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Ticket Summary Owner Type Priority Milestone Component
#61 change structure of tags Jari Häkkinen task blocker tracpages
#103 Create example extensions Nicklas Nordborg task blocker Extension examples v1.0 net.sf.basedb.examples.extensions
#105 Complete the move of the example code from BASE. Nicklas Nordborg task blocker Plugin examples v2.6 net.sf.basedb.examples.plugins
#107 Move the MEV specific code from BASE Nicklas Nordborg task blocker MEV Launcher v1.0 net.sf.basedb.mev
#114 Implement FTP Server Nicklas Nordborg task blocker net.sf.basedb.ftp
#216 Setup source code repository for GenePattern integration Nicklas Nordborg task blocker ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#220 MeV doesn't download files correctly Nicklas Nordborg defect blocker MEV Launcher v1.3 net.sf.basedb.mev
#257 Fix issues with the BGX reporter importer due to changes in the core api of BASE 2.15 Nicklas Nordborg task blocker Illumina package v1.5 net.sf.basedb.illumina
#311 Updates required for BASE 3 support Nicklas Nordborg task blocker Illumina package v1.7 net.sf.basedb.illumina
#314 Switch to GPL3 Nicklas Nordborg task blocker Example code v1.3 net.sf.basedb.examples.extensions
#315 Switch to GPL3 Martin Svensson task blocker FTP Server v1.2 net.sf.basedb.ftp
#326 Updates required for BASE 3 support Nicklas Nordborg Request blocker Reggie v2.0 net.sf.basedb.reggie
#340 Set subtype for all biomaterial items Jari Häkkinen task blocker Reggie v2.1 net.sf.basedb.reggie
#343 Partion wizard try to create a histology sample with itself as parent Nicklas Nordborg defect blocker Reggie v2.0.1 net.sf.basedb.reggie
#361 MeV TDMS exporter should only include reporter fields that are present in the experiment Nicklas Nordborg task blocker MeV Launcher v1.9 net.sf.basedb.mev
#507 'dil' items are created with incorrect value for PoolConc annotation Nicklas Nordborg defect blocker Reggie v2.13 net.sf.basedb.reggie
#539 Set "Disable log" flag on some annotation types Nicklas Nordborg enhancement blocker Reggie v2.16 net.sf.basedb.reggie
#578 Move to BASE 3.3 Nicklas Nordborg enhancement blocker Reggie v2.16 net.sf.basedb.reggie
#580 Authenticate users using YubiKey sticks Nicklas Nordborg task blocker YubiKey v1.0 net.sf.basedb.yubikey
#644 Can't start align job Nicklas Nordborg defect blocker Reggie v2.16.1 net.sf.basedb.reggie
#645 More than one parent item was found when starting align job Nicklas Nordborg defect blocker Reggie v2.16.1 net.sf.basedb.reggie
#676 Switch to AGPL v3 license Nicklas Nordborg task blocker Reggie v2.18 net.sf.basedb.reggie
#750 Changes required for BASE version 3.5 Nicklas Nordborg task blocker Reggie v3.3 net.sf.basedb.reggie
#825 Optimize library preparation and sequencing wizards for NextSeq Nicklas Nordborg enhancement blocker Reggie v4.0 net.sf.basedb.reggie
#842 Update to Hibernate 5 Nicklas Nordborg task blocker LabEnv v1.5 net.sf.basedb.labenv
#850 Encoding problems with JSON data Nicklas Nordborg defect blocker Reggie v4.1.1 net.sf.basedb.reggie
#879 Switch to BASE 3.8 Nicklas Nordborg task blocker Reggie v4.4 net.sf.basedb.reggie
#881 Implement INCA XML to CSV converter task blocker INCA XML to CSV converter 1.0 net.sf.basedb.inca
#889 Switch to BASE 3.9 Nicklas Nordborg task blocker Reggie v4.5 net.sf.basedb.reggie
#900 Switch to BASE 3.9.1 Nicklas Nordborg task blocker Reggie v4.6 net.sf.basedb.reggie
#973 Update to Hibernate 5.2 and BASE 3.12 olle task blocker LabEnv v1.6 net.sf.basedb.labenv
#982 Re-design the current pipeline Nicklas Nordborg task blocker 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
#998 Fix problems with unselected list items Nicklas Nordborg defect blocker Reggie v4.11.3 net.sf.basedb.reggie
#1056 Naming of child items Nicklas Nordborg defect blocker Reggie v4.19 net.sf.basedb.reggie
#1097 Switch to BASE 3.13.1 task blocker Relax v1.4 net.sf.basedb.relax
#1127 Thumbnails are not visible in BASE 3.15 Nicklas Nordborg task blocker Thumbnails v1.1 net.sf.basedb.thumbnails
#69 DBControl bad code style, beware and fix it! Jari Häkkinen defect critical se.lu.thep.affymetrix
#89 Installation program and documentation Johan Enell task critical Illumina package v1.0 net.sf.basedb.illumina
#90 Create array design from a bgx-file Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#93 Illumina SNP validator and meta-data extractor Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#100 Add Illumina SNP platform to the installation program Martin Svensson enhancement critical Illumina package v1.0 net.sf.basedb.illumina
#101 Import plug-in for SNP raw data Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#127 Update to final release of Apache Mina FTP server Nicklas Nordborg task critical FTP Server v1.0 net.sf.basedb.ftp
#132 ReplicateError: In witihn assays only one position of accepted replicate pairs are kept Jari Häkkinen defect critical se.lu.onk series plug-ins
#138 Importing data for multiple raw bioassays in one step Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#141 Rank invariant should not support configurations Martin Svensson defect critical Normalization package v1.0 net.sf.basedb.normalizers
#151 Use two queries instead of one in DetectionPValue.run() method Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#162 Upgrade to MeV 4.3 Nicklas Nordborg enhancement critical MEV Launcher v1.1 net.sf.basedb.mev
#163 Rank invariant normalization has a sorting bug Martin Svensson defect critical Normalization package v1.0 net.sf.basedb.normalizers
#178 The MeV launcher should use attached file instead of running BioAssaySetExporter Nicklas Nordborg enhancement critical MEV Launcher v1.1 net.sf.basedb.mev
#213 Cannot save MeV options Nicklas Nordborg defect critical MEV Launcher v1.3 net.sf.basedb.mev
#214 Move TDMS export to this extension Nicklas Nordborg task critical MEV Launcher v1.3 net.sf.basedb.mev
#217 GCT exporter Nicklas Nordborg task critical ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#221 Configure GenePattern server Nicklas Nordborg task critical ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#222 Utility for transfering file between BASE and a GenePattern server Nicklas Nordborg task critical ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#241 Add MeV Analysis file as a file type for bioassay sets Nicklas Nordborg task critical MeV Launcher v1.5 net.sf.basedb.mev
#242 Implement "Save to BASE" function in the MeV gui Nicklas Nordborg task critical MeV Launcher v1.5 net.sf.basedb.mev
#243 Create a sample MeV analysis file for testing purposes Nicklas Nordborg task critical MeV Launcher v1.5 net.sf.basedb.mev
#263 Release version 1.0 of the Agilent plug-in package Jari Häkkinen task critical Agilent package 1.0 net.sf.basedb.agilent
#264 Investigate and fix issues with external files introduced in BASE 2.16 Nicklas Nordborg task critical FTP Server v1.1 net.sf.basedb.ftp
#265 Investigate and fix issues with external files introduced in BASE 2.16 Nicklas Nordborg task critical Illumina package v1.6 net.sf.basedb.illumina
#266 Investigate and fix issues with external files introduced in BASE 2.16 Nicklas Nordborg task critical MeV Launcher v1.7 net.sf.basedb.mev
#291 Personal information registration Nicklas Nordborg task critical Reggie v1.0 net.sf.basedb.reggie
#335 Use item subtypes - step 1 Nicklas Nordborg task critical Reggie v2.0 net.sf.basedb.reggie
#348 Consent form registration wizard should allow 'Yes' in all cases Nicklas Nordborg enhancement critical Reggie v2.2 net.sf.basedb.reggie
#349 Copy consent information to multiple cases Nicklas Nordborg enhancement critical Reggie v2.2 net.sf.basedb.reggie
#350 Blood referral form registration wizard Nicklas Nordborg task critical Reggie v2.2 net.sf.basedb.reggie
#364 Put RNA aliquots on bioplate to be used by the Caliper machine Nicklas Nordborg task critical Reggie v2.4 net.sf.basedb.reggie
#365 Export bioplate information to a file that can be used by the Caliper machine Nicklas Nordborg task critical Reggie v2.4 net.sf.basedb.reggie
#370 Export run parameters to Caliper XML file Nicklas Nordborg task critical Reggie v2.4 net.sf.basedb.reggie
#371 Wizard that move histology samples to paraffin blocks Nicklas Nordborg task critical Reggie v2.7 net.sf.basedb.reggie
#379 Create "virtual" samples for cases when no specimen is received Nicklas Nordborg task critical Reggie v2.5 net.sf.basedb.reggie
#381 Handle core biopsies Nicklas Nordborg task critical Reggie v2.5 net.sf.basedb.reggie
#386 Qiacube/nanodrop wizard Nicklas Nordborg task critical Reggie v2.6 net.sf.basedb.reggie
#388 Lysate/Qiacube/NanoDrop lab tracking protocol Nicklas Nordborg task critical Reggie v2.6 net.sf.basedb.reggie
#407 Cannot import Caliper result if a QCRunDate is given Nicklas Nordborg defect critical Reggie v2.7 net.sf.basedb.reggie
#411 Enable core biopsy 'C' suffix for more sites Nicklas Nordborg enhancement critical Reggie v2.8 net.sf.basedb.reggie
#418 Dates are not parsed correctly by the sample report generator Nicklas Nordborg defect critical Reggie v2.9 net.sf.basedb.reggie
#422 Implement wizards for RNA->cDNA processing Nicklas Nordborg task critical Reggie v2.12 net.sf.basedb.reggie
#423 Implement wizards for cDNA->Library processing Nicklas Nordborg task critical Reggie v2.12 net.sf.basedb.reggie
#424 Select RNA items for library preparation Nicklas Nordborg task critical Reggie v2.12 net.sf.basedb.reggie
#451 Change 'storage location' for paraffin blocks and HE glass Nicklas Nordborg enhancement critical Reggie v2.10 net.sf.basedb.reggie
#456 Barcode layout wizard Nicklas Nordborg task critical Reggie v2.12 net.sf.basedb.reggie
#462 Implement a print function that can print complete pages Nicklas Nordborg task critical Reggie v2.11 net.sf.basedb.reggie
#474 Depend on BASE 3.2.2 Nicklas Nordborg task critical Reggie v2.12 net.sf.basedb.reggie
#478 Implement wizards for pooling Nicklas Nordborg task critical Reggie v2.12 net.sf.basedb.reggie
#481 Register prepared flow cells Nicklas Nordborg task critical Reggie v2.13 net.sf.basedb.reggie
#501 Generate lab protocol for clustering olle task critical Reggie v2.13 net.sf.basedb.reggie
#502 Design flow cells Nicklas Nordborg task critical Reggie v2.13 net.sf.basedb.reggie
#508 Library plates remain in the 'Create pooled libraries' wizard after pools have been created Nicklas Nordborg defect critical Reggie v2.13 net.sf.basedb.reggie
#533 Add secondary analysis section to Reggie Nicklas Nordborg task critical Reggie v2.16 net.sf.basedb.reggie
#540 Make sure Reggie works with BASE 3.3 Nicklas Nordborg task critical Reggie v2.15 net.sf.basedb.reggie
#552 PluginUtilities-0.2.jar is in incorrect location Martin Svensson defect critical Normalization package v1.1 net.sf.basedb.normalizers
#562 Re-design clustering and sequencing startup wizards Nicklas Nordborg enhancement critical Reggie v2.15 net.sf.basedb.reggie
#564 Update example extensions to new scripting pattern Nicklas Nordborg enhancement critical Example code v1.6 net.sf.basedb.examplecode
#566 Update print extension to new scripting pattern Nicklas Nordborg enhancement critical Print package v1.1 net.sf.basedb.print
#567 Update MEV extension to new scripting pattern Nicklas Nordborg enhancement critical MeV Launcher 1.11 net.sf.basedb.mev
#571 Update Reggie to new scripting pattern (first step) Nicklas Nordborg enhancement critical Reggie v2.16 net.sf.basedb.reggie
#583 Require 'embedding date' in 'Register paraffin blocks' wizard Nicklas Nordborg defect critical Reggie v2.15 net.sf.basedb.reggie
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