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Ticket Summary Owner Type Priority Milestone Component
#716 Add support for Reggie to the gold skin enhancement major Skin-collection 1.1 net.sf.basedb.skincollection
#707 Switch to Slf4j Nicklas Nordborg enhancement major Example code v1.7 net.sf.basedb.examplecode
#708 Add example skin Nicklas Nordborg task major Example code v1.7 net.sf.basedb.examplecode
#606 Switch to JDOM 2 Nicklas Nordborg task minor LabEnv v1.3 net.sf.basedb.labenv
#608 Update Labenv to new scripting pattern olle enhancement major LabEnv v1.3 net.sf.basedb.labenv
#706 Update LabEnv to use BASE database capabilties instead of SQLite Nicklas Nordborg task major LabEnv v1.3 net.sf.basedb.labenv
#714 Get rid of warning messages from HttpMethodBase olle enhancement minor LabEnv v1.3 net.sf.basedb.labenv
#715 Do not query the sensor for it's name every time olle enhancement minor LabEnv v1.3 net.sf.basedb.labenv
#703 Make print package compatible with skins Nicklas Nordborg enhancement major Print package v1.2 net.sf.basedb.print
#605 Switch to JDOM 2 Nicklas Nordborg task major Reggie v3.0 net.sf.basedb.reggie
#702 Use skin features in BASE 3.4 Nicklas Nordborg enhancement major Reggie v3.0 net.sf.basedb.reggie
#709 Depend on BASE 3.4 Nicklas Nordborg task critical Reggie v3.0 net.sf.basedb.reggie
#717 Auto-confirmation service Nicklas Nordborg task critical Reggie v3.0 net.sf.basedb.reggie
#720 Change major Reggie version to 3 Nicklas Nordborg enhancement major Reggie v3.0 net.sf.basedb.reggie
#721 Item not found: BioMaterialList[id=0] when trying to download HE glass labels Nicklas Nordborg defect minor Reggie v3.0 net.sf.basedb.reggie
#722 The count for Gene report wizard doesn't decrease after starting gene report Nicklas Nordborg defect minor Reggie v3.0 net.sf.basedb.reggie
#723 Retraction wizard - Step 2: Follow up olle task major Reggie v3.0 net.sf.basedb.reggie
#724 Summary counts on index page Nicklas Nordborg task minor Reggie v3.0 net.sf.basedb.reggie
#726 Improve performance of counter on index page Nicklas Nordborg enhancement major Reggie v3.0 net.sf.basedb.reggie
#629 Use annotations on protocols in the demux and mask/align step to set some program parameters Nicklas Nordborg enhancement major Reggie v3.1 net.sf.basedb.reggie
#730 Set target molarity in "Create pooled libraries" wizard Nicklas Nordborg enhancement major Reggie v3.1 net.sf.basedb.reggie
#731 Installation wizard should enable AutoProcessing annotation for raw bioassays Nicklas Nordborg defect trivial Reggie v3.1 net.sf.basedb.reggie
#732 Software item on aligned sequences is not set Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#733 The create pools wizard create pools with roman numerals as name Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#734 The create new mRNA plate wizard should reset RNA marked for re-processing Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#735 Can't modify number of slides created in the HE glass registration wizard Nicklas Nordborg defect major Reggie v3.1 net.sf.basedb.reggie
#736 Some HE glass may be stained with something else than HE Nicklas Nordborg enhancement major Reggie v3.1 net.sf.basedb.reggie
#737 Show last update date+time for counters Nicklas Nordborg enhancement minor Reggie v3.1 net.sf.basedb.reggie
#729 Check YubiKey password before user password Nicklas Nordborg enhancement critical YubiKey v1.2 net.sf.basedb.yubikey
#455 Flagged RNA re-processing wizard Nicklas Nordborg task major Reggie v3.2 net.sf.basedb.reggie
#738 Remove Cufflinks code from AlignJobCreator Nicklas Nordborg defect minor Reggie v3.2 net.sf.basedb.reggie
#739 Gene report doesn't pick up default path to template.pdf Nicklas Nordborg defect minor Reggie v3.2 net.sf.basedb.reggie
#740 Add support for reprocessing specimen Nicklas Nordborg task critical Reggie v3.2 net.sf.basedb.reggie
#741 AutoProcessing flag remains set on raw bioassays Nicklas Nordborg defect minor Reggie v3.2 net.sf.basedb.reggie
#742 Detect tiles with empty barcode files Nicklas Nordborg task major Reggie v3.2 net.sf.basedb.reggie
#743 The second trimmomatic step in demux script may not include options Nicklas Nordborg defect trivial Reggie v3.2 net.sf.basedb.reggie
#744 Lab protocol for RNAQC on BioAnalyzer Nicklas Nordborg task minor Reggie v3.2 net.sf.basedb.reggie
#745 Incorrect QiaCube positions in DNA/RNA/FlowThrough registration wizard Nicklas Nordborg defect minor Reggie v3.2 net.sf.basedb.reggie
#746 IHC-quality annotation Nicklas Nordborg enhancement major Reggie v3.2 net.sf.basedb.reggie
#747 Label file generated by the partition wizard should have even number of lables for each specimen Nicklas Nordborg enhancement minor Reggie v3.2 net.sf.basedb.reggie
#748 DNA/RNA/FlowThrough registration should have an option to load latest lot number Nicklas Nordborg enhancement minor Reggie v3.2 net.sf.basedb.reggie
#751 Set max-base-version to 3.5.0 Nicklas Nordborg task minor Reggie v3.2 net.sf.basedb.reggie
#725 MeLuDi v.1.1 bug fixes and improvements olle task major MeLuDi v1.2 net.sf.basedb.meludi
#753 Case summary breaks if no stained histology has GoodStain Nicklas Nordborg defect critical Reggie v3.2.1 net.sf.basedb.reggie
#754 Make case summary display more tolerant aginst problems Nicklas Nordborg enhancement major Reggie v3.2.1 net.sf.basedb.reggie
#755 Display unit for PF_READS in "Confirm demux" wizard Nicklas Nordborg enhancement minor Reggie v3.2.1 net.sf.basedb.reggie
#756 Display numbers with two decimals in the Flagged RNA wizard Nicklas Nordborg enhancement major Reggie v3.2.1 net.sf.basedb.reggie
#757 Some latest RNAQC items are not fetched in the Flagged RNA wizard Nicklas Nordborg defect critical Reggie v3.2.1 net.sf.basedb.reggie
#758 Open grid sceduler jobs with no job id in BASE Nicklas Nordborg defect major Reggie v3.2.1 net.sf.basedb.reggie
#760 Prepare for adding help texts in reggie wizards Nicklas Nordborg task trivial Reggie v3.2.1 net.sf.basedb.reggie
#759 MeLuDi v.1.2 bug fixes and improvements olle task major MeLuDI v1.2.1 net.sf.basedb.meludi
#765 Add 3x16 pool schema to create mRNA plate wizard Nicklas Nordborg enhancement major Reggie v3.2.2 net.sf.basedb.reggie
#766 The popup menu in the Assign barcode wizard is transparent Nicklas Nordborg defect minor Reggie v3.2.2 net.sf.basedb.reggie
#767 MeLuDI v.1.2.1 bug fixes and improvements olle task major MeLuDI v1.2.2 net.sf.basedb.meludi
#750 Changes required for BASE version 3.5 Nicklas Nordborg task blocker Reggie v3.3 net.sf.basedb.reggie
#761 Improve printing lists with multiple filter rows Nicklas Nordborg enhancement minor Print package v1.3 net.sf.basedb.print
#774 Comment for bioplate in mRNA registration is not updated Nicklas Nordborg defect major Reggie v3.3.1 net.sf.basedb.reggie
#775 Histology scoring wizard does not work Nicklas Nordborg defect critical Reggie v3.3.1 net.sf.basedb.reggie
#768 MeLuDI v.1.2.2 bug fixes and improvements olle task major MeLuDI v1.2.3 net.sf.basedb.meludi
#778 Can't create manual pool when there is no plate waiting Nicklas Nordborg defect critical Reggie v3.3.2 net.sf.basedb.reggie
#784 Can't create new histology work list Nicklas Nordborg defect critical Reggie v3.3.3 net.sf.basedb.reggie
#777 MeLuDI v.1.2.3 bug fixes and improvements olle task major MeLuDI v1.2.4 net.sf.basedb.meludi
#786 MeLuDI v.1.2.4 bug fixes and improvements olle task major MeLuDI v1.2.5 net.sf.basedb.meludi
#762 Pre-normalization changes due to NeoPrep Nicklas Nordborg task major Reggie v3.4 net.sf.basedb.reggie
#763 Change limit for NotEnoughRemaininQuantity flag in the extraction wizard Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#764 Support for neoprep in the library preparation Nicklas Nordborg task major Reggie v3.4 net.sf.basedb.reggie
#769 Retraction wizard - Additions to Step 2: Follow up olle task major Reggie v3.4 net.sf.basedb.reggie
#773 The mRNA wizard must be smarter when auto-selecting pre-normalized RNA Nicklas Nordborg enhancement critical Reggie v3.4 net.sf.basedb.reggie
#776 An old storage box position can be re-used for new specimens Nicklas Nordborg defect critical Reggie v3.4 net.sf.basedb.reggie
#779 Librararies with very high molarity gives "Low molarity" warning in pooling wizard Nicklas Nordborg defect major Reggie v3.4 net.sf.basedb.reggie
#780 Redesign Reggie start page Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#781 Clean up code in retraction wizard Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#787 Add support for BloodDNA items olle task major Reggie v3.4 net.sf.basedb.reggie
#788 NullPointerException when registering libraries Nicklas Nordborg defect minor Reggie v3.4 net.sf.basedb.reggie
#791 Upload microscope images in the histology scoring wizard Nicklas Nordborg enhancement major Reggie v3.4 net.sf.basedb.reggie
#793 Implement thumbnails for PNG and JPG images Nicklas Nordborg task critical Thumbnails v1.0 net.sf.basedb.thumbnails
#797 Implement thumbnails for PDF documents Nicklas Nordborg task major Thumbnails v1.0 net.sf.basedb.thumbnails
#792 MeLuDI v.1.2.5 bug fixes and improvements olle task major MeLuDI v1.3.1 net.sf.basedb.meludi
#749 Allow extraction of less than 12 samples Nicklas Nordborg enhancement minor Reggie v3.5 net.sf.basedb.reggie
#772 New sample annotation (LinkedSpecimen) to highlight prior specimen Nicklas Nordborg task major Reggie v3.5 net.sf.basedb.reggie
#790 Add new site: Jönköping Nicklas Nordborg task major Reggie v3.5 net.sf.basedb.reggie
#794 Improve visual difference between samples missing/having IHC annotation Nicklas Nordborg enhancement minor Reggie v3.5 net.sf.basedb.reggie
#795 Display image thumbnails in list view for stained samples Nicklas Nordborg enhancement major Reggie v3.5 net.sf.basedb.reggie
#796 Filter on image present/not present for stained samples Nicklas Nordborg enhancement major Reggie v3.5 net.sf.basedb.reggie
#798 Display thumbnail of gene report pdf in raw bioassays list and view page Nicklas Nordborg enhancement minor Reggie v3.5 net.sf.basedb.reggie
#799 TypeError: bestStain is null in case summary Jari Häkkinen defect minor Reggie v3.5 net.sf.basedb.reggie
#800 Add counter for total number of scored histology samples Nicklas Nordborg enhancement minor Reggie v3.5 net.sf.basedb.reggie
#803 Handle NanoDrop concentrations < 0 Nicklas Nordborg enhancement minor Reggie v3.5 net.sf.basedb.reggie
#804 Lab tracking protocol for Allprep isolation should include volume of RNAse free water Nicklas Nordborg enhancement major Reggie v3.6 net.sf.basedb.reggie
#805 LinkedSpecimen should set value for items with missing date Nicklas Nordborg enhancement minor Reggie v3.6 net.sf.basedb.reggie
#806 Confirmation wizards fail to report problems with deleting items as errors Nicklas Nordborg enhancement major Reggie v3.6 net.sf.basedb.reggie
#807 Flag RNA checkboxes should not be checked when inactive Nicklas Nordborg enhancement minor Reggie v3.6 net.sf.basedb.reggie
#808 Import wizard for frozen tissue dates Nicklas Nordborg enhancement major Reggie v3.6 net.sf.basedb.reggie
#809 Improve performance of demux+merge step Nicklas Nordborg enhancement critical Reggie v3.6 net.sf.basedb.reggie
#813 IndexOutOfBoundsException when selecting 7 lysates in the Lab Tracking Protocol for Allprep isolation wizard Nicklas Nordborg defect critical Reggie v3.6.1 net.sf.basedb.reggie
#802 MeLuDI v.1.3.1 bug fixes and improvements olle task major MeLuDI v1.3.2 net.sf.basedb.meludi
#815 MeLuDI v.1.3.2 bug fixes and improvements olle task major MeLuDI v1.3.3 net.sf.basedb.meludi
#810 Gene report combiner plug-in should be able to combine to a zip file Nicklas Nordborg enhancement major Reggie v3.7 net.sf.basedb.reggie
#811 Add support for adding personal information to the Gene report combiner plug-in Nicklas Nordborg enhancement major Reggie v3.7 net.sf.basedb.reggie
#812 Pilot report wizard Nicklas Nordborg task critical Reggie v3.7 net.sf.basedb.reggie
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