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Ticket Summary Owner Type Priority Milestone Component
#909 All counters disappear if the ProjectArchive server is not available Nicklas Nordborg defect minor Reggie v4.7 net.sf.basedb.reggie
#910 The Mark extracts for retraction wizard doesn't find all items in some cases Nicklas Nordborg defect major Reggie v4.7 net.sf.basedb.reggie
#912 Fix report delivery system Nicklas Nordborg defect critical Reggie v4.7.1 net.sf.basedb.reggie
#914 Add more columns to the blacklist Nicklas Nordborg task major INCA XML to CSV converter 1.1 net.sf.basedb.inca
#913 Implement a set of wizards for handling outtakes Nicklas Nordborg task critical Reggie v4.8 net.sf.basedb.reggie
#915 The AutoProcessing annotation is not reset after re-processing lysate Nicklas Nordborg defect major Reggie v4.8 net.sf.basedb.reggie
#916 The consent count report should not include all consents without date Nicklas Nordborg enhancement major Reggie v4.8 net.sf.basedb.reggie
#917 Add downloaded colum to yellow label tracking wizard Nicklas Nordborg enhancement major Reggie v4.8 net.sf.basedb.reggie
#918 Make it possible to filter on the Name column in the YellowLabel tracking wizard Nicklas Nordborg enhancement minor Reggie v4.8 net.sf.basedb.reggie
#920 GUI changes to delivery client Nicklas Nordborg enhancement minor Reggie v4.8 net.sf.basedb.reggie
#904 Implement an Open Grid Scheduler service extension Nicklas Nordborg task critical Open Grid Scheduler service v1.0 net.sf.basedb.opengrid
#905 Move Open Grid Scheduler functionality to a separate extension Nicklas Nordborg task critical Reggie v4.9 net.sf.basedb.reggie
#921 Delivery client should set session control in <base:page> taglib Nicklas Nordborg enhancement trivial Reggie v4.9 net.sf.basedb.reggie
#924 The progress bar may hide the final status message in wizards Nicklas Nordborg enhancement minor Reggie v4.9 net.sf.basedb.reggie
#925 Item not found: Group[....] in "Mark extracts for retraction" wizard Nicklas Nordborg defect minor Reggie v4.9 net.sf.basedb.reggie
#926 SCAN-B referral form generation improvements in Reggie olle task major Reggie v4.9 net.sf.basedb.reggie
#928 Define job subtypes and use them on Open Grid jobs Nicklas Nordborg enhancement major Reggie v4.9 net.sf.basedb.reggie
#929 The "All cases" field display null when running the Mark extracts for retraction wizard on a case with consent=no Nicklas Nordborg defect minor Reggie v4.9 net.sf.basedb.reggie
#930 The "Register sequencing started" may register without a start date Nicklas Nordborg defect minor Reggie v4.9 net.sf.basedb.reggie
#931 The "Register sequencing started" can't register if no analysis cluster is available Nicklas Nordborg defect major Reggie v4.9 net.sf.basedb.reggie
#932 Retraction wizard should be able to handle cases that only holds a consent Nicklas Nordborg defect major Reggie v4.9 net.sf.basedb.reggie
#922 Create an example of a custom extension point Nicklas Nordborg task critical Example code v1.8 net.sf.basedb.examplecode
#923 Move to Java 8 and BASE 3.10 Nicklas Nordborg task major Example code v1.8 net.sf.basedb.reggie
#935 The "Re-create report PDF" function doesn't work if raw bioassay is created after 2016-12-31 Nicklas Nordborg defect major Reggie v4.9.1 net.sf.basedb.reggie
#936 Improve the display of "Missing" in the YellowLabel tracking wizard Nicklas Nordborg enhancement minor Reggie v4.9.1 net.sf.basedb.reggie
#937 Improve filters in YellowLabel tracking wizard Nicklas Nordborg enhancement minor Reggie v4.9.1 net.sf.basedb.reggie
#942 Manually registering a sequencing as ended changes the job status to ERROR Nicklas Nordborg defect minor Reggie v4.9.1 net.sf.basedb.reggie
#944 Some sections in the installation wizard are hidden Nicklas Nordborg enhancement minor Reggie v4.9.1 net.sf.basedb.reggie
#947 Demux fails if all barcodes have been used Nicklas Nordborg defect critical Reggie v4.9.2 net.sf.basedb.reggie
#948 Can't create mRNA plate with External RNA or Stratagene Nicklas Nordborg defect major Reggie v4.9.2 net.sf.basedb.reggie
#950 New pool layouts: 1x24 and 2x24 with offset Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#951 BA PDF file should be optional in the "mRNA registration and quality control results" wizard Nicklas Nordborg enhancement minor Reggie v4.9.3 net.sf.basedb.reggie
#952 The "Register Caliper files" checkbox in the "Library registration" registration wizard should be unchecked by default Nicklas Nordborg enhancement trivial Reggie v4.9.3 net.sf.basedb.reggie
#953 Remove "unmapped.bam" file from Tophat results Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#954 The AddOrReplaceReadGroup step in Tophat alignment should replace SCAN-B ids with external id Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#955 fix_cufflinks_tracking_id.sh should be executed on transcripts.gtf Nicklas Nordborg enhancement major Reggie v4.9.3 net.sf.basedb.reggie
#963 The retraction wizard can't delete top-level data folder in project archive Nicklas Nordborg defect major Reggie v4.9.4 net.sf.basedb.reggie
#964 Mark extracts for retraction wizard should set consent=no on all cases and blood items related to the patient Nicklas Nordborg enhancement major Reggie v4.9.4 net.sf.basedb.reggie
#965 Retraction destruction wizard should set consent date to today on the new case item Nicklas Nordborg enhancement major Reggie v4.9.4 net.sf.basedb.reggie
#966 Monthly operation list export and INCA export should not include items with consent=no Nicklas Nordborg enhancement major Reggie v4.9.4 net.sf.basedb.reggie
#949 Update SSHj and Bouncy castle Nicklas Nordborg enhancement major External files support 1.3 net.sf.basedb.xfiles
#956 Add support for SHA-256 fingerprints on file servers Nicklas Nordborg enhancement major External files support 1.3 net.sf.basedb.xfiles
#959 Switch to BASE 3.11 Nicklas Nordborg task major External files support 1.3 net.sf.basedb.xfiles
#934 Improve API for uploading files Nicklas Nordborg enhancement major Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#943 Incorrect default value for <tmp-folder> in opengrid-config.xml defect trivial Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#957 Add support for SHA-256 fingerprints on file servers enhancement major Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#958 Switch to BASE 3.11 task major Open Grid Scheduler service v1.1 net.sf.basedb.opengrid
#946 Yubikey styelsheet is missing on the login page Nicklas Nordborg defect trivial YubiKey v1.4 net.sf.basedb.yubikey
#933 Add support for exporting files to a remote server to the Release exporter plug-in Nicklas Nordborg enhancement major Reggie v4.10 net.sf.basedb.reggie
#938 Release exporter should export files that can be imported on a different server Nicklas Nordborg enhancement critical Reggie v4.10 net.sf.basedb.reggie
#945 Re-design the installation wizard Nicklas Nordborg enhancement minor Reggie v4.10 net.sf.basedb.reggie
#960 Switch to BASE 3.11 Nicklas Nordborg task major Reggie v4.10 net.sf.basedb.reggie
#961 The partition wizard should set MultPieces to false if the checkbox is not checked Nicklas Nordborg enhancement minor Reggie v4.10 net.sf.basedb.reggie
#962 Add ReferenceDate annotation to Case Nicklas Nordborg task critical Reggie v4.10 net.sf.basedb.reggie
#967 Misaligned table columns in retraction follow up wizard Nicklas Nordborg defect trivial Reggie v4.10 net.sf.basedb.reggie
#968 Keep LiasonComment in some cases when destructing retracted items Nicklas Nordborg enhancement major Reggie v4.10 net.sf.basedb.reggie
#969 Changes to Frozen tissue date import wizard Nicklas Nordborg enhancement major Reggie v4.10 net.sf.basedb.reggie
#970 Specimen tube registration: Limit the value in "Number of tubes" to a single digit Nicklas Nordborg enhancement minor Reggie v4.10 net.sf.basedb.reggie
#972 Fix problems with bad URLs Nicklas Nordborg defect critical Reggie v4.10 net.sf.basedb.reggie
#939 Installation wizard for Relax server Nicklas Nordborg task critical Relax v1.0 net.sf.basedb.relax
#940 Release importer Nicklas Nordborg task critical Relax v1.0 net.sf.basedb.relax
#941 Create the Relax extension Nicklas Nordborg task critical Relax v1.0 net.sf.basedb.relax
#971 Storage box creation wizard Nicklas Nordborg task major Reggie v4.11 net.sf.basedb.reggie
#979 Define and import Pilot report annotations Nicklas Nordborg task major Reggie v4.11 net.sf.basedb.reggie
#980 Remove Tophat-alignment data files from release exporter Nicklas Nordborg enhancement major Reggie v4.11 net.sf.basedb.reggie
#981 Project archive need to use subfolders per site Nicklas Nordborg enhancement major Reggie v4.11 net.sf.basedb.reggie
#982 Re-design the current pipeline Nicklas Nordborg task blocker Reggie v4.11 net.sf.basedb.reggie
#983 Merge the Tophat alignment and Cufflinks job to a single job Nicklas Nordborg task critical Reggie v4.11 net.sf.basedb.reggie
#984 Remove the raw data import step for Cufflinks data Nicklas Nordborg task critical Reggie v4.11 net.sf.basedb.reggie
#985 Re-design the gene report generator so that it can produce the report using data from the cufflinks file Nicklas Nordborg task critical Reggie v4.11 net.sf.basedb.reggie
#986 Redesign the release exporter plug-in to make the cohort tables optional Nicklas Nordborg enhancement minor Reggie v4.11 net.sf.basedb.reggie
#988 New pool layout: 2x16 with offset Nicklas Nordborg enhancement major Reggie v4.11 net.sf.basedb.reggie
#989 Installation of Reggie 4.11 fails Nicklas Nordborg defect blocker Reggie v4.11.1 net.sf.basedb.reggie
#990 Release exporter looks for files in incorrect directory Nicklas Nordborg defect critical Reggie v4.11.2 net.sf.basedb.reggie
#991 Add "unclassified" to list of allowed values for the PILOT_Subtype annotation Nicklas Nordborg defect minor Reggie v4.11.2 net.sf.basedb.reggie
#992 NotEnoughRemainingQuantity in some cases when the remaining quantity is between the soft and hard target amounts Nicklas Nordborg defect major Reggie v4.11.2 net.sf.basedb.reggie
#993 Relative dates can be incorrect due to daylight savings time Nicklas Nordborg defect major Reggie v4.11.2 net.sf.basedb.reggie
#995 Project archive files are lacking access permission Nicklas Nordborg defect critical Reggie v4.11.2 net.sf.basedb.reggie
#996 The project archive service is running to often Nicklas Nordborg defect major Reggie v4.11.2 net.sf.basedb.reggie
#998 Fix problems with unselected list items Nicklas Nordborg defect blocker Reggie v4.11.3 net.sf.basedb.reggie
#999 Release exporter need to match Histology item based on partition date Nicklas Nordborg defect critical Reggie v4.11.3 net.sf.basedb.reggie
#997 Implement new secondary analysis pipeline Nicklas Nordborg task critical Reggie v4.12 net.sf.basedb.reggie
#1000 The release exporter should be able to export more raw bioassay annotations Nicklas Nordborg enhancement major Reggie v4.12 net.sf.basedb.reggie
#1001 Add HaplotypeCaller to Hisat align step Nicklas Nordborg enhancement major Reggie v4.13 net.sf.basedb.reggie
#1002 The release exporter should ignore directories and files that it has not permission to read Nicklas Nordborg defect minor Reggie v4.13 net.sf.basedb.reggie
#1003 Add support for disabling/pausing a pipeline Nicklas Nordborg enhancement major Reggie v4.13 net.sf.basedb.reggie
#1004 Auto-confirmation after demux should start Tophat/Hisat jobs independently of each other Nicklas Nordborg enhancement minor Reggie v4.13 net.sf.basedb.reggie
#1005 External data filtering and mapping wizard Nicklas Nordborg task major Reggie v4.13 net.sf.basedb.reggie
#1007 The release exporter should sort raw bioassay by external id when the "Use external ID" options is active Nicklas Nordborg enhancement major Reggie v4.13 net.sf.basedb.reggie
#987 Cohort exporter plugin Nicklas Nordborg task major Relax v1.1 net.sf.basedb.relax
#994 Level 3 exporter Nicklas Nordborg task critical Relax v1.1 net.sf.basedb.relax
#1006 External data filtering and mapping wizard Nicklas Nordborg task major Relax v1.1 net.sf.basedb.relax
#1008 The release exporter should be able to export expression data from the cufflinks file Nicklas Nordborg enhancement major Reggie v4.14 net.sf.basedb.reggie
#1010 2by16offset is missing from PoolSchema annotation Nicklas Nordborg defect minor Reggie v4.14 net.sf.basedb.reggie
#1011 Demux warning about a library with low PF_READS should include barcode Nicklas Nordborg enhancement minor Reggie v4.14 net.sf.basedb.reggie
#1012 Stratagene secondary analysis data files should be saved to the external archive Nicklas Nordborg enhancement minor Reggie v4.14 net.sf.basedb.reggie
#1013 Not enough RNA in some cases when the remaining quantity is between soft and hard target amount Nicklas Nordborg defect major Reggie v4.14 net.sf.basedb.reggie
#1014 Add column definition for "LibPlate" to derived bioassays and raw bioassays list pages Nicklas Nordborg enhancement major Reggie v4.14 net.sf.basedb.reggie
#1009 Genotype quality control wizard Nicklas Nordborg task major Reggie v4.15 net.sf.basedb.reggie
#1015 Add masking step to Hisat pipeline Nicklas Nordborg enhancement major Reggie v4.15 net.sf.basedb.reggie
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