todo update

[jabaws.git] / TODO.txt

diff --git a/TODO.txt b/TODO.txt
index d7ae747..1c907cf 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,4 +1,48 @@
+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
+ - test Muscle on the cluster\r
+ - test Muscle compilation\r
+ + probcons up-to-date\r
+ + clustal up-to-date \r
+ - update tcoffee (8.99 latest)\r
+ - update Mafft (6.857 latest)\r
++ make sure conf files are optional!\r
+\r

 TODO: \r
 TODO: \r

+Registry 1 week\r
+webservices - 1 week\r
+client - 1 week\r
+docs - 1 week\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
 \r
 FIXME: \r
 Conecting to JABAWS version 2 service\r

@@ -11,17 +55,17 @@ Exception in thread "main" java.lang.NullPointerException
        \r
 ScoreManager should output scores properly \r
 \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
 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
-Rename it to avoid confusion with jabaws client\r
++Add registry service to query services status\r

 \r
 \r

-Finish the client\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
 Add interface for Jalview annotation \r
 Add the method to return Jalview Annotation to SequenceAnnotation IF  \r