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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE part PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2011 Nicklas Nordborg |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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<chapter id="migrate_2_3" chunked="0"> |
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<?dbhtml filename="migrate.html" ?> |
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<title>Migrating code from BASE 2 to BASE 3</title> |
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|
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<para> |
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This section gives a brief overview what has changed between BASE 2 and |
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BASE 3 and how to migrate plug-in or extension code to BASE 3. |
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Do not expect that your code can be installed and function as intended |
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right out of the box. |
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</para> |
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|
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<sect1 id="migrate_2_3.compiling"> |
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<title>Compiling the code against BASE 3</title> |
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|
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<bridgehead>All deprecated methods and classes have been removed</bridgehead> |
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<para> |
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Before trying to compile your code against the BASE 3 API we recommend that |
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you make sure that you are not using any deprecated methods or classes |
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from the BASE 2.17 API. So the first step should always be to compile |
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your code against the latest BASE 2.17 release. Fix any warnings |
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according to the instructions in the javadoc. In most cases, there is a |
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simple replacment API that can be used instead. Since the deprecated API |
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has been removed in BASE 3 so has the instructions. You'll need to check |
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with the BASE 2.17 documentation which is located at: |
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</para> |
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|
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<itemizedlist> |
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<listitem> |
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<para><ulink url="https://base.thep.lu.se/chrome/site/2.17/html/index.html">https://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>: |
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User manual. |
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</para> |
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</listitem> |
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<listitem> |
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<para><ulink url="https://base.thep.lu.se/chrome/site/2.17/api/index.html">https://base.thep.lu.se/chrome/site/2.17/api/index.html</ulink>: |
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API documentation. |
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</para> |
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</listitem> |
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|
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</itemizedlist> |
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|
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<para> |
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Do not proceed until you are sure that your code is not using any |
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deprecated API. |
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</para> |
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|
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<bridgehead>BASE JAR files have new names</bridgehead> |
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|
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<para> |
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All JAR files with the BASE API has been renamed to better |
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follow the scheme used by many other projects. |
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</para> |
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|
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<table frame="all" id="migrate.jarfilenames"> |
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<title>JAR filename changes</title> |
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<tgroup cols="2" align="center"> |
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<colspec colname="oldname" align="left"/> |
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<colspec colname="newname" align="left"/> |
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<thead> |
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<row> |
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<entry> |
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Old filename |
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</entry> |
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<entry> |
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BASE 3 filename |
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</entry> |
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</row> |
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</thead> |
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<tbody> |
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<row> |
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<entry> |
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<filename>BASE2Core.jar</filename> |
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</entry> |
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<entry> |
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<filename>base-core-3.0.0.jar</filename> |
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</entry> |
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</row> |
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<row> |
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<entry> |
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<filename>BASE2CorePlugins.jar</filename> |
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</entry> |
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<entry> |
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<filename>base-coreplugins-3.0.0.jar</filename> |
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</entry> |
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</row> |
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<row> |
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<entry> |
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<filename>BASE2Webclient.jar</filename> |
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</entry> |
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<entry> |
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<filename>base-webclient-3.0.0.jar</filename> |
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</entry> |
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</row> |
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<row> |
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<entry> |
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<filename>BASE2WSClient.jar</filename> |
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</entry> |
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<entry> |
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<filename>base-webservices-client-3.0.0.jar</filename> |
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</entry> |
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</row> |
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</tbody> |
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</tgroup> |
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</table> |
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|
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<note> |
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Also note that the version number is included in the file name, |
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so the files will change when new versions are released. |
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You'll need to make sure that your build system can handle this. |
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The BASE JAR files can be downloaded from |
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<ulink url="https://base.thep.lu.se/chrome/site/files/base/jars/">https://base.thep.lu.se/chrome/site/files/base/jars/</ulink>. |
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</note> |
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|
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</sect1> |
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|
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<sect1 id="migrate_2_3.coreapi"> |
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|
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<title>Core API changes</title> |
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|
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<para> |
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There are lot's of other changes to the API between BASE 2 and BASE 3. |
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If your code is affected by those changes, you will have to update your |
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code. Since there are many changes, both big and small, it is not |
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possible to list everything here. One good way to find out more about |
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the changes is to use the BASE Trac or ask on the developers mailing |
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list. Some of the major changes are: |
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</para> |
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|
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<itemizedlist> |
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<listitem> |
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<para> |
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Removed the <methodname>Plugin.getAbout()</methodname> method |
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from the <interfacename docapi="net.sf.basedb.core.plugin">Plugin</interfacename> |
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interface. The information should instead be placed in the |
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<filename>META-INF/extensions.xml</filename> file inside the JAR |
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file that the plug-in is shipped in. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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<classname>HardwareType</classname>, <classname>SoftwareType</classname>, |
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<classname>ProtocolType</classname> and <classname>FileType</classname> |
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has been replaced with <classname |
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docapi="net.sf.basedb.core">ItemSubtype</classname>. |
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Additionally, several other items implement the new <interfacename |
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docapi="net.sf.basedb.core">Subtypable</interfacename> interface. |
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See <ulink url="https://base.thep.lu.se/ticket/1597">ticket #1597 (Subtypes of items)</ulink> |
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for more information. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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<classname>Label</classname> has been replaced with <classname docapi="net.sf.basedb.core">Tag</classname>. |
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<classname>LabeledExtract</classname> has been merged with <classname |
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docapi="net.sf.basedb.core">Extract</classname>. <classname>Hybridization</classname> has been |
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replaced with <classname docapi="net.sf.basedb.core">PhysicalBioAssay</classname>. |
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<classname>Scan</classname> and <classname>Image</classname> has been replaced with |
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<classname docapi="net.sf.basedb.core">DerivedBioAssay</classname>. The API for linking |
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parent/child biomaterial has been changed. The <property>pooled</property> property |
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of biomaterials has been removed. |
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The changes are driven by the support for sequencing experiments. The new items are |
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using the new subtype feature. For example, a hybridization in BASE 2 has been |
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converted to a physical bioassay in BASE 3 with the subtype 'Hybridization'. The |
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server admin can define additional subtypes. See |
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<ulink url="https://base.thep.lu.se/ticket/1153">ticket #1153 (Handling short read |
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transcript sequence data)</ulink> for more information. |
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|
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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<classname docapi="net.sf.basedb.core">RawBioAssay</classname> has |
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a direct link to <classname docapi="net.sf.basedb.core">Extract</classname> |
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instead of the <property>arrayIndex</property> property which has been |
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removed. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Removed validator and metadata reader properties from |
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<classname docapi="net.sf.basedb.core">DataFileType</classname>. |
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This feature is now implemented as extensions. The API is slightly |
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different and classes have been moved around a bit. See |
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<xref linkend="extensions_developer.fileset_validator"/> and |
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<ulink |
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url="https://base.thep.lu.se/ticket/1598">ticket #1598 (Use |
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the extensions system for data file validators and metadata readers)</ulink> for more information. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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A <classname docapi="net.sf.basedb.core">FileSet</classname> may |
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store more than one file for each <classname docapi="net.sf.basedb.core">DataFileType</classname> |
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which was not possible before. The API for adding files have changed. |
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See <ulink url="https://base.thep.lu.se/ticket/1604">ticket #1604 |
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(Support for multiple files of the same type in a FileSet)</ulink> for |
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more information. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Changes to the <interfacename docapi="net.sf.basedb.util.zip">FileUnpacker</interfacename> |
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interface. The <methodname>unpack()</methodname> method signature has changed and |
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any plug-ins that implement this interface need to be updated. The changes |
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make it possible to get information about the main zip/tar file that is being |
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unpacked. See <ulink |
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url="https://base.thep.lu.se/ticket/978">ticket #978 (Unzipped files never inherit |
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file type specified during upload)</ulink> for more information. |
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23 Sep 11 |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Encrypting passwords before logging in is no longer supported. The |
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<methodname>SessionControl.login()</methodname> has been changed to |
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reflect this. While this may seem like a reduction in security it is not. |
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26 Oct 11 |
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The previously used scheme with MD5 hashes can be cracked by brute-force on |
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a moderate computer today. If additional security is needed we recommend that |
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BASE is installed with HTTPS access only. See <ulink |
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url="https://base.thep.lu.se/ticket/1641">ticket #1641 (Use bcrypt for storing |
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26 Oct 11 |
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passwords instead of MD5)</ulink> for more information. |
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</para> |
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</listitem> |
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|
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</itemizedlist> |
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|
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</sect1> |
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|
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<sect1 id="migrate_2_3.packaging"> |
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<title>Packaging your plug-in so that it installs in BASE 3</title> |
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|
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<para> |
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The installation system for plug-ins and extensions has been reworked. We hope |
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that it is easier to install things now. Basically, the plug-in installation wizard |
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has been merged with the extensions installation wizard. If your package contain only |
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extensions it will probably install without changes. Packages with plug-ins need some |
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changes to the XML files. |
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</para> |
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|
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<itemizedlist> |
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<listitem> |
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<para> |
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The information that was in |
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<filename>META-INF/base-plugins.xml</filename>, should be moved to |
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<filename>META-INF/extensions.xml</filename>. The XML syntax in the new |
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file is different from the old file. You'll also need to put |
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the information was returned by the <methodname>Plugin.getAbout()</methodname> |
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method in this file. See <xref |
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linkend="plugin_developer.organize.autoinstallcompatible" /> |
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for more information. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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The information that was in |
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<filename>META-INF/base-configurations.xml</filename>, should be moved to |
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<filename>META-INF/plugin-configurations.xml</filename>. The XML syntax in the |
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new and old file is the same. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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All plug-ins and extensions are required to be installed in the directory specified by |
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<code>plugins.dir</code> setting in the <filename>base.config</filename> file. Sub-directories |
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are <emphasis>not</emphasis> searched any longer. |
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This is usually not something that you need to worry about as a developer except that |
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you should make sure the installation instruction are up to date. See |
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<xref linkend="plugins.installation" /> and |
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<ulink |
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url="https://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation |
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procedure for plug-ins, extensions and more...)</ulink> for more information. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Plug-ins/extensions that depend on 3-rd party JAR files are now recommended to include |
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those JAR file inside the <filename>META-INF/lib</filename> directory in the plug-in |
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JAR file. The <property>Class-Path</property> attribute in <filename>META-INF/MANIFEST.MF</filename> |
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must still be set. See <xref linkend="plugin_developer.organize"/> and <ulink |
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url="https://base.thep.lu.se/ticket/1594">ticket #1594 (JarClassLoader support for JARs within JARs)</ulink>. |
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</para> |
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</listitem> |
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|
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</itemizedlist> |
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|
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</sect1> |
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|
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</chapter> |