Changeset 5704


Ignore:
Timestamp:
Aug 22, 2011, 9:21:20 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1603: Developers migration guide

Updated the migration guide to make it up to date with the latest development.

File:
1 edited

Legend:

Unmodified
Added
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  • trunk/doc/src/docbook/developerdoc/migrate_2_3.xml

    r5640 r5704  
    4747      simple replacment API that can be used instead. Since the deprecated API
    4848      has been removed in BASE 3 so has the instructions. You'll need to check
    49       with the BASE 2.17 documentation which is located at
    50       <ulink url="http://base.thep.lu.se/chrome/site/2.17">http://base.thep.lu.se/chrome/site/2.17</ulink>.
    51     </para>
     49      with the BASE 2.17 documentation which is located at:
     50    </para>
     51   
     52    <itemizedlist>
     53      <listitem>
     54        <para><ulink url="http://base.thep.lu.se/chrome/site/2.17/html/index.html">http://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>:
     55        User manual.
     56        </para>
     57      </listitem>
     58      <listitem>
     59        <para><ulink url="http://base.thep.lu.se/chrome/site/2.17/api/index.html">http://base.thep.lu.se/chrome/site/2.17/api/index.html</ulink>:
     60        API documentation.
     61        </para>
     62      </listitem>
     63   
     64    </itemizedlist>
     65   
    5266    <para>
    5367      Do not proceed until you are sure that your code is not using any
     
    115129        <para>
    116130          <classname>Label</classname> has been replaced with <classname docapi="net.sf.basedb.core">Tag</classname>.
    117           <classname>LabeledExtract</classname> has been merged into <classname
     131          <classname>LabeledExtract</classname> has been merged with <classname
    118132          docapi="net.sf.basedb.core">Extract</classname>. <classname>Hybridization</classname> has been
    119133          replaced with <classname docapi="net.sf.basedb.core">PhysicalBioAssay</classname>.
    120134          <classname>Scan</classname> and <classname>Image</classname> has been replaced with
    121           <classname docapi="net.sf.basedb.core">BioAssayEvent</classname>,
    122           <classname docapi="net.sf.basedb.core">DerivedBioAssaySet</classname> and
    123           <classname docapi="net.sf.basedb.core">DerivedBioAssay</classname>.
     135          <classname docapi="net.sf.basedb.core">DerivedBioAssay</classname>. The API for linking
     136          parent/child biomaterial has been changed. The <property>pooled</property> property
     137          of biomaterials has been removed.
    124138          The changes are driven by the support for sequencing experiments. The new items are
    125139          using the new subtype feature. For example, a hybridization in BASE 2 has been
     
    185199        </para>
    186200      </listitem>
     201     
     202      <listitem>
     203        <para>
     204          All plug-ins and extensions are required to be installed in the directory specified by
     205          <code>plugins.dir</code> setting in the <filename>base.config</filename> file. Sub-directories
     206          are <emphasis>not</emphasis> searched any longer.
     207          This is usually not something that you need to worry about as a developer except that
     208          you should make sure the installation instruction are up to date. See <ulink
     209          url="http://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation
     210          procedure for plug-ins, extensions and more...)</ulink> for more information.
     211        </para>
     212      </listitem>
     213     
     214      <listitem>
     215        <para>
     216          Plug-ins/extensions that depend on 3-rd party JAR files are now recommended to include
     217          those JAR file inside the <filename>META-INF/lib</filename> directory in the plug-in
     218          JAR file. The <property>Class-Path</property> attribute in <filename>META-INF/MANIFEST.MF</filename>
     219          must still be set. See <xref linkend="plugin_developer.organize"/> and <ulink
     220          url="http://base.thep.lu.se/ticket/1594">ticket #1594 (JarClassLoader support for JARs within JARs)</ulink>.
     221        </para>
     222      </listitem>
     223     
    187224    </itemizedlist>
    188225   
    189     <para>
    190       Another change is that plug-ins and extensions are
    191       required to be installed in the directory specified by <code>plugins.dir</code>
    192       setting in the <filename>base.config</filename> file. This is usually not something that
    193       you need to worry about as a developer. See <ulink
    194       url="http://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation
    195       procedure for plug-ins, extensions and more...)</ulink> for more information.
    196     </para>
    197    
    198226  </sect1>
    199227 
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