Add JRonn runner, tester, methods to parse jronn output files.

[jabaws.git] / TODO.txt

TODO: \r
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Add globprot ws \r
Add ronn ws\r
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USE CASE - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE\r
- Receive user alignment \r
- use hmmerbuild to turn it to profile\r
- use hmmersearch to search the database \r
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#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE \r
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New data model for representing psiblast,blast,phmmer,jackhmmer results\r
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new parsers for the above programmes output (Stockholm MSA format?)\r
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Think hard on what to do with large output files? \r
e.g. serve the hits table in full, but retrieve alignments on demand.\r
What actually neeeds to be sent?   \r
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Add facility to distribute other results of the calculations like the trees and \r
annotation file for probcons. \r
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# END OF SEARCHING SEQUENCE DATABASE USECASE\r
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Good toString method for Limits (test with command line client -limits)\r
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JABA DOCS\r
(later) Define limits for presets - if required\r
(later) Add documentation on Presets, Parameters and Limits\r
(later) Explain how to define a limit\r
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Add test for repeated result collection from cluster engine\r
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(low) Pack the test cases and build file to run them in one of the distributives \r
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(low) Add logging facility to WSTester so more details of the problem can be reported\r
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(low) Statistics collector for engines (number of operations/timing)\r
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(later) WRAP Amps\r
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(later) Implement utility to rerun died tasks\r
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(later) Add recognition for executables for the different architectures\r
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(later) use Latch to manage engine reservations. Reservations for parallel jobs? \r
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DONE\r
WILL NOT DO: Progress bars - needs assessing how long does it take to run a task\r
DONE: LocalExecutor service must be shutdown on web application undeploy event not on JVM shutdown. \r
      This is because JVM is still running even after web application is shut down!\r
DONE: Use absolute path for web site download links as archives are not included into distro!\r
DONE: Rearrange web site docs - add links to the top of the page to the topics discussed below\r
DONE: Put the documentation for various executables online\r
DONE: Make left gradient image one-two characters larger + change "For developer ->For Developers"\r
DONE: test local/cluster execution - test Load balancer\r
DONE: Improve SimpleWS client so it can be scripted against: give user alignment and accept parameters\r
DONE: Make a configuration tester class (check that configuration files point to the executables, and they can be executed)\r
DONE: PUT CLIENT JAR INTO WEB-INF/LIB - most likely need to get rid of dist prefix in the build file\r
DONE: Different packages for download and dundee. generic vs specific settings. \r
DONE: JAVADOC\r
DONE: Refactor EngineResourcesLeak tester to hide a map implementation!\r
DONE: Compile executables for linux in the most generic way\r
DONE: Make different log4j configuration files / web services logs.\r
DONE: System manual\r
DONE: Developer doc\r
DONE: How to\r
DONE: Prepare different packages\r
DONE: extract commonly used names into variable in the build script\r
DONE: Test for high load conditions (TestNG?)\r
DONE: (low) Fix: Started jobs with unknown completion status reported as FINISHED by  msaws.getJobStatus(taskId) (see SimpleWSClient)\r
DONE: fix compile binaries script\r
DONE: Make script to change executable flag for linux systems\r
DONE: jobsout must be created within war\r
DONE: enable relative paths for local engine conf temp dir\r
COUND NOT REPRODUCE: fix cluster job status - RUNNING -> UNDEFINED\r
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\r
DONE: fix build scripts after reorganising project\r
DONE: package as war file for deployment\r
DONE: package for jalview distro for local execution\r
DONE: reorganise project into independent chunks\r
DONE: test Parameter & Option toCommand method\r
DONE: Replace WS methods with new CommandBuilder.toCommand()\r
DONE: Setting default values is validated as external method \r
DONE: Refactoring to extract data model, and engines is performed\r
DONE: Default value is adopted for passing new Option values to server side\r
DONE: Converting Options to commands delegated to CommandBuilder  \r
DONE: Make Arguments mutable to facilitate default value setting for WS\r
DONE: Matrix files for alignment programme\r
DONE: Clean up testcases\r
DONE: Replace List<String> as command line parameters abstraction to dedicated CommandBuilder class \r
DONE: Parallel execution for tcoffee jobs\r
DONE: Copyright added\r
DONE: WRAP ProbCons\r
DONE: think about time limits and cluster parameters for parallel execution - NativeSpecs for cluster is implemented\r
DONE: (low) Use for WS: (@WebParam(name = "name") String name) {\r
DONE: Implement rough policy for runtimes (e.g. do not run excessively long tasks on the local machine if cluster is available)\r
DONE: Write tomcat conf to expose WS\r
DONE: access control to web.xml\r
DONE: Statistics collector for WS\r
DONE: implements limits for web services\r
DONE: WS clients must be able to connect to a web service given the service url. \r
e.i. ws URL should not be compiled in using wsimport, but determined from \r
the configuration file.  \r
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DONE: Could not find configuration files if run from within servlet container\r
DONE: Add ways to get engine based on the key for everything but submission of the new tasks \r
DONE: Add cache to Cluster JOBID - so that at least jobs for which results have not been collected is cached.\r
DONE: FINISHED overrides FINISHED with time stamp!\r
DONE: Consider think about JobStatus and StatFileStatus\r
DONE: a method to read 3 chars at the beginning of the file to indicate a progress is added\r
DONE: ConfiguredExecutable<?> al = sexec.getResults(jobId); || Alignment ?\r
DONE: ClustalW - OUTput must be set !\r
DONE: Add accessor methods to get a DUMP of the process output \r
DONE: FilePuller should be cached to avoid excessive fs exercise\r
DONE: Test List of the processes (ensure no memory leaks)\r
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\r
DONE: Persist the task list to enable later result collection on the server side\r
DONE Wrap TCoffee\r
DONE: improve parameters handling - new schema + update for all parameters\r
DONE: Cluster jobs report submitting and result collecting/finishing time (for sync jobs only(!)) and cluster jobid in the corresponding files  \r
DONE: Local jobs report starting and finising times in files with corresponding names in the task directory  \r
DONE: Generalize getResult method for MSA runners\r
DONE: Create test suits\r
DONE: Convert junit tests to TestNG\r
DONE: Redirect output & error streams to the named files as some processed need this  \r
DONE: Extract generilyzed class with most of the method for individual executable to use\r
DONE: Refit wrappers to use the generalised class to avoid duplication  \r
DONE: Pass environment variable settings to the executable\r
DONE: Complete AsyncExecutors implementation\r
DONE: Look to unify methods for engines\r
DONE: Provide way around of generated directory setup for test cases(?)\r
DONE: Fix the test cases for local engine (need to set directory on executable explicitly)\r
DONE: Make log files for processes err and out for local execution\r
DONE: Trace where AsyncExcel called with null Executable and attempts to create a new directory repeatedly\r
DONE: directory generator\r
DONE: tests for cancel \r
DONE tests for getStatus\r
DONE  ws async\r
DONE: parametrized clustal operations\r
DONE: test large datasets handling \r
DONE: write load balancer \r
DONE: (low) task persistance\r
DONE: Look at CancellableTask if with Sync and AsyncExecutor \r