+TODO write some help on the executable.properties within this file! \r
+check that after binaries relocation build tasks point to correct locations!\r
+GET rid of binaries/help directory!\r
+update binaries\r
+ + muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs\r
+ - test Muscle on the cluster\r
+ - test Muscle compilation\r
+ + probcons up-to-date\r
+ + clustal up-to-date \r
+ - update tcoffee (8.99 latest)\r
+ - update Mafft (6.857 latest)\r
++ make sure conf files are optional!\r
+\r
TODO: \r
+Registry 1 week\r
+webservices - 1 week\r
+client - 1 week\r
+docs - 1 week\r
\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
+Cluster stats: \r
+ +cancelled should not be reported as incomplete!\r
+ -Remove hyperlinks from tasks which workdirs were removed \r
+ -graph generation \r
+ -user documentation (do not forget how to enable follow symlinks!)\r
+ -use the same name for output for different executables\r
+ +ant task to clean up clean stat db task before packing web app\r
+ +pack web apps with stat db (NOT TESTED!)\r
+ +change input size bites\r
+ +add help info for each column in the detailed job list table\r
+ +replace default -1 with ? \r
+ +delete and re-import the database to fix clustal input staff \r
\r
+add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor\r
\r
-Good toString method for Limits (test with command line client -limits)\r
+add to help: VirtualBox 4.0.4 works fine with JABAWS update links \r
+\r
+rename jaba.war to jabaws.war and make sure jabaws context path is used throughout. \r
+\r
+Current stat collector has to rely on file dates! \r
+\r
+Test all WS as names from Executables were removed\r
+\r
+Add default names for input and output in every executable and use them consistently\r
+throughts (e.g. in all WS). Best of all use the same name from SceletalExectuable \r
+For statistics. \r
+\r
+FIXME: \r
+Conecting to JABAWS version 2 service\r
+09-Feb-2011 15:27:53 compbio.ws.client.Jws2Client connect\r
+INFO: Connected successfully!\r
+Exception in thread "main" java.lang.NullPointerException\r
+ at compbio.ws.client.MetadataHelper.getParametersList(MetadataHelper.java:30)\r
+ at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)\r
+ at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)\r
+ \r
+ScoreManager should output scores properly \r
+\r
+Allow empty Parameters and Preset files! \r
+\r
+Check the WS input and reject it on submission rather then of access with error message\r
+\r
+Globprot need a proper reference to bio python and sav_gol binaries -> they should be \r
+somehow taken from disembl. \r
\r
-Add facility to distribute other results of the calculations like the trees and annotation file for probcons. \r
++Add registry service to query services status\r
\r
-Use absolute path for web site download links as archives are not included into distro! \r
++Refactor web services checker to enable a programmatic access to its methods.\r
++Finish the client\r
\r
+Add interface for Jalview annotation \r
+Add the method to return Jalview Annotation to SequenceAnnotation IF \r
\r
-(later) Define limits for presets\r
+Develop generic Interface to return Jalview annotation for easy to add new \r
+services (?) \r
\r
-Add documentation on Presets, Parameters and Limits\r
+Replace conservation.Method with server.ws.Method \r
+and try building WS. If this does not work - get rid of Method\r
\r
-Explain how to define a limit\r
+Output file parsing for stat reporting\r
+cluster engine stat of www-jws2 user\r
\r
-Rearrange web site docs - add links to the top of the page to the topics discussed below\r
+integrate the above to tweak the size of the local job\r
\r
-Put the documentation for various executables online\r
+Add AACon ws\r
+Add iupred ws http://iupred.enzim.hu/\r
+Add globprot ws - does not report raw scores, just regions\r
+Add ronn ws\r
\r
-Pack the test cases and build file to run them in one of the distributives \r
+Philogeny Mrbayes + Philip\r
+ \r
+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
\r
-Add test for repeated result collection from cluster engine \r
+#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE \r
\r
-Add logging facility to WSTester so more details of the problem can be reported\r
+New data model for representing psiblast,blast,phmmer,jackhmmer results\r
\r
-Make left gradient image one-two characters larger + change "For developer ->For Developers"\r
+new parsers for the above programmes output (Stockholm MSA format?)\r
\r
-PART DONE: test local/cluster execution - test Load balancer\r
+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 needs to be sent? \r
+\r
+Add facility to distribute other results of the calculations like the trees and \r
+annotation file for probcons. \r
+\r
+# END OF SEARCHING SEQUENCE DATABASE USECASE\r
+\r
+Good toString method for Limits (test with command line client -limits)\r
+\r
+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
+\r
+Add test for repeated result collection from cluster engine\r
+\r
+(low) Pack the test cases and build file to run them in one of the distributives \r
+\r
+(low) Add logging facility to WSTester so more details of the problem can be reported\r
\r
(low) Statistics collector for engines (number of operations/timing)\r
\r
\r
(later) Implement utility to rerun died tasks\r
\r
-(later) Progress bars - talk about (1. Proper time assessment vs low hustle option - dumping output to screen)\r
-\r
(later) Add recognition for executables for the different architectures\r
\r
(later) use Latch to manage engine reservations. Reservations for parallel jobs? \r
\r
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 donwload and dundee. generic vs specific settings. \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
git://source.jalview.org / jabaws.git / blobdiff