Timeline



Jun 18, 2008:

2:43 PM Changeset [4348] by Nicklas Nordborg
References #1038: Provide manual parameter for 'spotsize' in GAL …
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
1:48 PM Changeset [4345] by Nicklas Nordborg
Tagging version 2.7.1
1:47 PM Changeset [4344] by Nicklas Nordborg
Preparing release 2.7.1

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 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 …
1:14 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 …
11:20 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 …
11:01 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 …
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 …
9:26 AM Changeset [4335] by Nicklas Nordborg
References #1050: Add core support for storing analysed data in files …
8:01 AM Changeset [4334] by Nicklas Nordborg
References #1050: Add core support for storing analysed data in files …

Jun 16, 2008:

8:09 PM Ticket #1057 (Make it possible to access and change web service options on client side) created by Nicklas Nordborg
The current implementation of the client-side of the web services …
9:49 AM Ticket #1037 (Add 'id' column to all list pages) closed by Martin Svensson
fixed: (In [4333]) Fixes #1037 Add 'id' column to all list pages
9:49 AM Changeset [4333] by Martin Svensson
Fixes #1037 Add 'id' column to all list pages

Jun 12, 2008:

11:22 AM Changeset [4332] by Martin Svensson
References #1037 Most of the list pages can now show an item's ID.

Jun 11, 2008:

5:16 PM Ticket #1056 (Disk usage does not seem to report disk usage properly for experiments) created by Johan Vallon-Christersson
Defect? Experiments in BASE2 with lots of bioassaysets (and …
2:47 PM Ticket #1055 (Messaging system) created by Jari Häkkinen
The messaging system should allow users with proper credential to send …
9:12 AM Changeset [4331] by Martin Svensson
References #1037 The most important list pages are done.

Jun 10, 2008:

3:59 PM Ticket #1010 (Display progress reporter for plug-ins that are executing with the ...) closed by Martin Svensson
fixed: (In [4330]) Fixes #1010 Display progress reporter for plug-ins that …
3:59 PM Changeset [4330] by Martin Svensson
Fixes #1010 Display progress reporter for plug-ins that are executing …

Jun 5, 2008:

2:45 PM Ticket #1054 (Make it possible for the annotation importer to identify items by ...) created by Nicklas Nordborg
The current implementation only supports 'name' or 'externalId' as …
8:12 AM Ticket #1048 (Plugin configuration wizard display/parse incorrectly (when ...) closed by Nicklas Nordborg
wontfix: I have found what you are talking about. The issue here is that when …
8:01 AM Changeset [4329] by Nicklas Nordborg
Fixes #1047: Type.BOOLEAN.parseString() doesn't convert strings as expected
8:01 AM Ticket #1047 (Type.BOOLEAN.parseString() doesn't convert strings as expected) closed by Nicklas Nordborg
fixed: (In [4329]) Fixes #1047: Type.BOOLEAN.parseString() doesn't convert …
7:58 AM Changeset [4328] by Nicklas Nordborg
Fixes #1053: Values.getBoolean() is case-sensitive
7:58 AM Ticket #1053 (Values.getBoolean() is case-sensitive) closed by Nicklas Nordborg
fixed: (In [4328]) Fixes #1053: Values.getBoolean() is case-sensitive
7:55 AM Ticket #1053 (Values.getBoolean() is case-sensitive) created by Nicklas Nordborg
Trying to convert string values to boolean. Using lowercase strings, …

Jun 4, 2008:

1:35 PM Ticket #1052 (Core analysis plug-ins need to be aware of bioassaysets that use data ...) created by Nicklas Nordborg
This is related to #1029 and depends on #1050. All existing core …
1:29 PM Ticket #1051 (Add support in the GUI for accssing files used to store analysed data) created by Nicklas Nordborg
This is related to to #1029 and depends on #1050. The first thing is …
1:22 PM Ticket #1050 (Add core support for storing analysed data in files instead of in the ...) created by Nicklas Nordborg
This is related to #1029, but is only about changes needed in the core …
11:45 AM Ticket #1049 (Add the 'quadratic mean' to available Avg. method's for formulas.) created by Johan Vallon-Christersson
http://en.wikipedia.org/wiki/Quadratic_mean
10:56 AM Ticket #1048 (Plugin configuration wizard display/parse incorrectly (when ...) created by Johan Vallon-Christersson
When testing with file (parsing file) the rows above defined data …
10:08 AM Ticket #1047 (Type.BOOLEAN.parseString() doesn't convert strings as expected) created by Johan Vallon-Christersson
When importing Raw data (type = Agilent), data from the file is mapped …

Jun 3, 2008:

4:14 PM Changeset [4327] by Martin Svensson
References #1010 Using the SimpleProgressReporter? to get progress of …
3:07 PM Changeset [4326] by Nicklas Nordborg
Fixes #1045. References #1016.
3:07 PM Ticket #1045 (File list view creates an exception) closed by Nicklas Nordborg
fixed: (In [4326]) Fixes #1045. References #1016.
2:00 PM Ticket #1046 (Remember closed/expanded node status in the hierarchical tree of ...) created by Johan Vallon-Christersson
Currently, closed nodes in the hierarchical tree of Bioassay sets (in …
11:25 AM Changeset [4325] by Nicklas Nordborg
Fixes #1038: Provide manual parameter for 'spotsize' in GAL exporter
11:25 AM Ticket #1038 (Provide manual parameter for 'spotsize' in GAL exporter) closed by Nicklas Nordborg
fixed: (In [4325]) Fixes #1038: Provide manual parameter for 'spotsize' in …
11:07 AM Ticket #1045 (File list view creates an exception) created by Jari Häkkinen
When I try to view my files as ordinary user I get the below …
10:58 AM Changeset [4324] by Nicklas Nordborg
Fixes #532.
10:58 AM Ticket #532 (Read "Jobs" section) closed by Nicklas Nordborg
fixed: (In [4324]) Fixes #532.
9:41 AM Ticket #1036 (Implement 'service' extension point) closed by Nicklas Nordborg
fixed: Seems to be working fine right now.

Jun 2, 2008:

1:11 PM Ticket #1044 (MeV launch returns a 'jsp' extension not a 'jnlp') closed by Nicklas Nordborg
worksforme: It is a browser-related problem.
12:22 PM Ticket #1044 (MeV launch returns a 'jsp' extension not a 'jnlp') created by Jari Häkkinen
I am not sure if this should be in this ticket system or baseplugins …

May 30, 2008:

12:06 PM Changeset [4323] by Nicklas Nordborg
Fixes #1043: JarClassLoader?.getInstance() doesn't create a new class …
12:06 PM Ticket #1043 (JarClassLoader.getInstance() doesn't create a new class loader if a ...) closed by Nicklas Nordborg
fixed: (In [4323]) Fixes #1043: JarClassLoader?.getInstance() doesn't create a …
11:22 AM Ticket #1043 (JarClassLoader.getInstance() doesn't create a new class loader if a ...) created by Nicklas Nordborg
The documentation on the method says that a new class loader should be …
11:15 AM Changeset [4322] by Nicklas Nordborg
Fixes #1042: Improve error handling in the extensions system
11:15 AM Ticket #1042 (Improve error handling in the extensions system) closed by Nicklas Nordborg
fixed: (In [4322]) Fixes #1042: Improve error handling in the extensions system
10:58 AM Ticket #1042 (Improve error handling in the extensions system) created by Nicklas Nordborg
The extensions system contains code like the example below in several …

May 29, 2008:

3:02 PM Ticket #1041 (ZipException: error in opening zip file in JarClassLoader if a JAR ...) closed by Nicklas Nordborg
fixed: (In [4321]) Fixes #1041: ZipException?: error in opening zip file in …
3:02 PM Changeset [4321] by Nicklas Nordborg
Fixes #1041: ZipException?: error in opening zip file in JarClassLoader?
2:43 PM Ticket #1041 (ZipException: error in opening zip file in JarClassLoader if a JAR ...) created by Nicklas Nordborg
Here is the interesting parts of the stacktrace: […] The starting …
1:39 PM Changeset [4320] by Nicklas Nordborg
References #1036: Implement 'service' extension point Now it is ready …
11:38 AM Changeset [4319] by Nicklas Nordborg
Fixes #1040: Exceptions when stopping Tomcat
11:38 AM Ticket #1040 (Exceptions when stopping Tomcat) closed by Nicklas Nordborg
fixed: (In [4319]) Fixes #1040: Exceptions when stopping Tomcat
11:11 AM Ticket #1040 (Exceptions when stopping Tomcat) created by Nicklas Nordborg
This has been around for a long time... When stopping Tomcat using the …

May 28, 2008:

8:21 PM Ticket #408 (Implement FTP server) closed by Nicklas Nordborg
invalid: Moved to http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp
8:01 AM Ticket #1039 (link to list of plugins is broken) closed by Martin Svensson
fixed: The link is fixed
8:00 AM WikiStart edited by Martin Svensson
Repaired a broken link (diff)
12:15 AM Ticket #1039 (link to list of plugins is broken) created by Peter Johansson
Link on first page core plug-ins with sample configuration files

May 27, 2008:

12:21 PM Ticket #1038 (Provide manual parameter for 'spotsize' in GAL exporter) created by Nicklas Nordborg
Since the 'spotsize' column wasn't added until BASE 2.7 (#999), many …
11:55 AM Ticket #1037 (Add 'id' column to all list pages) created by Nicklas Nordborg
The internal ID of items is not visible anywhere in the web interface. …
10:16 AM Ticket #639 (exportPureMatrix method) closed by Jari Häkkinen
fixed: changeset:4318 adds functionality to export 2-channel data. ch1/ch2 …
10:08 AM Changeset [4318] by Jari Häkkinen
Addresses #639. Exporting plain matrix for 1 and 2 channel data.
9:36 AM Ticket #1036 (Implement 'service' extension point) created by Nicklas Nordborg
It could be useful to have an extension point that can be used for …
8:44 AM Changeset [4317] by Nicklas Nordborg
Fixes #1022: Add support for using regular expressions in queries
8:44 AM Ticket #1022 (Add support for using regular expressions in queries) closed by Nicklas Nordborg
fixed: (In [4317]) Fixes #1022: Add support for using regular expressions in …
8:17 AM Changeset [4316] by Jari Häkkinen
Removed obsolete/stray code.

May 26, 2008:

2:12 PM Changeset [4315] by Nicklas Nordborg
Fixes #1035: Exception when applying filter on multiple Item type in …
2:12 PM Ticket #1035 (Exception when applying filter on multiple Item type in some list views) closed by Nicklas Nordborg
fixed: (In [4315]) Fixes #1035: Exception when applying filter on multiple …
1:01 PM Ticket #967 (Assign the parent directory permissions to new files/directories) closed by Nicklas Nordborg
fixed: (In [4314]) Fixes #967: Assign the parent directory permissions to new …
1:01 PM Changeset [4314] by Nicklas Nordborg
Fixes #967: Assign the parent directory permissions to new …
11:52 AM Changeset [4313] by Nicklas Nordborg
References #981: Share all subdirectories and files when sharing a …
9:31 AM Changeset [4312] by Nicklas Nordborg
Fixes #981: Share all subdirectories and files when sharing a directory
9:31 AM Ticket #981 (Share all subdirectories and files when sharing a directory) closed by Nicklas Nordborg
fixed: (In [4312]) Fixes #981: Share all subdirectories and files when …

May 23, 2008:

3:12 PM Ticket #1035 (Exception when applying filter on multiple Item type in some list views) created by Johan Vallon-Christersson
Selecting to filter on two Item types in Trashcan table view, e.g., …
2:24 PM Changeset [4311] by Nicklas Nordborg
Fixes #1024: Allow users to select a specific job-agent when creating …
2:24 PM Ticket #1024 (Allow users to select a specific job-agent when creating a new job) closed by Nicklas Nordborg
fixed: (In [4311]) Fixes #1024: Allow users to select a specific job-agent …
2:08 PM Changeset [4310] by Jari Häkkinen
Fixes #1034
2:08 PM Ticket #1034 (Normalization: Lowess. Add information about reporter lists to plug-in ...) closed by Jari Häkkinen
fixed: (In [4310]) Fixes #1034
2:02 PM Ticket #1034 (Normalization: Lowess. Add information about reporter lists to plug-in ...) created by Jari Häkkinen
11:39 AM Ticket #1033 (Mark columns containing unique information in list views) created by Jari Häkkinen
It would be nice if the web interface could highlight information that …
11:33 AM Ticket #1032 (Apache server complains "Request-URI Too Large") created by Jari Häkkinen
In some cases the Apache server complains in the URI size. If one …

May 22, 2008:

3:51 PM Changeset [4309] by Martin Svensson
References #532. Chapter is ready to be read.

May 21, 2008:

10:49 PM Ticket #1030 (Normaliztion: Median ratio for 1-channel data should support scaling ...) closed by Jari Häkkinen
fixed: (In [4308]) Fixes #1030. User selects scaling/subtraction depending on …
10:49 PM Changeset [4308] by Jari Häkkinen
Fixes #1030. User selects scaling/subtraction depending on whether …
5:29 PM Changeset [4307] by Martin Svensson
References #532. Written main part of the Job section
3:39 PM Changeset [4306] by Nicklas Nordborg
References #1015: Add reporter list from tables that list …
1:22 PM Ticket #1031 (Filtering with selection lists) closed by Nicklas Nordborg
invalid: It is intentional and needed if using only a keybord and follows the …
1:13 PM Ticket #1031 (Filtering with selection lists) created by Jari Häkkinen
The selection list filters in list views works if the green check box …
1:11 PM Changeset [4305] by Nicklas Nordborg
References #1015: Add reporter list from tables that list …
8:47 AM Ticket #1027 (Annotation importer should be able to remove annotations) closed by Nicklas Nordborg
fixed: (In [4304]) Fixes #1027: Annotation importer should be able to remove …
8:47 AM Changeset [4304] by Nicklas Nordborg
Fixes #1027: Annotation importer should be able to remove annotations

May 20, 2008:

10:54 AM Ticket #1030 (Normaliztion: Median ratio for 1-channel data should support scaling ...) created by Jari Häkkinen
The current implementation translate the data to zero median for each …

May 19, 2008:

2:48 PM Ticket #987 (NullPointerException in "Test with file" function if no "data header ...) closed by Martin Svensson
fixed: (In [4303]) Fixes #987 NullPointerException? in "Test with file" …
2:48 PM Changeset [4303] by Martin Svensson
Fixes #987 NullPointerException? in "Test with file" function if no …
2:07 PM Changeset [4302] by Nicklas Nordborg
References #1016: Filter table using a reporter list I think this …
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