X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=TODO.txt;h=d7ae747ebbd61b3f33403238d49754f78f093876;hb=b5ed73498a3f12da3f6f8465ec115065ec98e931;hp=a2126517291dcab94923539de76147520ad4f037;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/TODO.txt b/TODO.txt index a212651..d7ae747 100644 --- a/TODO.txt +++ b/TODO.txt @@ -1,35 +1,81 @@ TODO: -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! +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.(Jws2Client.java:179) + at compbio.ws.client.Jws2Client.main(Jws2Client.java:483) + +ScoreManager should output scores properly +Check the WS input and reject it on submission rather then of access with error message -Good toString method for Limits (test with command line client -limits) +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. +Rename it to avoid confusion with jabaws client -Add facility to distribute other results of the calculations like the trees and annotation file for probcons. +Finish the client -Use absolute path for web site download links as archives are not included into distro! +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 (?) -(later) Define limits for presets +Replace conservation.Method with server.ws.Method +and try building WS. If this does not work - get rid of Method -Add documentation on Presets, Parameters and Limits +Output file parsing for stat reporting +cluster engine stat of www-jws2 user -Explain how to define a limit +integrate the above to tweak the size of the local job -Rearrange web site docs - add links to the top of the page to the topics discussed below +Add AACon ws +Add iupred ws http://iupred.enzim.hu/ +Add globprot ws - does not report raw scores, just regions +Add ronn ws -Put the documentation for various executables online +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 -Pack the test cases and build file to run them in one of the distributives +#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE -Add test for repeated result collection from cluster engine +New data model for representing psiblast,blast,phmmer,jackhmmer results -Add logging facility to WSTester so more details of the problem can be reported +new parsers for the above programmes output (Stockholm MSA format?) -Make left gradient image one-two characters larger + change "For developer ->For Developers" +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? -PART DONE: test local/cluster execution - test Load balancer +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) @@ -37,17 +83,23 @@ PART DONE: test local/cluster execution - test Load balancer (later) Implement utility to rerun died tasks -(later) Progress bars - talk about (1. Proper time assessment vs low hustle option - dumping output to screen) - (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 donwload and dundee. generic vs specific settings. +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