X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=TODO.txt;h=1c907cff06397c38ace588f0b5f63f97e0584dc6;hb=5d5b4fa33f708c00975d2f9810c4db5b86b5b6c8;hp=0acbf85324add92c95a0047754e9e63470deadd2;hpb=7e625752237ee07e815bfb28048bb0b1193b45c5;p=jabaws.git

diff --git a/TODO.txt b/TODO.txt
index 0acbf85..1c907cf 100644
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,4 +1,48 @@
+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
+ - test Muscle on the cluster
+ - test Muscle compilation
+ + probcons up-to-date
+ + clustal up-to-date 
+ - update tcoffee (8.99 latest)
+ - update Mafft (6.857 latest)
++ 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! 
+
+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
@@ -9,19 +53,19 @@ Exception in thread "main" java.lang.NullPointerException
 	at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)
 	at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)
 	
-	
-Need to pass predicted ranges to the client too - some are not straightforward to devise. 
-This may require changes to SequenceAnnotation
+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.
-Rename it to avoid confusion with jabaws client
++Add registry service to query services status
 
-Finish the client
++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