Sasha Sherstnev [Wed, 23 Oct 2013 15:49:07 +0000 (16:49 +0100)]
modify .gitignore to current JABAWS git structure
Sasha Sherstnev [Wed, 23 Oct 2013 12:23:05 +0000 (13:23 +0100)]
Changes to text on the website
Sasha Sherstnev [Mon, 14 Oct 2013 14:26:30 +0000 (15:26 +0100)]
Add an old jpred.pl script
Sasha Sherstnev [Mon, 14 Oct 2013 14:26:05 +0000 (15:26 +0100)]
Fix problems with tests
Sasha Sherstnev [Mon, 14 Oct 2013 14:20:41 +0000 (15:20 +0100)]
Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.
Sasha Sherstnev [Mon, 14 Oct 2013 09:58:40 +0000 (10:58 +0100)]
Define path to UNIREF database in conf/Executable.properties
Sasha Sherstnev [Mon, 14 Oct 2013 09:56:48 +0000 (10:56 +0100)]
Diable printing environmental variables in procInput.txt
Sasha Sherstnev [Mon, 14 Oct 2013 09:56:14 +0000 (10:56 +0100)]
Remove difinition of UNIREF for JABAWS from jpred.pl
Sasha Sherstnev [Fri, 4 Oct 2013 14:20:57 +0000 (15:20 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jabaws into develop
Sasha Sherstnev [Fri, 4 Oct 2013 14:20:30 +0000 (15:20 +0100)]
Update information on Jabaws VA
Sasha Sherstnev [Fri, 4 Oct 2013 14:20:01 +0000 (15:20 +0100)]
Fix bug with DB checking in jpred.pl
Sasha Sherstnev [Fri, 4 Oct 2013 14:19:04 +0000 (15:19 +0100)]
Comment code for future options
Jim Procter [Fri, 4 Oct 2013 12:39:31 +0000 (13:39 +0100)]
JWS-17 regression error - remove unnecessary throws statement
Jim Procter [Fri, 4 Oct 2013 12:16:28 +0000 (13:16 +0100)]
JWS-68 parameters cannot take multiple option names (this should have
been caught via configuration file validation - see JWS-73)
Sasha Sherstnev [Thu, 3 Oct 2013 12:33:45 +0000 (13:33 +0100)]
Slightly changed JSP page
Sasha Sherstnev [Thu, 3 Oct 2013 12:13:22 +0000 (13:13 +0100)]
Fix wrong error message
Sasha Sherstnev [Thu, 3 Oct 2013 12:10:50 +0000 (13:10 +0100)]
Fix problem with HTML code
Sasha Sherstnev [Thu, 3 Oct 2013 12:08:41 +0000 (13:08 +0100)]
Fix problem with old Probcons code: couldn't be complied with modern gcc since string.h is needed
Sasha Sherstnev [Wed, 2 Oct 2013 17:14:19 +0000 (18:14 +0100)]
Simplify code
Sasha Sherstnev [Mon, 30 Sep 2013 13:32:41 +0000 (14:32 +0100)]
Lots of changes for Jabaws 2.1 website
Sasha Sherstnev [Mon, 30 Sep 2013 13:32:05 +0000 (14:32 +0100)]
Re-build WS artefacts
Sasha Sherstnev [Mon, 30 Sep 2013 13:31:28 +0000 (14:31 +0100)]
Remove still unsupported methods of RegistryWS
Sasha Sherstnev [Mon, 30 Sep 2013 13:31:08 +0000 (14:31 +0100)]
Swtich off GA by default
Sasha Sherstnev [Mon, 30 Sep 2013 13:30:32 +0000 (14:30 +0100)]
Google analytics receives message with actual Jabaws version
Sasha Sherstnev [Mon, 30 Sep 2013 13:29:33 +0000 (14:29 +0100)]
Bug Fixg: testing RNAalifold jobs have been considered as real ones
Sasha Sherstnev [Mon, 30 Sep 2013 13:28:19 +0000 (14:28 +0100)]
test WS on internal server in the case of proxying
Sasha Sherstnev [Mon, 30 Sep 2013 13:27:18 +0000 (14:27 +0100)]
Add Jabaws version string available in Services
Sasha Sherstnev [Mon, 30 Sep 2013 13:26:03 +0000 (14:26 +0100)]
Roll back some changes in WSDL of RegistryWS for some time: restore back compatibility
Sasha Sherstnev [Mon, 30 Sep 2013 13:24:59 +0000 (14:24 +0100)]
Add Jabaws version id as publicly available string in webservices
Sasha Sherstnev [Mon, 30 Sep 2013 08:00:19 +0000 (09:00 +0100)]
Delete unneeded directory
Sasha Sherstnev [Fri, 27 Sep 2013 16:24:10 +0000 (17:24 +0100)]
Change Eclipse configuration
Sasha Sherstnev [Fri, 27 Sep 2013 14:27:53 +0000 (15:27 +0100)]
Remove old file
Sasha Sherstnev [Fri, 27 Sep 2013 14:27:20 +0000 (15:27 +0100)]
Improve JSP pages
Sasha Sherstnev [Fri, 27 Sep 2013 14:18:11 +0000 (15:18 +0100)]
Improve Eclipse project settings
Sasha Sherstnev [Thu, 26 Sep 2013 13:33:00 +0000 (14:33 +0100)]
Change default formatting
Sasha Sherstnev [Thu, 26 Sep 2013 13:30:04 +0000 (14:30 +0100)]
Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java and JobRunner.java -> ClusterRunner.java
Sasha Sherstnev [Tue, 24 Sep 2013 16:35:06 +0000 (17:35 +0100)]
Assign JABAService.V2_SERVICE_NAMESPACE to all new services: JpredWS, RNAalifoldWS, MSAprobsWS, GLprobsWS
Sasha Sherstnev [Tue, 24 Sep 2013 14:36:34 +0000 (15:36 +0100)]
Fix a problem with JSP page
Sasha Sherstnev [Tue, 24 Sep 2013 14:32:06 +0000 (15:32 +0100)]
Replace binaries with one compatible with the dundee cluster
Sasha Sherstnev [Tue, 24 Sep 2013 14:11:53 +0000 (15:11 +0100)]
Add all needed infrastructure for MSAprobs and GLprobs
Sasha Sherstnev [Tue, 24 Sep 2013 14:10:38 +0000 (15:10 +0100)]
Add measurement of execution time for servlets
Sasha Sherstnev [Tue, 24 Sep 2013 14:08:57 +0000 (15:08 +0100)]
Add GLprobs and MSAprobs to binaries
Sasha Sherstnev [Fri, 20 Sep 2013 14:32:07 +0000 (15:32 +0100)]
Refactoring: rename duplicated Util classes
Sasha Sherstnev [Fri, 20 Sep 2013 13:35:23 +0000 (14:35 +0100)]
add lost exception
Sasha Sherstnev [Fri, 20 Sep 2013 12:48:19 +0000 (13:48 +0100)]
Fix problems with tests
Sasha Sherstnev [Thu, 19 Sep 2013 13:44:57 +0000 (14:44 +0100)]
JWS-17 re-design behaviour of Option.toString
Sasha Sherstnev [Thu, 19 Sep 2013 12:47:25 +0000 (13:47 +0100)]
Re-generate WS artefacts: option.furtherDetails is xs:string now
Sasha Sherstnev [Thu, 19 Sep 2013 12:46:16 +0000 (13:46 +0100)]
JWS-17: fix problem with undefined URL for the furtherDetails tag
Sasha Sherstnev [Tue, 17 Sep 2013 16:12:56 +0000 (17:12 +0100)]
Add reference on Jronn
Sasha Sherstnev [Tue, 17 Sep 2013 14:35:24 +0000 (15:35 +0100)]
Final fixing of Jpred problem with casting
Sasha Sherstnev [Tue, 17 Sep 2013 14:20:15 +0000 (15:20 +0100)]
Fix probem with metadata
Sasha Sherstnev [Tue, 17 Sep 2013 10:46:10 +0000 (11:46 +0100)]
Remove unused imports
Sasha Sherstnev [Tue, 17 Sep 2013 10:22:48 +0000 (11:22 +0100)]
Clean up logging system
Sasha Sherstnev [Mon, 16 Sep 2013 16:22:00 +0000 (17:22 +0100)]
New Linux binaries for ViennaRNA
Sasha Sherstnev [Mon, 16 Sep 2013 16:21:35 +0000 (17:21 +0100)]
Fix bug with fail WS tests
Sasha Sherstnev [Mon, 16 Sep 2013 15:06:57 +0000 (16:06 +0100)]
Add info on new programs
Sasha Sherstnev [Mon, 16 Sep 2013 14:57:00 +0000 (15:57 +0100)]
Change JABAWS version at the website
Sasha Sherstnev [Mon, 16 Sep 2013 14:28:52 +0000 (15:28 +0100)]
Set right path to UNIREF at ningal
Sasha Sherstnev [Mon, 16 Sep 2013 14:17:02 +0000 (15:17 +0100)]
Re-design the ServiceStatus JSP page
Sasha Sherstnev [Mon, 16 Sep 2013 14:16:35 +0000 (15:16 +0100)]
Define proper test for JpredWS
Sasha Sherstnev [Mon, 16 Sep 2013 14:15:46 +0000 (15:15 +0100)]
Set right permissions for Jpred binaries
Sasha Sherstnev [Mon, 16 Sep 2013 14:15:10 +0000 (15:15 +0100)]
Made the binary executable at ningal
Sasha Sherstnev [Fri, 13 Sep 2013 15:45:35 +0000 (16:45 +0100)]
New set of presets for Jpred
Sasha Sherstnev [Fri, 13 Sep 2013 15:44:21 +0000 (16:44 +0100)]
New Jpred parameters and new set of Jpred presets
Sasha Sherstnev [Fri, 13 Sep 2013 15:43:32 +0000 (16:43 +0100)]
Fix problem with wrong casting Alignment -> JpredAlignment
Sasha Sherstnev [Fri, 13 Sep 2013 14:47:42 +0000 (15:47 +0100)]
Add SS prediction for multiple aligment into jpred.pl. Before this was a part of another script
Sasha Sherstnev [Thu, 12 Sep 2013 08:43:50 +0000 (09:43 +0100)]
Remove un-necessary Axis servlets
Sasha Sherstnev [Wed, 11 Sep 2013 16:17:31 +0000 (17:17 +0100)]
More commands...
Sasha Sherstnev [Wed, 11 Sep 2013 16:13:02 +0000 (17:13 +0100)]
Fix problem with the JpredWS service. Now Jws2Client is able to test the service
Sasha Sherstnev [Tue, 10 Sep 2013 15:10:56 +0000 (16:10 +0100)]
Log file for preparing of new version of wsdl and xsd files for all services
Sasha Sherstnev [Tue, 10 Sep 2013 15:10:37 +0000 (16:10 +0100)]
Improved Bld file
Sasha Sherstnev [Tue, 10 Sep 2013 15:09:58 +0000 (16:09 +0100)]
New version of wsdl and xsd files for all services
Sasha Sherstnev [Tue, 10 Sep 2013 15:08:09 +0000 (16:08 +0100)]
Re-formatting the file
Sasha Sherstnev [Tue, 10 Sep 2013 15:07:12 +0000 (16:07 +0100)]
File with main building commands
Sasha Sherstnev [Tue, 10 Sep 2013 15:06:14 +0000 (16:06 +0100)]
Add "safe type casting" warnings
Sasha Sherstnev [Tue, 10 Sep 2013 15:05:08 +0000 (16:05 +0100)]
Fix problem with unknown services ("forward" compatibility)
Sasha Sherstnev [Tue, 10 Sep 2013 15:02:58 +0000 (16:02 +0100)]
Add "safe type cast" warnings
Sasha Sherstnev [Mon, 9 Sep 2013 09:39:33 +0000 (10:39 +0100)]
Add lost description of RNAalifold from ViennaRNA
Sasha Sherstnev [Fri, 6 Sep 2013 16:23:22 +0000 (17:23 +0100)]
Merge branch 'JABAWS_Release_2_5' into develop
Conflicts:
.project
WEB-INF/sun-jaxws.xml
conf/Executable.properties
testsrc/compbio/data/sequence/SequenceUtilTester.java
webservices/compbio/data/msa/Category.java
webservices/compbio/ws/client/Jws2Client.java
webservices/compbio/ws/client/Services.java
webservices/compbio/ws/client/WSTester.java
webservices/compbio/ws/server/WSUtil.java
webservices/compbio/ws/server/resource/AAConWS.wsdl
webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
webservices/compbio/ws/server/resource/ClustalWS.wsdl
webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
webservices/compbio/ws/server/resource/DisemblWS.wsdl
webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
webservices/compbio/ws/server/resource/IUPredWS.wsdl
webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
webservices/compbio/ws/server/resource/JronnWS.wsdl
webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
webservices/compbio/ws/server/resource/MafftWS.wsdl
webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
webservices/compbio/ws/server/resource/MuscleWS.wsdl
webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
webservices/compbio/ws/server/resource/RegistryWS.wsdl
webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd
webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
wsbuild.xml
Sasha Sherstnev [Fri, 6 Sep 2013 15:33:09 +0000 (16:33 +0100)]
Merge branch 'JABAWS_Release_2_5' of https://source.jalview.org/git/jabaws into JABAWS_Release_2_5
Sasha Sherstnev [Fri, 6 Sep 2013 15:26:24 +0000 (16:26 +0100)]
Regenerate wsdl-s
Sasha Sherstnev [Fri, 6 Sep 2013 15:25:57 +0000 (16:25 +0100)]
Switch to olde namespace
Sasha Sherstnev [Fri, 6 Sep 2013 15:25:23 +0000 (16:25 +0100)]
Different code style
Sasha Sherstnev [Fri, 6 Sep 2013 14:29:24 +0000 (15:29 +0100)]
Switch JpredWS from SequenceAnnotation to MsaWS
Sasha Sherstnev [Fri, 6 Sep 2013 14:13:54 +0000 (15:13 +0100)]
Fix problem with path to the UNIREF database
Sasha Sherstnev [Fri, 6 Sep 2013 09:45:37 +0000 (10:45 +0100)]
Change project name
Sasha Sherstnev [Fri, 6 Sep 2013 09:29:59 +0000 (10:29 +0100)]
Fix problem with test data for RNAalifold
Sasha Sherstnev [Fri, 6 Sep 2013 09:29:42 +0000 (10:29 +0100)]
Replace logo files
Sasha Sherstnev [Thu, 5 Sep 2013 11:10:20 +0000 (12:10 +0100)]
Change version: 2.0.1 -> 2.5
Sasha Sherstnev [Thu, 5 Sep 2013 11:04:06 +0000 (12:04 +0100)]
Fix logging problem
Sasha Sherstnev [Thu, 5 Sep 2013 11:03:37 +0000 (12:03 +0100)]
Add missing binaty and statis library
Sasha Sherstnev [Thu, 5 Sep 2013 11:03:18 +0000 (12:03 +0100)]
Add missing doc files
Sasha Sherstnev [Thu, 5 Sep 2013 10:57:22 +0000 (11:57 +0100)]
Replace Progs/RNAalifold with x64 binary and add all other programs
Sasha Sherstnev [Thu, 5 Sep 2013 10:20:49 +0000 (11:20 +0100)]
Roll back JpredWS JABAWS namespace: from V3 to V2. V3 will be a Matrix
Sasha Sherstnev [Thu, 5 Sep 2013 10:19:18 +0000 (11:19 +0100)]
Fix a bug with wrong namespace
Sasha Sherstnev [Thu, 5 Sep 2013 10:18:26 +0000 (11:18 +0100)]
Use "right" namespace, i.e. the name from JABAService
Sasha Sherstnev [Thu, 5 Sep 2013 10:07:15 +0000 (11:07 +0100)]
Change JAXWS java code and wsdl for changed methods in RegistryWS
Sasha Sherstnev [Thu, 5 Sep 2013 09:52:55 +0000 (10:52 +0100)]
Other necessary changes
Sasha Sherstnev [Thu, 5 Sep 2013 09:52:28 +0000 (10:52 +0100)]
New version of the JABAWS client
Sasha Sherstnev [Thu, 5 Sep 2013 09:50:39 +0000 (10:50 +0100)]
Add new method
git://source.jalview.org / jabaws.git / log