Timeline



Mar 24, 2006:

5:26 PM Changeset [2112] by olle
Class and interface components in MagicDraw? files coreclasses.uml.xml …
3:58 PM Changeset [2111] by Nicklas Nordborg
Updated plot function
3:31 PM Changeset [2110] by Jari Häkkinen
Forgot information about database upgrade.
3:23 PM Changeset [2109] by Jari Häkkinen
Improved docs, and added information on how to upgrade existing BASE 2.
2:29 PM Changeset [2108] by Martin Svensson
Added taglib file for base-help
2:09 PM WikiStart edited by Jari Häkkinen
(diff)
11:45 AM Ticket #165 (Running updatedb.sh changes server settings.) created by Jari Häkkinen
Running the update database script reverts the information 'About', …
11:17 AM Changeset [2107] by Nicklas Nordborg
Added interface for administration of formulas.

Mar 23, 2006:

4:08 PM Changeset [2106] by Nicklas Nordborg
Formulas should use the getTitle() not getName() from formulas defined …
2:35 PM Ticket #155 (Export of annotations does not work) closed by Nicklas Nordborg
fixed
2:34 PM Changeset [2105] by Nicklas Nordborg
Fixes ticket #155: Export of annotations does not work
2:19 PM Ticket #164 (View all items in a project) created by Nicklas Nordborg
Create a new page that lists all items shared to a project.
2:07 PM Changeset [2104] by Nicklas Nordborg
Added Formula, test code and updated UML diagram.
8:01 AM Ticket #163 (The tree of bioassay sets in the analysis should include ...) created by Nicklas Nordborg
A transformation may not create any child bioassayset and those …

Mar 22, 2006:

4:03 PM Ticket #141 (When creating a new user the default quota is not preselected) closed by Martin Svensson
fixed: (In [2103]) Fixes #141. When creating a new user the default quota is …
4:03 PM Changeset [2103] by Martin Svensson
Fixes #141. When creating a new user the default quota is not preselected
3:53 PM Ticket #162 (Install help texts in flexisble way) created by Nicklas Nordborg
Currently there is no other way to install help texts than to …
3:51 PM Ticket #161 (Add support for showing help texts in the GUI) created by Nicklas Nordborg
The core has support for storing help texts related to client …
2:33 PM Ticket #154 (Filter is cleared) closed by Nicklas Nordborg
fixed: (In [2102]) Added new list page for bioassay data. Removed all old …
2:33 PM Changeset [2102] by Nicklas Nordborg
Added new list page for bioassay data. Removed all old pages from …
11:49 AM Ticket #118 (Not allowed to change password) closed by Martin Svensson
fixed: (In [2101]) Fixes #118.Not allowed to change password
11:49 AM Changeset [2101] by Martin Svensson
Fixes #118.Not allowed to change password
9:29 AM Changeset [2100] by Martin Svensson
Fixes #159.The Admin/Procotol? menu item is disabled even if the user …
9:29 AM Ticket #159 (The Admin/Procotol menu item is disabled even if the user has ...) closed by Martin Svensson
fixed: (In [2100]) Fixes #159.The Admin/Procotol? menu item is disabled even …
8:22 AM Ticket #160 (List pages should be able to list subset of items) created by Nicklas Nordborg
For example, the page that lists users should be able to list users …
8:15 AM Ticket #159 (The Admin/Procotol menu item is disabled even if the user has ...) created by Longfei Yu <lyu@…
About the permission. The original power user role does not have the …

Mar 21, 2006:

11:21 PM Ticket #158 (resizable annotation tab for most items but mostly needed for ...) created by rocca@…
Using Long Names for AnnotationType? declaration results in limited …
11:14 PM Ticket #157 (Display and link to associated items from list page) created by rocca@…
For Samples, Extracts, LabeledExtracts?, Hybridization, Scan and Raw …
4:04 PM Changeset [2099] by Nicklas Nordborg
Added list page for bioassays
4:03 PM Changeset [2098] by Martin Svensson
Fixes #119. Can't annotate sample in base 2 demo server
4:03 PM Ticket #119 (can't annotate sample in base 2 demo server) closed by Martin Svensson
fixed: (In [2098]) Fixes #119. Can't annotate sample in base 2 demo server
2:57 PM Changeset [2097] by Nicklas Nordborg
New list and view page design for bioassay sets. Rearranged HTML plot …
9:02 AM Changeset [2096] by Nicklas Nordborg
Added Tree utility class.

Mar 20, 2006:

10:50 AM Changeset [2095] by olle
Help/temporary packages net.sf.basedb.core-part and …
10:46 AM Ticket #156 (Creating a new file with the same name as a previously deleted file ...) created by Jari Häkkinen
The summary says it all. I suggest that the deleted flag should be …
10:43 AM Ticket #155 (Export of annotations does not work) created by Jari Häkkinen
Exporting samples with annotations generates the below stack trace. …
9:53 AM Changeset [2094] by Gregory Vincic
Merged trunk changes r2084:HEAD(2093) into branch
9:41 AM Changeset [2093] by olle
MagicDraw? file docexmples.uml.xml converted to Umbrello file …
9:23 AM Changeset [2092] by olle
MagicDraw? file dataclasses.uml.xml converted to Umbrello file …

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.
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