AAConWS further work

[jabaws.git] / TODO.txt

diff --git a/TODO.txt b/TODO.txt
index a212651..b6d15ed 100644 (file)
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+++ b/TODO.txt
@@ -1,35 +1,51 @@
 TODO: \r
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 TODO: \r
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-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
+Publish jabaws-discuss contact information\r

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

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-Good toString method for Limits (test with command line client -limits)\r
+integrate the above to tweak the size of the local job\r

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-Add facility to distribute other results of the calculations like the trees and annotation file for probcons. \r
+Add AACon ws\r
+Add iupred ws http://iupred.enzim.hu/\r
+Add globprot ws \r
+Add ronn ws\r

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-Use absolute path for web site download links as archives are not included into distro! \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

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

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-(later) Define limits for presets\r
+New data model for representing psiblast,blast,phmmer,jackhmmer results\r

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-Add documentation on Presets, Parameters and Limits\r
+new parsers for the above programmes output (Stockholm MSA format?)\r

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-Explain how to define a limit\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 neeeds to be sent?   \r

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-Rearrange web site docs - add links to the top of the page to the topics discussed below\r
+Add facility to distribute other results of the calculations like the trees and \r
+annotation file for probcons. \r

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-Put the documentation for various executables online\r
+# END OF SEARCHING SEQUENCE DATABASE USECASE\r

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-Pack the test cases and build file to run them in one of the distributives \r
+Good toString method for Limits (test with command line client -limits)\r

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-Add test for repeated result collection from cluster engine \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

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-Add logging facility to WSTester so more details of the problem can be reported\r
+Add test for repeated result collection from cluster engine\r

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-Make left gradient image one-two characters larger + change "For developer ->For Developers"\r
+(low) Pack the test cases and build file to run them in one of the distributives \r

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-PART DONE: test local/cluster execution - test Load balancer\r
+(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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 (low) Statistics collector for engines (number of operations/timing)\r
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@@ -37,17 +53,23 @@ PART DONE: test local/cluster execution - test Load balancer
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 (later) Implement utility to rerun died tasks\r
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 (later) Implement utility to rerun died tasks\r
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-(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
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 (later) use Latch to manage engine reservations. Reservations for parallel jobs? \r
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 DONE\r
 (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
 \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: 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
 DONE: JAVADOC\r
 DONE: Refactor EngineResourcesLeak tester to hide a map implementation!\r
 DONE: Compile executables for linux in the most generic way\r