Timeline



Nov 23, 2005:

8:31 PM Changeset [1657] by Nicklas Nordborg
Updated development status
4:06 PM Changeset [1656] by Nicklas Nordborg
Added Wells admin
2:58 PM Changeset [1655] by Nicklas Nordborg
Added plate events admin
2:55 PM Changeset [1654] by Nicklas Nordborg
Added HQL right join and support for WITH restriction in join clause
9:41 AM Changeset [1653] by Nicklas Nordborg
Added plate event types administration
8:54 AM Ticket #11 (Migration: AnnotationTransfer InvalidDataException not caught) closed by Gregory Vincic
fixed: Fixed. There is a problem concerning that Base 1 allows annotations …

Nov 22, 2005:

4:04 PM Changeset [1652] by Nicklas Nordborg
Added Array LIMS / plates
3:00 PM Changeset [1651] by Gregory Vincic
Removed some logging
2:59 PM Changeset [1650] by Nicklas Nordborg
Fixed bad UTF-8 characters
2:36 PM Changeset [1649] by Nicklas Nordborg
Fixed bug in ReporterFlatFileImporter? (Not converting values to …
1:37 PM Changeset [1648] by Gregory Vincic
Fixed bug with unavailable ArraySlides? and removed some logging
9:41 AM Changeset [1647] by Nicklas Nordborg
Plugin configuration

Nov 21, 2005:

2:44 PM Changeset [1646] by Nicklas Nordborg
Added plugin configuration admin
2:26 PM Changeset [1645] by Gregory Vincic
Setting different SELECT limit if QUICK_TRANSFER = yes
2:19 PM Changeset [1644] by Gregory Vincic
Removed calls to depraceted methods and fixed invalid use of null in …
10:53 AM Changeset [1643] by Gregory Vincic
Catching NumberFormatException?
10:34 AM Changeset [1642] by Gregory Vincic
Removed some logging
9:50 AM Ticket #11 (Migration: AnnotationTransfer InvalidDataException not caught) created by Gregory Vincic
The setValue methods on lines 143 through 156 in …
9:45 AM Changeset [1641] by Gregory Vincic
Annotations generating InvalidDataException? are not migrated
8:17 AM Changeset [1640] by Nicklas Nordborg
Abstract flat file importer now checks for thread interruption

Nov 18, 2005:

8:04 PM Changeset [1639] by Nicklas Nordborg
Set ID and Date keyword
8:00 PM Changeset [1638] by Nicklas Nordborg
Updated development status
3:24 PM Changeset [1637] by Gregory Vincic
Fixed bug with equal filenames and removed some logging
2:54 PM Changeset [1636] by Nicklas Nordborg
Jobs are not shareable, added server to view job
2:42 PM Changeset [1635] by Nicklas Nordborg
Updated some javadoc
2:00 PM Changeset [1634] by Nicklas Nordborg
Internal job queue is now functional
11:11 AM Changeset [1633] by Gregory Vincic
Logs migration ending
10:29 AM Changeset [1632] by Johan Enell
Added methods to handle String to int conversions
9:47 AM Changeset [1631] by Nicklas Nordborg
Modified SessionControl?.impersonateLogin() to create a new …
9:33 AM Changeset [1630] by Gregory Vincic
Fixed logging

Nov 17, 2005:

1:36 PM Changeset [1629] by Nicklas Nordborg
Added first version of internal job queue (not working)
1:21 PM Changeset [1628] by Johan Enell
added some svn properties
1:05 PM Changeset [1627] by Johan Enell
section tested
10:56 AM Changeset [1626] by Nicklas Nordborg
Added two new columns to job: server and estimated execution time. …
9:34 AM Changeset [1625] by Gregory Vincic
Changed error output to info
9:05 AM Changeset [1624] by Nicklas Nordborg
Added Log4j logger to migration since it didn't compile now that the …

Nov 16, 2005:

4:07 PM Changeset [1623] by Nicklas Nordborg
Removed Application.log methods
2:55 PM Changeset [1622] by Nicklas Nordborg
Plugins now leave better status reporters to jobs and messages.
1:32 PM Changeset [1621] by Nicklas Nordborg
Fixed bugs in configure columns and export
1:01 PM Changeset [1620] by Nicklas Nordborg
Added submit_jobs.jsp
12:57 PM Changeset [1619] by Nicklas Nordborg
Added View/Jobs?
11:23 AM Changeset [1618] by Nicklas Nordborg
Better file selection when importing File upload is now possible when …
10:52 AM Changeset [1617] by Nicklas Nordborg
Added some functions for better auto-detection of file formats

Nov 15, 2005:

4:53 PM Changeset [1616] by Johan Enell
section added to flatfileparser
4:10 PM Changeset [1615] by Nicklas Nordborg
Fixed bug in property value if no DbControl? was set
4:04 PM Changeset [1614] by Nicklas Nordborg
Fixed bug in column selection
3:52 PM Changeset [1613] by Nicklas Nordborg
First version of import reporters is now working
12:27 PM Changeset [1612] by Nicklas Nordborg
Started to implement import function
9:41 AM Changeset [1611] by Nicklas Nordborg
Added import_disabled.gif
9:22 AM Changeset [1610] by Nicklas Nordborg
Fixed classpath to log4j
9:21 AM Changeset [1609] by Nicklas Nordborg
Generic export can now handle data layer items
8:56 AM Changeset [1608] by Nicklas Nordborg
Fixed several bugs in Metadata to get View/Reporters? to work

Nov 14, 2005:

8:02 PM Changeset [1607] by Nicklas Nordborg
Updated development status
4:07 PM Changeset [1606] by Nicklas Nordborg
Added View/Reporters?
2:54 PM Changeset [1605] by Nicklas Nordborg
ExtendedProperty?.getTitle now returns the title instead of the name
11:27 AM Ticket #10 (Analysis: Hierarchical clustering) created by Johan Enell
Hierarchical clustering, bottom-up. The two closest points are merged …
11:08 AM Ticket #9 (Normalization: Lowess) created by Johan Enell
A plug-in for lowess normalization. For more info on LOWESS: …
10:55 AM Ticket #8 (PrintMapBlockFileImporter) created by Johan Enell
A importer plugin-in for print maps.
10:50 AM Ticket #7 (ReporterMapFlatFileImporter) closed by Johan Enell
fixed
10:50 AM Ticket #7 (ReporterMapFlatFileImporter) created by Johan Enell
A importer plug-in for reporter maps.
10:48 AM Ticket #6 (ReporterFlatFileImporter) closed by Johan Enell
fixed
10:48 AM Ticket #6 (ReporterFlatFileImporter) created by Johan Enell
A importer plug-in for reporter
10:46 AM Ticket #5 (RawDataFlatFileImporter) closed by Johan Enell
fixed
10:46 AM Ticket #5 (RawDataFlatFileImporter) created by Johan Enell
A importer plug-in for rawdata.
10:44 AM Ticket #4 (PlateFlatFileImporter) closed by Johan Enell
fixed
10:43 AM Ticket #4 (PlateFlatFileImporter) created by Johan Enell
An importer plug-in for plates.
10:41 AM Changeset [1604] by Nicklas Nordborg
Added ReporterType? admin
10:40 AM Changeset [1603] by Nicklas Nordborg
Added Removable interface to ReporterType?
10:23 AM Changeset [1602] by Nicklas Nordborg
Bug in reload timer. The same timer can't be reused.
9:33 AM Changeset [1601] by Nicklas Nordborg
Removed Swing timer from Keyring and replaced it with TimerTask?.
9:13 AM Changeset [1600] by Nicklas Nordborg
Added "debugEnabled" boolean so we don't have to generate log messages …
8:53 AM Changeset [1599] by Nicklas Nordborg
Moved log statements to log things before they happened.
8:43 AM Changeset [1598] by Nicklas Nordborg
Missing quotes around the "id" column when using sequences.
8:42 AM Changeset [1597] by Nicklas Nordborg
Fixed a bug where "ch1" was always selected instead of "ch1", …
8:40 AM Changeset [1596] by Nicklas Nordborg
Made dynamic table names shorter, since some databases (ie. Oracle) …
8:39 AM Changeset [1595] by Nicklas Nordborg
Fixed bug in TestUser? causing it to fail if executed on a too fast …
8:35 AM Changeset [1594] by Nicklas Nordborg
Fixed bug in FlatFileParser? which returned empty strings instead of …
8:06 AM Ticket #3 (Update doesn't create indexes) created by Nicklas Nordborg
When using the update option for the installation program …

Nov 11, 2005:

4:06 PM Changeset [1593] by Nicklas Nordborg
Default logging level set to warn
4:04 PM Changeset [1592] by Nicklas Nordborg
Added net.sf.basedb.core logger and removed calls to Application.log …
3:38 PM Changeset [1591] by Nicklas Nordborg
Replaced the Swing timer in Application with a jva.util.Timer running …
12:12 PM Changeset [1590] by Nicklas Nordborg
Fixed security hole in RawFunction? and changed Metadata to help with that.
9:56 AM Changeset [1589] by Nicklas Nordborg
Batch API and Query API now uses Log4j to log debuggin information. …
8:28 AM Changeset [1588] by Nicklas Nordborg
Fixed bugs in Install causing transactions to be left open if an item …
8:00 AM Changeset [1587] by Nicklas Nordborg
Added backticks to filters created by …
7:52 AM Changeset [1586] by Nicklas Nordborg
Help is now stored in table HelpTexts? since there was a problem with …

Nov 10, 2005:

4:02 PM Changeset [1585] by Nicklas Nordborg
IntensityCalculatorUtil? now checks that all raw bioassays are using …
3:00 PM Changeset [1584] by Nicklas Nordborg
Updated documentation and clean up some code. Fixed bug in …

Nov 9, 2005:

11:38 PM Ticket #2 (ability to add image files as annotation for samples) created by anup.parikh@…
We have images, of all our mutants under different conditions, that we …
4:00 PM Changeset [1583] by Nicklas Nordborg
Updated documentation and cleaned up code.
12:23 PM Changeset [1582] by Nicklas Nordborg
Fixed bug in TestExperiment?
12:15 PM Changeset [1581] by Nicklas Nordborg
Moved around JepUtil? to it's own package (net.sf.basedb.util.jep). …
12:15 PM Changeset [1580] by Gregory Vincic
Added ExperimentTransfer?

Nov 8, 2005:

7:09 PM Changeset [1579] by Johan Enell
added some @Override annotations
4:06 PM Changeset [1578] by Nicklas Nordborg
Added JepUtil? and TestJep? Added Log10Expression and LnExpression?
1:01 PM Changeset [1577] by Nicklas Nordborg
Can now create root bioassayset using INSERT INTO ... SELECT query.
11:59 AM Changeset [1576] by Nicklas Nordborg
Redesigned DynamicQuery? and added subclass for each type of query. …

Nov 7, 2005:

4:05 PM Changeset [1575] by Nicklas Nordborg
Added IntensityCalculatorUtil? and other classes needed by it: …
3:33 PM Changeset [1574] by Gregory Vincic
Added protocol column
2:39 PM Changeset [1573] by Gregory Vincic
Fixed old queries, default listing of scans now works
1:49 PM Changeset [1572] by Gregory Vincic
Documenting

Nov 4, 2005:

2:33 PM Changeset [1571] by Gregory Vincic
Added migration of reportermap
2:21 PM Changeset [1570] by Gregory Vincic
Initial revision of WizzzardTransfer?
2:21 PM Changeset [1569] by Gregory Vincic
Fixed quota using new byteQuota in base schemaVersion 1.2.20
1:27 PM Changeset [1568] by Johan Enell
PlateFlatFileImporter? complete
12:02 PM Changeset [1567] by Nicklas Nordborg
Updated javadoc and clean up the code Added BioAssaySet?.getPositionData
10:02 AM Changeset [1566] by Nicklas Nordborg
Extra values can now be selected by queries

Nov 3, 2005:

4:09 PM Changeset [1565] by Nicklas Nordborg
Small redesign of extra values: Added ExtraValue? class. DynamicQuery?
11:42 AM Changeset [1564] by Jari Häkkinen
Fixed typos.
11:00 AM Changeset [1563] by Gregory Vincic
Removing feature to delete files if transfer successful
10:56 AM Changeset [1562] by Nicklas Nordborg
Added PositionExtraValueBatcher? and updated dynamic batch documentation
10:50 AM Changeset [1561] by Gregory Vincic
Added schema version control and uncommented plugin related roles. …
1:48 AM Changeset [1560] by Jari Häkkinen
Added instructions on how to install from a source package, or a …
12:20 AM Changeset [1559] by Jari Häkkinen
Improved installation documentation.

Nov 2, 2005:

9:34 PM Changeset [1558] by Jari Häkkinen
Added info about the trac pages, also made demo servers to open in a …
5:56 PM Changeset [1557] by Johan Enell
PlateFlatFileImporter? first draft
4:03 PM Changeset [1556] by Nicklas Nordborg
Updated some documentation for extra value batching Added …
3:07 PM WikiStart edited by Jari Häkkinen
(diff)
2:57 PM Changeset [1555] by Nicklas Nordborg
Added SpotExtraValueBatcher? and other needed classes for it.
2:19 PM Changeset [1554] by Johan Enell
removed all set methods from the parameter types and made the …

Nov 1, 2005:

4:42 PM Changeset [1553] by Gregory Vincic
Documenting and refactoring some DbControl? variables
3:06 PM Ticket #1 (column names in flatfile parser) created by Johan Enell
The FlatFileParser? is only able to parse columnsnumbers, eg. \4\. The …
2:57 PM Changeset [1552] by Nicklas Nordborg
Updated documentation for Dynamic API
1:49 PM Changeset [1551] by Gregory Vincic
Fixed ArrayBlock? transfer which now saves Features properly. …
10:59 AM Changeset [1550] by Johan Enell
just corrected a small typo
9:08 AM Changeset [1549] by Nicklas Nordborg
RawDataBatcher? now looks for Affy featues in the AffyFeatures? table …

Oct 31, 2005:

5:22 PM Changeset [1548] by Gregory Vincic
Initial revision of ArrayBlockTransfer?. Added includeArrayBlock = yes …
4:49 PM Changeset [1547] by Gregory Vincic
Added experimental localMySQL transfer and a seperated …
4:46 PM Changeset [1546] by Gregory Vincic
Initial revision of ArrayTypePlateTransfer?
4:08 PM Changeset [1545] by Nicklas Nordborg
Fixed problem with DataQuery? not working when multiple raw data types …
3:49 PM Changeset [1544] by Nicklas Nordborg
DynamicQuery? can now join raw data
3:39 PM Changeset [1543] by Gregory Vincic
Initial revision of ArrayType?
1:07 PM Changeset [1542] by Nicklas Nordborg
DynamiQuery? now supports parameters and limits

Oct 28, 2005:

4:07 PM Changeset [1541] by Nicklas Nordborg
Started to investigate how limits should be implemented in dynamic queries.
2:48 PM Changeset [1540] by Nicklas Nordborg
DynamicQuery? may now join the reporters table
1:36 PM Changeset [1539] by Johan Enell
changed RawBioAssay? header value from varchar(255) to text
9:56 AM Changeset [1538] by Nicklas Nordborg
Implemented delete operation for BioAssaySet?, Transformation and VirtualDb?

Oct 27, 2005:

4:06 PM Changeset [1537] by Nicklas Nordborg
Added support for deleting DataCube?, DataCubeLayer? and DataCubeFilter?
3:40 PM Changeset [1536] by Johan Enell
handleHeader added
2:59 PM Changeset [1535] by Johan Enell
added some javadoc
2:23 PM Changeset [1534] by Johan Enell
RawDataFlatFileImporter? is operational
1:52 PM Changeset [1533] by Nicklas Nordborg
Dynamic batchers now updates the disk usage of the experiment.
1:19 PM Changeset [1532] by Gregory Vincic
Quick transfer is now configurable for testing purposes. Added some …
11:47 AM Changeset [1531] by Nicklas Nordborg
Fixed problem with closing and flushing of batchers.
9:54 AM Changeset [1530] by Johan Enell
added a totalinsert counter to the batch system corected the reporter …
9:34 AM Changeset [1529] by Nicklas Nordborg
Added -w option (wait for keypress before starting to delete items) to …

Oct 26, 2005:

3:58 PM Changeset [1528] by Nicklas Nordborg
Added MappingBatcher?
2:46 PM Changeset [1527] by Nicklas Nordborg
Cleaned up and documented BioAssay?, BioAssaySet?, Experiment, …
1:09 PM Changeset [1526] by Gregory Vincic
Seperation of RawBioAssay? and it's data into two classes. Also added …
1:08 PM Changeset [1525] by Gregory Vincic
Adding Image, and RawBioAssayParameters?
1:07 PM Changeset [1524] by Johan Enell
RawDataFlatFileImporter? imports data

Oct 25, 2005:

4:51 PM Changeset [1523] by Johan Enell
RawDataFlatFileImporter? configures and runs TODO: handleData(..)
4:31 PM Changeset [1522] by Johan Enell
changed the validation methods
4:28 PM Changeset [1521] by Johan Enell
changed the batch list creationplace
3:50 PM Changeset [1520] by Nicklas Nordborg
Added query aggregate expression. BioAssay? and BioAssaySet? now count …
1:36 PM Changeset [1519] by Nicklas Nordborg
Creating basic filtered bioassaysets is now working
11:21 AM Changeset [1518] by Nicklas Nordborg
First simple form of a query against the dynamic database is not working
11:12 AM Changeset [1517] by Gregory Vincic
Using the new image file transfer in UploadFileTransfer?
11:11 AM Changeset [1516] by Gregory Vincic
saveItem now expects the item to already be saved to the database
10:40 AM Changeset [1515] by Gregory Vincic
Adding Image file transfer
10:40 AM Changeset [1514] by Gregory Vincic
Adding done() statement
9:42 AM Changeset [1513] by Gregory Vincic
Adding done() statements
9:42 AM Changeset [1512] by Gregory Vincic
Adding getDuration() method
8:48 AM Changeset [1511] by Gregory Vincic
Added missing dependency control for protocolTransfer
8:48 AM Changeset [1510] by Gregory Vincic
Using recursive run(PreparedStatement?,int,int)
8:46 AM Changeset [1509] by Gregory Vincic
getReporterById handles exceptions
8:46 AM Changeset [1508] by Gregory Vincic
itemList is initiated within run(PreparedStatement? ps, int from, int …

Oct 24, 2005:

4:44 PM Changeset [1507] by Gregory Vincic
Adding done() statements
4:28 PM Changeset [1506] by Gregory Vincic
Adding comments and recoding MappedPlateTransfer?.
4:27 PM Changeset [1505] by Gregory Vincic
createItem now returns the created Extract instead of null
4:03 PM Changeset [1504] by Nicklas Nordborg
Added skeleton classes for DynamicQuery? and DynamicResultIterator?.
2:33 PM Changeset [1503] by Nicklas Nordborg
Added SpotBatcher?
11:53 AM Changeset [1502] by Nicklas Nordborg
Linking BioAssaySet?, BioAssay?, DataCube? and DataCubeColumn? and their …
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