Timeline



Apr 12, 2006:

5:35 PM Changeset [2162] by Johan Enell
It reads the configuration file but it doesnt store tha values

Apr 11, 2006:

4:52 PM Changeset [2161] by Johan Enell
createClient(...web...) was removed it is needed…

Apr 10, 2006:

8:25 AM Changeset [2160] by Martin Svensson
Added installation of HelpExporter? plugin

Apr 7, 2006:

5:25 PM Changeset [2159] by Martin Svensson
Fixes #179: Created plugin for exporting help texts
5:25 PM Ticket #179 (Create plugin for exporing help texts) closed by Martin Svensson
fixed: (In [2159]) Fixes #179: Created plugin for exporting help texts
3:58 PM Changeset [2158] by Nicklas Nordborg
Fixes #187: Add a New directory button to "Select directory" dialog
3:58 PM Ticket #187 (Add a New directory button to "Select directory" dialog) closed by Nicklas Nordborg
fixed: (In [2158]) Fixes #187: Add a New directory button to "Select …
3:45 PM Changeset [2157] by Nicklas Nordborg
Fixes #188: Readd the missing "Unload" button in Plugin definitions list
3:45 PM Ticket #188 (Readd the missing "Unload" button in Plugin definitions list) closed by Nicklas Nordborg
fixed: (In [2157]) Fixes #188: Readd the missing "Unload" button in Plugin …
3:04 PM Changeset [2156] by Nicklas Nordborg
Removed TODO from item that was done.
2:56 PM Ticket #139 (Write documentation: 5d) Analysis plug-ins) closed by Nicklas Nordborg
fixed: (In [2155]) Fixes #139: Write documentation: 5d) Analysis plug-ins …
2:56 PM Changeset [2155] by Nicklas Nordborg
Fixes #139: Write documentation: 5d) Analysis plug-ins Added another …
2:34 PM Ticket #188 (Readd the missing "Unload" button in Plugin definitions list) created by Nicklas Nordborg
The "Unload" button unloads the JAR file with an external plugin …
11:35 AM Ticket #137 (Write documentation 5b) Plug-ins for importing data) closed by Nicklas Nordborg
fixed: (In [2154]) Fixes #137: Write documentation 5b) Plug-ins for importing …
11:35 AM Changeset [2154] by Nicklas Nordborg
Fixes #137: Write documentation 5b) Plug-ins for importing data Added …
10:50 AM Changeset [2153] by Nicklas Nordborg
Classloader now ignores empty Class-Path attribute in the manifest file

Apr 6, 2006:

7:30 PM Ticket #187 (Add a New directory button to "Select directory" dialog) created by Nicklas Nordborg
This dialog is used in for example the "Move to" and "Save in" …
3:05 PM Changeset [2152] by Nicklas Nordborg
Fixed export function so it supports ReporterScore?
3:00 PM Changeset [2151] by Nicklas Nordborg
Added documentation 6a) How to write plug-ins
11:05 AM Ticket #186 (The InteractivePlugin.isInContext should return a String instead of boolean) created by Nicklas Nordborg
If so, the plugin could return null as a replacement for TRUE and a …
7:51 AM Ticket #126 (Add interface for managing reporter lists) closed by Nicklas Nordborg
fixed

Apr 5, 2006:

4:08 PM Ticket #185 (Refactor the Item class and DbControl and more...) created by Nicklas Nordborg
After adding the ReporterScore? which doesn't inherit from BasicItem?
3:37 PM Changeset [2150] by Nicklas Nordborg
Added page for viewing scores for reporters in reporter list. Added …

Apr 4, 2006:

3:50 PM Changeset [2149] by Nicklas Nordborg
First version of reporter list view Updated ReporterFlatFileImporter?
11:24 AM Changeset [2148] by Nicklas Nordborg
Changed copyright notice
11:21 AM Changeset [2147] by Nicklas Nordborg
Added PathParameterType? to allow plugins to ask for a File or …

Apr 3, 2006:

4:20 PM Changeset [2146] by Jari Häkkinen
Added devevloper information regarding database schema changes.
3:54 PM Changeset [2145] by Jari Häkkinen
Added a column in the download section indicating schema change.
3:32 PM Changeset [2144] by Jari Häkkinen
Added a comment about postgresql update problems.
3:27 PM Changeset [2143] by Jari Häkkinen
Added new revision to download 2.0RC1.2142
1:14 PM Ticket #184 (Running SQL/HQL after an update to the database) closed by Nicklas Nordborg
fixed: (In [2142]) Fixes #184: Running SQL/HQL after an update to the database.
1:14 PM Changeset [2142] by Nicklas Nordborg
Fixes #184: Running SQL/HQL after an update to the database.
8:07 AM Ticket #184 (Running SQL/HQL after an update to the database) created by Nicklas Nordborg
When updating the database there must be some way to update the values …
4:55 AM Ticket #183 (cannot add annotation and new Items) created by lyu@…
Dear all, After I downloaded the latest source code “2106 Mar 23, …

Mar 31, 2006:

11:30 PM Changeset [2141] by Jari Häkkinen
Added downloads for all demo server versions including original RC1.
8:16 PM Ticket #182 (Allow plugin parameters to use enumerations where one value is ...) created by Nicklas Nordborg
Ie. when the options are presented in a list the values displayed can …
4:13 PM Changeset [2140] by Johan Enell
config mathod created for Base1PluginExecuter
2:56 PM Ticket #176 (Running jobs with a project activated) closed by Nicklas Nordborg
fixed: (In [2139]) Fixes #176: Running jobs with a project activated INCLUDES …
2:56 PM Changeset [2139] by Nicklas Nordborg
Fixes #176: Running jobs with a project activated INCLUDES DATABASE …
2:15 PM Ticket #180 (Clear filter) closed by Nicklas Nordborg
fixed: (In [2138]) Fixes #180: Clear filter
2:15 PM Changeset [2138] by Nicklas Nordborg
Fixes #180: Clear filter
1:49 PM Ticket #124 (Plot function for analysed data) closed by Nicklas Nordborg
fixed: (In [2137]) Fixes #124: Plot function for analysed data
1:49 PM Changeset [2137] by Nicklas Nordborg
Fixes #124: Plot function for analysed data
12:07 PM Changeset [2136] by Johan Enell
added some javadoc
11:35 AM Changeset [2135] by Jari Häkkinen
Updated authors.
11:24 AM Changeset [2134] by Jari Häkkinen
Removing rf1 branch (moved to proteios).

Mar 30, 2006:

4:17 PM Ticket #181 (Import a plug-in configuration file from BASE 1) created by Johan Enell
An importer that reads a plug-in configuration from BASE 1 and creates …
3:55 PM Ticket #147 (Make normalization pinbased) closed by Johan Enell
fixed
3:49 PM Changeset [2133] by Johan Enell
corrected the counter
1:26 PM Changeset [2132] by Johan Enell
Lowess is pinbased
12:12 PM Changeset [2131] by Nicklas Nordborg
Replaced special JFreePlotServlet with the generic PlotServlet? which …
11:44 AM Changeset [2130] by Nicklas Nordborg
New bioassays now get the same name as their parent bioassay or raw …
11:31 AM Ticket #180 (Clear filter) created by Johan Enell
The funktion "clear filter" in the tables view should clear all …
11:09 AM Ticket #179 (Create plugin for exporing help texts) created by Nicklas Nordborg
This is needed so we don't have to edit the help texts directly in an …
11:08 AM Ticket #178 (Create plugin for importing help texts) created by Nicklas Nordborg
This could be used by the installation program to install help text. …
9:50 AM Ticket #161 (Add support for showing help texts in the GUI) closed by Martin Svensson
fixed: (In [2129]) Fixes #161 Add support for showing help texts in the GUI
9:50 AM Changeset [2129] by Martin Svensson
Fixes #161 Add support for showing help texts in the GUI
8:29 AM Ticket #177 (Store title and description of plugin parameters, not just the name) created by Nicklas Nordborg
When viewing the list of parameters sent to a job, the list only …
8:23 AM Ticket #176 (Running jobs with a project activated) created by Nicklas Nordborg
If a project is active when a job is created, the job must be executed …
8:01 AM Changeset [2128] by Gregory Vincic
Merged base/trunk revision 2116:2127 with base/branches/rf1
7:51 AM Changeset [2127] by olle
One new class diagram net_sf_basedb_core_plugin_02 with methods added …

Mar 29, 2006:

3:01 PM Ticket #29 (Filtering News on dates) closed by Nicklas Nordborg
duplicate: Is part of ticket #146: Write help text within the GUI.
2:56 PM Tickets #166,​167 batch updated by Nicklas Nordborg
fixed: (In [2126]) Fixes #166 and #167: * Make IntensityCalculator? an …
2:56 PM Changeset [2126] by Nicklas Nordborg
Fixes #166 and #167: * Make IntensityCalculator? an InteractivePlugin?
1:42 PM Ticket #145 (Plugin parameters with no default value get the string "null" as their ...) closed by Nicklas Nordborg
fixed: (In [2125]) Fixes #145: Plugin parameters with no default value get …
1:42 PM Changeset [2125] by Nicklas Nordborg
Fixes #145: Plugin parameters with no default value get the string …
11:19 AM Changeset [2124] by Jari Häkkinen
Creating branch for Dominics Annotation grouping stuff.
11:18 AM Changeset [2123] by olle
Umbrello class diagram showing inheritance between interfaces/classes …
11:18 AM Ticket #175 (Move core plugins to a standalone compilation unit) created by Nicklas Nordborg
It is a PITA to have to compile the entire core when working on the …
11:10 AM Ticket #174 (Batch creation of array slides) created by Nicklas Nordborg
It should be possible to create an ArrayBatch? and a bunch of …
11:09 AM Ticket #173 (Attach Hardware/Software to more items) created by Nicklas Nordborg
A request for beeing able to link a Hybridization to a hybridization …
11:06 AM Ticket #172 (Add externalId property to annotation type) created by Nicklas Nordborg
Tools for importing annotation types from other sources (ie. …
11:04 AM Ticket #171 (Experimental factor for experiments) created by Nicklas Nordborg
Experimental factors can be implemented as a link from Experiment to …
11:02 AM Ticket #170 (Categorize annotation types) created by Nicklas Nordborg
When having lots of annotation types for an item (say 50+) the …
8:41 AM Changeset [2122] by Nicklas Nordborg
Fixed some tooltip texts
8:37 AM Changeset [2121] by Nicklas Nordborg
Added gui for administrering help texts

Mar 28, 2006:

5:28 PM Changeset [2120] by Johan Enell
Median ratio is now pinbased
3:50 PM Changeset [2119] by Nicklas Nordborg
Added simple validation of formulas using JavaScript?.
3:47 PM Changeset [2118] by Nicklas Nordborg
Added some useful information (base version, browser, database …
1:50 PM Changeset [2117] by Gregory Vincic
Merged trunk revision 2093:2116 with branch rf1

Mar 27, 2006:

3:57 PM Changeset [2116] by Nicklas Nordborg
Plotting histogram is now working.
11:53 AM Changeset [2115] by Nicklas Nordborg
Selecting a different directory now updates the path in the "Save as" …
11:27 AM Ticket #169 (Use formulas for creating extra values) created by Nicklas Nordborg
The new Formula item is a very powerful way to calculate extra values …
11:26 AM Ticket #168 (Use formulas in table listings of bioassay data) created by Nicklas Nordborg
The new Formula item could prove very useful if used in table …
11:22 AM Ticket #165 (Running updatedb.sh changes server settings.) closed by Nicklas Nordborg
fixed: (In [2114]) Fixes #165: Running updatedb.sh changes server settings
11:22 AM Changeset [2114] by Nicklas Nordborg
Fixes #165: Running updatedb.sh changes server settings
11:17 AM Changeset [2113] by Nicklas Nordborg
Updated plot tool. It should now be possible to create scatter plots …
8:01 AM Ticket #167 (Create root bioassayset using other plugins than IntensityCalculator) created by Nicklas Nordborg
The current implementation has the IntensityCalculator? hardcoded in …
7:59 AM Ticket #166 (Make IntensityCalculator an InteractivePlugin) created by Nicklas Nordborg
and change it to use formulas from the database instead of from the …

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 …
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