#841 |
Change required BASE version to BASE 3.7
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.1
|
net.sf.basedb.reggie
|
#844 |
Switch to Java 8
|
olle
|
enhancement
|
major
|
LabEnv v1.4
|
net.sf.basedb.labenv
|
#845 |
Remove LabEnv references to Reggie
|
olle
|
task
|
major
|
LabEnv v1.4
|
net.sf.basedb.labenv
|
#846 |
Highlight YellowLabel specimen in sample processing wizards
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.1
|
net.sf.basedb.reggie
|
#847 |
Highlight YellowLabel specimen in library preparation wizards
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#848 |
Enabled/disable experimental features in reggie-config.xml
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.1
|
net.sf.basedb.reggie
|
#849 |
Demux wizard doesn't check that items have names that are accepted by downstream analysis steps
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#851 |
Retraction wizard - Step 2: Follow up should allow dates to be set as N/A
|
olle
|
task
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#852 |
Highlight YellowLabel specimen case summary
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#853 |
RNA marked for ReProcess should be auto-selected even if no RNAQC child item exists
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#855 |
Retraction follow-up and destruction wizards should make it easier to select existing cases
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#856 |
Highlight YellowLabel specimen in secondary analysis wizards
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#857 |
Highlight YellowLabel specimen in Flagged RNA wizard
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#858 |
Target volume for NeoPrep should be changed from 45 to 12.5
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.2
|
net.sf.basedb.reggie
|
#860 |
NeoPrep need other barcode variants
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.2.1
|
net.sf.basedb.reggie
|
#861 |
YellowLabel tracking wizard
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#863 |
Secondary analysis scripts should set permissions on created files in ProjectArchive
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#864 |
Implement a service that check and update file permission in ProjectArchive
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#865 |
Stray files wizard
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#867 |
Update SSH library
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#868 |
Update SSH library
|
Nicklas Nordborg
|
enhancement
|
major
|
External files support 1.2
|
net.sf.basedb.xfiles
|
#869 |
Switch to Java 8
|
Nicklas Nordborg
|
task
|
major
|
External files support 1.2
|
net.sf.basedb.xfiles
|
#870 |
Switch to BASE 3.7
|
Nicklas Nordborg
|
task
|
major
|
External files support 1.2
|
net.sf.basedb.xfiles
|
#871 |
NullPointerException when selecting a software item in the gene/pilot report wizard
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.2.1
|
net.sf.basedb.reggie
|
#873 |
Target volume for NeoPrep should be changed from 12.5 to 15
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.2.1
|
net.sf.basedb.reggie
|
#874 |
<reference-gidx> is incorrect in the default reggie-config.xml file
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#875 |
Soft and hard target amount for NeoPrep
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#876 |
NeoPrep library registration without Caliper files
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.3
|
net.sf.basedb.reggie
|
#878 |
The YellowLabel wizard display Library *.dil items instead of Library items
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.3.1
|
net.sf.basedb.reggie
|
#880 |
MeLuDI v.1.4.2 bug fixes and improvements
|
olle
|
task
|
major
|
MeLuDI v1.4.3
|
net.sf.basedb.meludi
|
#883 |
Add support for progress reporting to the Reggie wizard API
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.4
|
net.sf.basedb.reggie
|
#885 |
The ProjectArchive permission checker should use smaller batches with chmod commands
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.4
|
net.sf.basedb.reggie
|
#888 |
INCA statistics
|
olle
|
task
|
major
|
Reggie v4.5
|
net.sf.basedb.reggie
|
#890 |
Remove calls to methods deprecated in BASE 3.9
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.5
|
net.sf.basedb.reggie
|
#892 |
Add support for enforcing YubiKey login depending on client
|
Nicklas Nordborg
|
enhancement
|
major
|
YubiKey v1.3
|
net.sf.basedb.yubikey
|
#893 |
Add support for using login+password+yubikey otp when logging in
|
Nicklas Nordborg
|
enhancement
|
major
|
YubiKey v1.3
|
net.sf.basedb.yubikey
|
#894 |
Update YubiKey JAR file
|
Nicklas Nordborg
|
task
|
major
|
YubiKey v1.3
|
net.sf.basedb.yubikey
|
#895 |
Switch to Java 8 and BASE 3.9
|
Nicklas Nordborg
|
task
|
major
|
YubiKey v1.3
|
net.sf.basedb.yubikey
|
#897 |
Generate SCAN-B referral forms in Reggie
|
olle
|
task
|
major
|
Reggie v4.7
|
net.sf.basedb.reggie
|
#898 |
INCA import should create trimmed tab-delimited file with synonymized data
|
olle
|
task
|
major
|
Reggie v4.6
|
net.sf.basedb.reggie
|
#901 |
Set multiple paths for run-archive
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.6
|
net.sf.basedb.reggie
|
#902 |
Incorrect counter on reggie start page
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.6
|
net.sf.basedb.reggie
|
#906 |
Create alias for Patient, Case, Specimen and Blood items for external use
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.7
|
net.sf.basedb.reggie
|
#908 |
Support for re-processing from lysate
|
Nicklas Nordborg
|
enhancement
|
major
|
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
|
#911 |
MeLuDI should support multiple projects
|
olle
|
task
|
major
|
MeLuDI v1.5.0
|
net.sf.basedb.meludi
|
#914 |
Add more columns to the blacklist
|
Nicklas Nordborg
|
task
|
major
|
INCA XML to CSV converter 1.1
|
net.sf.basedb.inca
|
#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
|
#923 |
Move to Java 8 and BASE 3.10
|
Nicklas Nordborg
|
task
|
major
|
Example code v1.8
|
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
|
#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
|
#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
|
#934 |
Improve API for uploading files
|
Nicklas Nordborg
|
enhancement
|
major
|
Open Grid Scheduler service v1.1
|
net.sf.basedb.opengrid
|
#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
|
#948 |
Can't create mRNA plate with External RNA or Stratagene
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.9.2
|
net.sf.basedb.reggie
|
#949 |
Update SSHj and Bouncy castle
|
Nicklas Nordborg
|
enhancement
|
major
|
External files support 1.3
|
net.sf.basedb.xfiles
|
#950 |
New pool layouts: 1x24 and 2x24 with offset
|
Nicklas Nordborg
|
enhancement
|
major
|
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
|
#956 |
Add support for SHA-256 fingerprints on file servers
|
Nicklas Nordborg
|
enhancement
|
major
|
External files support 1.3
|
net.sf.basedb.xfiles
|
#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
|
#959 |
Switch to BASE 3.11
|
Nicklas Nordborg
|
task
|
major
|
External files support 1.3
|
net.sf.basedb.xfiles
|
#960 |
Switch to BASE 3.11
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.10
|
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
|
#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
|
#971 |
Storage box creation wizard
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.11
|
net.sf.basedb.reggie
|
#974 |
A project should not be required
|
olle
|
task
|
major
|
LabEnv v1.6
|
net.sf.basedb.labenv
|
#975 |
Clean up unused javascript code
|
olle
|
task
|
major
|
LabEnv v1.6
|
net.sf.basedb.labenv
|
#976 |
Running 'ant update-version' doesn't update the version number in labenv.js
|
olle
|
defect
|
major
|
LabEnv v1.6
|
net.sf.basedb.labenv
|
#977 |
Re-design the Lab-sensor info page
|
olle
|
enhancement
|
major
|
LabEnv v1.6
|
net.sf.basedb.labenv
|
#978 |
Re-design the Lab sensor alarms page
|
olle
|
enhancement
|
major
|
LabEnv v1.6
|
net.sf.basedb.labenv
|
#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
|
#987 |
Cohort exporter plugin
|
Nicklas Nordborg
|
task
|
major
|
Relax v1.1
|
net.sf.basedb.relax
|
#988 |
New pool layout: 2x16 with offset
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.11
|
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
|
#996 |
The project archive service is running to often
|
Nicklas Nordborg
|
defect
|
major
|
Reggie v4.11.2
|
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
|
#1003 |
Add support for disabling/pausing a pipeline
|
Nicklas Nordborg
|
enhancement
|
major
|
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
|
#1006 |
External data filtering and mapping wizard
|
Nicklas Nordborg
|
task
|
major
|
Relax v1.1
|
net.sf.basedb.relax
|
#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
|
#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
|
#1009 |
Genotype quality control wizard
|
Nicklas Nordborg
|
task
|
major
|
Reggie v4.15
|
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
|
#1015 |
Add masking step to Hisat pipeline
|
Nicklas Nordborg
|
enhancement
|
major
|
Reggie v4.15
|
net.sf.basedb.reggie
|