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Ticket Summary Owner Type Priority Milestone Component
#263 Release version 1.0 of the Agilent plug-in package Jari Häkkinen task critical Agilent package 1.0 net.sf.basedb.agilent
#359 Changes related to new GUI in BASE 3.1 Nicklas Nordborg enhancement minor Example code v1.4 net.sf.basedb.examplecode
#376 Create some example extensions that add list columns Nicklas Nordborg task major Example code v1.5 net.sf.basedb.examplecode
#377 Create some example extensions for the item overview Nicklas Nordborg task major Example code v1.5 net.sf.basedb.examplecode
#410 Create an example extensions for logging Nicklas Nordborg task major Example code v1.5 net.sf.basedb.examplecode
#564 Update example extensions to new scripting pattern Nicklas Nordborg enhancement critical Example code v1.6 net.sf.basedb.examplecode
#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
#922 Create an example of a custom extension point Nicklas Nordborg task critical Example code v1.8 net.sf.basedb.examplecode
#103 Create example extensions Nicklas Nordborg task blocker Extension examples v1.0 net.sf.basedb.examples.extensions
#189 Add toolbar extension examples Nicklas Nordborg task major Extension examples v1.1 net.sf.basedb.examples.extensions
#198 Change source files to UTF-8 Nicklas Nordborg task minor Extension examples v1.1 net.sf.basedb.examples.extensions
#233 Add example that uses the alternate approach for invoking servlets Nicklas Nordborg enhancement major Extension examples v1.2 net.sf.basedb.examples.extensions
#247 net.sf.basedb.normalizers: qQuantileNormalization crashes when normalizing filtered bioassay sets Jari Häkkinen defect major Normalization package v1.1 net.sf.basedb.examples.extensions
#282 Add example of an edit-dialog extension Nicklas Nordborg task major Example code v1.3 net.sf.basedb.examples.extensions
#283 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor Example code v1.3 net.sf.basedb.examples.extensions
#309 Merge example plug-ins and extensions into one package Nicklas Nordborg task major Example code v1.3 net.sf.basedb.examples.extensions
#310 Update extension examples to BASE 3 Nicklas Nordborg task major Example code v1.3 net.sf.basedb.examples.extensions
#314 Switch to GPL3 Nicklas Nordborg task blocker Example code v1.3 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
#199 Change source files to UTF-8 Nicklas Nordborg task minor Plugin examples v2.x net.sf.basedb.examples.plugins
#281 Plug-in should suggest better job names Nicklas Nordborg enhancement major Example code v1.3 net.sf.basedb.examples.plugins
#287 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect major Plugin examples v2.x net.sf.basedb.examples.plugins
#289 Add 'download-lib' target to ant buildfile and remove checked in BASE jar file Nicklas Nordborg enhancement minor Plugin examples v2.x net.sf.basedb.examples.plugins
#106 Move the example web services code from the BASE server Nicklas Nordborg task major Web services examples v2.6 net.sf.basedb.examples.webservices
#200 Change source files to UTF-8 Nicklas Nordborg task minor Web services examples v3.0 net.sf.basedb.examples.webservices
#288 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor Web services examples v3.0 net.sf.basedb.examples.webservices
#290 Add 'download-lib' target to ant buildfile and remove checked in BASE jar file Nicklas Nordborg enhancement minor Web services examples v3.0 net.sf.basedb.examples.webservices
#327 Update web service examples to BASE 3 Nicklas Nordborg task major Web services examples v3.0 net.sf.basedb.examples.webservices
#338 Update Ajax2 to 1.6.1 Nicklas Nordborg task major Web services examples v3.1 net.sf.basedb.examples.webservices
#460 Update Axis2 Nicklas Nordborg enhancement minor Web service examples 3.2 net.sf.basedb.examples.webservices
#114 Implement FTP Server Nicklas Nordborg task blocker net.sf.basedb.ftp
#127 Update to final release of Apache Mina FTP server Nicklas Nordborg task critical FTP Server v1.0 net.sf.basedb.ftp
#128 Warning when ftp-config.xml is missing Nicklas Nordborg enhancement major net.sf.basedb.ftp
#201 Change source files to UTF-8 Nicklas Nordborg task minor FTP Server v1.1 net.sf.basedb.ftp
#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
#269 Update ftp server library version Nicklas Nordborg task major FTP Server v1.1 net.sf.basedb.ftp
#272 Handle CWD . commands correctly Nicklas Nordborg enhancement minor FTP Server v1.1 net.sf.basedb.ftp
#276 Version should autopropagate from build.xml Nicklas Nordborg task minor FTP Server v1.1 net.sf.basedb.ftp
#284 Change "source" and "target" compilation options to 1.6 Nicklas Nordborg defect minor FTP Server v1.2 net.sf.basedb.ftp
#313 Updates required for BASE 3 support Martin Svensson task major FTP Server v1.2 net.sf.basedb.ftp
#315 Switch to GPL3 Martin Svensson task blocker FTP Server v1.2 net.sf.basedb.ftp
#329 Set active project when using FTP Nicklas Nordborg task major FTP Server v1.2 net.sf.basedb.ftp
#332 Update to FTP server lib 1.0.6 Nicklas Nordborg task major FTP Server v1.2 net.sf.basedb.ftp
#589 FTP service should install client item when service is started first time Nicklas Nordborg enhancement minor FTP Server v1.3 net.sf.basedb.ftp
#616 External files with a file server can't be downloaded Nicklas Nordborg defect major FTP Server v1.4 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
#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
#223 Add target in build.xml for downloading required GenePattern jar files Nicklas Nordborg task major ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#224 Add a "Test" button on the GenePattern 'edit server' page Nicklas Nordborg enhancement major ZZ GenePattern integration v1.0 net.sf.basedb.genepattern
#304 Implement HDFS external file support Nicklas Nordborg task major HDFS package v1.0 net.sf.basedb.hdfs
#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
#91 Import Illumina Bead Summary(IBS) files as raw data Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#92 Create Illumina SNP raw data type Johan Enell defect 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
#94 Import reporter annotations from bgx files Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#95 Intensity calculator for Illumina expression data Jari Häkkinen task major Illumina package v1.1 net.sf.basedb.illumina
#98 Implement validator and metadata extractor plug-in for BGX files Martin Svensson task major 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
#102 Intensity calculator for Illumina SNP data Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#104 Add information that BASE2WSClient.jar is needed to compile the plug-ins Jari Häkkinen defect major Illumina package v1.1 net.sf.basedb.illumina
#109 Add information to the wiki page on how to give feedback on the Illumina package Nicklas Nordborg task major Illumina package v1.1 net.sf.basedb.illumina
#110 Illumina detection P-value plug-in Jari Häkkinen enhancement major Illumina package v1.1 net.sf.basedb.illumina
#111 Update Illumina wiki pages and related documentation before release Jari Häkkinen task major Illumina package v1.1 net.sf.basedb.illumina
#112 Illumina plug-in installer script fails (in some cases) Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#113 Add support for more variations of Illumina detection P-value calculations Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#121 BGX-importer should 0-pad Array_Address_ID if the BGX-file doesn't have done that already Martin Svensson enhancement major Illumina package v1.2 net.sf.basedb.illumina
#126 Illumina SNP ... files are now supported (by the BASEcore) in the BASE analysis tree Nicklas Nordborg enhancement major Illumina package v1.x net.sf.basedb.illumina
#138 Importing data for multiple raw bioassays in one step Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#140 Add support in build.xml for automatic download of BASE jar files Nicklas Nordborg enhancement minor Illumina package v1.2 net.sf.basedb.illumina
#142 Illumina installer plugin cannot be installed in some cases Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#143 Illumina plug-in package installer requests wrong permissions Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#149 Error: The query has already been executed (Illumina detection P-value calculation) Nicklas Nordborg defect major net.sf.basedb.illumina
#150 Fix layout of DetectionPValue.java Nicklas Nordborg task minor Illumina package v1.2 net.sf.basedb.illumina
#151 Use two queries instead of one in DetectionPValue.run() method Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#155 New error handling option for duplicated features when creating array design from a bgx-file Nicklas Nordborg enhancement minor net.sf.basedb.illumina
#164 Improve documentation on how to upgrade the illumina plug-in package Martin Svensson task major Illumina package v1.3 net.sf.basedb.illumina
#170 Result dialouge after batch importing several raw bioassays is somewhat confusing Martin Svensson defect major Illumina package v1.3 net.sf.basedb.illumina
#171 IBS raw data importer should be able to handle floats in some columns Martin Svensson enhancement major Illumina package v1.3 net.sf.basedb.illumina
#173 Remove the float to integer conversions in beadstudio2ibs.pl when ticket:171 is fixed and 1.3 is released Martin Svensson defect major Illumina package v1.3 net.sf.basedb.illumina
#174 Change license to GPL 3 for the illumina package? Martin Svensson enhancement major Illumina package v1.3 net.sf.basedb.illumina
#175 Update the ant script to include contrib directory when creating package. Nicklas Nordborg enhancement major Illumina package v1.3 net.sf.basedb.illumina
#180 Overview plot extensions for Illumina expression Martin Svensson task major Illumina package v1.4 net.sf.basedb.illumina
#182 Illumina probes not found message should be documented Martin Svensson task major Illumina package v1.4 net.sf.basedb.illumina
#196 Illumina methylation arrays ... Nicklas Nordborg defect major Illumina package v1.x net.sf.basedb.illumina
#202 Change source files to UTF-8 Nicklas Nordborg task minor Illumina package v1.4 net.sf.basedb.illumina
#204 Add option to include all available negative controls in detection P-value calculation Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#205 Change link README_PluginDetails to point to tags at next release Jari Häkkinen defect major Illumina package v1.4 net.sf.basedb.illumina
#207 Illumina DASL arrays Nicklas Nordborg enhancement major net.sf.basedb.illumina
#215 BGX reporter importer hangs if the [Controls] section has less than 6 columns Nicklas Nordborg task major Illumina package v1.4 net.sf.basedb.illumina
#227 Illumina detection P-value plug-in description must be improved Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#230 Illumina detection P-value Control outlier cut-off parameter cannot be zero Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#231 Illumina detection P-value fails if no negative controls are available in the bio assayset Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#232 Fix deprecation warnings in detection P-value plug-in Nicklas Nordborg task major Illumina package v1.4 net.sf.basedb.illumina
#235 Illumina package: Add instructions on how to remove 'Illumina' raw data type from the server Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#236 Reporter import of Illumina BGX file fails on section [controls] Nicklas Nordborg defect major net.sf.basedb.illumina
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