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Ticket Summary Owner Type Priority Milestone Component
#724 Summary counts on index page Nicklas Nordborg task minor Reggie v3.0 net.sf.basedb.reggie
#737 Show last update date+time for counters Nicklas Nordborg enhancement minor Reggie v3.1 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
#741 AutoProcessing flag remains set on raw bioassays Nicklas Nordborg defect minor 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
#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
#749 Allow extraction of less than 12 samples Nicklas Nordborg enhancement minor Reggie v3.5 net.sf.basedb.reggie
#751 Set max-base-version to 3.5.0 Nicklas Nordborg task minor Reggie v3.2 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
#761 Improve printing lists with multiple filter rows Nicklas Nordborg enhancement minor Print package v1.3 net.sf.basedb.print
#766 The popup menu in the Assign barcode wizard is transparent Nicklas Nordborg defect minor Reggie v3.2.2 net.sf.basedb.reggie
#788 NullPointerException when registering libraries Nicklas Nordborg defect minor Reggie v3.4 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
#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
#805 LinkedSpecimen should set value for items with missing date Nicklas Nordborg enhancement minor 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
#814 New 1x16 pool layout that is offset to the left Nicklas Nordborg enhancement minor Reggie v3.7 net.sf.basedb.reggie
#819 Printable lab protocol from Create aliquots on Bioanalyzer/Caliper plates wizard Nicklas Nordborg enhancement minor Reggie v3.7 net.sf.basedb.reggie
#820 Add "Inconclusive" as an option to the IHCQuality annotation Nicklas Nordborg enhancement minor Reggie v3.7 net.sf.basedb.reggie
#823 Do not include items with only Read permission in selection lists Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#824 fix_tophat_unmapped_reads.py has been renamed to tophat-recondition.py Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#829 Display RNA box position in the lab protocol from "Create aliquots on Bioanalyzer/Caliper plates" wizard Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#831 Losing connection to Open grid cluster Nicklas Nordborg defect minor Reggie v4.0 net.sf.basedb.reggie
#832 Specimen tube registration wizard should create new storage boxes Nicklas Nordborg task minor Reggie v4.0 net.sf.basedb.reggie
#833 The "Plasma/serum" checkbox in the Blood referral form registration wizard (step 3) should not be checked for site '99' Nicklas Nordborg enhancement minor Reggie v4.0 net.sf.basedb.reggie
#839 Change YellowLabel status in "Pathology referral form registration" wizard Nicklas Nordborg enhancement minor Reggie v4.1 net.sf.basedb.reggie
#843 Set <max-base-version> to 3.8.0 olle task minor LabEnv v1.4 net.sf.basedb.labenv
#854 Fix "Remaining quantity" filter in "Manual select" function Nicklas Nordborg defect minor Reggie v4.2 net.sf.basedb.reggie
#859 ProjectArchive should be shared with USE permission to the project Nicklas Nordborg enhancement minor Reggie v4.2 net.sf.basedb.reggie
#862 Import frozen tissue date wizard should have PatientCurator role Nicklas Nordborg defect minor Reggie v4.2.1 net.sf.basedb.reggie
#877 Add counter for consent forms Nicklas Nordborg enhancement minor Reggie v4.3 net.sf.basedb.reggie
#882 It is not possible for a user with PatientCurator role to use the "Re-create report PDFs" button in the YellowLabel wizard Nicklas Nordborg defect minor Reggie v4.4 net.sf.basedb.reggie
#884 Check timeouts for SSH commands Nicklas Nordborg enhancement minor Reggie v4.4 net.sf.basedb.reggie
#896 INCA import should include laterality mapping column olle task minor Reggie v4.6 net.sf.basedb.reggie
#907 Remove code that can create patient items from the follow-up blood registration wizard Nicklas Nordborg enhancement minor Reggie v4.7 net.sf.basedb.reggie
#909 All counters disappear if the ProjectArchive server is not available Nicklas Nordborg defect minor Reggie v4.7 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
#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
#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
#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
#945 Re-design the installation wizard Nicklas Nordborg enhancement minor Reggie v4.10 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
#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
#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
#986 Redesign the release exporter plug-in to make the cohort tables optional Nicklas Nordborg enhancement minor Reggie v4.11 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
#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
#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
#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
#1020 Change novel-splicesite-outfile parameter to Hisat Nicklas Nordborg enhancement minor Reggie v4.15 net.sf.basedb.reggie
#1033 The INCA export wizard should only export personal numbers Nicklas Nordborg enhancement minor Reggie v4.16 net.sf.basedb.reggie
#1040 Set max BASE version to 3.13 Nicklas Nordborg task minor Reggie v4.16 net.sf.basedb.reggie
#1042 The release exporter fails if the release server has a specified port Nicklas Nordborg defect minor Reggie v4.16 net.sf.basedb.reggie
#1045 Display FrozenTissueDate annotation in case summary Nicklas Nordborg enhancement minor Reggie v4.17 net.sf.basedb.reggie
#1047 HaplotypeCaller should be wrapped with stdwrap.sh Nicklas Nordborg enhancement minor Reggie v4.18 net.sf.basedb.reggie
#1052 The FrozenTissueDate importer fails if ProvID is the first or last column Nicklas Nordborg defect minor Reggie v4.18 net.sf.basedb.reggie
#1058 The "Download labels" button in the DNA/RNA/FlowThrough registration wizard doesn't work Nicklas Nordborg defect minor Reggie v4.19 net.sf.basedb.reggie
#1059 NullPointerException when running the Genotype quality control wizard and no patient has been registered for a specimen Nicklas Nordborg defect minor Reggie v4.19 net.sf.basedb.reggie
#1060 Copy consent in referral form registration wizard Nicklas Nordborg enhancement minor Reggie v4.19 net.sf.basedb.reggie
#1065 It should be possible to search with PAD and RCCID number in case summary Nicklas Nordborg enhancement minor Reggie v4.19.1 net.sf.basedb.reggie
#1066 Specimen tube registration wizard should allow different sampling and RNA later dates Nicklas Nordborg enhancement minor Reggie v4.20 net.sf.basedb.reggie
#1069 Reggie should check actual active roles and not just membership Nicklas Nordborg defect minor Reggie v4.20 net.sf.basedb.reggie
#1079 The FrozenTissue date importer should ignore lines without date Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1082 HaplotypeCaller should not write command line parameters in result file Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1083 Add mBAF plot column to derived bioassay list Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1085 Remove the temporary hack for handling FlowThrough names with .f suffix Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1088 Keep Session Alive problems Nicklas Nordborg defect minor Reggie v4.21 net.sf.basedb.reggie
#1089 The Delivery client login should specify which login manager it uses Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1101 Annotation type categories for raw data types Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1102 The level3 exporter should use script templates enhancement minor Relax v1.4 net.sf.basedb.relax
#1105 Lower-case 'c/d' suffix in the specimen tube registration wizard should be auto-converted to upper case Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1106 A pre-registered consent should prevent the "copy consent" function from appearing Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1107 Search by PATnnnn names in case summary Nicklas Nordborg enhancement minor Reggie v4.21 net.sf.basedb.reggie
#1111 Changes in the INCA import Nicklas Nordborg enhancement minor Reggie v4.22 net.sf.basedb.reggie
#1112 Add a predefined option in the referral form registration when a case is registered without referral form Nicklas Nordborg enhancement minor Reggie v4.22 net.sf.basedb.reggie
#1113 Switch to JSON.simple 1.1.1-1 Nicklas Nordborg task minor Reggie v4.22 net.sf.basedb.reggie
#1114 Remove null="false" from "otp_requried" column definition Nicklas Nordborg defect minor OTP login v1.3 net.sf.basedb.otp
#1157 Case summary changes due to MIPs pipeline Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1158 FASTQ files for external samples should not have the prefix in their names Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1163 Start demux wizard may display the same sequencing run multiple times if it is marked for re-process Nicklas Nordborg defect minor Reggie v4.23 net.sf.basedb.reggie
#1166 Add configuration setting for disabling counting stray folders Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1167 Safer debugging of release exporter plug-in Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1169 The private-key file of a file-server is ignored in the installation servlet Nicklas Nordborg defect minor Reggie v4.23 net.sf.basedb.reggie
#1170 The private-key file of a file-server is ignored in the installation servlet Nicklas Nordborg defect minor Relax v1.6 net.sf.basedb.relax
#1171 Hisat alignment stops without error if the genotype VCF file can't be parsed Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
#1172 The message in the "Secondary analysis cleanup" wizard is confusing Nicklas Nordborg enhancement minor Reggie v4.23 net.sf.basedb.reggie
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