Write help on 
 + execution stats
 + new menu bar background 
 - new page background(?)
 - merge developers help pages
 - new VM 
 - new properties e.g. jar
 - registry
 - change log 
 - main page should point to JABA 1   
 - Document the Limits for presets
 - JAVA DOCS
 - defaults changed - e.g. limits are disabled - explain how to enable
 - cluster settings are commented out 
 - Describe requirements 
Python > 2.2
Perl > 5.0
Java > 6
For compilation 
C++
C
Gnu make
   
- Check progress tracking on large sequence.

- Add more detailed tests for webservices? 

+ TODO write some help on the executable.properties within this file! 

- check that after binaries relocation build tasks point to correct locations!


add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor

rename jaba.war to jabaws.war and make sure jabaws context path is used throughout. 


? Replace conservation.Method with server.ws.Method and try building WS. If this does not work - get rid of Method

integrate the above to tweak the size of the local job


(later) Add documentation on Presets, Parameters and Limits
(later) Explain how to define a limit

Add test for repeated result collection from cluster engine



DONE

version 2

DONE: Current stat collector has to rely on file dates! 
DONE: Help information? - relative - client to add host and context info
DONE: statistics - result files 
DONE: Good toString method for Limits (test with command line client -limits)
DONE: install JABA 1 stat server 
DONE: Get path to Java executable from JAVA_HOME ? (for Jronn AACon) 

DONE:  GET rid of binaries/help directory!
DONE:  update binaries
 DONE:  muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs
 DONE:  test Muscle on the cluster
 DONE:  test Muscle compilation
 DONE:  probcons up-to-date
 DONE:  clustal up-to-date 
 DONE:  update tcoffee (8.99 latest) source code updated  docs updated 
 DONE:  tcoffee compilation for IA32 
 DONE:  update Mafft (6.857 latest) for win/lin32/lin64 and sources, no docs updates
DONE:  make sure conf files are optional!

Cluster stats: 
 DONE: cancelled should not be reported as incomplete!
 DONE: ant task to clean up clean stat db task before packing web app
 DONE: pack web apps with stat db (NOT TESTED!)
 DONE: change input size bites
 DONE: add help info for each column in the detailed job list table
 DONE: replace default -1 with ? 
 DONE: delete and re-import the database to fix clustal input staff    

DONE:  Test all WS as names from Executables were removed
DONE:  Add default names for input and output in every executable and use them consistently
  throughts (e.g. in all WS). Best of all use the same name from SceletalExectuable 
  For statistics. 

DONE:  FIXED Conecting to JABAWS version 2 service
  09-Feb-2011 15:27:53 compbio.ws.client.Jws2Client connect
  INFO: Connected successfully!
  Exception in thread "main" java.lang.NullPointerException
	at compbio.ws.client.MetadataHelper.getParametersList(MetadataHelper.java:30)
	at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)
	at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)

DONE:  ScoreManager should output scores properly 
DONE:  Allow empty Parameters and Preset files! 
DONE:  Check the WS input and reject it on submission rather then of access with error message

DONE: Add registry service to query services status
DONE: Refactor web services checker to enable a programmatic access to its methods.
DONE: Finish the client
DONE: Add AACon ws
DONE: Add iupred ws http://iupred.enzim.hu/
DONE: Add globprot ws - does not report raw scores, just regions
DONE: Add ronn ws
DONE: Define limits for presets - if required
DONE: Add logging facility to WSTester so more details of the problem can be reported
DONE: Statistics collector for engines (number of operations/timing)


version 1

DONE: LocalExecutor service must be shutdown on web application undeploy event not on JVM shutdown. 
      This is because JVM is still running even after web application is shut down!
DONE: Use absolute path for web site download links as archives are not included into distro!
DONE: Rearrange web site docs - add links to the top of the page to the topics discussed below
DONE: Put the documentation for various executables online
DONE: Make left gradient image one-two characters larger + change "For developer ->For Developers"
DONE: test local/cluster execution - test Load balancer
DONE: Improve SimpleWS client so it can be scripted against: give user alignment and accept parameters
DONE: Make a configuration tester class (check that configuration files point to the executables, and they can be executed)
DONE: PUT CLIENT JAR INTO WEB-INF/LIB - most likely need to get rid of dist prefix in the build file
DONE: Different packages for download and dundee. generic vs specific settings. 
DONE: JAVADOC
DONE: Refactor EngineResourcesLeak tester to hide a map implementation!
DONE: Compile executables for linux in the most generic way
DONE: Make different log4j configuration files / web services logs.
DONE: System manual
DONE: Developer doc
DONE: How to
DONE: Prepare different packages
DONE: extract commonly used names into variable in the build script
DONE: Test for high load conditions (TestNG?)
DONE: (low) Fix: Started jobs with unknown completion status reported as FINISHED by  msaws.getJobStatus(taskId) (see SimpleWSClient)
DONE: fix compile binaries script
DONE: Make script to change executable flag for linux systems
DONE: jobsout must be created within war
DONE: enable relative paths for local engine conf temp dir
COUND NOT REPRODUCE: fix cluster job status - RUNNING -> UNDEFINED
DONE: throw JobSubmission exception with appropriate method instead - (low) code discoverer/tester for ws - e.g. after war deployment to find out what actually works
DONE: fix build scripts after reorganising project
DONE: package as war file for deployment
DONE: package for jalview distro for local execution
DONE: reorganise project into independent chunks
DONE: test Parameter & Option toCommand method
DONE: Replace WS methods with new CommandBuilder.toCommand()
DONE: Setting default values is validated as external method 
DONE: Refactoring to extract data model, and engines is performed
DONE: Default value is adopted for passing new Option values to server side
DONE: Converting Options to commands delegated to CommandBuilder  
DONE: Make Arguments mutable to facilitate default value setting for WS
DONE: Matrix files for alignment programme
DONE: Clean up testcases
DONE: Replace List<String> as command line parameters abstraction to dedicated CommandBuilder class 
DONE: Parallel execution for tcoffee jobs
DONE: Copyright added
DONE: WRAP ProbCons
DONE: think about time limits and cluster parameters for parallel execution - NativeSpecs for cluster is implemented
DONE: (low) Use for WS: (@WebParam(name = "name") String name) {
DONE: Implement rough policy for runtimes (e.g. do not run excessively long tasks on the local machine if cluster is available)
DONE: Write tomcat conf to expose WS
DONE: access control to web.xml
DONE: Statistics collector for WS
DONE: implements limits for web services
DONE: WS clients must be able to connect to a web service given the service url. 
e.i. ws URL should not be compiled in using wsimport, but determined from 
the configuration file.  

DONE: Could not find configuration files if run from within servlet container
DONE: Add ways to get engine based on the key for everything but submission of the new tasks 
DONE: Add cache to Cluster JOBID - so that at least jobs for which results have not been collected is cached.
DONE: FINISHED overrides FINISHED with time stamp!
DONE: Consider think about JobStatus and StatFileStatus
DONE: a method to read 3 chars at the beginning of the file to indicate a progress is added
DONE: ConfiguredExecutable<?> al = sexec.getResults(jobId); || Alignment ?
DONE: ClustalW - OUTput must be set !
DONE: Add accessor methods to get a DUMP of the process output 
DONE: FilePuller should be cached to avoid excessive fs exercise
DONE: Test List of the processes (ensure no memory leaks)
PART DONE - On the client on shutdown remember the task list - server tasks could be loaded and executed from saved run configurations, client should decide for themselves what they want
DONE: Persist the task list to enable later result collection on the server side
DONE Wrap TCoffee
DONE: improve parameters handling - new schema + update for all parameters
DONE: Cluster jobs report submitting and result collecting/finishing time (for sync jobs only(!)) and cluster jobid in the corresponding files  
DONE: Local jobs report starting and finising times in files with corresponding names in the task directory  
DONE: Generalize getResult method for MSA runners
DONE: Create test suits
DONE: Convert junit tests to TestNG
DONE: Redirect output & error streams to the named files as some processed need this  
DONE: Extract generilyzed class with most of the method for individual executable to use
DONE: Refit wrappers to use the generalised class to avoid duplication  
DONE: Pass environment variable settings to the executable
DONE: Complete AsyncExecutors implementation
DONE: Look to unify methods for engines
DONE: Provide way around of generated directory setup for test cases(?)
DONE: Fix the test cases for local engine (need to set directory on executable explicitly)
DONE: Make log files for processes err and out for local execution
DONE: Trace where AsyncExcel called with null Executable and attempts to create a new directory repeatedly
DONE: directory generator
DONE: tests for cancel 
DONE tests for getStatus
DONE  ws async
DONE: parametrized clustal operations
DONE: test large datasets handling 
DONE: write load balancer 
DONE: (low) task persistance
DONE: Look at CancellableTask if with Sync and AsyncExecutor