

@1575

18 years 
Nicklas Nordborg 
Added IntensityCalculatorUtil? and other classes needed by it: …



@1574

18 years 
Gregory Vincic 
Added protocol column



@1573

18 years 
Gregory Vincic 
Fixed old queries, default listing of scans now works



@1572

18 years 
Gregory Vincic 
Documenting



@1571

18 years 
Gregory Vincic 
Added migration of reportermap



@1570

18 years 
Gregory Vincic 
Initial revision of WizzzardTransfer?



@1569

18 years 
Gregory Vincic 
Fixed quota using new byteQuota in base schemaVersion 1.2.20



@1568

18 years 
Johan Enell 
PlateFlatFileImporter? complete



@1567

18 years 
Nicklas Nordborg 
Updated javadoc and clean up the code
Added BioAssaySet?.getPositionData



@1566

18 years 
Nicklas Nordborg 
Extra values can now be selected by queries



@1565

18 years 
Nicklas Nordborg 
Small redesign of extra values: Added ExtraValue? class.
DynamicQuery? …



@1564

18 years 
Jari Häkkinen 
Fixed typos.



@1563

18 years 
Gregory Vincic 
Removing feature to delete files if transfer successful



@1562

18 years 
Nicklas Nordborg 
Added PositionExtraValueBatcher? and updated dynamic batch
documentation



@1561

18 years 
Gregory Vincic 
Added schema version control and uncommented plugin related roles. …



@1560

18 years 
Jari Häkkinen 
Added instructions on how to install from a source package, or a …



@1559

18 years 
Jari Häkkinen 
Improved installation documentation.



@1558

18 years 
Jari Häkkinen 
Added info about the trac pages, also made demo servers to open in a …



@1557

18 years 
Johan Enell 
PlateFlatFileImporter?
first draft



@1556

18 years 
Nicklas Nordborg 
Updated some documentation for extra value batching
Added …



@1555

18 years 
Nicklas Nordborg 
Added SpotExtraValueBatcher? and other needed classes for it.



@1554

18 years 
Johan Enell 
removed all set methods from the parameter types and made the …



@1553

18 years 
Gregory Vincic 
Documenting and refactoring some DbControl? variables



@1552

18 years 
Nicklas Nordborg 
Updated documentation for Dynamic API



@1551

18 years 
Gregory Vincic 
Fixed ArrayBlock? transfer which now saves Features properly. …



@1550

18 years 
Johan Enell 
just corrected a small typo



@1549

18 years 
Nicklas Nordborg 
RawDataBatcher? now looks for Affy featues in the AffyFeatures? table …



@1548

18 years 
Gregory Vincic 
Initial revision of ArrayBlockTransfer?. Added includeArrayBlock = yes …



@1547

18 years 
Gregory Vincic 
Added experimental localMySQL transfer and a seperated …



@1546

18 years 
Gregory Vincic 
Initial revision of ArrayTypePlateTransfer?



@1545

18 years 
Nicklas Nordborg 
Fixed problem with DataQuery? not working when multiple raw data types …



@1544

18 years 
Nicklas Nordborg 
DynamicQuery? can now join raw data



@1543

18 years 
Gregory Vincic 
Initial revision of ArrayType?



@1542

18 years 
Nicklas Nordborg 
DynamiQuery? now supports parameters and limits



@1541

18 years 
Nicklas Nordborg 
Started to investigate how limits should be implemented in dynamic queries.



@1540

18 years 
Nicklas Nordborg 
DynamicQuery? may now join the reporters table



@1539

18 years 
Johan Enell 
changed RawBioAssay? header value from varchar(255) to text



@1538

18 years 
Nicklas Nordborg 
Implemented delete operation for BioAssaySet?, Transformation and VirtualDb?



@1537

18 years 
Nicklas Nordborg 
Added support for deleting DataCube?, DataCubeLayer? and DataCubeFilter? …



@1536

18 years 
Johan Enell 
handleHeader added



@1535

18 years 
Johan Enell 
added some javadoc



@1534

18 years 
Johan Enell 
RawDataFlatFileImporter? is operational



@1533

18 years 
Nicklas Nordborg 
Dynamic batchers now updates the disk usage of the experiment.



@1532

18 years 
Gregory Vincic 
Quick transfer is now configurable for testing purposes. Added some …



@1531

18 years 
Nicklas Nordborg 
Fixed problem with closing and flushing of batchers.



@1530

18 years 
Johan Enell 
added a totalinsert counter to the batch system
corected the reporter …



@1529

18 years 
Nicklas Nordborg 
Added w option (wait for keypress before starting to delete items) to …



@1528

18 years 
Nicklas Nordborg 
Added MappingBatcher?



@1527

18 years 
Nicklas Nordborg 
Cleaned up and documented BioAssay?, BioAssaySet?, Experiment, …



@1526

18 years 
Gregory Vincic 
Seperation of RawBioAssay? and it's data into two classes. Also added …



@1525

18 years 
Gregory Vincic 
Adding Image, and RawBioAssayParameters?



@1524

18 years 
Johan Enell 
RawDataFlatFileImporter? imports data



@1523

18 years 
Johan Enell 
RawDataFlatFileImporter? configures and runs
TODO: handleData(..)



@1522

18 years 
Johan Enell 
changed the validation methods



@1521

18 years 
Johan Enell 
changed the batch list creationplace



@1520

18 years 
Nicklas Nordborg 
Added query aggregate expression.
BioAssay? and BioAssaySet? now count …



@1519

18 years 
Nicklas Nordborg 
Creating basic filtered bioassaysets is now working



@1518

18 years 
Nicklas Nordborg 
First simple form of a query against the dynamic database is not working



@1517

18 years 
Gregory Vincic 
Using the new image file transfer in UploadFileTransfer?



@1516

18 years 
Gregory Vincic 
saveItem now expects the item to already be saved to the database



@1515

18 years 
Gregory Vincic 
Adding Image file transfer



@1514

18 years 
Gregory Vincic 
Adding done() statement



@1513

18 years 
Gregory Vincic 
Adding done() statements



@1512

18 years 
Gregory Vincic 
Adding getDuration() method



@1511

18 years 
Gregory Vincic 
Added missing dependency control for protocolTransfer



@1510

18 years 
Gregory Vincic 
Using recursive run(PreparedStatement?,int,int)



@1509

18 years 
Gregory Vincic 
getReporterById handles exceptions



@1508

18 years 
Gregory Vincic 
itemList is initiated within run(PreparedStatement? ps, int from, int …



@1507

18 years 
Gregory Vincic 
Adding done() statements



@1506

18 years 
Gregory Vincic 
Adding comments and recoding MappedPlateTransfer?.



@1505

18 years 
Gregory Vincic 
createItem now returns the created Extract instead of null



@1504

18 years 
Nicklas Nordborg 
Added skeleton classes for DynamicQuery? and DynamicResultIterator?.



@1503

18 years 
Nicklas Nordborg 
Added SpotBatcher?



@1502

18 years 
Nicklas Nordborg 
Linking BioAssaySet?, BioAssay?, DataCube? and DataCubeColumn? and their …



@1501

18 years 
Nicklas Nordborg 
Start linking BioAssaySet? to DataCube?
Added DataCubeLayer? and …



@1500

18 years 
Nicklas Nordborg 
Postgres is now fully working.



@1499

18 years 
Nicklas Nordborg 
Added BioAssay?
More implementation of Experiment, Transformation and …



@1498

18 years 
Gregory Vincic 
Documenting



@1497

18 years 
Gregory Vincic 
Added prepareStatement() method



@1496

18 years 
Gregory Vincic 
Small fixes here and there



@1495

18 years 
Gregory Vincic 
Using itemList to save items



@1494

18 years 
Gregory Vincic 
Added done() statement



@1493

18 years 
Gregory Vincic 
Removed debug log



@1492

18 years 
Gregory Vincic 
Initial revision



@1491

18 years 
Gregory Vincic 
Added getById()



@1490

18 years 
Gregory Vincic 
Using getSampleById and getAnnotationTypeById



@1489

18 years 
Gregory Vincic 
Temporary removal of fileTransfers



@1488

18 years 
Gregory Vincic 
MeasuredBioMaterials? are not saved anymore during …



@1487

18 years 
Gregory Vincic 
Adding done() statement



@1486

18 years 
Gregory Vincic 
Progress now indicates number of rows that have been processed even if …



@1485

18 years 
Gregory Vincic 
Initial revision



@1484

18 years 
Gregory Vincic 
Protocol associated files are now first uploaded with …



@1483

18 years 
Nicklas Nordborg 
Added Transformation and BioAssaySet?



@1482

18 years 
Gregory Vincic 
Adding done() statement



@1481

18 years 
Gregory Vincic 
Id's are now mapped using an wrapper item before saving. After items …



@1480

18 years 
Nicklas Nordborg 
Implemented RawBioAssay?.isUsed



@1479

18 years 
Nicklas Nordborg 
Test program now test putting raw bioassays in experiments.



@1478

18 years 
Nicklas Nordborg 
Added c3p0 connection pool and updated license information
for …



@1477

18 years 
Nicklas Nordborg 
Added db.dynamic.catalog and db.dynamic.schema options.
Added database …



@1476

18 years 
Nicklas Nordborg 
Added DataCube?
Renamed Dynamic* to Virtual*
Updated documentation …


