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:

8:38 AM Ticket #178 (Create plugin for importing help texts) updated by Martin Svensson
Status changed
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
11:06 AM Ticket #152 (Error text on rawdata importer plugin) updated by Nicklas Nordborg
Description, Milestone changed
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 …
10:01 AM Ticket #148 (Should read permission in BASE 1 be migrated as read/use permission in ...) updated by Nicklas Nordborg
Owner, Component changed
7:52 AM Ticket #139 (Write documentation: 5d) Analysis plug-ins) updated by Nicklas Nordborg
Status changed
7:51 AM Ticket #137 (Write documentation 5b) Plug-ins for importing data) updated by Nicklas Nordborg
Status changed
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...) updated by Nicklas Nordborg
Priority changed
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.
8:09 AM Ticket #184 (Running SQL/HQL after an update to the database) updated by Nicklas Nordborg
Status changed
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 …
8:01 AM Ticket #183 (cannot add annotation and new Items) updated by Nicklas Nordborg
Please supply the original exceptions. Not the one you got after …
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 …
2:23 PM Ticket #126 (Add interface for managing reporter lists) updated by Nicklas Nordborg
Status changed
2:23 PM Ticket #176 (Running jobs with a project activated) updated by Nicklas Nordborg
Status changed
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
1:24 PM Ticket #150 (Affymetrix support) updated by Jari Häkkinen
Status changed
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).
7:53 AM Ticket #20 (Display and link to associated item from view page) updated by Nicklas Nordborg
Milestone changed
7:52 AM Ticket #157 (Display and link to associated items from list page) updated by Nicklas Nordborg
Milestone changed

Mar 30, 2006:

4:18 PM Ticket #181 (Import a plug-in configuration file from BASE 1) updated by Johan Enell
Status changed
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 …
4:03 PM Ticket #160 (List pages should be able to list subset of items) updated by Johan Enell
Owner changed
3:57 PM Ticket #157 (Display and link to associated items from list page) updated by Johan Enell
Owner, Milestone changed
3:55 PM Ticket #147 (Make normalization pinbased) closed by Johan Enell
fixed
3:55 PM Ticket #147 (Make normalization pinbased) updated by Johan Enell
Status changed
3:52 PM Ticket #147 (Make normalization pinbased) updated by Johan Enell
Component, Status changed
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. …
9:54 AM Ticket #162 (Install help texts in flexisble way) updated by Martin Svensson
Status changed
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 …
11:16 AM Ticket #167 (Create root bioassayset using other plugins than IntensityCalculator) updated by Nicklas Nordborg
Status changed
11:15 AM Ticket #166 (Make IntensityCalculator an InteractivePlugin) updated by Nicklas Nordborg
Status changed
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 …
8:04 AM Ticket #161 (Add support for showing help texts in the GUI) updated by Martin Svensson
Status changed
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)
11:47 AM Ticket #165 (Running updatedb.sh changes server settings.) updated by Jari Häkkinen
Description changed
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
3:54 PM Ticket #146 (Add help text to the web gui) updated by Nicklas Nordborg
Description changed
3:53 PM Ticket #161 (Add support for showing help texts in the GUI) updated by Nicklas Nordborg
Description changed
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 …
3:48 PM Ticket #146 (Add help text to the web gui) updated by Nicklas Nordborg
Owner changed
2:58 PM Ticket #157 (Display and link to associated items from list page) updated by Nicklas Nordborg
Milestone changed
2:57 PM Ticket #158 (resizable annotation tab for most items but mostly needed for ...) updated by Nicklas Nordborg
Milestone changed
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 …
8:35 AM Ticket #159 (The Admin/Procotol menu item is disabled even if the user has ...) updated by Martin Svensson
Status changed
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
11:23 AM Ticket #145 (Plugin parameters with no default value get the string "null" as their ...) updated by Johan Enell
Instead of null it now writes the empty string. But now the action for …
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.
9:50 AM Ticket #124 (Plot function for analysed data) updated by Nicklas Nordborg
Status changed
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) updated by Johan Enell
Description changed
1:16 PM Ticket #152 (Error text on rawdata importer plugin) updated by Johan Enell
Description changed
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 …
1:04 PM Ticket #1 (column names in flatfile parser) updated by Johan Enell
Owner changed
1:03 PM Ticket #1 (column names in flatfile parser) updated by Johan Enell
Owner, Status changed
1:03 PM Ticket #147 (Make normalization pinbased) updated by Johan Enell
Status changed
1:02 PM Ticket #151 (Space in filenames) updated by Johan Enell
Maybe thats not the problem. I can't view any file. I get an error …
11:41 AM Ticket #119 (can't annotate sample in base 2 demo server) updated by Martin Svensson
Status changed
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 …
8:08 AM Ticket #23 (Apply button in popup windows?) updated by Nicklas Nordborg
Priority changed
8:08 AM Ticket #141 (When creating a new user the default quota is not preselected) updated by Nicklas Nordborg
Owner changed
8:07 AM Ticket #119 (can't annotate sample in base 2 demo server) updated by Nicklas Nordborg
Owner, Status changed
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