Sasha Sherstnev [Fri, 6 Dec 2013 18:13:14 +0000 (18:13 +0000)]
partly working security: registration form, authorization, simple authentification
Sasha Sherstnev [Fri, 6 Dec 2013 17:39:14 +0000 (17:39 +0000)]
Partly working security: registration form, authorisaztion, simple authentication
Sasha Sherstnev [Thu, 5 Dec 2013 14:25:55 +0000 (14:25 +0000)]
Add posibility to look at failed jobs
Sasha Sherstnev [Thu, 5 Dec 2013 09:44:49 +0000 (09:44 +0000)]
Fix problem due to new internal java beans
Sasha Sherstnev [Thu, 5 Dec 2013 09:20:42 +0000 (09:20 +0000)]
Merge branch 'servlets' of https://source.jalview.org/git/proteocache into servlets
Conflicts:
server/compbio/controllers/SequenceController.java
Sasha Sherstnev [Thu, 5 Dec 2013 09:18:02 +0000 (09:18 +0000)]
Add basic security jars to the project
Natasha Sherstneva [Tue, 3 Dec 2013 17:45:52 +0000 (17:45 +0000)]
create DateBean, UserBean, TotalBean
Sasha Sherstnev [Tue, 3 Dec 2013 14:04:05 +0000 (14:04 +0000)]
Add additional checks of input parameters
Sasha Sherstnev [Tue, 3 Dec 2013 11:45:29 +0000 (11:45 +0000)]
Merge branch 'servlets'
Natasha Sherstneva [Tue, 3 Dec 2013 11:39:07 +0000 (11:39 +0000)]
create ProteinBean
Sasha Sherstnev [Mon, 2 Dec 2013 14:49:49 +0000 (14:49 +0000)]
Clean up JSP code
Sasha Sherstnev [Mon, 2 Dec 2013 14:49:35 +0000 (14:49 +0000)]
Fix problem with different date formats
Sasha Sherstnev [Mon, 2 Dec 2013 14:48:59 +0000 (14:48 +0000)]
Add additional checks of input parameters from html forms
Sasha Sherstnev [Mon, 2 Dec 2013 14:48:24 +0000 (14:48 +0000)]
Remove system prints
Sasha Sherstnev [Mon, 2 Dec 2013 12:31:55 +0000 (12:31 +0000)]
New internal supporting JSP
Sasha Sherstnev [Mon, 2 Dec 2013 11:58:08 +0000 (11:58 +0000)]
Improve UI of the website
Remove java code from JSP
Sasha Sherstnev [Fri, 29 Nov 2013 16:53:21 +0000 (16:53 +0000)]
Improve visibility of the website
Sasha Sherstnev [Fri, 29 Nov 2013 16:52:54 +0000 (16:52 +0000)]
Bug fixed: wrong class object in the logging
Sasha Sherstnev [Fri, 29 Nov 2013 16:52:31 +0000 (16:52 +0000)]
Fix problem with the bean
Sasha Sherstnev [Fri, 29 Nov 2013 16:51:53 +0000 (16:51 +0000)]
Modify ant build process for the new project structure
Sasha Sherstnev [Fri, 29 Nov 2013 12:20:17 +0000 (12:20 +0000)]
Merge branch 'master' into servlets
Conflicts:
WEB-INF/web.xml
website/AllReports.jsp
website/Index.jsp
website/ReportSequenceProtein.jsp
Sasha Sherstnev [Fri, 29 Nov 2013 12:16:24 +0000 (12:16 +0000)]
Improve front-end view of the website
Sasha Sherstnev [Fri, 29 Nov 2013 12:16:00 +0000 (12:16 +0000)]
Convert servlets into Spring controllers
Sasha Sherstnev [Fri, 29 Nov 2013 12:15:30 +0000 (12:15 +0000)]
improve configuration of the main Spring servlet
Sasha Sherstnev [Fri, 29 Nov 2013 12:14:52 +0000 (12:14 +0000)]
New bootstrap added
Sasha Sherstnev [Fri, 29 Nov 2013 12:14:17 +0000 (12:14 +0000)]
Add servlets for queries with IP
Sasha Sherstnev [Fri, 29 Nov 2013 12:12:58 +0000 (12:12 +0000)]
Remove old bootstrap
Natasha Sherstneva [Thu, 28 Nov 2013 14:46:25 +0000 (14:46 +0000)]
the new query jobs by ip
Sasha Sherstnev [Wed, 27 Nov 2013 19:07:08 +0000 (19:07 +0000)]
First working Spring-based version
Natasha Sherstneva [Tue, 26 Nov 2013 09:24:09 +0000 (09:24 +0000)]
PROT-7 fixed a problem with reportProteinSequence
Sasha Sherstnev [Mon, 25 Nov 2013 11:35:01 +0000 (11:35 +0000)]
Make all necessary changes for combining old and new servlets
Sasha Sherstnev [Mon, 25 Nov 2013 11:28:38 +0000 (11:28 +0000)]
Merge branch 'servlets'
Natasha Sherstneva [Mon, 25 Nov 2013 11:22:40 +0000 (11:22 +0000)]
PROT-7 add reportjobbyaday
Natasha Sherstneva [Mon, 25 Nov 2013 11:20:19 +0000 (11:20 +0000)]
PROT-7 add servletjobbyday
Sasha Sherstnev [Mon, 25 Nov 2013 11:04:43 +0000 (11:04 +0000)]
delete renamed class
Sasha Sherstnev [Mon, 25 Nov 2013 11:04:31 +0000 (11:04 +0000)]
Merge branch 'servlets'
Conflicts:
datadb/compbio/cassandra/StructureProteinPrediction.java
server/compbio/statistic/CassandraRequester.java
Natasha Sherstneva [Mon, 25 Nov 2013 10:41:17 +0000 (10:41 +0000)]
PROT-7 fixed reports jobs by a day
Sasha Sherstnev [Fri, 22 Nov 2013 18:34:55 +0000 (18:34 +0000)]
Improved style
Sasha Sherstnev [Fri, 22 Nov 2013 18:30:11 +0000 (18:30 +0000)]
Improve table style
Sasha Sherstnev [Fri, 22 Nov 2013 18:25:37 +0000 (18:25 +0000)]
Improve presentation of job on the web (servlet ServletSequenceProtein)
Sasha Sherstnev [Fri, 22 Nov 2013 12:29:29 +0000 (12:29 +0000)]
Some tweaks with Reporting JSPs
Sasha Sherstnev [Fri, 22 Nov 2013 11:52:17 +0000 (11:52 +0000)]
Merge branch 'servlets'
Conflicts:
.classpath
Natasha Sherstneva [Fri, 22 Nov 2013 11:46:09 +0000 (11:46 +0000)]
PROT-7 fixed report by dates
Sasha Sherstnev [Fri, 22 Nov 2013 11:27:37 +0000 (11:27 +0000)]
Switch off archiving by default
Sasha Sherstnev [Fri, 22 Nov 2013 11:26:36 +0000 (11:26 +0000)]
First working code for archinving Jpred jobs
Sasha Sherstnev [Fri, 22 Nov 2013 11:26:12 +0000 (11:26 +0000)]
make internal object private
Sasha Sherstnev [Fri, 22 Nov 2013 11:25:35 +0000 (11:25 +0000)]
some code for reporting Cassansdra status
Sasha Sherstnev [Fri, 22 Nov 2013 11:25:02 +0000 (11:25 +0000)]
New ProteoCache configuration
Sasha Sherstnev [Fri, 22 Nov 2013 11:24:38 +0000 (11:24 +0000)]
Fix problems with Eclipse settings
Sasha Sherstnev [Thu, 21 Nov 2013 12:43:16 +0000 (12:43 +0000)]
Merge branch 'servlets'
Sasha Sherstnev [Thu, 21 Nov 2013 12:42:03 +0000 (12:42 +0000)]
Better defaults for the JSP
Natasha Sherstneva [Thu, 21 Nov 2013 12:35:56 +0000 (12:35 +0000)]
PROT-7 fixed ServletProteinSequence
Sasha Sherstnev [Thu, 21 Nov 2013 12:08:52 +0000 (12:08 +0000)]
correct wb.xml
Natasha Sherstneva [Thu, 21 Nov 2013 09:35:40 +0000 (09:35 +0000)]
Change structure of CFMerge branch 'servlets' of https://source.jalview.org/git/proteocache into servlets
Natasha Sherstneva [Thu, 21 Nov 2013 09:35:04 +0000 (09:35 +0000)]
PROT-4 fixed remover
Sasha Sherstnev [Wed, 20 Nov 2013 16:51:30 +0000 (16:51 +0000)]
Merge branch 'servlets'
Natasha Sherstneva [Wed, 20 Nov 2013 14:55:59 +0000 (14:55 +0000)]
PROT-4 updated CF JobDateInfo (add new columns), JpredArchive (add column ExecutionStatus), add new CF FailLog
Sasha Sherstnev [Wed, 20 Nov 2013 13:46:01 +0000 (13:46 +0000)]
PROT-6 Fix problem with missing proteocache.jar in proteocache.war
Natasha Sherstneva [Tue, 19 Nov 2013 22:34:59 +0000 (22:34 +0000)]
PROT-4 updated structure ProteinData (change primary key, add column ExecTime), JpredArchive (add column FinalStatus), CassandraRemover almost finished
Sasha Sherstnev [Tue, 19 Nov 2013 15:28:58 +0000 (15:28 +0000)]
PROT-6 A first working, but not tested ant-based build system prepared
Sasha Sherstnev [Tue, 19 Nov 2013 15:28:15 +0000 (15:28 +0000)]
Remove internal FastaReader/FastaSequence and replace this with classes from JABAWS
Sasha Sherstnev [Tue, 19 Nov 2013 15:27:29 +0000 (15:27 +0000)]
Replace old textng jar with new one
Natasha Sherstneva [Mon, 18 Nov 2013 21:37:08 +0000 (21:37 +0000)]
Merge branch 'master' into servlets
Natasha Sherstneva [Mon, 18 Nov 2013 21:31:47 +0000 (21:31 +0000)]
PROT-4 Initial code for remover servlet
Natasha Sherstneva [Mon, 18 Nov 2013 21:27:49 +0000 (21:27 +0000)]
PROT-5 jars for the histogram servlet
Natasha Sherstneva [Mon, 18 Nov 2013 21:24:54 +0000 (21:24 +0000)]
PROT-5 template for the histogram servlet (still not working )
Sasha Sherstnev [Wed, 13 Nov 2013 14:19:35 +0000 (14:19 +0000)]
Better proteocache configuration for tests with real Jpred
Sasha Sherstnev [Wed, 13 Nov 2013 14:18:33 +0000 (14:18 +0000)]
Add still-not-working code for archiving jobs
Sasha Sherstnev [Tue, 12 Nov 2013 18:31:30 +0000 (18:31 +0000)]
Code for Jpred Job java Bean
Sasha Sherstnev [Tue, 12 Nov 2013 18:30:45 +0000 (18:30 +0000)]
RIntroduce Bean for Jpred job
Sasha Sherstnev [Tue, 12 Nov 2013 18:30:20 +0000 (18:30 +0000)]
Change JpredArchive table
Sasha Sherstnev [Tue, 12 Nov 2013 15:23:04 +0000 (15:23 +0000)]
Re-design the parser for inserting alignment-only and failed jobs
Sasha Sherstnev [Tue, 12 Nov 2013 15:22:07 +0000 (15:22 +0000)]
Fix bug for inserting job without known predictions
Sasha Sherstnev [Mon, 11 Nov 2013 18:31:24 +0000 (18:31 +0000)]
Switch off fillin new tables by default
Sasha Sherstnev [Mon, 11 Nov 2013 17:25:16 +0000 (17:25 +0000)]
Fix problem with filling new tables
Sasha Sherstnev [Mon, 11 Nov 2013 16:58:32 +0000 (16:58 +0000)]
Rebuild tables for queries
Sasha Sherstnev [Sat, 9 Nov 2013 11:48:07 +0000 (11:48 +0000)]
Merge branch 'servlets'
Conflicts:
datadb/compbio/cassandra/CassandraNativeConnector.java
server/compbio/statistic/CassandraRequester.java
Sasha Sherstnev [Sat, 9 Nov 2013 11:45:38 +0000 (11:45 +0000)]
Remive interface
Sasha Sherstnev [Sat, 9 Nov 2013 11:44:23 +0000 (11:44 +0000)]
Add filling new tables with data from old tables
Sasha Sherstnev [Sat, 9 Nov 2013 11:43:30 +0000 (11:43 +0000)]
Re-engineering of database I/O
Natasha Sherstneva [Fri, 8 Nov 2013 15:03:49 +0000 (15:03 +0000)]
new type date request
Natasha Sherstneva [Fri, 8 Nov 2013 14:16:19 +0000 (14:16 +0000)]
finished report log
Sasha Sherstnev [Fri, 8 Nov 2013 14:03:34 +0000 (14:03 +0000)]
Merge branch 'master' into servlets
Conflicts:
server/compbio/listeners/ServletSequenceProtein.java
server/compbio/statistic/CassandraRequester.java
Sasha Sherstnev [Fri, 8 Nov 2013 13:59:53 +0000 (13:59 +0000)]
Merge branch 'master' into servlets
Conflicts:
.classpath
datadb/compbio/cassandra/CassandraNativeConnector.java
datadb/compbio/cassandra/JpredParserHTTP.java
datadb/compbio/cassandra/JpredParserLocalFile.java
server/compbio/listeners/ContextListener.java
server/compbio/statistic/CassandraRequester.java
website/QuerySequenceProtein.jsp
website/ReportLength.jsp
website/ReportNew.jsp
Sasha Sherstnev [Fri, 8 Nov 2013 13:49:38 +0000 (13:49 +0000)]
Update classpath
Sasha Sherstnev [Fri, 8 Nov 2013 13:47:37 +0000 (13:47 +0000)]
Updated website
Sasha Sherstnev [Fri, 8 Nov 2013 13:47:17 +0000 (13:47 +0000)]
Updated website
Sasha Sherstnev [Fri, 8 Nov 2013 13:46:48 +0000 (13:46 +0000)]
Remove keyspace name from queries
Sasha Sherstnev [Fri, 8 Nov 2013 13:28:29 +0000 (13:28 +0000)]
Fix problems with Natasha's code
Natasha Sherstneva [Thu, 7 Nov 2013 13:32:02 +0000 (13:32 +0000)]
fix data report, protein report
Conflicts:
.classpath
datadb/compbio/cassandra/CassandraNativeConnector.java
Sasha Sherstnev [Fri, 8 Nov 2013 13:10:05 +0000 (13:10 +0000)]
Add lost JRE
Natasha Sherstneva [Thu, 7 Nov 2013 14:09:34 +0000 (14:09 +0000)]
add class with structure
Natasha Sherstneva [Thu, 7 Nov 2013 13:32:02 +0000 (13:32 +0000)]
fix data report, protein report
Conflicts:
.classpath
datadb/compbio/cassandra/CassandraNativeConnector.java
website/AllReports.jsp
Sasha Sherstnev [Fri, 8 Nov 2013 12:11:41 +0000 (12:11 +0000)]
Still not-working system for reading cassandra
Sasha Sherstnev [Fri, 8 Nov 2013 12:11:18 +0000 (12:11 +0000)]
Improved cassandra support
Sasha Sherstnev [Fri, 8 Nov 2013 11:26:45 +0000 (11:26 +0000)]
Start documentation
Natasha Sherstneva [Fri, 8 Nov 2013 11:10:46 +0000 (11:10 +0000)]
fix query log info, jobs by counter
Sasha Sherstnev [Fri, 8 Nov 2013 10:22:23 +0000 (10:22 +0000)]
Add PropertyHelper for running ProteoCache
Sasha Sherstnev [Fri, 8 Nov 2013 10:21:41 +0000 (10:21 +0000)]
Add properties configuration to the system
Sasha Sherstnev [Fri, 8 Nov 2013 10:20:24 +0000 (10:20 +0000)]
Fix logging system and add jabaws libs into the system
git://source.jalview.org / proteocache.git / log