with SMTP server settings.

Adam
 
sum732 responded:  2007-01-10 06:41
I did what you suggested. Uninstalled CPAS and installed it again. I selected a new password and user name. But there is no effect. It is again stuck at module "portal". It shows me "core", "query", " wiki" Version 1.70 ready to use. It is NOT moving further from "portal". The page seems to refresh itself after couple of seconds. Any ideas what is going on?? Please help.

I also noticed that at the top right hand corner it is showing my old user name (email add), not the one which i entered recently.
 
sum732 responded:  2007-01-10 08:01
Hello Adam,

OK so i found few things, all this while i was using the installer that came with CPAS. So i uninstalled CPAS and installed it again. Gave and new user name and password as the first user, in the next step i selected to install the express version. It again got stuck at "portal". And as i mentioned earlier, i noticed that at top right hand corner it was showing me my old user name. I did the following: signed out, logged back in with my *new* user name and password, by doing so i was able to go the pass "portal", but then again it got stuck at the next step. So i repeated the procedure. Each time i log back in, it will NOT show me my NEW user name but the old one. After repeated attempts i was able to install successfully.
In the page, " customize CPAS sever" i can see all my old entries. This told me that something is wrong as why is my old settings still exists. So i used uninstaller on windows (control panel-> add remove programs-->CPAS, Apache, Postgre). Also removed what ever i can from *regedit". This time when i installed CPAS again, there was no problem. However, in "customize CPAS" old setting still exists. In top right hand corner it is again showing my old user name and when i go to "Manage Site" -> "create project" old project are shown, although if i click on them an error is shown, "404: Page Not Found - 404: page not found". It seems that old tables are delete but somehow not removed completely.

What needs to be done to *completely remove* each and every instance of CPAS and tables created by other applications, so that i can begin fresh??

Thanks
Sudeep
 
adam responded:  2007-01-10 11:02
Sounds like CPAS is successfully installed and running, but your database is still in a very bad state.

I'm assuming you have no useful data in your database. If so, try the following steps:

- Shut down the "CPAS Apache Tomcat 5.5" service (use the Administrative Tools/Services UI or the command line)
- Open "pgAdmin III", the GUI administrative tool for PostgreSQL
- Connect to the localhost server (you'll need your PostgreSQL credentials to do this)
- Expand "Databases"
- Right click "cpas" and "Delete/Drop"
- Start the "CPAS Apache Tomcat 5.5" service

CPAS should start and create the database from scratch. You will pick a CPAS admin email & password again and all modules should install. If anything fails, stop what you're doing, post the first error that occurs and attach your cpas.log file (in tomcat/logs).
 
sum732 responded:  2007-01-15 07:58
Hello,
So far all is well. CAPS is up and running and i am able to run my own datasets. Although old "projects" are still shown, but for the moment NOT paying that much attention to them.
Thanks for your assistance