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Documentation Templates for UseCase and Software Design

Not everyone will be using case tools. We need to provide simple a page or
two template for the use case and software design.

Essentially we need to provide headings and subheadings of what is expected
from developers.

Original issue reported on code.google.com by [email protected] on 20 Jan 2010 at 5:58

Flow Exception: Classification by Seyer...

I ran this flow with sample rate set to 44100 and the flow crashed with the
exception below

Retrieving test file paths for set: 34
Got 83 tracks, resolving to files
Resolving files for 83 tracks
tracks in set:
Query returned data on 2215 files, filtering
mapped 0 files to tracks

mapped 0 files to tracks
returning file list length: 83
Got file list length: 83, preparing output
2010.01.26 13:51:03.011::WARNING:  java.lang.NullPointerException  
[org.meandre.core.engine.WrappedComponent.run]
<4535431591/instance/collectionselector/0:20>
2010.01.26 13:51:03.291::SEVERE:  Aborting execution. Component
http://imirsel.org/classification/classification_seyerlehner/classification_seye
rlehner1264535431591/instance/collectionselector/0
requested execution termination.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
</407724774/1264535423820-token/mr-proper:21>
2010.01.26 13:51:03.292::SEVERE:  Aborting execution. Requested execution
termination propagated.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
</407724774/1264535423820-token/mr-proper:21>
2010.01.26 13:51:03.292::SEVERE:  Disposing WebUI.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
</407724774/1264535423820-token/mr-proper:21>
Flow Aborted Tue Jan 26 13:51:03 CST 2010
http://imirsel.org/classification/classification_seyerlehner/classification_seye
rlehner1264535431591/0AFFFFFE2CFA/1264535460189/407724774/1264535423820-token/
Probe Disposed

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 7:53

Implement Beat detection evaluator and file reader util classes

Implement Beat detection evaluator and file reader util classes in M2K and 
component wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 4 Feb 2010 at 1:55

Meandre servers leaky memory

Meandre servers are leaking memory as they try and read the security realms
file.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 12:41

flow description field truncated

Flow description field is truncated to 256 characters -it needs to be of
smalltext type.

Original issue reported on code.google.com by [email protected] on 29 Jan 2010 at 2:59

Console goodbye again

I noticed the console is not working again -I see

GET
/services/jobs/job_console.json?uri=http://imirsel.org/analysis/structure/struct
ure_mauch/structure_mauch1264699491759/0A0101012D5E/1264699503326/1847510476/126
4699488342-token/'

 HTTP Response Code 403 -> Forbidden  
[org.imirsel.meandre.client.MeandreBaseClient.verifyResponseOK]
<511307135@qtp-697745840-4:17>



which indicates  trouble at the meandre end.

Original issue reported on code.google.com by [email protected] on 28 Jan 2010 at 5:36

Modify the FlowService to create/update template flows

The flowservice during the deployment should install the template flows.

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 3:00

Evaluation components should take the dataset as a parameter and use it on the result pages output.

Evaluation components should take the dataset as a parameter and use it on
the result pages output. At present macro classification evaluator uses
string 'OverallPublishedResults' and does not tell you what dataset the
results are for.

We need to take both evaluation name and dataset name/description and add
them to the results pages.

Original issue reported on code.google.com by [email protected] on 28 Jan 2010 at 7:28

firewall rules on gserve033.lis.illinois.edu

Dan,

Can you modify the iptables rules on  gserve033.lis.illinois.edu so that
cloud.cs.illinois.edu can connect to the mysql running on this box. 
Alejandro is running scripts on the cloud to download jamendo track  database.


I added 
iptables -I INPUT 3 -i eth0 -p udp --dport mysql -s 128.174.252.0/23 -j ACCEPT

and 

iptables -I INPUT 3 -i eth0 -p tcp --dport mysql -s 128.174.252.0/23 -j ACCEPT



But no luck.

Thanks
Amit

Original issue reported on code.google.com by [email protected] on 24 Jan 2010 at 2:22

Migrate Meandre Servers to Cluster nodes

The meandre servers are all on nema -they need to be moved to the cluster
nodes.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 2:19

Implement Chord detection evaluator and file reader util classes

Implement Chord detection evaluator and file reader util classes in M2K and 
component wrappers 
in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 4 Feb 2010 at 1:54

Blocking: #71

Produce API for evaluation components and MIREX file readers/writers

Produce an API (interface, maybe abstract implementation) for evaluation 
components and MIREX 
file readers/writers that all such code should implement/extend.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:36

Executing a job should take you directly to the job output

Executing a job should take you directly to the job output rather than job
list page. 

If the job has not yet been scheduled display job status

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 12:31

Testing and build platform for MIREX and IMIRSEL

We require a testing and build machine for MIREX. It was decided to spare a
8 core 32 gig box for this. Dan mentions he can do this soonish.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 2:16

nema user accounts settings, homedirs does not show

-bash: /home/mertbay/.ssh/authorized_keys: No such file or directory
chmod: cannot access `/home/mertbay/.ssh/authorized_keys': No such file or
directory
chmod: cannot access `/home/mertbay': No such file or directory

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 11:53

Job status does not updated when executed.

What steps will reproduce the problem?
1.  After job started, the jobstatus stays as "submitted" 


What is the expected output? What do you see instead?
It should be "started"

Original issue reported on code.google.com by [email protected] on 24 Jan 2010 at 2:46

Select Job as Submission Should redirect to FlowFormManager.getFlowTemplate?id=10

After a user selects job as submission -redirect to the 

FlowFormManager.getFlowTemplate?id=10

So that the user can run the MIREX evaluation.

-Needed for Stephen's demo.

Amit

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 2:35

Deployment documentation

Deployment documentation including that for the demo and production needs
to be written for flowservice (including meandre servers), diy
webapplication in two contexts
-Testing and production

It should cover
1. The list of services that need to be running before the application is run.
2. The ports and proxy settings for these services.
3. What to check to make sure that these services are deployed correctly.
4. The information needed by the monitoring service (nagios) to check
status of the service.

Original issue reported on code.google.com by [email protected] on 20 Jan 2010 at 6:03

nema-raid readonly

Trying to install Matlab so that it's shared with the nodes


[root@compute-1-2 nema-raid]# mkdir -p share/apps
mkdir: cannot create directory `share': Permission denied
[root@compute-1-2 nema-raid]# 


Can you check please.

Thanks
Amit

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 11:48

Hide flow components

The components like fork need to be marked as hidden for a flow. This is a
per flow property not something that can be implemented at the level of the
components.

Original issue reported on code.google.com by [email protected] on 29 Jan 2010 at 3:50

json uri is not mapped in the dispatcher

Guojun -this one is for you


HTTP Response Code 403 -> Forbidden  
[org.imirsel.meandre.client.MeandreBaseClient.verifyResponseOK]
<1287887392@qtp-697745840-5:12>
680693 [1287887392@qtp-697745840-5] INFO
org.apache.commons.httpclient.auth.AuthChallengeProcessor - basic
authentication scheme selected
2010.01.26 13:30:08.049::SEVERE:  Problem contacting the Meandre Server at
'nema.lis.uiuc.edu', port:11709, as user:'admin' 
 GET /services/jobs/job_console.json?uri=' 
 HTTP Response Code 403 -> Forbidden  
[org.imirsel.meandre.client.MeandreBaseClient.verifyResponseOK]
<1287887392@qtp-697745840-5:12>
Show Job here: Classification: Andreas F. Ehmann
ST

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 7:35

Update Tag evaluator to current NEMA standard

Migrate Tag evaluator and file reader util classes in M2K to new evaluator API 
and build component 
wrappers in Components project. Implement JUnit tests based on past MIREX 
submission output.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:49

compute nodes of nema can't connect to mysql on nema

The database (meandrestore) on nema has proper permission and I am able to
connect from other hosts. When I try and connect from the compute nodes
mysql client just hangs with no message. Can you help Dan -I am running out
of ideas, unless there is a specific iptables rule to deny access from
compute nodes?

Original issue reported on code.google.com by [email protected] on 25 Jan 2010 at 4:47

mysql connection dropped

After a couple of days of inactivity, middleware drops the mysql database
connection.




Yikes!

org.springframework.transaction.CannotCreateTransactionException: Could not
open Hibernate Session for transaction; nested exception is
org.hibernate.TransactionException: JDBC begin failed: 
    at
org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(Hibernate
TransactionManager.java:541)
    at
org.springframework.transaction.support.AbstractPlatformTransactionManager.getTr
ansaction(AbstractPlatformTransactionManager.java:350)
    at
org.springframework.transaction.interceptor.TransactionAspectSupport.createTrans
actionIfNecessary(TransactionAspectSupport.java:262)
    at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(Transa
ctionInterceptor.java:101)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInv
ocationInterceptor.java:89)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.j
ava:204)
    at $Proxy25.getFlowTemplates(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor55.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils
.java:307)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(Ref
lectiveMethodInvocation.java:182)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:149)
    at
org.springframework.remoting.support.RemoteInvocationTraceInterceptor.invoke(Rem
oteInvocationTraceInterceptor.java:77)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.j
ava:204)
    at $Proxy25.getFlowTemplates(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.ja
va:205)
    at
org.springframework.remoting.support.DefaultRemoteInvocationExecutor.invoke(Defa
ultRemoteInvocationExecutor.java:38)
    at
org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(Remote
InvocationBasedExporter.java:78)
    at
org.springframework.remoting.rmi.RmiBasedExporter.invoke(RmiBasedExporter.java:7
2)
    at
org.springframework.remoting.rmi.RmiInvocationWrapper.invoke(RmiInvocationWrappe
r.java:72)
    at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:305)
    at sun.rmi.transport.Transport$1.run(Transport.java:159)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.Transport.serviceCall(Transport.java:155)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:535)
    at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:790)
    at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:649)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:8
85)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
    at java.lang.Thread.run(Thread.java:619)
    at
org.springframework.remoting.support.RemoteInvocationUtils.fillInClientStackTrac
eIfPossible(RemoteInvocationUtils.java:47)
    at
org.springframework.remoting.rmi.RmiClientInterceptor.doInvoke(RmiClientIntercep
tor.java:347)
    at
org.springframework.remoting.rmi.RmiClientInterceptor.invoke(RmiClientIntercepto
r.java:258)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.j
ava:204)
    at $Proxy34.getFlowTemplates(Unknown Source)
    at
org.imirsel.nema.webapp.controller.FlowController.getTemplateFlows(FlowControlle
r.java:95)
    at sun.reflect.GeneratedMethodAccessor100.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.springframework.web.servlet.mvc.multiaction.MultiActionController.invokeName
dMethod(MultiActionController.java:473)
    at
org.springframework.web.servlet.mvc.multiaction.MultiActionController.handleRequ
estInternal(MultiActionController.java:410)
    at
org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractCon
troller.java:153)
    at
org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(Simple
ControllerHandlerAdapter.java:48)
    at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.j
ava:875)
    at
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.ja
va:809)
    at
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet
.java:571)
    at
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:501
)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
    at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1166)
    at
com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:118
)
    at
com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:52)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1157)
    at
org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
    at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
    at
org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90
)
    at
org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.jav
a:406)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1157)
    at
org.imirsel.nema.webapp.filter.LocaleFilter.doFilterInternal(LocaleFilter.java:7
4)
    at
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilte
r.java:76)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1157)
    at
com.opensymphony.clickstream.ClickstreamFilter.doFilter(ClickstreamFilter.java:4
2)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1157)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:359)
    at
org.springframework.security.intercept.web.FilterSecurityInterceptor.invoke(Filt
erSecurityInterceptor.java:109)
    at
org.springframework.security.intercept.web.FilterSecurityInterceptor.doFilter(Fi
lterSecurityInterceptor.java:83)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.ui.ExceptionTranslationFilter.doFilterHttp(Exceptio
nTranslationFilter.java:101)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.providers.anonymous.AnonymousProcessingFilter.doFil
terHttp(AnonymousProcessingFilter.java:105)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.ui.rememberme.RememberMeProcessingFilter.doFilterHt
tp(RememberMeProcessingFilter.java:116)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.wrapper.SecurityContextHolderAwareRequestFilter.doF
ilterHttp(SecurityContextHolderAwareRequestFilter.java:91)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.ui.basicauth.BasicProcessingFilter.doFilterHttp(Bas
icProcessingFilter.java:172)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.ui.AbstractProcessingFilter.doFilterHttp(AbstractPr
ocessingFilter.java:268)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.ui.logout.LogoutFilter.doFilterHttp(LogoutFilter.ja
va:87)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.ui.SessionFixationProtectionFilter.doFilterHttp(Ses
sionFixationProtectionFilter.java:61)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.context.HttpSessionContextIntegrationFilter.doFilte
rHttp(HttpSessionContextIntegrationFilter.java:235)
    at
org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilt
er.java:53)
    at
org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFilter(F
ilterChainProxy.java:371)
    at
org.springframework.security.util.FilterChainProxy.doFilter(FilterChainProxy.jav
a:174)
    at
org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFi
lterProxy.java:236)
    at
org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterPr
oxy.java:167)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1157)
    at
org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(Characte
rEncodingFilter.java:96)
    at
org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilte
r.java:76)
    at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.jav
a:1157)
    at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
    at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
    at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
    at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
    at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
    at
org.mortbay.jetty.handler.ContextHandlerCollection.handle(ContextHandlerCollecti
on.java:230)
    at
org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
    at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
    at org.mortbay.jetty.Server.handle(Server.java:326)
    at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
    at
org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.ja
va:923)
    at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:547)
    at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
    at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
    at
org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
    at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
Caused by: org.hibernate.TransactionException: JDBC begin failed: 
    at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:68)
    at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326)
    at
org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(Hibernate
TransactionManager.java:510)
    ... 129 more
Caused by: com.mysql.jdbc.CommunicationsException: Communications link
failure due to underlying exception: 

** BEGIN NESTED EXCEPTION ** 

java.io.EOFException

STACKTRACE:

java.io.EOFException
    at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1963)
    at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2375)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2874)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1623)
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1715)
    at com.mysql.jdbc.Connection.execSQL(Connection.java:3243)
    at com.mysql.jdbc.Connection.setAutoCommit(Connection.java:5371)
    at sun.reflect.GeneratedMethodAccessor16.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
com.mchange.v2.c3p0.impl.C3P0PooledConnection$ProxyConnectionInvocationHandler.i
nvoke(C3P0PooledConnection.java:712)
    at com.mchange.v2.c3p0.impl.$Proxy15.setAutoCommit(Unknown Source)
    at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:63)
    at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326)
    at
org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(Hibernate
TransactionManager.java:510)
    at
org.springframework.transaction.support.AbstractPlatformTransactionManager.getTr
ansaction(AbstractPlatformTransactionManager.java:350)
    at
org.springframework.transaction.interceptor.TransactionAspectSupport.createTrans
actionIfNecessary(TransactionAspectSupport.java:262)
    at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(Transa
ctionInterceptor.java:101)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInv
ocationInterceptor.java:89)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.j
ava:204)
    at $Proxy25.getFlowTemplates(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor55.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils
.java:307)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(Ref
lectiveMethodInvocation.java:182)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:149)
    at
org.springframework.remoting.support.RemoteInvocationTraceInterceptor.invoke(Rem
oteInvocationTraceInterceptor.java:77)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:171)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.j
ava:204)
    at $Proxy25.getFlowTemplates(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.ja
va:205)
    at
org.springframework.remoting.support.DefaultRemoteInvocationExecutor.invoke(Defa
ultRemoteInvocationExecutor.java:38)
    at
org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(Remote
InvocationBasedExporter.java:78)
    at
org.springframework.remoting.rmi.RmiBasedExporter.invoke(RmiBasedExporter.java:7
2)
    at
org.springframework.remoting.rmi.RmiInvocationWrapper.invoke(RmiInvocationWrappe
r.java:72)
    at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:305)
    at sun.rmi.transport.Transport$1.run(Transport.java:159)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.rmi.transport.Transport.serviceCall(Transport.java:155)
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:535)
    at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:790)
    at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:649)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:8
85)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
    at java.lang.Thread.run(Thread.java:619)


** END NESTED EXCEPTION **



Last packet sent to the server was 1 ms ago.
    at
com.mchange.v2.c3p0.impl.C3P0PooledConnection$ProxyConnectionInvocationHandler.i
nvoke(C3P0PooledConnection.java:733)
    at com.mchange.v2.c3p0.impl.$Proxy15.setAutoCommit(Unknown Source)
    at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:63)
    ... 131 more

Original issue reported on code.google.com by [email protected] on 1 Feb 2010 at 2:34

use property files to store meandre server information in the flowservice

The compile time dependency to know the list of the meandre servers is not
flexible. Can we discuss the need to move the client list to a property
file and that property file could be loaded from the Classpath. Also make
the number of servers including the username/password for the servers and
the head server address a property in the property file.

Original issue reported on code.google.com by [email protected] on 19 Jan 2010 at 6:47

Standardize maven profiles

Standardize the maven profiles to support development and production
resources. -Required for flowservice, diy and nema repository service.

Original issue reported on code.google.com by [email protected] on 20 Jan 2010 at 6:05

Cluster reconfiguration

As per discussions with Dan/Kris and Mert. The IMIRSEL clusters need to be
reconfigured -he will send a proposal.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 2:14

Implement Cover song evaluator and file reader

Implement Cover song evaluator and file reader util classes in M2K and 
component wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:51

Fix Hudson proxy

Hudson proxy on nema is screwed up because of relative/absolute links
issue. Fix that.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 2:17

nema(DIY)-probes moduler does not compile.

What steps will reproduce the problem?
1. nema-probes does not compile under maven. 

What is the expected output? What do you see instead?



[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository appfuse (http://static.appfuse.org/repository)
Downloading:
http://openjena.org/repo//org/meandre/meandre-annotation/1.4.8/meandre-annotatio
n-1.4.8.pom
[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository jena (http://openjena.org/repo/)
Downloading:
http://nema.lis.uiuc.edu/artifactory/repo/org/meandre/meandre-annotation/1.4.8/m
eandre-annotation-1.4.8.pom
[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository nema-artifactory-repo (http://nema.lis.uiuc.edu/artifactory/repo)
Downloading:
http://nema.lis.uiuc.edu/artifactory/remote-repos/org/meandre/meandre-annotation
/1.4.8/meandre-annotation-1.4.8.pom
[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository nema-artifactory-remote
(http://nema.lis.uiuc.edu/artifactory/remote-repos)
Downloading:
http://repo1.maven.org/maven2/org/meandre/meandre-annotation/1.4.8/meandre-annot
ation-1.4.8.pom
[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository central (http://repo1.maven.org/maven2)
Downloading:
http://www.monkproject.org/maven2/org/meandre/meandre-annotation/1.4.8/meandre-a
nnotation-1.4.8.pom
[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository monk (http://www.monkproject.org/maven2)
Downloading:
http://tanesha.net/maven2/org/meandre/meandre-annotation/1.4.8/meandre-annotatio
n-1.4.8.pom
[INFO] Unable to find resource 'org.meandre:meandre-annotation:pom:1.4.8'
in repository taneshanet (http://tanesha.net/maven2)
Downloading:
http://repo1.maven.org/maven2/org/imirsel/nema-temp-repository/0.1-SNAPSHOT/nema
-temp-repository-0.1-SNAPSHOT.pom
[INFO] Unable to find resource
'org.imirsel:nema-temp-repository:pom:0.1-SNAPSHOT' in repository central
(http://repo1.maven.org/maven2)
Downloading:
http://static.appfuse.org/repository/org/imirsel/nema-temp-repository/0.1-SNAPSH
OT/nema-temp-repository-0.1-SNAPSHOT.pom
[INFO] Unable to find resource
'org.imirsel:nema-temp-repository:pom:0.1-SNAPSHOT' in repository appfuse
(http://static.appfuse.org/repository)
Downloading:
http://openjena.org/repo//org/imirsel/nema-temp-repository/0.1-SNAPSHOT/nema-tem
p-repository-0.1-SNAPSHOT.pom
[INFO] Unable to find resource
'org.imirsel:nema-temp-repository:pom:0.1-SNAPSHOT' in repository jena
(http://openjena.org/repo/)
Downloading:
http://nema.lis.uiuc.edu/artifactory/repo/org/imirsel/nema-temp-repository/0.1-S
NAPSHOT/nema-temp-repository-0.1-SNAPSHOT.pom
[INFO] Unable to find resource
'org.imirsel:nema-temp-repository:pom:0.1-SNAPSHOT' in repository
nema-artifactory-repo (http://nema.lis.uiuc.edu/artifactory/repo)
Downloading:
http://nema.lis.uiuc.edu/artifactory/remote-repos/org/imirsel/nema-temp-reposito
ry/0.1-SNAPSHOT/nema-temp-repository-0.1-SNAPSHOT.pom
[INFO] Unable to find resource
'org.imirsel:nema-temp-repository:pom:0.1-SNAPSHOT' in repository
nema-artifactory-remote (http://nema.lis.uiuc.edu/artifactory/remote-repos)
Downloading:
http://repo1.maven.org/maven2/opensymphony/quartz/1.6.0/quartz-1.6.0.pom
[INFO] Unable to find resource 'opensymphony:quartz:pom:1.6.0' in
repository central (http://repo1.maven.org/maven2)
Downloading:
http://static.appfuse.org/repository/opensymphony/quartz/1.6.0/quartz-1.6.0.pom
[INFO] Unable to find resource 'opensymphony:quartz:pom:1.6.0' in
repository appfuse (http://static.appfuse.org/repository)
Downloading:
http://openjena.org/repo//opensymphony/quartz/1.6.0/quartz-1.6.0.pom
[INFO] Unable to find resource 'opensymphony:quartz:pom:1.6.0' in
repository jena (http://openjena.org/repo/)
Downloading:
http://nema.lis.uiuc.edu/artifactory/repo/opensymphony/quartz/1.6.0/quartz-1.6.0
.pom
[INFO] Unable to find resource 'opensymphony:quartz:pom:1.6.0' in
repository nema-artifactory-repo (http://nema.lis.uiuc.edu/artifactory/repo)
Downloading:
http://nema.lis.uiuc.edu/artifactory/remote-repos/opensymphony/quartz/1.6.0/quar
tz-1.6.0.pom
[INFO] Unable to find resource 'opensymphony:quartz:pom:1.6.0' in
repository nema-artifactory-remote
(http://nema.lis.uiuc.edu/artifactory/remote-repos)
[INFO] [compiler:compile {execution: default-compile}]
[INFO] Compiling 67 source files to
/Users/imirsel/Documents/workspaceGoolge/nema/webapp/target/classes
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Compilation failure

/Users/imirsel/Documents/workspaceGoolge/nema/webapp/src/main/java/org/imirsel/n
ema/webapp/controller/FlowFormController.java:[38,23]
package org.imirsel.util does not exist

/Users/imirsel/Documents/workspaceGoolge/nema/webapp/src/main/java/org/imirsel/n
ema/webapp/controller/FlowController.java:[101,20]
cannot find symbol
symbol  : method toUpperCase()
location: class org.imirsel.nema.model.Flow.FlowType

/Users/imirsel/Documents/workspaceGoolge/nema/webapp/src/main/java/org/imirsel/n
ema/webapp/controller/JobController.java:[169,39]
incompatible types
found   : org.imirsel.nema.model.Flow.FlowType
required: java.lang.String

/Users/imirsel/Documents/workspaceGoolge/nema/webapp/src/main/java/org/imirsel/n
ema/webapp/controller/FlowFormController.java:[244,19]
cannot find symbol
symbol  : variable FlowTypeUtils
location: class org.imirsel.nema.webapp.controller.FlowFormController


[INFO] ------------------------------------------------------------------------
[INFO] For more information, run Maven with the -e switch
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 14 seconds
[INFO] Finished at: Wed Jan 20 16:47:10 CST 2010
[INFO] Final Memory: 42M/81M
[INFO] ------------------------------------------------------------------------

Original issue reported on code.google.com by [email protected] on 20 Jan 2010 at 11:13

Implement Tempo evaluator and file reader

Implement Tempo evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:47

Create new database nemadatarepositorydev with updated schema

This one is for Kris;

I am doing a test deploy for 0.5.0 with the newest everything including
repository. I see you have updated the datamodel for the repository, can
you create another small database and name it nemadatarepositorydev with
the data that is uptodate. Put it on the nema box.

As it stands, The exception I am getting is

populating types map with query: SELECT * FROM task_type
Feb 3, 2010 9:10:19 PM
org.imirsel.nema.repository.RepositoryClientConnectionPool <init>
SEVERE: Failed to initialise RepositoryClientConnectionPool!
com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: Table
'nemadatarepository.task_type' doesn't exist
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:936)

Original issue reported on code.google.com by [email protected] on 4 Feb 2010 at 3:19

Implement Multi-F0 evaluator and file reader

Implement Multi-F0  evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:45

Blocking: #72

Implement Melody evaluator and file reader util classes

Implement Melody evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 4 Feb 2010 at 1:53

Backup system

Spec/purchase backup system for all major data stores

Original issue reported on code.google.com by [email protected] on 22 Jan 2010 at 4:03

Better scrolling text pane for console output and data refresh

Put console output in a scrolling text pane on job output page (so page
length remains constant).
Investigate simple JS components for this - needs to not fully redraw with
each update.
May need to offer a service that gets output from Meandre (only full output
is retrievable) and converts into a stream. Store stream position so new
output can be efficiently clipped to add to the stream.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 12:34

Flow Exception: Classification by Andy

Below is an exception while running classification By Andy

-Uses Small Demo dataset







010.01.26 13:01:19.324::INFO:  Flow Started: Tue Jan 26 13:01:19 CST 2010
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/0AFFFFFE2CFA/1264532479263/349336750/1264532455592-token/
 http://compute-1-3.local:11515/  
[org.imirsel.probes.NemaFlowNotification.probeFlowStart]
<3/349336750/1264532455592-token/mr-probe:25>
2010.01.26 13:01:19.323::INFO:  Executing flow
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/0AFFFFFE2CFA/1264532479263/349336750/1264532455592-token/
  [org.meandre.core.engine.Executor.execute] <btpool0-4:17>
2010.01.26 13:01:19.324::INFO:  Flow Started: 2  
[org.imirsel.probes.NemaFlowNotification.probeFlowStart]
<3/349336750/1264532455592-token/mr-probe:25>
2010.01.26 13:01:19.333::INFO:  10.1.1.1:59778/admin --> GET -->
http://c1-3:11514/services/execute/uri_flow.txt <--
token=1264532455592-token   [sun.reflect.NativeMethodAccessorImpl.invoke0]
<btpool0-3:14>
Initialized
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/instance/traintestgatekeeper/1
RUNBINARY: PROCESS WORKING DIR:
/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resources/nem
a/http__imirsel.org_classification_classification_ehmann_classification_ehmann12
64532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_
Initialized
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/instance/runbinarytwoinput/2
Initialized
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/instance/runbinaryoneinput/1
Initialized
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/instance/classificationevaluator/0
Initialized
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/instance/collectionselector/0
Writing out train and test files for dataset_id=10
File encoding constraints: 
    channels:   1
    encoding:   wav
    clip-type:  30
    sample-rate:    22050
2010.01.26 13:01:19.370::INFO:  Connecting to server:
jdbc:mysql://nema.lis.uiuc.edu:3306/nemadatarepository?noAccessToProcedureBodies
=true
  [org.imirsel.nema.repository.DatabaseConnector.connect]
<4532460891/instance/collectionselector/0:26>
Populating types map with query: SELECT * FROM track_metadata_definitions
3: Album
2: Artist
4: Composer
1: Genre
5: Key
6: Title
Populating types map with query: SELECT * FROM file_metadata_definitions
4: bitrate
3: channels
5: clip-type
1: encoding
2: sample-rate
Populating types map with query: SELECT * FROM task_type
2: classification
4: evaluation
3: feature extraction
5: similarity estimation
7: structural segmentation
6: tag classification
Populating types map with query: SELECT * FROM set_type_definitions
1: collection_subset
3: test
2: train
4: validation
Retrieving test file paths for set: 34
Got 83 tracks, resolving to files
Resolving files for 83 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 83 files to tracks
returning file list length: 83
Got file list length: 83, preparing output
Retrieving ground-truth data and file paths for set: 35
Got 167 tracks, resolving to files
Resolving files for 167 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 167 files to tracks
returning file list length: 167
Got file list length: 167, retrieving metadata
Retrieving test file paths for set: 36
Got 84 tracks, resolving to files
Resolving files for 84 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 84 files to tracks
returning file list length: 84
Got file list length: 84, preparing output
Retrieving ground-truth data and file paths for set: 37
Got 166 tracks, resolving to files
Resolving files for 166 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 166 files to tracks
returning file list length: 166
Got file list length: 166, retrieving metadata
Retrieving test file paths for set: 38
Got 83 tracks, resolving to files
Resolving files for 83 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 83 files to tracks
returning file list length: 83
Got file list length: 83, preparing output
Retrieving ground-truth data and file paths for set: 39
Got 167 tracks, resolving to files
Resolving files for 167 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 167 files to tracks
returning file list length: 167
Got file list length: 167, retrieving metadata
Writing out Groundtruth and Extraction list files for dataset_id=10
File encoding constraints: 
    channels:   1
    encoding:   wav
    clip-type:  30
    sample-rate:    22050
2010.01.26 13:01:41.286::INFO:  Connecting to server:
jdbc:mysql://nema.lis.uiuc.edu:3306/nemadatarepository?noAccessToProcedureBodies
=true
  [org.imirsel.nema.repository.DatabaseConnector.connect]
<4532460891/instance/collectionselector/0:26>
Populating types map with query: SELECT * FROM track_metadata_definitions
3: Album
2: Artist
4: Composer
1: Genre
5: Key
6: Title
Populating types map with query: SELECT * FROM file_metadata_definitions
4: bitrate
3: channels
5: clip-type
1: encoding
2: sample-rate
Populating types map with query: SELECT * FROM task_type
2: classification
4: evaluation
3: feature extraction
5: similarity estimation
7: structural segmentation
6: tag classification
Populating types map with query: SELECT * FROM set_type_definitions
1: collection_subset
3: test
2: train
4: validation
Retrieving ground-truth data and file paths for set: 33
Got 250 tracks, resolving to files
Resolving files for 250 tracks
tracks in set:
Query returned data on 31304 files, filtering
mapped 250 files to tracks
returning file list length: 250
Got file list length: 250, retrieving metadata
Feature Extraction file
no.0:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/extra
ctlist-33.txt
Ground-truth file
no.0:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/gt-33
.txt
Train 
no.0:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/train
-35.txt
Test 
no.0:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/test-
34.txt
Train 
no.1:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/train
-37.txt
Test 
no.1:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/test-
36.txt
Train 
no.2:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/train
-39.txt
Test 
no.2:/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resource
s/nema/http__imirsel.org_classification_classification_ehmann_classification_ehm
ann1264532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/test-
38.txt
Determining location of results files for each system for each experiment
fold...
    retrieving files for
/home/meandre/apps/projects/Meandre-Infrastructure-1.4.8/published_resources/nem
a/http__imirsel.org_classification_classification_ehmann_classification_ehmann12
64532460891_0AFFFFFE2CFA_1264532479263_349336750_1264532455592-token_/results
        got 0 files
reading result data files...
    reading ehmann
Performing individual classification evals...
    evaluating ehmann
Plotting overall confusion matrices...
2010.01.26 13:01:45.531::WARNING:  java.lang.NullPointerException  
[org.meandre.core.engine.WrappedComponent.run]
<60891/instance/classificationevaluator/0:27>
2010.01.26 13:01:46.196::SEVERE:  Aborting execution. Component
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/instance/classificationevaluator/0
requested execution termination.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
</349336750/1264532455592-token/mr-proper:28>
2010.01.26 13:01:46.196::SEVERE:  Aborting execution. Requested execution
termination propagated.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
</349336750/1264532455592-token/mr-proper:28>
2010.01.26 13:01:46.197::SEVERE:  Disposing WebUI.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
</349336750/1264532455592-token/mr-proper:28>
Flow Aborted Tue Jan 26 13:01:46 CST 2010
http://imirsel.org/classification/classification_ehmann/classification_ehmann126
4532460891/0AFFFFFE2CFA/1264532479263/349336750/1264532455592-token/
Probe Disposed

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 7:14

Implement Onset evaluator and file reader

Implement Onset evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Careful thought should go into how the paramete sweeps will be implemented.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:50

Change default collections on demo flows to all point to small demo collection

Some demo flows point to collections other than the small demo collections.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 12:28

This is a test

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


Please use labels and text to provide additional information.

Original issue reported on code.google.com by [email protected] on 21 Jan 2010 at 6:44

Implement AudioSim stats and human evaluator, utils and file reader

Implement AudioSim stats and human evaluator, Evalutron 6k prep utils and dist 
mat file reader util 
classes in M2K and component wrappers in Components project. Implement JUnit 
tests based on 
past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:52

Implement Key evaluator and file reader

Implement Key evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 2 Feb 2010 at 11:48

When logged in as admin, menu overlaps tag line

When the logged in user is an admin, the menu is overlapped regardless of
window size, necessitating a page layout change.

Original issue reported on code.google.com by [email protected] on 27 Jan 2010 at 1:10

Attachments:

admin_menu.png

Implement structure evaluator and file reader util classes

Implement structure evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 4 Feb 2010 at 1:56

job.jsp refreshes console when it should not

job.jsp refreshes console even when the job is finished or aborted. It
should not.

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 2:26

flowservice maven compile issue

What steps will reproduce the problem?
1. mvn deploy -Pproduction -Dmaven.test.skip=true
in the flowservice project causes an exception. Both with/Without profile.


%> mvn deploy -Pproduction -Dmaven.test.skip=true
gserve112:/content/workspace2009/flowservice 103 % sh ./deploy.sh 
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building nema-flow-service
[INFO]    task-segment: [deploy]
[INFO] ------------------------------------------------------------------------
[INFO] [resources:resources {execution: default-resources}]
[WARNING] File encoding has not been set, using platform encoding MacRoman,
i.e. build is platform dependent!
[WARNING] Using platform encoding (MacRoman actually) to copy filtered
resources, i.e. build is platform dependent!
[INFO] Copying 4 resources
[WARNING] POM for 'org.meandre:meandre-core:pom:1.4.8:compile' is invalid.

Its dependencies (if any) will NOT be available to the current build.
[INFO] [compiler:compile {execution: default-compile}]
[INFO] Nothing to compile - all classes are up to date
[INFO] [resources:testResources {execution: default-testResources}]
[WARNING] Using platform encoding (MacRoman actually) to copy filtered
resources, i.e. build is platform dependent!
[INFO] Copying 4 resources
[INFO] Preparing hibernate3:hbm2ddl
[WARNING] Removing: hbm2ddl from forked lifecycle, to prevent recursive
invocation.
[INFO] [resources:resources {execution: default-resources}]
[WARNING] File encoding has not been set, using platform encoding MacRoman,
i.e. build is platform dependent!
[WARNING] Using platform encoding (MacRoman actually) to copy filtered
resources, i.e. build is platform dependent!
[INFO] Copying 4 resources
Downloading:
http://repository.codehaus.org/${jdbc/groupId}/${jdbc.artifactId}/${jdbc.version
}/${jdbc.artifactId}-${jdbc.version}.pom
[INFO] ------------------------------------------------------------------------
[ERROR] FATAL ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Invalid uri
'http://repository.codehaus.org/${jdbc/groupId}/${jdbc.artifactId}/${jdbc.versio
n}/${jdbc.artifactId}-${jdbc.version}.pom':
escaped absolute path not valid
[INFO] ------------------------------------------------------------------------
[INFO] Trace
java.lang.IllegalArgumentException: Invalid uri
'http://repository.codehaus.org/${jdbc/groupId}/${jdbc.artifactId}/${jdbc.versio
n}/${jdbc.artifactId}-${jdbc.version}.pom':
escaped absolute path not valid
    at
hidden.org.apache.commons.httpclient.HttpMethodBase.<init>(HttpMethodBase.java:2
22)
    at
hidden.org.apache.commons.httpclient.methods.GetMethod.<init>(GetMethod.java:89)
    at
org.apache.maven.wagon.shared.http.AbstractHttpClientWagon.fillInputData(Abstrac
tHttpClientWagon.java:547)
    at org.apache.maven.wagon.StreamWagon.getInputStream(StreamWagon.java:116)
    at org.apache.maven.wagon.StreamWagon.getIfNewer(StreamWagon.java:88)
    at org.apache.maven.wagon.StreamWagon.get(StreamWagon.java:61)
    at
org.apache.maven.artifact.manager.DefaultWagonManager.getRemoteFile(DefaultWagon
Manager.java:491)
    at
org.apache.maven.artifact.manager.DefaultWagonManager.getArtifact(DefaultWagonMa
nager.java:372)
    at
org.apache.maven.artifact.manager.DefaultWagonManager.getArtifact(DefaultWagonMa
nager.java:327)
    at
org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolve(DefaultArtifa
ctResolver.java:216)
    at
org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolve(DefaultArtifa
ctResolver.java:90)
    at
org.apache.maven.project.DefaultMavenProjectBuilder.findModelFromRepository(Defa
ultMavenProjectBuilder.java:558)
    at
org.apache.maven.project.DefaultMavenProjectBuilder.buildFromRepository(DefaultM
avenProjectBuilder.java:251)
    at
org.apache.maven.project.artifact.MavenMetadataSource.retrieveRelocatedProject(M
avenMetadataSource.java:163)
    at
org.apache.maven.project.artifact.MavenMetadataSource.retrieveRelocatedArtifact(
MavenMetadataSource.java:94)
    at
org.apache.maven.artifact.resolver.DefaultArtifactCollector.recurse(DefaultArtif
actCollector.java:388)
    at
org.apache.maven.artifact.resolver.DefaultArtifactCollector.collect(DefaultArtif
actCollector.java:74)
    at
org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolveTransitively(D
efaultArtifactResolver.java:316)
    at
org.apache.maven.artifact.resolver.DefaultArtifactResolver.resolveTransitively(D
efaultArtifactResolver.java:304)
    at
org.apache.maven.plugin.DefaultPluginManager.ensurePluginContainerIsComplete(Def
aultPluginManager.java:828)
    at
org.apache.maven.plugin.DefaultPluginManager.getConfiguredMojo(DefaultPluginMana
ger.java:640)
    at
org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.ja
va:461)
    at
org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycl
eExecutor.java:678)
    at
org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(Def
aultLifecycleExecutor.java:540)
    at
org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycle
Executor.java:519)
    at
org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures
(DefaultLifecycleExecutor.java:371)
    at
org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultL
ifecycleExecutor.java:332)
    at
org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExec
utor.java:181)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:356)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:137)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)
    at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:41)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
    at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
    at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
    at org.codehaus.classworlds.Launcher.main(Launcher.java:375)
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4 seconds
[INFO] Finished at: Tue Jan 19 12:39:21 CST 2010
[INFO] Final Memory: 23M/1018M
[INFO] ------------------------------------------------------------------------

Original issue reported on code.google.com by [email protected] on 19 Jan 2010 at 6:44

Mirex Evaluation Flow: Exceptions

Mert/Andy and Kris,


When I try and run the MIREX evaluation flow (the results aggregrator flow)
I get this exception


Can you you guys help and debug?

Amit

got file list length: 500, retrieving metadata
Determining location of results files for each system for each experiment
fold...
reading result data files...
2010.01.26 08:04:29.459::WARNING:  java.lang.NegativeArraySizeException  
[org.meandre.core.engine.WrappedComponent.run]
<ce/classificationevaluationsaggregator/0:16>
2010.01.26 08:04:30.442::SEVERE:  Aborting execution. Component
http://imirsel.org/evaluation/mirex_evaluation/mirex_evaluation1264514653709/ins
tance/classificationevaluationsaggregator/0
requested execution termination.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
<1689106892/1264514649713-token/mr-proper:17>
2010.01.26 08:04:30.442::SEVERE:  Aborting execution. Requested execution
termination propagated.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
<1689106892/1264514649713-token/mr-proper:17>
2010.01.26 08:04:30.443::SEVERE:  Disposing WebUI.  
[org.meandre.core.engine.MrProper.checkTerminationFlag]
<1689106892/1264514649713-token/mr-proper:17>
Flow Aborted Tue Jan 26 08:04:30 CST 2010
http://imirsel.org/evaluation/mirex_evaluation/mirex_evaluation1264514653709/80A
E9A4A2D5E/1264514665148/1689106892/1264514649713-token/
Probe Disposed

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 2:17

Mirex Evaluation Flow -Improvements

The flow throws an exception when the flows dataset does not match that of
the one selected in the Mirex Evaluation flow.

Mirex Evaluation flow should not require the dataset id, it should get that
from the flows selected as submission.

Original issue reported on code.google.com by [email protected] on 26 Jan 2010 at 2:44

Implement QBSH evaluator and file reader util classes

Implement QBSH evaluator and file reader util classes in M2K and component 
wrappers in 
Components project. Implement JUnit tests based on past MIREX submission output.

Original issue reported on code.google.com by [email protected] on 4 Feb 2010 at 1:57

flowservice: EmailNotificationSender.loadUnsentNotifications exception

When I start the flow service this is the exception I get. It is a clean 
install.


org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 
'notificationSender': Invocation of init method failed; nested exception is 
java.lang.NullPointerException
    at 
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProces
sor.postProc
essBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:147)
    at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.app
lyBeanPost
ProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:350)
    at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.ini
tializeBean(A
bstractAutowireCapableBeanFactory.java:1331)
    at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doC
reateBean(
AbstractAutowireCapableBeanFactory.java:473)
    at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.r
un(Abstract
AutowireCapableBeanFactory.java:409)
    at java.security.AccessController.doPrivileged(Native Method)
    at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.cre
ateBean(Abs
tractAutowireCapableBeanFactory.java:380)
    at 
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(Abstra
ctBeanFactor
y.java:264)
    at 
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingle
ton(DefaultSi
ngletonBeanRegistry.java:222)
    at 
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(Abstract
BeanFactory.
java:261)
    at 
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBe
anFactory.ja
va:185)
    at 
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBe
anFactory.ja
va:164)
    at 
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstanti
ateSingletons(
DefaultListableBeanFactory.java:429)
    at 
org.springframework.context.support.AbstractApplicationContext.finishBeanFactory
Initialization(
AbstractApplicationContext.java:728)
    at 
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractA
pplicationCo
ntext.java:380)
    at 
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassP
athXmlAppli
cationContext.java:139)
    at 
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassP
athXmlAppli
cationContext.java:83)
    at org.imirsel.nema.flowservice.FlowServiceApp.main(FlowServiceApp.java:33)
Caused by: java.lang.NullPointerException
    at 
org.imirsel.nema.flowservice.EmailNotificationSender.loadUnsentNotifications(Ema
ilNotificationSe
nder.java:74)
    at org.imirsel.nema.flowservice.EmailNotificationSender.init(EmailNotificationSender.java:69)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

Original issue reported on code.google.com by [email protected] on 22 Jan 2010 at 3:55

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