Timeline



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
Status, Owner 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

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
3:56 PM Ticket #119 (can't annotate sample in base 2 demo server) updated by Jari Häkkinen
Priority changed
3:55 PM Ticket #119 (can't annotate sample in base 2 demo server) updated by Jari Häkkinen
Priority changed
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
3:52 PM Ticket #145 (Plugin parameters with no default value get the string "null" as their ...) updated by Jari Häkkinen
Owner changed
3:51 PM Ticket #143 (Typo in raw data type name for Affymetrix) updated by Jari Häkkinen
Status, Owner changed
3:49 PM Ticket #142 (Changing Preference to S or XS prevents from Seeing Annotations ...) updated by Jari Häkkinen
Status, Owner changed
3:47 PM Ticket #139 (Write documentation: 5d) Analysis plug-ins) updated by Jari Häkkinen
Version, Milestone changed
3:47 PM Ticket #137 (Write documentation 5b) Plug-ins for importing data) updated by Jari Häkkinen
Milestone, Version changed
3:46 PM Ticket #135 (Write documentation: 3c) Internals of the core API - Plugin system) updated by Jari Häkkinen
Milestone changed
3:46 PM Ticket #127 (Experiment explorer) updated by Jari Häkkinen
Milestone, Version changed
3:45 PM Ticket #126 (Add interface for managing reporter lists) updated by Jari Häkkinen
Milestone changed
3:44 PM Ticket #125 (Create filtered bioassay sets) updated by Jari Häkkinen
Milestone, Version changed
Filtering in analysis.
3:43 PM Ticket #124 (Plot function for analysed data) updated by Jari Häkkinen
Priority, Milestone, Version changed
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 …
3:39 PM Ticket #118 (Not allowed to change password) updated by Jari Häkkinen
Owner changed
3:37 PM Ticket #118 (Not allowed to change password) updated by Jari Häkkinen
Milestone changed
3:36 PM Ticket #108 (Logging the change history of an item) updated by Jari Häkkinen
Milestone changed
3:35 PM Ticket #2 (ability to add image files as annotation for samples) closed by Jari Häkkinen
wontfix: Replaced with ticket:107
3:33 PM Ticket #103 (Display name of current item in 'Set access permissions' dialog) updated by Jari Häkkinen
Owner, Milestone, Version changed
3:30 PM Ticket #97 (Trashcan functionality) updated by Jari Häkkinen
Milestone, Version changed
3:29 PM Ticket #96 (Inherit annotations) updated by Jari Häkkinen
Milestone, Version changed
3:27 PM Ticket #86 (New importer: Plate mapping) updated by Jari Häkkinen
Milestone changed
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
3:18 PM Ticket #37 (New/Edit user - Handling of duplicate login) updated by Jari Häkkinen
Summary changed
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
3:10 PM Ticket #10 (Analysis: Hierarchical clustering) updated by Jari Häkkinen
Milestone changed
3:10 PM Ticket #3 (Update doesn't create indexes) updated by Jari Häkkinen
Milestone changed
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.
1:55 PM Ticket #142 (Changing Preference to S or XS prevents from Seeing Annotations ...) updated by Nicklas Nordborg
Status changed
The calulatation of the heigth for the input form is missing a …
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 #131 (Write documentation 4a) Schematic overview of BASE) updated by Nicklas Nordborg
Type changed
12:48 PM Ticket #133 (Write documentation: 3c) Internals of the core API - Data validation) updated by Nicklas Nordborg
Type changed
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
12:15 PM Ticket #131 (Write documentation 4a) Schematic overview of BASE) updated by Nicklas Nordborg
Summary changed
12:14 PM Ticket #131 (Write documentation 4a) Schematic overview of BASE) created by Nicklas Nordborg
12:04 PM Ticket #128 (tomcat5.5 has to be reinstalled after upgrading BASE jars.) updated by Jari Häkkinen
Status changed
12:04 PM Ticket #130 (Is the java compiler fix still needed for tomcat5.5) updated by Jari Häkkinen
Status changed
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:

3:32 PM Ticket #123 (The textformat of item types in Edit role ->Permissions doesn't agree ...) updated by Martin Svensson
Summary changed
11:16 AM Ticket #122 (Creation of ArrayDesign: AffyChip check box does not work) updated by Martin Svensson
Owner, Status changed
11:09 AM Ticket #123 (The textformat of item types in Edit role ->Permissions doesn't agree ...) updated by Martin Svensson
Status changed
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 3, 2006:

5:08 PM Ticket #119 (can't annotate sample in base 2 demo server) updated by Nicklas Nordborg
Priority, Component changed
This is probably a bug in the AnnotationSet.initPermissions method. …

Mar 2, 2006:

11:03 AM Ticket #118 (Not allowed to change password) updated by Johan Enell
Component, Owner changed
10:21 AM Ticket #117 (Failure to Create Raw BioAssay (tested on 2 different installs: linux ...) updated by Jari Häkkinen
The demo server has been upgraded and should not show the problem …
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:

5:31 PM Ticket #119 (can't annotate sample in base 2 demo server) updated by Johan Enell
Version, Milestone changed
5:30 PM Ticket #121 (create new raw bioassay error) updated by Johan Enell
Milestone, Version changed
5:30 PM Ticket #117 (Failure to Create Raw BioAssay (tested on 2 different installs: linux ...) updated by Johan Enell
Milestone changed
5:29 PM Ticket #120 (create new experiment error) updated by Johan Enell
Milestone changed
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 …
1:38 PM Ticket #119 (can't annotate sample in base 2 demo server) updated by Johan Enell
Status, Component changed
Annotations isnt migrated correct. Permission r in base1 must be …
12:27 PM Ticket #119 (can't annotate sample in base 2 demo server) updated by Jari Häkkinen
Status, Owner changed
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 …
9:02 AM Ticket #119 (can't annotate sample in base 2 demo server) updated by Jari Häkkinen
Status, Owner changed

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 26, 2006:

10:18 PM Ticket #117 (Failure to Create Raw BioAssay (tested on 2 different installs: linux ...) updated by Jari Häkkinen
Owner, Status changed
Creating a new 'Experiment' or 'Raw Bioassay' fails (menu File -> New …
Note: See TracTimeline for information about the timeline view.