Timeline



Jul 4, 2008:

2:23 PM Ticket #1079 (Raw data import takes very long time to fail when user exceeds quota) updated by Nicklas Nordborg
I just tested this on my development machine, and the failure happened …
2:04 PM Ticket #1066 (Reset all filters functionality request) closed by Nicklas Nordborg
fixed: (In [4376]) Fixes #1066: Reset all filters functionality request
2:04 PM Changeset [4376] by Nicklas Nordborg
Fixes #1066: Reset all filters functionality request
1:48 PM Ticket #1079 (Raw data import takes very long time to fail when user exceeds quota) created by Jari Häkkinen
Raw data imports that usually takes 30-40 seconds to successfully …
12:54 PM Ticket #1066 (Reset all filters functionality request) updated by Nicklas Nordborg
Priority, Status, Owner, Milestone changed
12:15 PM Ticket #1078 (Copyright in 'About' BASE should contain year 2008) closed by Nicklas Nordborg
fixed: (In [4375]) Fixes #1078: Copyright in 'About' BASE should contain year 2008
12:15 PM Changeset [4375] by Nicklas Nordborg
Fixes #1078: Copyright in 'About' BASE should contain year 2008
12:15 PM Ticket #1078 (Copyright in 'About' BASE should contain year 2008) updated by Nicklas Nordborg
Owner, Priority, Status, Milestone changed
12:14 PM Changeset [4374] by Nicklas Nordborg
Fixes #1046: Remember closed/expanded node status in the hierarchical …
12:14 PM Ticket #1046 (Remember closed/expanded node status in the hierarchical tree of ...) closed by Nicklas Nordborg
fixed: (In [4374]) Fixes #1046: Remember closed/expanded node status in the …
12:13 PM Ticket #1046 (Remember closed/expanded node status in the hierarchical tree of ...) updated by Nicklas Nordborg
Milestone, Owner, Status, Priority changed
11:37 AM Changeset [4373] by Nicklas Nordborg
Fixes #1071: Help text for default configuration selection for …
11:37 AM Ticket #1071 (Help text for default configuration selection for Base1PluginExecuter ...) closed by Nicklas Nordborg
fixed: (In [4373]) Fixes #1071: Help text for default configuration selection …
11:37 AM Ticket #1071 (Help text for default configuration selection for Base1PluginExecuter ...) updated by Nicklas Nordborg
Milestone, Priority, Status, Owner changed
11:23 AM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Nicklas Nordborg
Description changed
11:23 AM batchimport-3.txt attached to Ticket #1028 by Nicklas Nordborg
3rd version of developers view
11:22 AM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Nicklas Nordborg
(In [4372]) References #1028: Plug-in for batch upload/modification of …
11:22 AM Changeset [4372] by Nicklas Nordborg
References #1028: Plug-in for batch upload/modification of items …

Jul 3, 2008:

7:51 AM Changeset [4371] by Nicklas Nordborg
Merged patch release 2.7.2 to the trunk.

Jul 2, 2008:

10:36 PM Ticket #1078 (Copyright in 'About' BASE should contain year 2008) created by Jari Häkkinen
7:11 PM Ticket #1046 (Remember closed/expanded node status in the hierarchical tree of ...) updated by Johan Vallon-Christersson
Noticed that it is not remembered after logout/login. Could this be …
4:30 PM Milestone BASE 2.7.2 completed
Bug fixes for 2.7.1. Revision log: log:branches/2.7-stable@4345:4369
4:29 PM DownloadPage edited by Jari Häkkinen
Releasing 2.7.2 (diff)
4:22 PM Changeset [4370] by Jari Häkkinen
Changes for the future release 2.7.3
3:55 PM Changeset [4369] by Jari Häkkinen
Tagging version 2.7.2
3:54 PM Changeset [4368] by Jari Häkkinen
Preparing release 2.7.2
3:51 PM Changeset [4367] by Jari Häkkinen
Fixes #1077. Changed help text on step parameter, also changed default …
3:51 PM Ticket #1077 (Lowess normalization broken) closed by Jari Häkkinen
fixed: (In [4367]) Fixes #1077. Changed help text on step parameter, also …
1:23 PM Changeset [4366] by Nicklas Nordborg
References #1028: Plug-in for batch upload/modification of items …
1:23 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Nicklas Nordborg
(In [4366]) References #1028: Plug-in for batch upload/modification of …
1:13 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Nicklas Nordborg
Summary changed
10:33 AM Changeset [4365] by Jari Häkkinen
Minor changes to text.
9:04 AM Changeset [4364] by Nicklas Nordborg
References #1077: Lowess normalization broken Added warning in update …
9:04 AM Ticket #1077 (Lowess normalization broken) updated by Nicklas Nordborg
(In [4364]) References #1077: Lowess normalization broken Added …
8:56 AM Changeset [4363] by Jari Häkkinen
Addresses #1077. A couple of more issues found. Further quality …
8:56 AM Ticket #1077 (Lowess normalization broken) updated by Jari Häkkinen
(In [4363]) Addresses #1077. A couple of more issues found. Further …
8:47 AM Ticket #1077 (Lowess normalization broken) reopened by Jari Häkkinen
8:47 AM Ticket #1077 (Lowess normalization broken) updated by Jari Häkkinen
Further issues found, reopening this ticket.

Jul 1, 2008:

4:30 PM Changeset [4362] by Jari Häkkinen
Fixes #1074.
4:30 PM Ticket #1074 (Base1PluginExecuter: BASE1 text field parameter is not working properly) closed by Jari Häkkinen
fixed: (In [4362]) Fixes #1074.
4:30 PM Ticket #1074 (Base1PluginExecuter: BASE1 text field parameter is not working properly) updated by Jari Häkkinen
Description changed
4:25 PM Ticket #1074 (Base1PluginExecuter: BASE1 text field parameter is not working properly) updated by Jari Häkkinen
BASE 1 field type string and text will be parsed and new line is …
1:44 PM Ticket #1077 (Lowess normalization broken) updated by Nicklas Nordborg
(In [4361]) References #1077: Lowess normalization broken Added …
1:43 PM Changeset [4361] by Nicklas Nordborg
References #1077: Lowess normalization broken Added script for …
11:59 AM Changeset [4360] by Jari Häkkinen
Fixes #1077.
11:59 AM Ticket #1077 (Lowess normalization broken) closed by Jari Häkkinen
fixed: (In [4360]) Fixes #1077.
11:42 AM Ticket #1077 (Lowess normalization broken) updated by Jari Häkkinen
Owner, Status, Description changed
11:40 AM Changeset [4359] by Nicklas Nordborg
Fixes #1076: Backwards incompatible change in MedianRatioNormalization
11:40 AM Ticket #1076 (Backwards incompatible change in MedianRatioNormalization plugin) closed by Nicklas Nordborg
fixed: (In [4359]) Fixes #1076: Backwards incompatible change in …
11:26 AM Ticket #1075 (Lowess normalization fails on trunk but works on latest 2.7-stable) updated by Jari Häkkinen
Summary changed
11:16 AM Ticket #1076 (Backwards incompatible change in MedianRatioNormalization plugin) updated by Nicklas Nordborg
Status, Owner changed
11:10 AM Ticket #1077 (Lowess normalization broken) created by Jari Häkkinen
This problem affects all versions of BASE2. As pointed out in the …
11:08 AM Changeset [4358] by Nicklas Nordborg
Fixes #1075: Lowess normaliztion fails on trunk but works on latest …
11:08 AM Ticket #1075 (Lowess normalization fails on trunk but works on latest 2.7-stable) closed by Nicklas Nordborg
fixed: (In [4358]) Fixes #1075: Lowess normaliztion fails on trunk but works …
9:51 AM Ticket #1075 (Lowess normalization fails on trunk but works on latest 2.7-stable) updated by Nicklas Nordborg
The same problem exists in the Median-ratio normalization plug-in.
9:19 AM Ticket #1076 (Backwards incompatible change in MedianRatioNormalization plugin) created by Nicklas Nordborg
The fix to #1030 which was included in the 2.7.1 release, removed the …
8:49 AM Ticket #1075 (Lowess normalization fails on trunk but works on latest 2.7-stable) updated by Nicklas Nordborg
Owner, Component, Status changed
I get the same error. Looking at the SQL, it seems like the table …

Jun 30, 2008:

10:51 PM Ticket #1075 (Lowess normalization fails on trunk but works on latest 2.7-stable) created by Jari Häkkinen
Running trunk version lowess on my development machine creates the …
7:31 PM Ticket #1074 (Base1PluginExecuter: BASE1 text field parameter is not working properly) updated by Jari Häkkinen
Status changed
7:31 PM Ticket #1074 (Base1PluginExecuter: BASE1 text field parameter is not working properly) created by Jari Häkkinen
Text field parameters in BASE1 are treated specially in that they are …
2:48 PM Changeset [4357] by Nicklas Nordborg
References #1072: Core plug-in versions should follow BASE versions …
2:48 PM Ticket #1072 (Core plug-in versions should follow BASE versions) updated by Nicklas Nordborg
(In [4357]) References #1072: Core plug-in versions should follow BASE …
2:47 PM Ticket #1072 (Core plug-in versions should follow BASE versions) closed by Nicklas Nordborg
fixed: (In [4356]) Fixes #1072: Core plug-in versions should follow BASE versions
2:47 PM Changeset [4356] by Nicklas Nordborg
Fixes #1072: Core plug-in versions should follow BASE versions
2:32 PM Ticket #1072 (Core plug-in versions should follow BASE versions) updated by Nicklas Nordborg
Owner, Status changed
2:32 PM Ticket #1073 (Store current plug-in version when running a job) closed by Nicklas Nordborg
fixed: (In [4355]) Fixes #1073: Store current plug-in version when running a job
2:32 PM Changeset [4355] by Nicklas Nordborg
Fixes #1073: Store current plug-in version when running a job
1:55 PM Ticket #1073 (Store current plug-in version when running a job) updated by Nicklas Nordborg
Status, Owner changed
11:10 AM Ticket #1073 (Store current plug-in version when running a job) created by Nicklas Nordborg
It may be useful to know the version number of a plug-in that was used …
11:06 AM Ticket #1072 (Core plug-in versions should follow BASE versions) created by Nicklas Nordborg
The version number of the core plug-ins as reported by the …
8:41 AM Changeset [4354] by Nicklas Nordborg
Fixes #1070: Excess memory usage when creating root bioassayset with …
8:41 AM Ticket #1070 (Excess memory usage when creating root bioassayset with different ...) closed by Nicklas Nordborg
fixed: (In [4354]) Fixes #1070: Excess memory usage when creating root …

Jun 27, 2008:

2:45 PM Ticket #1071 (Help text for default configuration selection for Base1PluginExecuter ...) created by Jari Häkkinen
Selecting the Base1PluginExecuter as plug-in to run will show the …
2:34 PM Changeset [4353] by Nicklas Nordborg
References #1070: Excess memory usage when creating root bioassayset …
2:34 PM Ticket #1070 (Excess memory usage when creating root bioassayset with different ...) updated by Nicklas Nordborg
(In [4353]) References #1070: Excess memory usage when creating root …
2:34 PM Ticket #1070 (Excess memory usage when creating root bioassayset with different ...) updated by Nicklas Nordborg
I think this may be fixed now. The memory usage is is much lower. Here …
9:24 AM Ticket #1070 (Excess memory usage when creating root bioassayset with different ...) updated by Nicklas Nordborg
Status, Owner changed

Jun 26, 2008:

8:38 PM Ticket #1070 (Excess memory usage when creating root bioassayset with different ...) created by Nicklas Nordborg
Although the implementation is correct I tag this as a defect since …
11:11 AM Ticket #1069 (New mode for Import reporters to reporterlist - Add existing without ...) created by Johan Vallon-Christersson
When importing reporters to a reporterlist from file (using Reporter …
9:51 AM Ticket #1068 (Sorting spotdata on a formula-based column where the formula contains ...) closed by Nicklas Nordborg
fixed: (In [4352]) Fixes #1068: Sorting spotdata on a formula-based column …
9:51 AM Changeset [4352] by Nicklas Nordborg
Fixes #1068: Sorting spotdata on a formula-based column where the …
9:33 AM Ticket #1068 (Sorting spotdata on a formula-based column where the formula contains ...) updated by Nicklas Nordborg
Owner, Status changed
There is a similar problem in Experiment explorer: […]
9:32 AM Ticket #1068 (Sorting spotdata on a formula-based column where the formula contains ...) created by Nicklas Nordborg
[…]
9:30 AM Ticket #1065 (Can't display spot-data columns that are based on formulas returning ...) closed by Nicklas Nordborg
duplicate: I think the fix in #1067 is better. * Using CAST in the SQL will …
9:25 AM Changeset [4351] by Nicklas Nordborg
Fixes #1067: Can't display spot-data columns that are based on …
9:25 AM Ticket #1067 (Can't display spot-data columns that are based on formulas returning ...) closed by Nicklas Nordborg
fixed: (In [4351]) Fixes #1067: Can't display spot-data columns that are …

Jun 25, 2008:

3:42 PM Ticket #1065 (Can't display spot-data columns that are based on formulas returning ...) updated by Nicklas Nordborg
Description changed
3:42 PM Ticket #1067 (Can't display spot-data columns that are based on formulas returning ...) created by Nicklas Nordborg
This is the same problem as in ticket #1065. I have been investigating …
1:02 PM Ticket #1065 (Can't display spot-data columns that are based on formulas returning ...) updated by Nicklas Nordborg
I have now checked MySQL also and the result is different from …
12:47 PM Ticket #1066 (Reset all filters functionality request) updated by Nicklas Nordborg
I think we can have two levels: * Reset in-memory settings * Reset …
12:28 PM Ticket #1066 (Reset all filters functionality request) created by Jari Häkkinen
In some cases filtering of list views and inclusion of columns to list …
12:13 PM Ticket #1065 (Can't display spot-data columns that are based on formulas returning ...) updated by Nicklas Nordborg
I made a quick check and the result is that the return type is varying …
11:50 AM Ticket #1065 (Can't display spot-data columns that are based on formulas returning ...) updated by Nicklas Nordborg
Priority, Summary, Component, Milestone changed
It seems like the chromosome column in question comes from a formula …
10:54 AM Ticket #1065 (Can't display spot-data columns that are based on formulas returning ...) created by Jari Häkkinen
See also #1067. I was looking at spot data and with a few columns …
9:57 AM Ticket #1064 (Add support for dry-run to the plug-in system) created by Nicklas Nordborg
There is a wish in ticket #1028 that it should be possible to run a …

Jun 24, 2008:

3:01 PM Ticket #1063 (Read doc/src/docbook/overviewdoc/features.xml) updated by Jari Häkkinen
Summary changed
3:00 PM Changeset [4350] by Jari Häkkinen
Fixes #1062.
3:00 PM Ticket #1062 (Add information about Illumina plugin to platform section in doc) closed by Jari Häkkinen
fixed: (In [4350]) Fixes #1062.

Jun 23, 2008:

10:35 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
Description changed
Major revision of the user perspective, and the sample openoffice is …
10:33 PM batchimport_userperspective-3.txt attached to Ticket #1028 by Jari Häkkinen
9:32 PM Ticket #1063 (Read doc/src/docbook/overviewdoc/features.xml) created by Jari Häkkinen
Was: Add information about supported microarray platforms to web site …
9:28 PM Ticket #1062 (Add information about Illumina plugin to platform section in doc) updated by Jari Häkkinen
Status changed
9:28 PM Ticket #1062 (Add information about Illumina plugin to platform section in doc) created by Jari Häkkinen
2:43 PM Ticket #1037 (Add 'id' column to all list pages) updated by Nicklas Nordborg
(In [4349]) References #1037: Add 'id' column to all list pages Fixed …
2:43 PM Changeset [4349] by Nicklas Nordborg
References #1037: Add 'id' column to all list pages Fixed incorrect …
8:07 AM Ticket #1060 (Bug? - Overview plots fail after BASE 2.7.1 update) closed by Nicklas Nordborg
invalid: I don't think this has anything to do with the 2.7.1 update. It is …
7:56 AM Ticket #1061 (Error: Run plugin: Formula intensity calculator) closed by Nicklas Nordborg
invalid: You need to give the base2@myserver.edu user access to the dynamic …

Jun 19, 2008:

11:37 PM Ticket #1061 (Error: Run plugin: Formula intensity calculator) created by base
When attempting to run this plugin, I get this MySQL error: CREATE …
4:34 PM Ticket #1060 (Bug? - Overview plots fail after BASE 2.7.1 update) created by Johan Vallon-Christersson
After updating to BASE 2.7.1 (Lund onk installation) overview plots …
10:46 AM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
Description changed
Updated spreadsheet, sample information to the labeled extracts step …
8:29 AM Ticket #1059 (JasperException: Unable to find setter method for attribute: direction ...) updated by Nicklas Nordborg
Summary, Version, Priority changed
I have checked with IBM's java runtime (version 6) and I get the same …

Jun 18, 2008:

8:31 PM Ticket #1059 (JasperException: Unable to find setter method for attribute: direction ...) updated by base
Yes, that fixed the problem! Thanks a lot.
7:30 PM Ticket #1059 (JasperException: Unable to find setter method for attribute: direction ...) updated by Nicklas Nordborg
Have you tried using Sun's Java runtime?
6:18 PM Ticket #1059 (JasperException: Unable to find setter method for attribute: direction ...) updated by base
Replying to nicklas: > I think this is a Tomcat-related …
2:43 PM Changeset [4348] by Nicklas Nordborg
References #1038: Provide manual parameter for 'spotsize' in GAL …
2:43 PM Ticket #1038 (Provide manual parameter for 'spotsize' in GAL exporter) updated by Nicklas Nordborg
(In [4348]) References #1038: Provide manual parameter for 'spotsize' …
2:19 PM Changeset [4347] by Nicklas Nordborg
Merged patch release 2.7.1 to the trunk
2:06 PM Milestone BASE 2.7.1 completed
Bug fixes for 2.7. Revision log: log:branches/2.7-stable@4296:4345
2:06 PM DownloadPage edited by Nicklas Nordborg
Releasing 2.7.1 (diff)
2:02 PM Changeset [4346] by Nicklas Nordborg
Changes for future release 2.7.2
1:52 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
Description changed
batchimport_userperspective.txt updated.
1:51 PM batchimport_userperspective-2.txt attached to Ticket #1028 by Jari Häkkinen
1:49 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
Description changed
1:48 PM Changeset [4345] by Nicklas Nordborg
Tagging version 2.7.1
1:47 PM Changeset [4344] by Nicklas Nordborg
Preparing release 2.7.1
1:46 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
I added a spreadsheet with sample sheets for use with the batch item …
1:42 PM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
In the batchimport.txt document there is a discussion on multi-item …
8:48 AM Ticket #1059 (JasperException: Unable to find setter method for attribute: direction ...) updated by Nicklas Nordborg
I think this is a Tomcat-related problem. Which Tomcat5 version are …

Jun 17, 2008:

11:36 PM Ticket #1059 (JasperException: Unable to find setter method for attribute: direction ...) created by base
I'm attempting to use BASE 2.6.3. I only have Tomcat5 available, and …
2:54 PM Ticket #1010 (Display progress reporter for plug-ins that are executing with the ...) updated by Martin Svensson
(In [4343]) References #1010
2:54 PM Changeset [4343] by Martin Svensson
References #1010
2:53 PM Changeset [4342] by Martin Svensson
Fixes #1010
2:53 PM Ticket #1010 (Display progress reporter for plug-ins that are executing with the ...) closed by Martin Svensson
fixed: (In [4342]) Fixes #1010
2:06 PM Ticket #1056 (Disk usage does not seem to report disk usage properly for experiments) closed by Nicklas Nordborg
fixed: (In [4341]) Fixes #1056: Disk usage does not seem to report disk usage …
2:06 PM Changeset [4341] by Nicklas Nordborg
Fixes #1056: Disk usage does not seem to report disk usage properly …
1:44 PM Ticket #1056 (Disk usage does not seem to report disk usage properly for experiments) updated by Nicklas Nordborg
Component, Owner, Status, Milestone changed
I can confirm this. There seems to be an issue with synchronizing the …
1:14 PM Changeset [4340] by Nicklas Nordborg
Fixes #1054: Make it possible for the annotation importer to identify …
1:14 PM Ticket #1054 (Make it possible for the annotation importer to identify items by ...) closed by Nicklas Nordborg
fixed: (In [4340]) Fixes #1054: Make it possible for the annotation importer …
1:12 PM Ticket #1010 (Display progress reporter for plug-ins that are executing with the ...) reopened by Martin Svensson
The progress reporter does not finish, instead it hangs even if the …
1:02 PM Ticket #1058 (Metadata.getPropertyValue() fails to get value for the 'id' property) closed by Nicklas Nordborg
fixed: (In [4339]) Fixes #1058: Metadata.getPropertyValue() fails to get …
1:02 PM Changeset [4339] by Nicklas Nordborg
Fixes #1058: Metadata.getPropertyValue() fails to get value for the …
1:02 PM Ticket #1058 (Metadata.getPropertyValue() fails to get value for the 'id' property) created by Nicklas Nordborg
This makes it impossible to export the id value from data tables …
11:21 AM Ticket #1054 (Make it possible for the annotation importer to identify items by ...) updated by Nicklas Nordborg
Status, Owner changed
11:20 AM Ticket #1050 (Add core support for storing analysed data in files instead of in the ...) closed by Nicklas Nordborg
fixed: Seems to be working ok.
11:19 AM Ticket #1051 (Add support in the GUI for accssing files used to store analysed data) closed by Nicklas Nordborg
fixed: (In [4338]) Fixes #1051: Add support in the GUI for accssing files …
11:19 AM Changeset [4338] by Nicklas Nordborg
Fixes #1051: Add support in the GUI for accssing files used to store …
11:07 AM Ticket #1028 (Plug-in for batch upload/modification of items) updated by Jari Häkkinen
Description changed
11:02 AM batchimport_userperspective.txt attached to Ticket #1028 by Jari Häkkinen
First draft of a users view
11:01 AM Changeset [4337] by Nicklas Nordborg
Fixes #1052: Core analysis plug-ins need to be aware of bioassaysets …
11:01 AM Ticket #1052 (Core analysis plug-ins need to be aware of bioassaysets that use data ...) closed by Nicklas Nordborg
fixed: (In [4337]) Fixes #1052: Core analysis plug-ins need to be aware of …
11:01 AM Ticket #1057 (Make it possible to access and change web service options on client side) updated by Martin Svensson
Owner changed
10:05 AM Ticket #1055 (Messaging system) updated by Jari Häkkinen
Description changed
9:54 AM Ticket #1052 (Core analysis plug-ins need to be aware of bioassaysets that use data ...) updated by Nicklas Nordborg
Description changed
9:51 AM Ticket #1049 (Add the 'quadratic mean' to available Avg. method's for formulas.) closed by Martin Svensson
fixed: (In [4336]) Fixes #1049 Add the 'quadratic mean' to available Avg. …
9:51 AM Changeset [4336] by Martin Svensson
Fixes #1049 Add the 'quadratic mean' to available Avg. method's for …
9:29 AM Ticket #1052 (Core analysis plug-ins need to be aware of bioassaysets that use data ...) updated by Nicklas Nordborg
Owner, Status changed
9:26 AM Changeset [4335] by Nicklas Nordborg
References #1050: Add core support for storing analysed data in files …
9:26 AM Ticket #1050 (Add core support for storing analysed data in files instead of in the ...) updated by Nicklas Nordborg
(In [4335]) References #1050: Add core support for storing analysed …
8:03 AM Ticket #1051 (Add support in the GUI for accssing files used to store analysed data) updated by Nicklas Nordborg
Owner, Status changed
8:01 AM Changeset [4334] by Nicklas Nordborg
References #1050: Add core support for storing analysed data in files …
8:01 AM Ticket #1050 (Add core support for storing analysed data in files instead of in the ...) updated by Nicklas Nordborg
(In [4334]) References #1050: Add core support for storing analysed …
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