-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
-+ 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
+reset execution statistic in VM!\r
+\r
++ regerate javadoc\r
++ server war - obtaining command line binaries \r
+\r
+Write help on \r
+ + execution stats\r
+ + new menu bar background \r
+ - new page background(?)\r
+ - merge developers help pages\r
+ - new VM \r
+ - new properties e.g. jar\r
+ - registry\r
+ - change log \r
+ - main page should point to JABA 1 \r
+ - Document the Limits for presets\r
+ - JAVA DOCS\r
+ - defaults changed - e.g. limits are disabled - explain how to enable\r
+ - cluster settings are commented out \r
+ - Describe requirements \r
+Python > 2.2\r
+Perl > 5.0\r
+Java > 6\r
+For compilation \r
+C++\r
+C\r
+Gnu make\r
+ \r
+- Check progress tracking on large sequence.\r
+\r
+- Add more detailed tests for webservices? \r
+\r
++ TODO write some help on the executable.properties within this file! \r
+\r
+- check that after binaries relocation build tasks point to correct locations!\r
\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
-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 registry service to query services status\r
-\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
-Develop generic Interface to return Jalview annotation for easy to add new \r
-services (?) \r
-\r
-Replace conservation.Method with server.ws.Method \r
-and try building WS. If this does not work - get rid of Method\r
\r
-Output file parsing for stat reporting\r
-cluster engine stat of www-jws2 user\r
+? Replace conservation.Method with server.ws.Method and try building WS. If this does not work - get rid of Method\r
\r
integrate the above to tweak the size of the local job\r
\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
-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
-#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE \r
-\r
-New data model for representing psiblast,blast,phmmer,jackhmmer results\r
-\r
-new parsers for the above programmes output (Stockholm MSA format?)\r
-\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
+DONE\r
+\r
+version 2\r
+\r
+DONE: Current stat collector has to rely on file dates! \r
+DONE: Help information? - relative - client to add host and context info\r
+DONE: statistics - result files \r
+DONE: Good toString method for Limits (test with command line client -limits)\r
+DONE: install JABA 1 stat server \r
+DONE: Get path to Java executable from JAVA_HOME ? (for Jronn AACon) \r
+\r
+DONE: GET rid of binaries/help directory!\r
+DONE: update binaries\r
+ DONE: muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs\r
+ DONE: test Muscle on the cluster\r
+ DONE: test Muscle compilation\r
+ DONE: probcons up-to-date\r
+ DONE: clustal up-to-date \r
+ DONE: update tcoffee (8.99 latest) source code updated docs updated \r
+ DONE: tcoffee compilation for IA32 \r
+ DONE: update Mafft (6.857 latest) for win/lin32/lin64 and sources, no docs updates\r
+DONE: make sure conf files are optional!\r
+\r
+Cluster stats: \r
+ DONE: cancelled should not be reported as incomplete!\r
+ DONE: ant task to clean up clean stat db task before packing web app\r
+ DONE: pack web apps with stat db (NOT TESTED!)\r
+ DONE: change input size bites\r
+ DONE: add help info for each column in the detailed job list table\r
+ DONE: replace default -1 with ? \r
+ DONE: delete and re-import the database to fix clustal input staff \r
+\r
+DONE: Test all WS as names from Executables were removed\r
+DONE: 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
+DONE: FIXED 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
-(later) WRAP Amps\r
+DONE: ScoreManager should output scores properly \r
+DONE: Allow empty Parameters and Preset files! \r
+DONE: Check the WS input and reject it on submission rather then of access with error message\r
\r
-(later) Implement utility to rerun died tasks\r
+DONE: Add registry service to query services status\r
+DONE: Refactor web services checker to enable a programmatic access to its methods.\r
+DONE: Finish the client\r
+DONE: Add AACon ws\r
+DONE: Add iupred ws http://iupred.enzim.hu/\r
+DONE: Add globprot ws - does not report raw scores, just regions\r
+DONE: Add ronn ws\r
+DONE: Define limits for presets - if required\r
+DONE: Add logging facility to WSTester so more details of the problem can be reported\r
+DONE: Statistics collector for engines (number of operations/timing)\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
+version 1\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
git://source.jalview.org / jabaws.git / blobdiff