X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=blobdiff_plain;f=TODO.txt;h=4dc9f9b0c35c8a43b6d508caf5501217dbd1e579;hp=dbd8400f81c539aea466af84ace18930ed8e6527;hb=HEAD;hpb=3b7b9e0a5fe1f6f3d57874a5ae63aaedf6a35ef3 diff --git a/TODO.txt b/TODO.txt index dbd8400..4dc9f9b 100644 --- a/TODO.txt +++ b/TODO.txt @@ -1,125 +1,120 @@ -TODO: -Registry 1 week -webservices - 1 week -client - 1 week -docs - 1 week +reset execution statistic in VM! + ++ regerate javadoc ++ server war - obtaining command line binaries + +Write help on + + execution stats + + new menu bar background + - new page background(?) + - merge developers help pages + - new VM + - new properties e.g. jar + - registry + - change log + - main page should point to JABA 1 + - Document the Limits for presets + - JAVA DOCS + - defaults changed - e.g. limits are disabled - explain how to enable + - cluster settings are commented out + - Describe requirements +Python > 2.2 +Perl > 5.0 +Java > 6 +For compilation +C++ +C +Gnu make + +- Check progress tracking on large sequence. + +- Add more detailed tests for webservices? + ++ TODO write some help on the executable.properties within this file! + +- check that after binaries relocation build tasks point to correct locations! -Cluster stats: - +cancelled should not be reported as incomplete! - -Remove hyperlinks from tasks which workdirs were removed - -graph generation - -user documentation (do not forget how to enable follow symlinks!) - -use the same name for output for different executables - +ant task to clean up clean stat db task before packing web app - +pack web apps with stat db (NOT TESTED!) - +change input size bites - +add help info for each column in the detailed job list table - +replace default -1 with ? - +delete and re-import the database to fix clustal input staff add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor -add to help: VirtualBox 4.0.4 works fine with JABAWS update links - rename jaba.war to jabaws.war and make sure jabaws context path is used throughout. -Current stat collector has to rely on file dates! - -Test all WS as names from Executables were removed - -Add default names for input and output in every executable and use them consistently -throughts (e.g. in all WS). Best of all use the same name from SceletalExectuable -For statistics. - -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 - -Allow empty Parameters and Preset files! - -Check the WS input and reject it on submission rather then of access with error message - -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. -+Finish the client - -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 (?) - -Replace conservation.Method with server.ws.Method -and try building WS. If this does not work - get rid of Method -Output file parsing for stat reporting -cluster engine stat of www-jws2 user +? Replace conservation.Method with server.ws.Method and try building WS. If this does not work - get rid of Method integrate the above to tweak the size of the local job -Add AACon ws -Add iupred ws http://iupred.enzim.hu/ -Add globprot ws - does not report raw scores, just regions -Add ronn ws -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 - -#END OF - TURN ALIGNMENT INTO PROFILE AND SEARCH SEQUENCE DATABASE USECASE - -New data model for representing psiblast,blast,phmmer,jackhmmer results - -new parsers for the above programmes output (Stockholm MSA format?) - -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? - -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) +DONE + +version 2 + +DONE: Current stat collector has to rely on file dates! +DONE: Help information? - relative - client to add host and context info +DONE: statistics - result files +DONE: Good toString method for Limits (test with command line client -limits) +DONE: install JABA 1 stat server +DONE: Get path to Java executable from JAVA_HOME ? (for Jronn AACon) + +DONE: GET rid of binaries/help directory! +DONE: update binaries + DONE: muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs + DONE: test Muscle on the cluster + DONE: test Muscle compilation + DONE: probcons up-to-date + DONE: clustal up-to-date + DONE: update tcoffee (8.99 latest) source code updated docs updated + DONE: tcoffee compilation for IA32 + DONE: update Mafft (6.857 latest) for win/lin32/lin64 and sources, no docs updates +DONE: make sure conf files are optional! + +Cluster stats: + DONE: cancelled should not be reported as incomplete! + DONE: ant task to clean up clean stat db task before packing web app + DONE: pack web apps with stat db (NOT TESTED!) + DONE: change input size bites + DONE: add help info for each column in the detailed job list table + DONE: replace default -1 with ? + DONE: delete and re-import the database to fix clustal input staff + +DONE: Test all WS as names from Executables were removed +DONE: Add default names for input and output in every executable and use them consistently + throughts (e.g. in all WS). Best of all use the same name from SceletalExectuable + For statistics. + +DONE: FIXED 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) -(later) WRAP Amps +DONE: ScoreManager should output scores properly +DONE: Allow empty Parameters and Preset files! +DONE: Check the WS input and reject it on submission rather then of access with error message -(later) Implement utility to rerun died tasks +DONE: Add registry service to query services status +DONE: Refactor web services checker to enable a programmatic access to its methods. +DONE: Finish the client +DONE: Add AACon ws +DONE: Add iupred ws http://iupred.enzim.hu/ +DONE: Add globprot ws - does not report raw scores, just regions +DONE: Add ronn ws +DONE: Define limits for presets - if required +DONE: Add logging facility to WSTester so more details of the problem can be reported +DONE: Statistics collector for engines (number of operations/timing) -(later) Add recognition for executables for the different architectures -(later) use Latch to manage engine reservations. Reservations for parallel jobs? +version 1 -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!