Timeline



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 …

Oct 21, 2005:

3:01 PM Changeset [1501] by Nicklas Nordborg
Start linking BioAssaySet? to DataCube? Added DataCubeLayer? and …
10:36 AM Changeset [1500] by Nicklas Nordborg
Postgres is now fully working.

Oct 20, 2005:

8:40 PM Changeset [1499] by Nicklas Nordborg
Added BioAssay? More implementation of Experiment, Transformation and …
1:36 PM Changeset [1498] by Gregory Vincic
Documenting
11:42 AM Changeset [1497] by Gregory Vincic
Added prepareStatement() method
11:03 AM Changeset [1496] by Gregory Vincic
Small fixes here and there
11:02 AM Changeset [1495] by Gregory Vincic
Using itemList to save items
11:01 AM Changeset [1494] by Gregory Vincic
Added done() statement
11:01 AM Changeset [1493] by Gregory Vincic
Removed debug log
11:01 AM Changeset [1492] by Gregory Vincic
Initial revision
11:00 AM Changeset [1491] by Gregory Vincic
Added getById()
10:59 AM Changeset [1490] by Gregory Vincic
Using getSampleById and getAnnotationTypeById
8:53 AM Changeset [1489] by Gregory Vincic
Temporary removal of fileTransfers

Oct 19, 2005:

10:10 PM Changeset [1488] by Gregory Vincic
MeasuredBioMaterials? are not saved anymore during …
10:01 PM Changeset [1487] by Gregory Vincic
Adding done() statement
10:01 PM Changeset [1486] by Gregory Vincic
Progress now indicates number of rows that have been processed even if …
9:55 PM Changeset [1485] by Gregory Vincic
Initial revision
9:55 PM Changeset [1484] by Gregory Vincic
Protocol associated files are now first uploaded with …
3:57 PM Changeset [1483] by Nicklas Nordborg
Added Transformation and BioAssaySet?
3:44 PM Changeset [1482] by Gregory Vincic
Adding done() statement
3:40 PM Changeset [1481] by Gregory Vincic
Id's are now mapped using an wrapper item before saving. After items …
2:38 PM Changeset [1480] by Nicklas Nordborg
Implemented RawBioAssay?.isUsed
2:12 PM Changeset [1479] by Nicklas Nordborg
Test program now test putting raw bioassays in experiments.
12:25 PM Changeset [1478] by Nicklas Nordborg
Added c3p0 connection pool and updated license information for …
11:33 AM Changeset [1477] by Nicklas Nordborg
Added db.dynamic.catalog and db.dynamic.schema options. Added database …

Oct 18, 2005:

3:58 PM Changeset [1476] by Nicklas Nordborg
Added DataCube? Renamed Dynamic* to Virtual* Updated documentation …
11:43 AM Changeset [1475] by Nicklas Nordborg
Implemented dynamic table creation Added PositionBatcher?

Oct 17, 2005:

4:08 PM Changeset [1474] by Nicklas Nordborg
Added DynamicTables? data-, core- and test-layer class, plus supporting …
12:06 PM Changeset [1473] by Nicklas Nordborg
Added ChildItem? and made all child classes extend from this instead of …
9:53 AM Changeset [1472] by Nicklas Nordborg
Added ClassUtil?

Oct 16, 2005:

2:47 AM Changeset [1471] by Jari Häkkinen
Changed repository location.

Oct 14, 2005:

2:56 PM Changeset [1470] by Nicklas Nordborg
Added some data layer classes for experiments and analysis Added core …
11:34 AM Changeset [1469] by Nicklas Nordborg
Removed unneeded import from FileData?
11:23 AM Changeset [1468] by Nicklas Nordborg
Fixed mysterious bug that caused IE to select the wrong property in …
11:08 AM Changeset [1467] by Nicklas Nordborg
Another fix for MySQL/Postgres compatibility
11:07 AM Changeset [1466] by Nicklas Nordborg
Added Postgres driver and fixed some of the bugs having to do with …
10:53 AM Changeset [1465] by Gregory Vincic
createItem(ResultSet?) is no longer abstract
10:19 AM Changeset [1464] by Gregory Vincic
Rewrote createItem and added createImage() method
10:18 AM Changeset [1463] by Gregory Vincic
Adding runUnBatched() method
10:18 AM Changeset [1462] by Gregory Vincic
Fixing bug for empty descriptions

Oct 13, 2005:

8:21 PM Changeset [1461] by Nicklas Nordborg
Updated development status
4:33 PM Changeset [1460] by Gregory Vincic
Assorted changes including itemlist.js
3:31 PM Changeset [1459] by Gregory Vincic
Using new progress and MappedPlateTransfer? now uses one progress for …
2:36 PM Changeset [1458] by Gregory Vincic
Using threaded progress report
2:36 PM Changeset [1457] by Gregory Vincic
Removing old progress methods dot, firstdot and lastdot
2:33 PM Changeset [1456] by Gregory Vincic
Initial revision of ProgressThread?.
2:31 PM Changeset [1455] by Nicklas Nordborg
Updated to Hibernate 3.1 and changed DataQuery? to use stateless …
11:18 AM Changeset [1454] by Gregory Vincic
Making class public
11:18 AM Changeset [1453] by Gregory Vincic
Making it possible to dump resultset on error
11:17 AM Changeset [1452] by Gregory Vincic
Adding logging
11:16 AM Changeset [1451] by Gregory Vincic
Fixing permission denied problem for existing files
11:16 AM Changeset [1450] by Gregory Vincic
Removing unused methods
11:15 AM Changeset [1449] by Gregory Vincic
Adding log method which dumps a ResultSet?
11:14 AM Changeset [1448] by Gregory Vincic
Making class public

Oct 12, 2005:

2:50 PM Changeset [1447] by Nicklas Nordborg
Ok, here is the Batcher again
2:49 PM Changeset [1446] by Nicklas Nordborg
Added Batcher interface changed DbControl? to use it instead of the …
2:39 PM Changeset [1445] by Nicklas Nordborg
FileUtil?.getDirectoryTree now loads shared/others directories as well
12:03 PM Changeset [1444] by Nicklas Nordborg
Fixed bug in AbstractEntityQuery? that ignored Query.setFirstResult …
11:59 AM Changeset [1443] by Nicklas Nordborg
Added QueryRuntimeFilterManager? to make it easier to enable/disable …
11:55 AM Changeset [1442] by Nicklas Nordborg
Added generics parameter to FeatureBatcher?.
10:41 AM Changeset [1441] by Nicklas Nordborg
Query API documentation and it's javadoc is now finished
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