Changeset 5820


Ignore:
Timestamp:
Oct 24, 2011, 12:46:11 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Last part of the "Write documentation" chapter and FAQ and Apecix sections.

Location:
trunk/doc/src
Files:
7 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/appendix/base.config.xml

    r5782 r5820  
    437437        <para>
    438438        The priority to give to jobs. The priority is a value between 1 and 10.
    439         See <ulink url="http://java.sun.com/javase/6/docs/api/java/lang/Thread.html"
    440         >http://java.sun.com/javase/6/docs/api/java/lang/Thread.html</ulink>
     439        See <ulink url="http://download.oracle.com/javase/6/docs/api/java/lang/Thread.html"
     440        >http://download.oracle.com/javase/6/docs/api/java/lang/Thread.html</ulink>
    441441        for more information about thread priorities.
    442442        </para>
  • trunk/doc/src/docbook/appendix/coreplugins.xml

    r5782 r5820  
    3131
    3232  <para>
    33     A categorized list of all plug-ins installed with a pristine BASE
    34     installation. Some plug-ins must be configured before use,
     33    Here is a categorized list of all plug-ins installed with a pristine BASE
     34    installation. Some plug-ins must be configured before use. The
    3535    requirements are listed below and configuration samples are given
    3636    for for plug-ins that supports/requires configurations. Use the
     
    5454    <variablelist>
    5555      <varlistentry>
    56         <term>Base1PluginExecuter</term>
    57         <listitem>
    58           <para>
    59             Simulates the plug-in runner from Base 1.2.
    60           </para>
    61           <para>
    62             <emphasis>Since BASE 2.2, no configuration needed for the
    63             Base1PluginExecuter but may be required for the underlying
    64             BASE version 1.2 plug-ins.</emphasis>
    65           </para>
    66         </listitem>
    67       </varlistentry>
    68 
    69       <varlistentry>
    70         <term>JEP extra value calculator</term>
    71         <listitem>
    72           <para>
    73             Calculates extra values for a bioassay set.
    74           </para>
    75           <para>
    76             <emphasis>Since BASE 2.1, no configuration needed.</emphasis>
    77           </para>
    78         </listitem>
    79       </varlistentry>
    80 
    81       <varlistentry>
    82         <term>JEP filter plug-in</term>
    83         <listitem>
    84           <para>
    85             Bioassay set filter. Expressions parsed with JEP.
    86           </para>
    87           <para>
    88             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
    89           </para>
    90         </listitem>
    91       </varlistentry>
    92 
    93       <varlistentry>
    94         <term>JEP intensity transformer</term>
    95         <listitem>
    96           <para>
    97             Transforms the intensities of a bioassayset.
    98           </para>
    99           <para>
    100             <emphasis>Since BASE 2.1, no configuration needed.</emphasis>
    101           </para>
    102         </listitem>
    103       </varlistentry>
    104      
    105       <varlistentry>
     56        <term>BASE 1 plug-in executor</term>
     57        <listitem>
     58          <para>
     59            Simulates the plug-in runner from Base 1.2. Must be configured
     60            before use. The recommended approach is to use the plug-in configuration
     61            file from the BASE 1.2 installation. See <xref linkend="plugins.installation.base1"
     62            /> for more information.
     63          </para>
     64        </listitem>
     65      </varlistentry>
     66
     67      <varlistentry>
     68        <term>External program executor</term>
     69        <listitem>
     70          <para>
     71            Export data from BASE and execute an external program for analysis.
     72            Afterwards, data can be imported back to BASE. A configuration is needed
     73            to run this plug-in. The plug-in is very flexible and can handle several
     74            export/import data formats (which can be extended by
     75            adding special export/import plug-ins). Here is a list of the built-in
     76            exporter/importer implementations.
     77          </para>
     78         
     79          <itemizedlist>
     80            <listitem>
     81              <para>
     82              <emphasis>BASEFile exporter for the ExternalProgramExecutor</emphasis>: Exporter implementation
     83              that export data in BASE file format.
     84              </para>
     85            </listitem>
     86            <listitem>
     87              <para>
     88              <emphasis>BASEfile importer for the ExternalProgramExecutor</emphasis>: Importer implementation
     89              that can import data in BASEfile format.
     90              </para>
     91            </listitem>
     92            <listitem>
     93              <para>
     94              <emphasis>BFS exporter for the ExternalProgramExecutor</emphasis>: Exporter implementation
     95              that export data in BFS file format.
     96              </para>
     97            </listitem>
     98            <listitem>
     99              <para>
     100              <emphasis>BFS importer for the ExternalProgramExecutor</emphasis>: Importer implementation
     101              that can import data in BFS file format.
     102              </para>
     103            </listitem>
     104            <listitem>
     105              <para>
     106              <emphasis>File-only importer for the ExternalProgramExecutor</emphasis>: Importer implementation
     107              that simply upload all created files to BASE.
     108              </para>
     109            </listitem>
     110          </itemizedlist>
     111         
     112          <note>
     113            <para>
     114            This plug-in can in theory handle everything (and more) that the
     115            <emphasis>BASE 1 plug-in executor</emphasis> can, except that it doesn't do
     116            any translation of field names used in BASE 1.
     117            </para>
     118          </note>
     119         
     120        </listitem>
     121      </varlistentry>
     122
     123      <varlistentry>
     124        <term>Formula extra value calculator</term>
     125        <listitem>
     126          <para>
     127            Calculates extra values for a bioassay set using a user-defined
     128            formula. No configuration is needed.
     129          </para>
     130        </listitem>
     131      </varlistentry>
     132
     133      <varlistentry>
     134        <term>Formula filter</term>
     135        <listitem>
     136          <para>
     137            Filters a bioassay set using a user-defined formula.
     138            No configuration is needed.
     139          </para>
     140        </listitem>
     141      </varlistentry>
     142
     143      <varlistentry>
     144        <term>Formula intensity transformer</term>
     145        <listitem>
     146          <para>
     147            Creates a new bioassay set with transformed intensity values using a
     148            user-defined formula. No configuration is needed.
     149          </para>
     150        </listitem>
     151      </varlistentry>
     152
     153      <varlistentry>
     154        <term>Manual derived bioassay creator</term>
    106155        <term>Manual transformation</term>
    107156        <listitem>
     
    109158            Allows a user to manually register an external analysis procedure that has
    110159            happened outside of BASE and to register the parameters used and the generated
    111             output files.
    112           </para>
    113           <para>
    114             <emphasis>
    115               Since BASE 2.12. Configuration is needed to register possible parameters
    116               and output files.
    117             </emphasis>
     160            output files. On plug-in create a derived bioassay set and the other
     161            a transformation/bioassay set. Both plug-ins need a configuration to
     162            register possible parameters and output files.
    118163          </para>
    119164        </listitem>
     
    124169        <listitem>
    125170          <para>
    126             Normalisation using LOWESS algorithm.
    127           </para>
    128           <para>
    129             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     171            Normalisation using LOWESS algorithm. No configuration is
     172            needed.
    130173          </para>
    131174        </listitem>
     
    136179        <listitem>
    137180          <para>
    138             Normalisation based on median ratio.
    139           </para>
    140           <para>
    141             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     181            Normalisation based on median ratio. No configuration is needed.
    142182          </para>
    143183        </listitem>
     
    150190    <title>Core export plug-ins</title>
    151191
     192    <para>
     193      Unless otherwise noted, none of the export plug-ins
     194      need a configuration.
     195    </para>
     196
    152197    <variablelist>
    153198      <varlistentry>
     
    157202            Exports bioassay set data to serial or matrix BASEfile format.
    158203          </para>
    159           <para>
    160             <emphasis>Since BASE 2.12, no configuration needed.</emphasis>
    161           </para>
    162204        </listitem>
    163205      </varlistentry>
    164206     
    165207      <varlistentry>
     208        <term>BFS exporter</term>
     209        <listitem>
     210          <para>
     211            Exports bioassay set data to BFS format.
     212          </para>
     213        </listitem>
     214      </varlistentry>
     215     
     216      <varlistentry>
    166217        <term>GAL exporter</term>
    167218        <listitem>
     
    169220            Exports the features of an array design to a GAL file.
    170221          </para>
    171           <para>
    172             <emphasis>Since BASE 2.7, no configuration needed.</emphasis>
    173           </para>
    174222        </listitem>
    175223      </varlistentry>
     
    181229            Exports help texts to an XML file.
    182230          </para>
    183           <para>
    184             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
    185           </para>
    186231        </listitem>
    187232      </varlistentry>
     
    191236        <listitem>
    192237          <para>
    193             Exports files and directories as an archive-file.
    194           </para>
    195           <para>
    196             <emphasis>Since BASE 2.4, no configuration needed.</emphasis>
    197           </para>
     238            Exports files and directories as an archive-file. A configuration
     239            is needed to specify compression format. Support for the following
     240            formats are included in BASE:
     241          </para>
     242         
     243          <itemizedlist>
     244            <listitem>
     245              <para>
     246              <emphasis>BZipped TAR archive</emphasis>: Collects the selected files/directories
     247              into a TAR file and compress it with BZIP2.
     248              </para>
     249            </listitem>
     250            <listitem>
     251              <para>
     252              <emphasis>GZipped TAR archive</emphasis>: Collects the selected files/directories
     253              into a TAR file and compress it with GZIP.
     254              </para>
     255            </listitem>
     256            <listitem>
     257              <para>
     258              <emphasis>TAR archive</emphasis>: Collects the selected files/directories
     259              into an uncompressed TAR file.
     260              </para>
     261            </listitem>
     262            <listitem>
     263              <para>
     264              <emphasis>ZIP archive</emphasis>: Collects the selected files/directories
     265              into a ZIP file.
     266              </para>
     267            </listitem>
     268          </itemizedlist>
     269         
     270          <para>
     271            See <xref linkend="plugin_developer.other.packer"/> for information
     272            about implementing support for other file formats. 
     273          </para>
     274         
    198275        </listitem>
    199276      </varlistentry>
     
    205282            Exports plate mappings.
    206283          </para>
    207           <para>
    208             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
    209           </para>
    210284        </listitem>
    211285      </varlistentry>
     
    217291            Exports plug-in configurations to an XML file.
    218292          </para>
    219           <para>
    220             <emphasis>Since BASE 2.1, no configuration needed.</emphasis>
    221           </para>
    222293        </listitem>
    223294      </varlistentry>
     
    227298        <listitem>
    228299          <para>
    229             Exports table listings in the web-interface.
    230           </para>
    231           <para>
    232             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     300            Exports data from table listings in the web-interface to
     301            a TAB-separated text file or XML file.
    233302          </para>
    234303        </listitem>
     
    267336            the reporters, since the CDF file doesn't contains any
    268337            annotation information. Probesets already in BASE will not
    269             be affected by the import.
    270           </para>
    271           <para>
    272             <emphasis>Since BASE 2.4, no configuration needed.</emphasis>
     338            be affected by the import. No configuration is needed.
    273339          </para>
    274340        </listitem>
     
    280346          <para>
    281347            Imports annotation to any annotatable item in BASE.
    282           </para>
    283           <para>
    284             <emphasis>Since BASE 2.4, no configuration needed.</emphasis>
     348            Configurations are supported but not required.
     349          </para>
     350        </listitem>
     351      </varlistentry>
     352
     353      <varlistentry>
     354        <term>GTF reporter importer</term>
     355        <listitem>
     356          <para>
     357            Imports reporter information from GTF (Gene transfer format)
     358            files. Configurations are supported but not required. BASE
     359            has pre-installed configurations that uses the gene_id or transcript_id
     360            as reporter id.
     361          </para>
     362        </listitem>
     363      </varlistentry>
     364
     365      <varlistentry>
     366        <term>GTF reporter map importer</term>
     367        <listitem>
     368          <para>
     369            Imports array design features from GTF (Gene transfer format)
     370            files. A configuration is needed. BASE has pre-installed
     371            configurations that uses the gene_id or transcript_id
     372            as reporter id.
    285373          </para>
    286374        </listitem>
     
    291379        <listitem>
    292380          <para>
    293             Imports help texts from an XML file into BASE.
    294           </para>
    295           <para>
    296             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     381            Imports help texts from an XML file into BASE.
     382            No configuration is needed.
    297383          </para>
    298384        </listitem>
     
    303389        <listitem>
    304390          <para>
    305             This plug-in is used to import raw data from Illumina data
    306             files.
    307           </para>
    308           <para>
    309             <emphasis>Since BASE 2.4, no configuration needed.</emphasis>
     391            This plug-in is used to import raw data from Illumina BeadStudion
     392            data files. No configuration is needed.
    310393          </para>
    311394        </listitem>
     
    316399        <listitem>
    317400          <para>
    318             Imports plates from a simple flat file.
    319           </para>
    320           <para>
    321             <emphasis>Since BASE 2.0, available configurations: </emphasis>
    322             <ulink url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/plate_importer_384wells.xml?format=raw">384
    323             wells-plate</ulink> and <ulink
    324             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/plate_importer_96wells.xml?format=raw">96 wells-plate</ulink>
     401            Imports plates from a simple flat file. A configuration is needed.
     402            BASE has pre-installed configurations for 96- and 384-well plates.
    325403          </para>
    326404        </listitem>
     
    331409        <listitem>
    332410          <para>
    333             Imports plate mappings.
    334           </para>
    335           <para>
    336             <emphasis>BASE 2.0, no configuration needed.</emphasis>
     411            Imports plate mappings exported by the <emphasis>Plate mapping exporter</emphasis>.
     412            No configuration is needed.
    337413          </para>
    338414        </listitem>
     
    344420        <listitem>
    345421          <para>
    346             Imports plug-in configurations from an XML file.
    347           </para>
    348           <para>
    349             <emphasis>Since BASE 2.1, no configuration needed.</emphasis>
     422            Imports plug-in configurations from an XML file. No configuration
     423            is needed.
    350424          </para>
    351425        </listitem>
     
    356430        <listitem>
    357431          <para>
    358             Imports array designs from a print map.
    359           </para>
    360           <para>
    361             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     432            Imports array design features from TAM or MwBR files. This plug-in
     433            require that the array design is connected with plates. No
     434            configuration is needed.
    362435          </para>
    363436        </listitem>
     
    368441        <listitem>
    369442          <para>
    370             Imports raw data from a text file.
    371           </para>
    372           <para>
    373             <emphasis>Since BASE 2.0, available configurations:</emphasis>
    374             <ulink
    375             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/raw_data_importer_genepix-cy3_cy5.xml?format=raw">cy3/cy5
    376             GenePix</ulink> and <ulink
    377             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/raw_data_importer_genepix-cy5_cy3.xml?format=raw">cy5/cy3
    378             GenePix</ulink>
    379           </para>
    380         </listitem>
    381       </varlistentry>
    382 
     443            Imports raw data from a text file. A configuration is needed.
     444            BASE has pre-installed configurations for GenePix and Cufflinks
     445            data files.
     446          </para>
     447        </listitem>
     448      </varlistentry>
    383449
    384450      <varlistentry>
     
    386452        <listitem>
    387453          <para>
    388             Import reporter (probeset) information from a file.
     454            Import reporter (probeset) information from a file. A configuration
     455            is not needed, but is recommended. BASE has pre-installed configurations
     456            for several different file types.
    389457          </para>
    390458          <para>
     
    392460            configurations:</emphasis>
    393461          </para>
    394           <para>
    395             GenePix related <ulink
    396             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/reporter_importer_96wells.xml?format=raw">96
    397             wells</ulink>, <ulink
    398             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/reporter_importer_384wells.xml?format=raw">384
    399             wells</ulink>, and <ulink
    400             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/reporter_importer_genepix.xml?format=raw">GenePix</ulink>.
    401           </para>
    402           <para>
    403             Affymetrix related, these samples import a small amount of
    404             information: <ulink
    405             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/reporter_importer_affymetrix.xml?format=raw">HG-U133_Plus_2
    406             and MG_U74Av2</ulink> and <ulink
    407             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/reporter_importer_affymetrix2.xml?format=raw">HG-U133A</ulink>.
    408             The samples may work on other Affymetrix chips, the listed
    409             ones are tested and known to work.
    410           </para>
    411462        </listitem>
    412463      </varlistentry>
     
    416467        <listitem>
    417468          <para>
    418             Imports GenePix features from a gpr-file.
    419           </para>
    420           <para>
    421             <emphasis>Since BASE 2.0, <ulink
    422             url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/reporter_map_importer_genepix.xml?format=raw">GenePix</ulink>
    423             sample configuration available.</emphasis>
     469            Imports array design features from text files. This plug-in can
     470            be used without connection to plates. A configuration is needed.
     471            BASE has pre-installed configurations for some file formats.
    424472          </para>
    425473        </listitem>
     
    433481      <para>
    434482        The batch import plug-ins all work similarly and their usage
    435         is described in <xref linkend="import_data" />.
     483        is described in <xref linkend="import_data.batch" />. All
     484        batch importers have support for configurations but can also
     485        be used without.
    436486      </para>
    437487
     
    443493              Imports and updates array batches in a batch.
    444494            </para>
    445             <para>
    446               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    447             </para>
    448495          </listitem>
    449496        </varlistentry>
     
    455502              Imports and updates array designs in a batch.
    456503            </para>
    457             <para>
    458               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    459             </para>
    460504          </listitem>
    461505        </varlistentry>
     
    467511              Imports and updates array slides in a batch.
    468512            </para>
    469             <para>
    470               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
     513          </listitem>
     514        </varlistentry>
     515
     516        <varlistentry>
     517          <term>Bioplate importer</term>
     518          <listitem>
     519            <para>
     520              Imports and updates bioplates in a batch. Note that this
     521              import can't be used to put biomaterial on the bioplates.
    471522            </para>
    472523          </listitem>
     
    479530              Imports and updates biosources in a batch.
    480531            </para>
    481             <para>
    482               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
     532          </listitem>
     533        </varlistentry>
     534
     535        <varlistentry>
     536          <term>Derived bioassay importer</term>
     537          <listitem>
     538            <para>
     539              Imports and updates derived bioassays in a batch.
    483540            </para>
    484541          </listitem>
     
    491548              Imports and updates extracts in a batch.
    492549            </para>
    493             <para>
    494               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    495             </para>
    496           </listitem>
    497         </varlistentry>
    498 
    499         <varlistentry>
    500           <term>Hybridization importers</term>
    501           <listitem>
    502             <para>
    503               Imports and updates hybridizations in a batch.
    504             </para>
    505             <para>
    506               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    507             </para>
    508           </listitem>
    509         </varlistentry>
    510 
    511         <varlistentry>
    512           <term>Labeled extract importer</term>
    513           <listitem>
    514             <para>
    515               Imports and updates labeled extracts in a batch.
    516             </para>
    517             <para>
    518               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
     550          </listitem>
     551        </varlistentry>
     552
     553        <varlistentry>
     554          <term>Physical bioassay importer</term>
     555          <listitem>
     556            <para>
     557              Imports and updates physical bioassays in a batch.
    519558            </para>
    520559          </listitem>
     
    527566              Imports and updates raw bioassays in a batch.
    528567            </para>
    529             <para>
    530               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    531             </para>
    532568          </listitem>
    533569        </varlistentry>
     
    539575              Imports and updates samples in a batch.
    540576            </para>
    541             <para>
    542               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    543             </para>
    544           </listitem>
    545         </varlistentry>
    546 
    547         <varlistentry>
    548           <term>Scan importer</term>
    549           <listitem>
    550             <para>
    551               Imports and updates scans in a batch.
    552             </para>
    553             <para>
    554               <emphasis>Since BASE 2.8, no configuration required.</emphasis>
    555             </para>
    556           </listitem>
    557         </varlistentry>
     577          </listitem>
     578        </varlistentry>
     579
    558580      </variablelist>
    559581
     
    570592        <listitem>
    571593          <para>
    572             Calculate intensities from raw data.
    573           </para>
    574           <para>
    575             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     594            Calculate intensities from raw data using a user-defined formula.
     595            No configuration is needed, but formulas must be defined using
     596            <menuchoice>
     597              <guimenu>View</guimenu>
     598              <guimenuitem>Formulas</guimenuitem>
     599            </menuchoice>.
    576600          </para>
    577601        </listitem>
     
    592616          <para>
    593617            Converts a full-size image into JPEG images for each spot.
    594           </para>
    595           <para>
    596             <emphasis>Since BASE 2.0, no configuration needed.</emphasis>
     618            No configuration is needed.
    597619          </para>
    598620        </listitem>
     
    605627            Unpacks a tar file on the BASE file system. It also
    606628            supports TAR files compressed with GZIP or BZIP
    607             algorithms.
    608           </para>
    609           <para>
    610             <emphasis>Since BASE 2.1, no configuration needed.</emphasis>
     629            algorithms. This plug-in can be used to automatically
     630            unpack files during upload. No configuration is needed.
    611631          </para>
    612632        </listitem>
     
    617637        <listitem>
    618638          <para>
    619             Unpacks zip and jar file on the BASE's file system.
    620           </para>
    621           <para>
    622             <emphasis>Since BASE 2.1, no configuration needed.</emphasis>
     639            Unpacks ZIP and JAR files on the BASE's file system.
     640            This plug-in can be used to automatically unpack files
     641            during upload. No configuration is needed.
    623642          </para>
    624643        </listitem>
  • trunk/doc/src/docbook/appendix/incompatible.xml

    r5782 r5820  
    5252    <para>
    5353      The list of changes made in the various BASE 2.x releases can be found
    54       in the <ulink url="http://base.thep.lu.se/chrome/site/2.17/html/index.html"
     54      in the <ulink url="http://base.thep.lu.se/chrome/site/2.17/html/appendix/appendix.incompatible.html"
    5555      >BASE 2.17 documentation</ulink>.
    5656    </para>
  • trunk/doc/src/docbook/developer/core_ref.xml

    r5781 r5820  
    29162916              <programlisting language="java">
    29172917<![CDATA[
    2918 // DerivedBioAssaySet.java
     2918// DerivedBioAssay.java
    29192919@Override
    29202920@SubtypableRelatedItems({Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAYSET, Item.SOFTWARE, Item.HARDWARE, Item.PROTOCOL})
  • trunk/doc/src/docbook/developer/documentation.xml

    r5819 r5820  
    13481348      <para>
    13491349        All classes and diagrams are in a single UML file. It can be
    1350         found at <filename>&lt;base-dir&gt;/doc/src/uml/base.mdzip</filename>
     1350        found at <filename>&lt;base-dir&gt;/doc/src/uml/baseuml.mdzip</filename>
    13511351      </para>
    13521352     
     
    14531453          <para>
    14541454            To achieve this we have slightly altered the meaning of some UML symbols.
    1455             For example we use the access modified symbols (+, ~ and -) to indicate
     1455            For example we use the access modifier symbols (+, ~ and -) to indicate
    14561456            if a property is updatable or not.
     1457            Some of the information needed is specified as <emphasis>tagged values</emphasis>
     1458            that can be attached to a class.
     1459            Double-click on the new class to bring up it's properties dialog
     1460            box. Switch to the <guilabel>Tags</guilabel> configuration page.
    14571461          </para>
    1458 
    1459           <sect4 id="magicdraw.classes.data.tags">
    1460             <title>Setting tagged values</title>
     1462         
     1463            <figure id="magicdraw.figures.classtags">
     1464              <title>Setting tagged values</title>
     1465              <screenshot>
     1466                <mediaobject>
     1467                  <imageobject>
     1468                    <imagedata
     1469                      scalefit="1" width="100%"
     1470                      fileref="figures/magicdraw/classtags.png" format="PNG" />
     1471                  </imageobject>
     1472                </mediaobject>
     1473              </screenshot>
     1474            </figure>
    14611475           
    14621476            <para>
    1463               Some of the information needed is specified as <emphasis>tagged values</emphasis>
    1464               that can be attached to a class.
    1465               Double-click on the new class to bring up it's properties dialog
    1466               box. Switch to the <guilabel>Tags</guilabel> configuration page.
    1467               We have defined the following tags:
    1468             </para>
    1469              
     1477            We have defined the following tags:
     1478            </para>
     1479           
    14701480            <variablelist>
    14711481            <varlistentry>
     
    15261536              </listitem>
    15271537            </varlistentry>
     1538            <varlistentry>
     1539              <term><guilabel>discriminator-value</guilabel></term>
     1540              <listitem>
     1541                <para>
     1542                Used for classes that share the underlying database table. The
     1543                discriminator value is used so that Hibernate knows which subclass
     1544                to create.
     1545                </para>
     1546              </listitem>
     1547            </varlistentry>
    15281548            </variablelist>
    15291549           
    1530             <figure id="magicdraw.figures.classtags">
    1531               <title>Setting tagged values</title>
    1532               <screenshot>
    1533                 <mediaobject>
    1534                   <imageobject>
    1535                     <imagedata
    1536                       scalefit="1" width="100%"
    1537                       fileref="figures/magicdraw/classtags.png" format="PNG" />
    1538                   </imageobject>
    1539                 </mediaobject>
    1540               </screenshot>
    1541             </figure>
    1542           </sect4>
    1543          
    1544           <sect4 id="magicdraw.classes.data.properties">
    1545             <title>Specifying simple properties for a class</title>
    15461550            <para>
    15471551              Simple properties are strings, numbers, dates, etc. that are part of an object.
     
    15701574            <listitem>
    15711575              <para>
    1572               If null values are allowed or not: specify a multiplicity of 1 if a
    1573               non-null value is required.
     1576              If null values are allowed or not. Specify a multiplicity of 1 if a
     1577              non-null value is required, but only if the underlying datatype
     1578              can hold null values.
    15741579              </para>
    15751580            </listitem>
     
    16141619                </mediaobject>
    16151620              </screenshot>
    1616             </figure>         
    1617           </sect4>
    1618          
    1619           <sect4 id="magicdraw.classes.data.associations">
    1620             <title>Associations to other classes</title>
     1621            </figure>
    16211622
    16221623            <para>
     
    16681669            </para>         
    16691670
    1670           </sect4>
    16711671
    16721672          <para>
     
    17871787            </para>
    17881788          </listitem>
     1789          <listitem>
     1790            <para>
     1791            Core class: Use this style for all primary core classes in a diagram. It will
     1792            display all info that we are interested in.
     1793            </para>
     1794          </listitem>
     1795         
    17891796          </itemizedlist>     
    17901797        </sect3>
     
    18651872        General information about Javadoc and how it is written in a proper way can be found
    18661873        at
    1867         <ulink url="http://java.sun.com/j2se/javadoc/writingdoccomments/index.html">
    1868           http://java.sun.com/j2se/javadoc/writingdoccomments/index.html</ulink>.
     1874        <ulink url="http://www.oracle.com/technetwork/java/javase/documentation/index-137868.html"
     1875          >http://www.oracle.com/technetwork/java/javase/documentation/index-137868.html</ulink>.
    18691876        The rule when coding in Base is that all packages, classes, interfaces, public
    18701877        methods and public attributes must be commented in Javadoc style. It is also
     
    18891896              <listitem>
    18901897                <para>
    1891                   If a comment only should be shown in the internal documentation
    1892                   and not in the public, it should be tagged with
    1893                   <synopsis>@base.internal</synopsis>
     1898                  If a comment is mostly related to the inner workings of
     1899                  BASE, it should be tagged with <synopsis>@base.internal</synopsis>
    18941900                </para>
    18951901              </listitem>
     
    19371943              </varlistentry>
    19381944              <varlistentry>
    1939                 <term><synopsis>@version</synopsis></term>
     1945                <term><synopsis>@since</synopsis></term>
    19401946                <listitem>
    1941                   <para>From which version of Base the class is available.</para>
     1947                  <para>The BASE verion when this class or interface was added.</para>
    19421948                </listitem>
    19431949              </varlistentry>
  • trunk/doc/src/docbook/faq/faqs.xml

    r5782 r5820  
    485485        </qandaentry>
    486486
    487         <qandaentry>
    488           <question>
    489             <para>Unzipped files never inherit file type specified
    490             during upload, why?</para>
    491           </question>
    492           <answer>
    493             <para>
    494               Unfortunately this is an "unfixable" defect. The API for
    495               unpacking files is a kind of plug-in interface
    496               (FileUnpacker) that has been made public. The "mistake"
    497               is that the API does not include any information from
    498               the file upload dialog except the directory to upload to
    499               (not even the file name is included). Introducing new
    500               method or parameters will break the API and we prefer to
    501               not do that.
    502             </para>
    503             <para>
    504               As a workaround to this problem the extension of each
    505               file is checked against the list of MIME types
    506               (<menuchoice>
    507                 <guimenu>Administrate</guimenu>
    508                 <guimenuitem>Types</guimenuitem>
    509                 <guimenuitem>Mime Types</guimenuitem>
    510               </menuchoice>).
    511               If a MIME type with the same extension is found and has
    512               been connected to a file type, this file type is
    513               transferred to the file. This will obviously only work
    514               for non-generic file
    515               extensions, <emphasis>eg.</emphasis>, .gpr for GenePix
    516               raw data files, .cel for Affymetrix CEL files, etc.
    517             </para>
    518           </answer>
    519         </qandaentry>
    520487      </qandaset>
    521488
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