proteocache.git
7 years agoAdd mode comments to the classes master
Alexander Sherstnev [Wed, 6 Aug 2014 08:32:14 +0000 (09:32 +0100)]
Add mode comments to the classes

7 years agoRemove trash
Alexander Sherstnev [Fri, 1 Aug 2014 10:44:26 +0000 (11:44 +0100)]
Remove trash

7 years agoMerge branch 'master' of https://source.jalview.org/git/proteocache
Alexander Sherstnev [Fri, 1 Aug 2014 10:21:12 +0000 (11:21 +0100)]
Merge branch 'master' of https://source.jalview.org/git/proteocache

7 years agofix html errors
Sasha Sherstnev [Fri, 1 Aug 2014 08:07:38 +0000 (09:07 +0100)]
fix html errors

7 years agopdf version of the presentation
Sasha Sherstnev [Thu, 31 Jul 2014 19:59:13 +0000 (20:59 +0100)]
pdf version of the presentation

7 years agoFigure for ProteoCache structure
Sasha Sherstnev [Thu, 31 Jul 2014 19:20:43 +0000 (20:20 +0100)]
Figure for ProteoCache structure

7 years agoAdd new method to ProteoCacheWS web service
Sasha Sherstnev [Tue, 4 Feb 2014 16:20:29 +0000 (16:20 +0000)]
Add new method to ProteoCacheWS web service

7 years agoImprove javadoc
Sasha Sherstnev [Tue, 4 Feb 2014 16:19:27 +0000 (16:19 +0000)]
Improve javadoc

7 years agoFix bug with deleted Cassandra table column
Sasha Sherstnev [Tue, 4 Feb 2014 16:18:55 +0000 (16:18 +0000)]
Fix bug with deleted Cassandra table column

7 years agoSimplify the jobdateinfo table (remove Total, Program, Version)
Sasha Sherstnev [Mon, 3 Feb 2014 14:05:26 +0000 (14:05 +0000)]
Simplify the jobdateinfo table (remove Total, Program, Version)

7 years agoTemporary fix problem with wrong Jpred version
Sasha Sherstnev [Mon, 3 Feb 2014 14:04:31 +0000 (14:04 +0000)]
Temporary fix problem with wrong Jpred version

7 years agoAllow less full jobs (with failed status) to be reported
Sasha Sherstnev [Mon, 3 Feb 2014 14:03:51 +0000 (14:03 +0000)]
Allow less full jobs (with failed status) to be reported

7 years agoFix problem with the JSP
Sasha Sherstnev [Mon, 3 Feb 2014 14:03:30 +0000 (14:03 +0000)]
Fix problem with the JSP

7 years agoAdd file needed for WS deployment on Tomcat DAO
Sasha Sherstnev [Mon, 3 Feb 2014 10:32:20 +0000 (10:32 +0000)]
Add file needed for WS deployment on Tomcat

7 years agoRe-generated WSDL
Sasha Sherstnev [Mon, 3 Feb 2014 10:28:44 +0000 (10:28 +0000)]
Re-generated WSDL

7 years agoAdd explicit URL object
Sasha Sherstnev [Mon, 3 Feb 2014 10:27:39 +0000 (10:27 +0000)]
Add explicit URL object

7 years agoAdd comments to bean internal data
Sasha Sherstnev [Mon, 3 Feb 2014 10:26:34 +0000 (10:26 +0000)]
Add comments to bean internal data

7 years agoFix problem with monospace font
Sasha Sherstnev [Mon, 3 Feb 2014 10:26:07 +0000 (10:26 +0000)]
Fix problem with monospace font

7 years agoAdd documentation to the classes
Sasha Sherstnev [Fri, 31 Jan 2014 16:51:47 +0000 (16:51 +0000)]
Add documentation to the classes

7 years agoAdd new operation to the ProteoCache WS
Sasha Sherstnev [Fri, 31 Jan 2014 16:36:14 +0000 (16:36 +0000)]
Add new operation to the ProteoCache WS

7 years agoSimplify the code
Sasha Sherstnev [Fri, 31 Jan 2014 16:35:24 +0000 (16:35 +0000)]
Simplify the code

7 years agoMerge branch 'DAO'
Sasha Sherstnev [Fri, 31 Jan 2014 16:34:26 +0000 (16:34 +0000)]
Merge branch 'DAO'

Conflicts:
datadb/compbio/cassandra/CassandraReaderOld.java

7 years agoApply formatting
Sasha Sherstnev [Fri, 31 Jan 2014 14:37:32 +0000 (14:37 +0000)]
Apply formatting

7 years agoFirst working web service for quering proteocache DB PROT-9-webservice
Sasha Sherstnev [Fri, 31 Jan 2014 14:30:32 +0000 (14:30 +0000)]
First working web service for quering proteocache DB

7 years agoMerge branch 'DAO' of https://source.jalview.org/git/proteocache into DAO
Natasha Sherstneva [Fri, 31 Jan 2014 10:37:32 +0000 (10:37 +0000)]
Merge branch 'DAO' of https://source.jalview.org/git/proteocache into DAO

Conflicts:
datadb/compbio/cassandra/CassandraReaderOld.java
server/compbio/statistic/CassandraRequester.java

7 years agoDeleted CassandraRequest.java and CassandraReaderOld.java
Natasha Sherstneva [Fri, 31 Jan 2014 10:25:22 +0000 (10:25 +0000)]
Deleted CassandraRequest.java and CassandraReaderOld.java

7 years agoClean up the code
Sasha Sherstnev [Wed, 29 Jan 2014 14:24:15 +0000 (14:24 +0000)]
Clean up the code

7 years agoMerge branch 'master' into PROT-9-webservice
Sasha Sherstnev [Wed, 29 Jan 2014 14:06:00 +0000 (14:06 +0000)]
Merge branch 'master' into PROT-9-webservice

7 years agoChange main menu fro anonymous users
Sasha Sherstnev [Wed, 29 Jan 2014 13:56:37 +0000 (13:56 +0000)]
Change main menu fro anonymous users

7 years agoSwitichin between different Jpred installations
Sasha Sherstnev [Wed, 29 Jan 2014 08:07:37 +0000 (08:07 +0000)]
Switichin between different Jpred installations

7 years agoAdd reporting servlet time execution
Sasha Sherstnev [Wed, 29 Jan 2014 08:04:02 +0000 (08:04 +0000)]
Add reporting servlet time execution

7 years agoFi bug for wrong job selection
Sasha Sherstnev [Wed, 29 Jan 2014 08:03:26 +0000 (08:03 +0000)]
Fi bug for wrong job selection

7 years agoA new MVC model paramter for "no jobs found"
Sasha Sherstnev [Wed, 29 Jan 2014 08:02:28 +0000 (08:02 +0000)]
A new MVC model paramter for "no jobs found"

7 years agoBlock job report if no jobs are found
Sasha Sherstnev [Wed, 29 Jan 2014 08:01:53 +0000 (08:01 +0000)]
Block job report if no jobs are found

7 years agoupdate path to some dynamic pages
Sasha Sherstnev [Mon, 27 Jan 2014 15:58:28 +0000 (15:58 +0000)]
update path to some dynamic pages

7 years agoAdd detailed statistics on delated jobs
Sasha Sherstnev [Mon, 27 Jan 2014 14:54:10 +0000 (14:54 +0000)]
Add detailed statistics on delated jobs

7 years agoClean up the code
Sasha Sherstnev [Mon, 27 Jan 2014 14:53:16 +0000 (14:53 +0000)]
Clean up the code

7 years agoAdd simple statistics to the project home page
Sasha Sherstnev [Mon, 27 Jan 2014 14:51:18 +0000 (14:51 +0000)]
Add simple statistics to the project home page

7 years agoMove the class to engine
Sasha Sherstnev [Mon, 27 Jan 2014 14:50:52 +0000 (14:50 +0000)]
Move the class to engine

7 years agoImprove stability of Cassandra API calls (commands are checked)
Sasha Sherstnev [Mon, 27 Jan 2014 14:49:54 +0000 (14:49 +0000)]
Improve stability of Cassandra API calls (commands are checked)

7 years agoImprove call of earliest and current dates (through protected methods)
Sasha Sherstnev [Mon, 27 Jan 2014 14:48:18 +0000 (14:48 +0000)]
Improve call of earliest and current dates (through protected methods)

7 years agoMerge branch 'DAO'
Sasha Sherstnev [Thu, 23 Jan 2014 14:33:17 +0000 (14:33 +0000)]
Merge branch 'DAO'

Conflicts:
server/compbio/controllers/JobController.java

7 years ago1. Fix bug in SequenceReader
Sasha Sherstnev [Thu, 23 Jan 2014 14:26:59 +0000 (14:26 +0000)]
1. Fix bug in SequenceReader
2. Simpligy links to dynamic pages

7 years ago1. Fix problem with slow servlets (wrong forming CVS line)
Sasha Sherstnev [Thu, 23 Jan 2014 14:01:03 +0000 (14:01 +0000)]
1. Fix problem with slow servlets (wrong forming CVS line)
2. Add servlet time execution for admin role

7 years agoMerge branch 'DAO' of https://source.jalview.org/git/proteocache into DAO
Natasha Sherstneva [Thu, 23 Jan 2014 11:01:21 +0000 (11:01 +0000)]
Merge branch 'DAO' of https://source.jalview.org/git/proteocache into DAO

7 years agofixed Execution Time Statistics report
Natasha Sherstneva [Thu, 23 Jan 2014 10:57:45 +0000 (10:57 +0000)]
fixed Execution Time Statistics report

7 years agoIntroduce new table for programs and necessary infrastructure for the table
Sasha Sherstnev [Wed, 22 Jan 2014 12:00:21 +0000 (12:00 +0000)]
Introduce new table for programs and necessary infrastructure for the table

7 years agoMerge branch 'DAO'
Sasha Sherstnev [Wed, 22 Jan 2014 09:28:01 +0000 (09:28 +0000)]
Merge branch 'DAO'

7 years agoadd check for a Cassandra request
Sasha Sherstnev [Wed, 22 Jan 2014 09:26:48 +0000 (09:26 +0000)]
add check for a Cassandra request

7 years agofixed Execution time report
Natasha Sherstneva [Tue, 21 Jan 2014 14:08:38 +0000 (14:08 +0000)]
fixed Execution time report

7 years agoAdd delay for reading new jobs
Sasha Sherstnev [Tue, 21 Jan 2014 09:39:44 +0000 (09:39 +0000)]
Add delay for reading new jobs

7 years agoAdd javadoc
Sasha Sherstnev [Tue, 21 Jan 2014 09:39:11 +0000 (09:39 +0000)]
Add javadoc

7 years agoWrong link
Sasha Sherstnev [Tue, 21 Jan 2014 09:38:35 +0000 (09:38 +0000)]
Wrong link

7 years agoFix problem with new table column names: ProgrammeName -> ProgramName, Version -...
Sasha Sherstnev [Mon, 20 Jan 2014 16:03:46 +0000 (16:03 +0000)]
Fix problem with new table column names: ProgrammeName -> ProgramName, Version -> ProgramVersion

7 years agoMerge branch 'DAO'
Sasha Sherstnev [Mon, 20 Jan 2014 15:24:16 +0000 (15:24 +0000)]
Merge branch 'DAO'

Conflicts:
conf/Proteocache.properties

7 years agoAdd reference to the production Cassandra deployment
Sasha Sherstnev [Mon, 20 Jan 2014 15:22:09 +0000 (15:22 +0000)]
Add reference to the production Cassandra deployment

7 years agoReplace java 1.6 -> 1.7 in Eclipse
Sasha Sherstnev [Mon, 20 Jan 2014 15:21:40 +0000 (15:21 +0000)]
Replace java 1.6 -> 1.7 in Eclipse

7 years agoenable removing DB records from the Web (with admin role)
Sasha Sherstnev [Mon, 20 Jan 2014 15:20:26 +0000 (15:20 +0000)]
enable removing DB records from the Web (with admin role)

7 years agoEdit comments
Sasha Sherstnev [Mon, 20 Jan 2014 15:19:36 +0000 (15:19 +0000)]
Edit comments

7 years agoImprove web view of the project (real pages for removal of DB records)
Sasha Sherstnev [Mon, 20 Jan 2014 15:17:35 +0000 (15:17 +0000)]
Improve web view of the project (real pages for removal of DB records)

7 years agoMerge branch 'DAO' of https://source.jalview.org/git/proteocache into DAO
Natasha Sherstneva [Mon, 20 Jan 2014 11:01:33 +0000 (11:01 +0000)]
Merge branch 'DAO' of https://source.jalview.org/git/proteocache into DAO

7 years agoinserted 2 columns: version and pragramme name
Natasha Sherstneva [Mon, 20 Jan 2014 10:56:16 +0000 (10:56 +0000)]
inserted 2 columns: version and pragramme name

7 years agoMerge branch 'DAO'
Sasha Sherstnev [Fri, 17 Jan 2014 11:27:27 +0000 (11:27 +0000)]
Merge branch 'DAO'

7 years agochanged a dayly jobs statistic query
Natasha Sherstneva [Wed, 15 Jan 2014 19:34:23 +0000 (19:34 +0000)]
changed a dayly jobs statistic query

7 years agoForm CSV file if results are not null
Sasha Sherstnev [Wed, 15 Jan 2014 17:14:29 +0000 (17:14 +0000)]
Form CSV file if results are not null

7 years agoAdd direct links to Jpred jobs
Sasha Sherstnev [Mon, 13 Jan 2014 13:31:27 +0000 (13:31 +0000)]
Add direct links to Jpred jobs

7 years agomove jsp for reports to a separate dir
Sasha Sherstnev [Fri, 10 Jan 2014 16:35:59 +0000 (16:35 +0000)]
move jsp for reports to a separate dir

7 years agoApply formatting
Sasha Sherstnev [Fri, 10 Jan 2014 16:35:28 +0000 (16:35 +0000)]
Apply formatting

7 years agoMerge branch 'DAO'
Sasha Sherstnev [Fri, 10 Jan 2014 15:15:38 +0000 (15:15 +0000)]
Merge branch 'DAO'

Conflicts:
server/compbio/controllers/DailyStatisticsController.java
server/compbio/controllers/SequenceController.java

7 years agoAttempt to resolve the problem with java on cluster...
Sasha Sherstnev [Fri, 10 Jan 2014 15:01:02 +0000 (15:01 +0000)]
Attempt to resolve the problem with java on cluster...

7 years agoRemove obsolete javascript code
Sasha Sherstnev [Fri, 10 Jan 2014 15:00:27 +0000 (15:00 +0000)]
Remove obsolete javascript code

7 years agoDummy controller for proteomes
Sasha Sherstnev [Fri, 10 Jan 2014 14:59:59 +0000 (14:59 +0000)]
Dummy controller for proteomes

7 years agoAdd a bit of javascripting to the project
Sasha Sherstnev [Fri, 10 Jan 2014 14:56:08 +0000 (14:56 +0000)]
Add a bit of javascripting to the project

7 years agoAdd datatables-1.9.4 and jquery-1.10.2 libraries
Sasha Sherstnev [Fri, 10 Jan 2014 14:55:28 +0000 (14:55 +0000)]
Add datatables-1.9.4 and jquery-1.10.2 libraries

7 years agoComment strang and potentially erroneous code
Sasha Sherstnev [Fri, 10 Jan 2014 14:53:36 +0000 (14:53 +0000)]
Comment strang and potentially erroneous code

7 years agoAdd the "Reload" and "CSV" buttons
Sasha Sherstnev [Fri, 10 Jan 2014 14:53:06 +0000 (14:53 +0000)]
Add the "Reload" and "CSV" buttons

7 years agoTiny "view" correction
Sasha Sherstnev [Fri, 10 Jan 2014 14:52:31 +0000 (14:52 +0000)]
Tiny "view" correction

7 years agoadd menu elements for dealing with proteomes
Sasha Sherstnev [Fri, 10 Jan 2014 14:52:02 +0000 (14:52 +0000)]
add menu elements for dealing with proteomes

7 years agonew readers for the queries
Natasha Sherstneva [Fri, 10 Jan 2014 10:29:01 +0000 (10:29 +0000)]
new readers for the queries

7 years agoRename the dynamic page generated with the controller
Sasha Sherstnev [Thu, 9 Jan 2014 15:59:16 +0000 (15:59 +0000)]
Rename the dynamic page generated with the controller

7 years agoAdd exceptions and internal checks for Cassandra requests
Sasha Sherstnev [Thu, 9 Jan 2014 15:53:12 +0000 (15:53 +0000)]
Add exceptions and internal checks for Cassandra requests

7 years agoAdd CSS element for tables with scrollbars
Sasha Sherstnev [Thu, 9 Jan 2014 15:43:45 +0000 (15:43 +0000)]
Add CSS element for tables with scrollbars

7 years agoFix problem with radio button
Sasha Sherstnev [Thu, 9 Jan 2014 15:43:12 +0000 (15:43 +0000)]
Fix problem with radio button

7 years agoAdd a possible path to the Jpred archive in the cluster
Sasha Sherstnev [Thu, 9 Jan 2014 15:41:22 +0000 (15:41 +0000)]
Add a possible path to the Jpred archive in the cluster

7 years agoAdd areal group logo picture
Sasha Sherstnev [Thu, 9 Jan 2014 15:40:31 +0000 (15:40 +0000)]
Add areal group logo picture

7 years agoMake all servlets available to admins
Sasha Sherstnev [Fri, 20 Dec 2013 11:39:29 +0000 (11:39 +0000)]
Make all servlets available to admins

7 years agoWrong web form action fixed
Sasha Sherstnev [Fri, 20 Dec 2013 11:38:11 +0000 (11:38 +0000)]
Wrong web form action fixed

7 years agoCentralize initial examples of job id and IP
Sasha Sherstnev [Fri, 20 Dec 2013 11:37:35 +0000 (11:37 +0000)]
Centralize initial examples of job id and IP

7 years agoFix the problem with the disappearing link to the job archive file
Sasha Sherstnev [Fri, 20 Dec 2013 11:36:48 +0000 (11:36 +0000)]
Fix the problem with the disappearing link to the job archive file

7 years agoEnabling archiving by default
Sasha Sherstnev [Fri, 20 Dec 2013 08:33:34 +0000 (08:33 +0000)]
Enabling archiving by default

7 years agoRemove obsolete raw servlets
Sasha Sherstnev [Fri, 20 Dec 2013 08:33:03 +0000 (08:33 +0000)]
Remove obsolete raw servlets

7 years agoAdd "template" figures for non-existing logos and javascript for checking svg support...
Sasha Sherstnev [Fri, 20 Dec 2013 08:32:11 +0000 (08:32 +0000)]
Add "template" figures for non-existing logos and javascript for checking svg support in browser

7 years agoadd dummy file into results
Sasha Sherstnev [Fri, 20 Dec 2013 08:31:33 +0000 (08:31 +0000)]
add dummy file into results

7 years agoAdd direct link to the job archive file (raw data)
Sasha Sherstnev [Fri, 20 Dec 2013 08:30:35 +0000 (08:30 +0000)]
Add direct link to the job archive file (raw data)

7 years agoMove one method and som internal data form DailyStatisticsController.java to BasicCo...
Sasha Sherstnev [Fri, 20 Dec 2013 08:29:49 +0000 (08:29 +0000)]
Move one method and som internal data form  DailyStatisticsController.java to BasicController.java

7 years agoFix problm with username
Sasha Sherstnev [Fri, 20 Dec 2013 08:29:25 +0000 (08:29 +0000)]
Fix problm with username

7 years agoRemove obsolete classes
Sasha Sherstnev [Thu, 19 Dec 2013 12:38:26 +0000 (12:38 +0000)]
Remove obsolete classes

7 years agoComment wrong code
Sasha Sherstnev [Thu, 19 Dec 2013 12:37:45 +0000 (12:37 +0000)]
Comment wrong code

7 years agoAdd private methods instead of exteranl dependency
Sasha Sherstnev [Thu, 19 Dec 2013 12:37:11 +0000 (12:37 +0000)]
Add private methods instead of exteranl dependency

7 years agoAdd private method instead of an exteran dependence
Sasha Sherstnev [Thu, 19 Dec 2013 12:34:36 +0000 (12:34 +0000)]
Add private method instead of an exteran dependence