X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=TODO.txt;h=5d66c70f5166b06ced1bc25be0d70f4112e90c40;hb=a88671f0eaf790609936850c72c58624219ec726;hp=7ca26257e3b7596850d18bbbbb28bc8d0e45136d;hpb=b67f9b9dd77fa8f57d515842b8382b88d85cc029;p=jabaws.git diff --git a/TODO.txt b/TODO.txt index 7ca2625..5d66c70 100644 --- a/TODO.txt +++ b/TODO.txt @@ -1,111 +1,35 @@ +Add more detailed tests for webservices? + +? ideally should introduce native Mac support (and maybe abandon native windows support in +favour of VM) + TODO write some help on the executable.properties within this file! check that after binaries relocation build tasks point to correct locations! -GET rid of binaries/help directory! -update binaries - + muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs -+ make sure conf files are optional! - -TODO: -Registry 1 week -webservices - 1 week -client - 1 week -docs - 1 week 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! +To change this you need +1) Collect all the stats in old format into the DB +2) Update the code to get the date out of the file. +Can be done once JABAWS 1 is replaced with 2. -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) - +Document the Limits for presets JABA DOCS -(later) Define limits for presets - if required + (later) Add documentation on Presets, Parameters and Limits (later) Explain how to define a limit @@ -113,20 +37,63 @@ 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 -(later) WRAP Amps +version 2 -(later) Implement utility to rerun died tasks +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! -(later) Add recognition for executables for the different architectures +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) use Latch to manage engine reservations. Reservations for parallel jobs? +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 + +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) + + +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!