TODO: 
Registry 1 week
webservices - 1 week
client - 1 week
docs - 1 week

Cluster stats: 
 +cancelled should not be reported as incomplete!
 -Remove hyperlinks from tasks which workdirs were removed 
 -graph generation 
 -user documentation (do not forget how to enable follow symlinks!)
 -use the same name for output for different executables
 +ant task to clean up clean stat db task before packing web app
 +pack web apps with stat db (NOT TESTED!)
 +change input size bites
 +add help info for each column in the detailed job list table
 +replace default -1 with ? 
 +delete and re-import the database to fix clustal input staff    

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

add to help: VirtualBox 4.0.4 works fine with JABAWS update links 

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

Current stat collector has to rely on file dates! 

Test all WS as names from Executables were removed

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. 

FIXME: 
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)
	
ScoreManager should output scores properly 

Allow empty Parameters and Preset files! 

Check the WS input and reject it on submission rather then of access with error message

Globprot need a proper reference to bio python and sav_gol binaries -> they should be 
somehow taken from disembl. 

+Add registry service to query services status

+Refactor web services checker to enable a programmatic access to its methods.
+Finish the client

Add interface for Jalview annotation 
Add the method to return Jalview Annotation to SequenceAnnotation IF  

Develop generic Interface to return Jalview annotation for easy to add new 
services (?) 

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

Output file parsing for stat reporting
cluster engine stat of www-jws2 user

integrate the above to tweak the size of the local job

Add AACon ws
Add iupred ws http://iupred.enzim.hu/
Add globprot ws - does not report raw scores, just regions
Add ronn ws

Philogeny Mrbayes + Philip
 
USE CASE - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE
- Receive user alignment 
- use hmmerbuild to turn it to profile
- use hmmersearch to search the database 

#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE 

New data model for representing psiblast,blast,phmmer,jackhmmer results

new parsers for the above programmes output (Stockholm MSA format?)

Think hard on what to do with large output files? 
e.g. serve the hits table in full, but retrieve alignments on demand.
What actually needs to be sent?   

Add facility to distribute other results of the calculations like the trees and 
annotation file for probcons. 

# END OF SEARCHING SEQUENCE DATABASE USECASE

Good toString method for Limits (test with command line client -limits)

JABA DOCS
(later) Define limits for presets - if required
(later) Add documentation on Presets, Parameters and Limits
(later) Explain how to define a limit

Add test for repeated result collection from cluster engine

(low) Pack the test cases and build file to run them in one of the distributives 

(low) Add logging facility to WSTester so more details of the problem can be reported

(low) Statistics collector for engines (number of operations/timing)

(later) WRAP Amps

(later) Implement utility to rerun died tasks

(later) Add recognition for executables for the different architectures

(later) use Latch to manage engine reservations. Reservations for parallel jobs? 

DONE
WILL NOT DO: Progress bars - needs assessing how long does it take to run a task
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