Timeline



Mar 18, 2006:

4:34 PM Ticket #128 (tomcat5.5 has to be reinstalled after upgrading BASE jars.) closed by Jari Häkkinen
worksforme: No, not anymore, something magic has taken place.
3:00 PM Changeset [2091] by Jari Häkkinen
Changed 'about' copyright statement.

Mar 17, 2006:

11:58 PM Changeset [2090] by Jari Häkkinen
New package download revision.
5:37 PM Changeset [2089] by Johan Enell
Changed between to be low <= x AND x < high Database independent
3:06 PM Changeset [2088] by olle
Packages net.sf.basedb.core, net.sf.basedb.core.authentication, …
11:30 AM Changeset [2087] by Nicklas Nordborg
Added first version of HTML plot tool
11:20 AM Ticket #154 (Filter is cleared) created by Johan Enell
The filter on the rawdata table is cleared everytime the page is updated.
9:46 AM Changeset [2086] by Nicklas Nordborg
Added Log2Function, ChannelFunction? and JepExpressionFunction? These …

Mar 16, 2006:

4:39 PM Changeset [2085] by olle
MagicDraw? file coreclasses.uml.xml converted to Umbrello file …
3:27 PM Changeset [2084] by Gregory Vincic
Core refactoring, creating a distinction between core features and …
10:40 AM Changeset [2083] by Nicklas Nordborg
Added Type.isNumerical() method
9:51 AM Changeset [2082] by Gregory Vincic
Added max height and width for images and set antialias to false
8:05 AM Changeset [2081] by Jari Häkkinen
Added a more visible link to milestones.

Mar 15, 2006:

2:13 PM Changeset [2080] by Johan Enell
changed exception handling in method doImport
2:12 PM Ticket #151 (Space in filenames) closed by Johan Enell
fixed: Must copy the web.xml to WEB-INF
1:29 PM Ticket #153 (More progress from importer plug-ins) created by Johan Enell
Add line/s in the progress info. Maybe change to features or spot or …
1:16 PM Ticket #152 (Error text on rawdata importer plugin) created by Johan Enell
When trying to import data on a none empty rawdata the errormessage …
11:13 AM Ticket #151 (Space in filenames) created by Johan Enell
If you upload a file with spaces the file can't be found. When using …
11:02 AM Ticket #130 (Is the java compiler fix still needed for tomcat5.5) closed by Jari Häkkinen
fixed: (In [2079]) Fixes #130. The tomcat fix is not needed anymore, updated …
11:02 AM Changeset [2079] by Jari Häkkinen
Fixes #130. The tomcat fix is not needed anymore, updated documentation.
10:53 AM Changeset [2078] by Martin Svensson
Name of item types in view_role now agree with the names of item types …
10:53 AM Ticket #123 (The textformat of item types in Edit role ->Permissions doesn't agree ...) closed by Martin Svensson
fixed: (In [2078]) Name of item types in view_role now agree with the names …
8:18 AM Changeset [2077] by Nicklas Nordborg
Help, FAQ and Report a bug links were linked to the wrong page if no …

Mar 14, 2006:

1:25 PM Changeset [2076] by Martin Svensson
Started to add some procedures to test permissions in BASE2

Mar 13, 2006:

4:15 PM Ticket #143 (Typo in raw data type name for Affymetrix) closed by Jari Häkkinen
fixed
4:15 PM Changeset [2075] by Jari Häkkinen
Resolved ticket:143
3:54 PM Ticket #150 (Affymetrix support) created by Jari Häkkinen
3:53 PM Ticket #149 (Plugin bridge that allows BASE1 plug-ins to be run in BASE2) created by Jari Häkkinen
3:41 PM Ticket #148 (Should read permission in BASE 1 be migrated as read/use permission in ...) created by Jari Häkkinen
Items shared to groups should be migrated as read/use, otherwise it is …
3:35 PM Ticket #2 (ability to add image files as annotation for samples) closed by Jari Häkkinen
wontfix: Replaced with ticket:107
3:22 PM Ticket #78 (pinbase median ratio normalization) closed by Jari Häkkinen
fixed: Replace with ticket:147
3:21 PM Ticket #147 (Make normalization pinbased) created by Jari Häkkinen
3:17 PM Ticket #146 (Add help text to the web gui) created by Jari Häkkinen
This ticket is now part of tickets #268, #269, #270, #271 and #272.
3:11 PM Ticket #19 (Show/hide option for various section on a "view item" page) closed by Jari Häkkinen
wontfix
2:12 PM Ticket #145 (Plugin parameters with no default value get the string "null" as their ...) created by Nicklas Nordborg
If no default value is set for a plugin parameter, the input field for …
2:01 PM Ticket #144 (Overhaul of BASE web site) created by Jari Häkkinen
BASE 2 should replace BASE 1 as the main event at BASE web site.
1:22 PM Ticket #143 (Typo in raw data type name for Affymetrix) created by rocca@…
a very minor thing to change in the …
1:08 PM Ticket #142 (Changing Preference to S or XS prevents from Seeing Annotations ...) created by rocca@…
Bug seen on demo-server + my own installation: when changing display …
12:53 PM Ticket #141 (When creating a new user the default quota is not preselected) created by Nicklas Nordborg
The quota that happens to be sorted first in the list is the one that …
12:48 PM Ticket #140 (Write documentation: 5e) Secondary file storage) created by Nicklas Nordborg
12:47 PM Ticket #139 (Write documentation: 5d) Analysis plug-ins) created by Nicklas Nordborg
12:46 PM Ticket #138 (Write documentation: 5c) Authentication plug-ins) created by Nicklas Nordborg
12:46 PM Ticket #137 (Write documentation 5b) Plug-ins for importing data) created by Nicklas Nordborg
12:44 PM Ticket #136 (Write documentation: 3c) Internals of the core API - Job queue management) created by Nicklas Nordborg
12:44 PM Ticket #135 (Write documentation: 3c) Internals of the core API - Plugin system) created by Nicklas Nordborg
12:43 PM Ticket #134 (Write documentation: 3c) Internals of the core API - Checking quota) created by Nicklas Nordborg
12:43 PM Ticket #133 (Write documentation: 3c) Internals of the core API - Data validation) created by Nicklas Nordborg
12:42 PM Ticket #132 (Write documentation: 3c) Internals of the core API - Transaction handling) created by Nicklas Nordborg
12:14 PM Ticket #131 (Write documentation 4a) Schematic overview of BASE) created by Nicklas Nordborg
12:04 PM Ticket #130 (Is the java compiler fix still needed for tomcat5.5) created by Jari Häkkinen
Test a late release of tomcat5.5 to find out whether the recipe on …
12:03 PM Ticket #129 (Interface for inheriting annotations) closed by Nicklas Nordborg
duplicate: Same as #96.
12:02 PM Ticket #129 (Interface for inheriting annotations) created by Nicklas Nordborg
And add support for using the annotations in the analysis.
11:57 AM Ticket #128 (tomcat5.5 has to be reinstalled after upgrading BASE jars.) created by Jari Häkkinen
11:57 AM Ticket #127 (Experiment explorer) created by Nicklas Nordborg
Add interface similar to the Experiment explorer found in BASE 1.
11:55 AM Ticket #126 (Add interface for managing reporter lists) created by Nicklas Nordborg
It should also be possible to use the reporter lists in the analysis.
11:53 AM Ticket #125 (Create filtered bioassay sets) created by Nicklas Nordborg
Add functionality to create filtered bioassay sets.
11:51 AM Ticket #124 (Plot function for analysed data) created by Nicklas Nordborg
Plot function similar to the BASE 1 plot function to plot analysed data.
9:13 AM Changeset [2074] by Johan Enell
changed the imports
9:05 AM Changeset [2073] by Johan Enell
write empty string instead of null
8:32 AM Ticket #122 (Creation of ArrayDesign: AffyChip check box does not work) closed by Nicklas Nordborg
fixed
8:32 AM Changeset [2072] by Nicklas Nordborg
Fixed bug #122: Creation of ArrayDesign?: AffyChip? check box does not work

Mar 10, 2006:

11:09 AM Ticket #123 (The textformat of item types in Edit role ->Permissions doesn't agree ...) created by Martin Svensson
The Item types under a role's permissions are written in singular …

Mar 9, 2006:

12:38 PM Ticket #122 (Creation of ArrayDesign: AffyChip check box does not work) created by rocca@…
Despite ticking the AffyChip? box, the design is created as non affy

Mar 6, 2006:

1:34 PM Changeset [2071] by Martin Svensson
Testprocedures for projectadmin and updated newcommands
1:29 PM Changeset [2070] by Martin Svensson
Updated the text and corrected misspellings

Mar 2, 2006:

10:18 AM Changeset [2069] by Jari Häkkinen
Updated information on downloadable RC1 version.
9:30 AM Changeset [2068] by Gregory Vincic
Fixed handling of null parameter values. Null values are written as …

Mar 1, 2006:

5:28 PM Ticket #120 (create new experiment error) closed by Johan Enell
duplicate: Known and fixes #117
5:25 PM Ticket #121 (create new raw bioassay error) closed by Johan Enell
duplicate: Known and fixed #117
4:12 PM Ticket #121 (create new raw bioassay error) created by anonymous
java.lang.NullPointerException? on page …
4:10 PM Ticket #120 (create new experiment error) created by anonymous
java.lang.NullPointerException? on page …

Feb 28, 2006:

4:17 PM Changeset [2067] by Gregory Vincic
Query needs to include shared plugins for users to use all available …
11:37 AM Changeset [2066] by Jari Häkkinen
Checked in information explaining that downloadable RC1 is not the …
9:48 AM Changeset [2065] by Johan Enell
The method getRawDataType didnt return null for id = null
9:47 AM Ticket #117 (Failure to Create Raw BioAssay (tested on 2 different installs: linux ...) closed by Johan Enell
fixed: The method RawDataTypes?.getRawDataType(String id) threw an exception …

Feb 27, 2006:

12:26 PM Ticket #119 (can't annotate sample in base 2 demo server) created by r.maccallr@…
Hi Jari/others, When I'm using my guest509 username on the base2 demo …
11:34 AM Ticket #118 (Not allowed to change password) created by anonymous
When trying to change my password i get the following error message: …

Feb 24, 2006:

2:35 PM Ticket #8 (PrintMapBlockFileImporter) closed by Jari Häkkinen
fixed
2:17 PM Ticket #117 (Failure to Create Raw BioAssay (tested on 2 different installs: linux ...) created by rocca@…
Dear BASE Attemping to create a Raw Bioassay objects results in the …
1:36 PM Ticket #116 (Analyze of experiment fails) closed by Jari Häkkinen
duplicate: Sorry, this is a known issue and there is a solution, see ticket:99

Feb 23, 2006:

10:42 PM Ticket #9 (Normalization: Lowess) closed by Jari Häkkinen
fixed: It is now a part of the BASE core plug-ins.
10:40 PM Milestone BASE 2.0 RC1 completed
This release is aimed at being the first release that we will …
10:39 PM Ticket #116 (Analyze of experiment fails) created by Jari Häkkinen
The analyze experiment feature does not work. Trying to create a new …
10:13 PM Ticket #115 (DemoServer internal error on startup) closed by Jari Häkkinen
fixed: Tomcat 5 stopped working. Nothing helped, I even resorted to CPR but …
4:22 PM Ticket #115 (DemoServer internal error on startup) created by sdavis2@…
Got this when trying to start the base2 server: Server error! The …
4:05 PM Changeset [2064] by Jari Häkkinen
Fixed spelling error.
3:16 PM Changeset [2063] by Nicklas Nordborg
Releasing RC1
3:10 PM Changeset [2062] by Gregory Vincic
small bug in last query
2:52 PM Changeset [2061] by Johan Enell
Made some corrections on Lowess
2:30 PM Changeset [2060] by Jari Häkkinen
Bumped to RC1.
2:20 PM Changeset [2059] by Jari Häkkinen
Information about people involved in BASE 2, presently and in the past.
2:13 PM Changeset [2058] by Nicklas Nordborg
Make sure the correct web.xml (/src/web.xml.in) is copied by ant dist.
11:42 AM Changeset [2057] by Nicklas Nordborg
Added CompileAll? servlet
8:45 AM Changeset [2056] by Martin Svensson
Correct some misspellings
12:28 AM Changeset [2055] by Jari Häkkinen
Added subversion properties to .html files.
12:22 AM Changeset [2054] by Jari Häkkinen
Added svn:ignore to exclude api direcotry.

Feb 22, 2006:

11:55 PM Changeset [2053] by Jari Häkkinen
Added subversion properties to .xml files.
11:48 PM Changeset [2052] by Jari Häkkinen
Added copyright and license notice.
4:20 PM Changeset [2051] by Martin Svensson
Adapted and updated documents to the new listpages
2:55 PM Changeset [2050] by Nicklas Nordborg
Exclude Oracle JDBC driver from "ant dist"
2:33 PM Ticket #114 (Default values for plugin parameters are not shown.) closed by Nicklas Nordborg
fixed
2:32 PM Changeset [2049] by Nicklas Nordborg
Fixed ticket #114: Default values for plugin parameters are not shown.
2:19 PM Changeset [2048] by Nicklas Nordborg
Directory.createHomeDirectory no longer shares the new directories to …
2:03 PM Changeset [2047] by Nicklas Nordborg
Fixed rounding errors while parsing and formatting byte values.
1:30 PM Changeset [2046] by Nicklas Nordborg
Fixed bug where projects keys didn't get loaded correctly due to a …
12:09 PM Changeset [2045] by Nicklas Nordborg
Fixed problem where the InternalStorageController? sets the location of …
11:02 AM Changeset [2044] by Jari Häkkinen
Updated copyright notice.
10:58 AM Changeset [2043] by Jari Häkkinen
Added information on how to create a plug-in.
10:49 AM Ticket #113 (Re-upload a file should have a checkbox option to verify against old MD5) closed by Nicklas Nordborg
fixed
10:49 AM Changeset [2042] by Nicklas Nordborg
Fixed ticket #113: Re-upload a file should have a checkbox option to …
9:49 AM Ticket #112 (view/download of files with national characters doesn't work) closed by Nicklas Nordborg
fixed: This link may be useful: http://java2.5341.com/msg/76475.html
9:48 AM Changeset [2041] by Nicklas Nordborg
Fixed ticket #112: view/download of files with national characters …
8:49 AM Changeset [2040] by Nicklas Nordborg
Now creates child bioassays. Moved batcher.close() and dc.commit() to …
8:43 AM Ticket #114 (Default values for plugin parameters are not shown.) created by Nicklas Nordborg
The web client ignores default values for plugin parameters and just …

Feb 21, 2006:

4:21 PM Ticket #74 (HibernateUtil doesn't find configuration file if installation path ...) closed by Martin Svensson
fixed
4:20 PM Changeset [2039] by Martin Svensson
Fixed ticket #74: HibernateUtil? doesn't find configuration file if …
3:44 PM Changeset [2038] by Nicklas Nordborg
Added SecondaryStorageController? and InternalStorageController?. More …
3:26 PM Changeset [2037] by Johan Enell
added ignore to log4j.properties
2:56 PM Changeset [2036] by Johan Enell
LowessNormalization? added
2:55 PM Ticket #113 (Re-upload a file should have a checkbox option to verify against old MD5) created by Nicklas Nordborg
If the checkbox is checked the upload will be rejected if the MD5 of …
2:04 PM Ticket #112 (view/download of files with national characters doesn't work) created by Nicklas Nordborg
For example a file named: två View link in browser: …
11:22 AM Ticket #70 (Lazy creation of PreparedStatments in BasicBatcher.) closed by Nicklas Nordborg
wontfix: Well, we are probably better of creating the statements in the …
11:21 AM Changeset [2035] by Nicklas Nordborg
Fixed ticket #70: Lazy creation of PreparedStatments? in BasicBatcher?. …
11:14 AM Ticket #71 (java.sql.Date is hardcoded in BasicBatcher) closed by Nicklas Nordborg
fixed
11:13 AM Changeset [2034] by Nicklas Nordborg
Fixed ticket #71: java.sql.Date is hardcoded in BasicBatcher?
8:36 AM Changeset [2033] by Nicklas Nordborg
Removed unused import
8:25 AM Changeset [2032] by Nicklas Nordborg
Fucking eclipse!
8:23 AM Changeset [2031] by Nicklas Nordborg
Removed unused imports

Feb 20, 2006:

3:59 PM Changeset [2030] by Nicklas Nordborg
Fixed ticket #91: Export fails if there are too many items (MySQL only)
3:59 PM Ticket #91 (Export fails if there are too many items (MySQL only)) closed by Nicklas Nordborg
fixed
12:29 PM Changeset [2029] by Nicklas Nordborg
Fixed ticket #101: Add try / catch around all Query.iterate methods in …
12:27 PM Ticket #101 (Add try / catch around all Query.iterate methods in list pages) closed by Nicklas Nordborg
fixed
11:36 AM Ticket #69 (Funny looking line showing when last tab is visible) closed by Nicklas Nordborg
worksforme
11:29 AM Ticket #80 (RawDataPropertyExpression.getColumn should cache column information) closed by Nicklas Nordborg
fixed
11:26 AM Changeset [2028] by Nicklas Nordborg
Fixed ticket #80: RawDataPropertyExpression?.getColumn should cache …
11:17 AM Changeset [2027] by Gregory Vincic
Fixed column order in the configuration view
10:24 AM Changeset [2026] by Nicklas Nordborg
Added some more intensity formulas to raw data types. Ticket #90: Add …
10:24 AM Ticket #90 (Add more raw data types with intensity formulas to default settings) closed by Nicklas Nordborg
fixed
9:28 AM Changeset [2025] by Nicklas Nordborg
Fixed ticket #68: Application.BUILD should be updated automatically.
9:27 AM Ticket #68 (Application.BUILD should be updated automatically.) closed by Nicklas Nordborg
fixed: The "ant dist" command now uses the "svnversion" command to get the …
8:20 AM Ticket #111 (The User columns don't have the same order when all columns are shown) closed by Nicklas Nordborg
worksforme

Feb 17, 2006:

4:59 PM Changeset [2024] by Martin Svensson
Updated testdocument for List columns,Filter and User admin
4:47 PM Ticket #75 (Remove unused code in migrate package) closed by Gregory Vincic
fixed: Fixed
4:47 PM Changeset [2023] by Gregory Vincic
Fixed ticket #75 removing warnings and unused code
3:51 PM Changeset [2022] by Nicklas Nordborg
Fixed ticket #89: Check list of hardware / software that the …
3:51 PM Ticket #88 (Installation should add print robots) closed by Nicklas Nordborg
fixed
3:50 PM Ticket #89 (Check list of hardware / software that the installation program is adding) closed by Nicklas Nordborg
fixed
3:06 PM Changeset [2021] by Nicklas Nordborg
Install can now update existing database and add missing items.
3:04 PM Ticket #111 (The User columns don't have the same order when all columns are shown) created by Martin Svensson
The columns in userlist don't get the same order when selecting All …
1:48 PM Changeset [2020] by Jari Häkkinen
Using original gif (instead for generated png) image for html.
1:25 PM Changeset [2019] by Jari Häkkinen
Added web dev status figure to the test document.
12:42 PM Changeset [2018] by Nicklas Nordborg
Removed Filter. It has now been completely replaced by ItemContext?.
11:59 AM Changeset [2017] by Nicklas Nordborg
Removed TableInfo? class since all list pages now use the ItemContext?
9:57 AM Changeset [2016] by Nicklas Nordborg
Changed system id:s to upper case
9:49 AM Changeset [2015] by Nicklas Nordborg
Quota now use the new list and view page design
9:29 AM Ticket #110 (Potential threading problem in /www/analyze/index.jsp) closed by Gregory Vincic
fixed: Fixed. Index is now generated with the javascript treeline.js
9:28 AM Changeset [2014] by Gregory Vincic
Fixed ticket #110
9:17 AM Changeset [2013] by Jari Häkkinen
Made section numbers coherrent with the web interface dev status image.
8:53 AM Ticket #31 (Changing list columns - list of visible columns becomes empty) closed by Gregory Vincic
fixed
8:45 AM Changeset [2012] by Nicklas Nordborg
Mime types now use the new list and view page design
8:31 AM Changeset [2011] by Nicklas Nordborg
Quota types now use the new list and view page design
8:24 AM Changeset [2010] by Nicklas Nordborg
File types now use the new list and view page design
8:19 AM Ticket #110 (Potential threading problem in /www/analyze/index.jsp) created by Nicklas Nordborg
The file /www/analyze/index.jsp has declared a: […] The index is …
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