Changeset 5706


Ignore:
Timestamp:
Aug 23, 2011, 3:20:30 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

User documentation chapter 10 to 15. Added new chapter about "Item subtypes". Removed sections about protocol types, hardware types and software types. Merged "Hardware" and "Software" into a single chapter.

Added some menu separators in the New annotation type menu.

As usual, screen shots have not yet been updated.

Location:
trunk
Files:
1 added
3 deleted
10 edited
1 moved

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r5675 r5706  
    13141314    <mkdir dir="${docbook.html.out}/userdoc/analysis"/>
    13151315    <mkdir dir="${docbook.html.out}/userdoc/filesystem"/>
    1316     <mkdir dir="${docbook.html.out}/userdoc/hardware"/>
     1316    <mkdir dir="${docbook.html.out}/userdoc/subtypes"/>
     1317    <mkdir dir="${docbook.html.out}/userdoc/wares"/>
    13171318    <mkdir dir="${docbook.html.out}/userdoc/import"/>
    13181319    <mkdir dir="${docbook.html.out}/userdoc/export"/>
     
    13211322    <mkdir dir="${docbook.html.out}/userdoc/protocols"/>
    13221323    <mkdir dir="${docbook.html.out}/userdoc/reporters"/>
    1323     <mkdir dir="${docbook.html.out}/userdoc/software"/>
    13241324    <mkdir dir="${docbook.html.out}/userdoc/trashcan"/>
    13251325    <mkdir dir="${docbook.html.out}/userdoc/webclient"/>
  • trunk/doc/src/docbook/userdoc/annotations.xml

    r5682 r5706  
    5757      <emphasis>Protocols</emphasis>
    5858      and
    59       <emphasis>BioAssaysets</emphasis>
     59      <emphasis>Bioassay sets</emphasis>
    6060    </para>
    6161
     
    7676      &gbNew; button. This behaves differently
    7777      than other buttons found elsewhere and you must select
    78       one of the 8 different types which can be split in 4 main groups.
     78      one of the 9 different types which can be split in 4 main groups.
    7979    </para>
    8080
     
    323323          </listitem>
    324324        </varlistentry>
    325 
    326         <varlistentry>
    327           <term><guilabel>Min/max value</guilabel></term>
    328           <listitem>
    329             <para>
    330               Available for numerical annotation types only.
    331               Specifies the minimum and maximum allowed value.
    332               If left empty, the bound(s) are undefined and any
    333               value is allowed.
    334             </para>
    335           </listitem>
    336         </varlistentry>
    337325       
    338326        <varlistentry>
     
    597585      </para>
    598586    </example>
     587   
     588    <tip>
     589      <para>
     590      If you use the same name for a category as for an item subtype (see <xref linkend="subtypes" />)
     591      the annotations in this category will be selected by default when editing an item item
     592      by that subtype. This can be useful when you have two or more subtypes of the same
     593      main item type and a different set of annotations that should be used on each subtype.
     594      For example, <emphasis>Labeled extract</emphasis> and <emphasis>Library</emphasis>
     595      are subtypes of <emphasis>Extract</emphasis>, which probably have different annotation
     596      types.
     597      </para>
     598    </tip>
     599   
    599600  </sect1>
    600601
     
    781782        BASE includes a plug-in for importing annotations to multiple items
    782783        in one go. The plug-in read annotation values from a simple column-based
    783         text file. Usually, a tab is used as the delimiter between columns.
     784        text file. Usually, a tab is used as the delimiter between columns, but this
     785        is configurable.
    784786        The first row should contain the column headers. One column should contain
    785787        the name or the external ID of the item. The rest of the columns can each be
  • trunk/doc/src/docbook/userdoc/index.xml

    r4509 r5706  
    3535  <include file="annotations.xml"/>
    3636  <include file="platforms.xml" />
     37  <include file="subtypes.xml" />
    3738  <include file="protocols.xml"/>
    38   <include file="hardware.xml"/>
    39   <include file="software.xml"/>
     39  <include file="wares.xml"/>
    4040  <include file="array_lims.xml"/>
    4141  <include file="biomaterials.xml"/>
  • trunk/doc/src/docbook/userdoc/platforms.xml

    r4509 r5706  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <chapter id="platforms">
     26<chapter id="platforms" chunked="0">
    2727  <?dbhtml dir="platforms"?>
    2828  <title>Experimental platforms and data file types</title>
     
    285285        <para>
    286286        Make it possible to validate and extract metadata from attached files.
    287         This is done by plug-ins. A data file type may specify which plug-in
    288         to use for validation and metadata extraction. Currently, BASE ships
    289         with plug-ins for CEL and CDF files.
     287        This is done by extensions. Currently, BASE ships
     288        with extensions for CEL and CDF files, but the administrator may have installed
     289        extensions for other file types. See <xref linkend="extensions_developer.fileset_validator"/>
     290        for more information about creating extensions.
    290291        </para>
    291292      </listitem>
     
    372373      </varlistentry>
    373374      <varlistentry>
    374         <term><guilabel>Validator</guilabel></term>
    375         <listitem>
    376           <para>
    377             The name of the Java class that can be used to
    378             validate if a given file is a valid file of this type.
    379             The class must implement the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileValidator</interfacename>
    380             interface. <nohelp>See <xref linkend="plugin_developer.other.datafiles" />.</nohelp>
    381           </para>
    382         </listitem>
    383       </varlistentry>
    384       <varlistentry>
    385         <term><guilabel>Metadata reader</guilabel></term>
    386         <listitem>
    387           <para>
    388             The name of the Java class that can be used to
    389             extract metadata from a file of this type.
    390             The class must implement the <interfacename docapi="net.sf.basedb.core.filehandler">DataFileMetadataReader</interfacename>
    391             interface. <nohelp>See <xref linkend="plugin_developer.other.datafiles" />.</nohelp>
    392           </para>
    393         </listitem>
    394       </varlistentry>
    395       <varlistentry>
    396375        <term><guilabel>Description</guilabel></term>
    397376        <listitem>
     
    423402        <listitem>
    424403          <para>
    425             Mark this checkbox if you want to validate the selected files.
    426             The checkbox is automatically selected if you remove or select
    427             a different file.
    428           </para>
    429         </listitem>
    430       </varlistentry>
    431       <varlistentry>
    432         <term><guilabel>Extract metadata</guilabel></term>
    433         <listitem>
    434           <para>
    435             Mark this checkbox if you want to extract metadata from the
    436             selected files. The checkbox is automatically selected if you
    437             remove or select a different file.
     404            Mark this checkbox if you want to validate and extract metadata
     405            from the selected files. The checkbox is automatically checked
     406            if you remove or select a different file.
    438407          </para>
    439408        </listitem>
     
    443412      <note>
    444413        <para>
    445           Validation and metadata extraction is only done for file types
    446           which has registered a plug-in that can do the validation and
    447           metadata extraction. The checkboxes are always present
    448           event if the file types for a particular platform doesn't
    449           have any validator or metadata extractor.
     414          Validation and metadata extraction is performed by extensions.
     415          The checkbox is only visible if there is at least one
     416          installed extension that supports validation of the
     417          current file types.
    450418        </para>
    451419      </note>
  • trunk/doc/src/docbook/userdoc/project_permission.xml

    r5705 r5706  
    653653      </sect2>
    654654     
     655      <sect2 id ="project_permissions.project.defaults">
     656        <title>Default items</title>
     657       
     658        <para>TODO</para>
     659       
     660      </sect2>
     661     
    655662      <sect2 id="project_permission.projects.items">
    656663        <title>Working with the items in the project</title>
  • trunk/doc/src/docbook/userdoc/protocols.xml

    r4509 r5706  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <chapter id="protocols_protocoltypes">
     26<chapter id="protocols" chunked="0">
    2727  <?dbhtml dir="protocols"?>
    28   <title>Protocols and protocol types</title>
    29   <para>
    30     Information about laboratory standard operating procedure
    31     and protocols can be tracked in BASE using two structures,
    32     the use of which is detailed in the following sections.
    33   </para>
    34   <sect1 id="protocoltypes">
    35     <title>Protocol types</title>
     28  <title>Protocols</title>
    3629
    37     <helptext external_id="protocoltype.view.properties"
    38       title="Protocol Types">
    39       <para>
    40         <guilabel>Protocol Type</guilabel>
    41         allows classification of protocols based on their
    42         usage and purpose in the laboratory workflow. By
    43         default, BASE creates the 8 main Protocol types and
    44         those correspond to the main protocol families
    45         identified by MIAME requirements and applied in a
    46         canonical DNA microarray experiment meant for
    47         surveying gene expression. These 8 protocol types
    48         are namely
    49         <guilabel>Printing</guilabel>,
    50         <guilabel>Sampling</guilabel>,
    51         <guilabel>Pooling</guilabel>,
    52         <guilabel>Extraction</guilabel>,
    53         <guilabel>Labeling</guilabel>,
    54         <guilabel>Hybridization</guilabel>,
    55         <guilabel>Scanning</guilabel> and
    56         <guilabel>Feature extraction</guilabel>.
    57       </para>
    58       <para>
    59         New applications of DNA microarray technology, for
    60         instance DNA binding site identification, imposes
    61         the creation of new protocol type in addition to
    62         those built-in in BASE.
    63       </para>
    64       <tip>
    65         <title>Follow MIAME recommendations</title>
    66         <para>
    67           It is advised to define the protocol type
    68           <guilabel>Name</guilabel>
    69           so that it is compatible with the
    70           MIAME requirements and recommendations issues by
    71           microarray data repositories.
    72         </para>
    73       </tip>
    74     </helptext>
     30    <para>
     31      A protocol is a document describing some kind of process that
     32      is typically performed in the lab to create an item
     33      of some type (for example, how to create an extract from a sample).
     34      It can also represent a procedure for running software programs to
     35      extract measured data (for example, from a scanned microarray image).
     36      A protocol in the simplest form is just a name with an optional link to a file.
     37      The file may for example be a PDF or some other document with a more
     38      detailed description.
     39    </para>
    7540   
    7641    <para>
    77       You can manage the protocol types by going to
    78       <menuchoice>
     42      Protocols are typically added to a BASE server by an administrator
     43      and can be managed from <menuchoice>
    7944        <guimenu>Administrate</guimenu>
    80         <guimenuitem>Types</guimenuitem>
    81         <guisubmenu>Protocol Type</guisubmenu>
     45        <guimenuitem>Protocols</guimenuitem>
    8246      </menuchoice>.
    8347    </para>
     48
     49     
    8450    <figure
    85       id="protocols.figures.protocoltype">
    86       <title>Protocol type properties</title>
     51      id="protocols.figures.edit_protocol">
     52      <title>Protocol properties</title>
    8753      <screenshot>
    8854        <mediaobject>
    8955          <imageobject>
    9056            <imagedata
    91               fileref="figures/edit_protocoltype.png" format="PNG" />
     57              fileref="figures/edit_protocol.png" format="PNG" />
    9258          </imageobject>
    9359        </mediaobject>
    9460      </screenshot>
    9561    </figure>
    96    
    97     <helptext external_id="protocoltype.edit"
    98       title="Edit protocol type">
    99    
    100       <variablelist>
    101       <varlistentry>
    102         <term><guilabel>Name</guilabel></term>
    103         <listitem>
    104           <para>
    105             The name of the protocol type.
    106           </para>
    107         </listitem>
    108       </varlistentry>
    109       <varlistentry>
    110         <term><guilabel>Description</guilabel></term>
    111         <listitem>
    112           <para>
    113             A description of the protocol type.
    114           </para>
    115         </listitem>
    116       </varlistentry>
    117       </variablelist>
    118     </helptext>
    119   </sect1>
    120 
    121   <sect1 id="protocols">
    122     <title>Protocols</title>
    123     <para>
    124       In BASE, protocols can be created by two routes. Either
    125       from the single-item view of a protocol type or from the
    126       list view of protocols.
    127     </para>
    128     <sect2 id="protocols.properties">
    129       <title>Protocol properties</title>
    130      
    131       <figure
    132         id="protocols.figures.edit_protocol">
    133         <title>Protocol properties</title>
    134         <screenshot>
    135           <mediaobject>
    136             <imageobject>
    137               <imagedata
    138                 fileref="figures/edit_protocol.png" format="PNG" />
    139             </imageobject>
    140           </mediaobject>
    141         </screenshot>
    142       </figure>
    14362     
    14463      <helptext external_id="protocol.edit"
     
    14867        This tab allows users to enter essential
    14968        information about a protocol.
     69        </para>
    15070       
    15171        <variablelist>
     
    16484            The protocol type of the protocol. The list
    16585            may evolve depending on additions by the server
    166             administrator.
     86            administrator. Selecting the proper protocol type
     87            is important and enables BASE to automatically guess
     88            the most likely protocol when creating new items.
     89            <nohelp>
     90            See <xref linkend="subtypes" /> for more information.
     91            </nohelp>
     92            </para>
     93          </listitem>
     94        </varlistentry>
     95        <varlistentry>
     96          <term><guilabel>External ID</guilabel></term>
     97          <listitem>
     98            <para>
     99            An ID identifying this protocol in an external
     100            database. The value does not have to be unique.
    167101            </para>
    168102          </listitem>
     
    173107            <para>
    174108            A document containing the protocol description,     
    175             e.g. pdf documents from kit providers to
     109            e.g. PDF documents from kit providers to
    176110            the protocol. Use the <guibutton>Select</guibutton>
    177111            button to select or upload a file.
     
    188122        </varlistentry>
    189123        </variablelist>
    190         </para>   
    191124       
    192125        <seeother>
     
    194127        </seeother>
    195128      </helptext>
    196     </sect2>
    197129   
    198     <sect2 id="protocols.parameters">
     130    <sect1 id="protocols.parameters">
    199131      <title>Protocol parameters</title>
    200132
     
    264196     
    265197      </helptext>
    266     </sect2>
    267 
    268198  </sect1>
    269199</chapter>
  • trunk/doc/src/docbook/userdoc/reporters.xml

    r4889 r5706  
    145145      </para>
    146146     
    147       <tip>
    148         <title>Exchanging plug-in configurations</title>
    149         <para>
    150           As for any other plug-in, configuration parameters
    151           can be saved as an XML file and exchanged with
    152           another BASE instance, thereby reducing
    153           configuration burden (provided the two instances have
    154           identical <filename>extended-properties.xml</filename> files).
    155           See <xref linkend="resources.coreplugins" /> for information
    156           about available configuration files.
    157         </para>
    158       </tip>
    159 
    160147      <note>
    161148        <title>Dealing with Affymetrix probesets</title>
     
    176163          the associated CDF file to import the missing probesets into
    177164          BASE, make sure not to upgrade existing reporters when
    178           starting the plug-in. The CDF file contains no annotation
    179           information and consequently annotation information is
    180           removed if the CDF used to upgrade annotations.
     165          starting the plug-in.
    181166        </para>
    182167      </note>
     
    341326          A common problem is to delete reporters that has been accidentally
    342327          created. The regular web interface is usually no good since it
    343           only allows you to select at most 99 reporters at a time. To solve
     328          only allows you to delete a limited number of reporters at a time. To solve
    344329          this problem the reporter import plug-in can be used in delete mode.
    345330          You can use the same file as you used when importing. Just select
     
    369354      BASE allows for defining sets of reporters for a
    370355      particular use, for instance to define a list of
    371       reporters to be used on an array. There are two ways to do
     356      reporters to be used on an array. There are several ways to do
    372357      so:
    373358    </para>
    374     <orderedlist>
     359    <itemizedlist>
    375360      <listitem>
    376361        <para>
     
    379364            <guimenu>View</guimenu>
    380365            <guimenuitem>Reporters</guimenuitem>
    381           </menuchoice> page.
     366          </menuchoice> page. This creates a reporter list with the current
     367          selection or filtered out reporters.
    382368        </para>
    383369      </listitem>
     
    389375            <guimenu>View</guimenu>
    390376            <guimenuitem>Reporter lists</guimenuitem>
    391           </menuchoice> page.
    392         </para>
    393       </listitem>
    394       </orderedlist>
     377          </menuchoice> page. This creates an initially empty reporter list
     378          that can be filled later.
     379        </para>
     380      </listitem>
     381     
     382      <listitem>
     383        <para>
     384          Use the <guibutton>New reporter list</guibutton> button on the
     385          <guilabel>Features</guilabel> tab on the single-item view page
     386          for an array design. This creates a reporter list with all or some of
     387          the reporters used on the array design.
     388        </para>
     389      </listitem>
     390     
     391      <listitem>
     392        <para>
     393          Use the <guibutton>New reporter list</guibutton> button on the
     394          <guilabel>Raw data</guilabel> tab on the single-item view page
     395          for a raw bioassay. This creates a reporter list with all or some of
     396          the reporters used by the raw bioassay.
     397        </para>
     398      </listitem>
     399     
     400      <listitem>
     401        <para>
     402          Use the <guibutton>New reporter list</guibutton> button on the
     403          <guilabel>Spot data</guilabel> tab on the single-item view page
     404          for a bioassay set in the experiment analysis section.
     405          This creates a reporter list with all or some of
     406          the reporters used by the current bioassay set.
     407        </para>
     408      </listitem>
     409     
     410      <listitem>
     411        <para>
     412          Use the <guibutton>New reporter list</guibutton> button on the
     413          <guilabel>Reporter search</guilabel> tab in experiment explorer.
     414          This creates a reporter list with all or some of
     415          the reporters used by the current bioassay set.
     416        </para>
     417      </listitem>
     418     
     419      </itemizedlist>
    395420     
    396421      <figure
     
    437462            <para>
    438463            Select one of the options for specifying which reporters
    439             should be included in the list.
    440             <note>
    441               This option is only available when creating a
    442               reporter list from the
    443               <menuchoice>
    444                 <guimenu>View</guimenu>
    445                 <guimenuitem>Reporters</guimenuitem>
    446               </menuchoice> page, not when editing
    447               an existing list or creating it from the
    448               <menuchoice>
    449                 <guimenu>View</guimenu>
    450                 <guimenuitem>Reporter lists</guimenuitem>
    451               </menuchoice> page.
    452             </note>
    453            
    454             <tip>
    455               <para>
    456               To add or remove reporters to the list use the
    457               <guilabel>Reporters</guilabel> tab on the single-item
    458               view page of a reporter list. This tab lists all
    459               reporters in the list and there are functions for
    460               removing, adding and importing reporters to the list.
    461               </para>
    462             </tip>
    463            
     464            should be included in the list. This option is only available
     465            when creating a new reporter list, not when editing an existing
     466            list.
    464467            </para>
    465468          </listitem>
     
    474477        </varlistentry>
    475478        </variablelist>
     479
     480        <tip>
     481          <para>
     482          To add or remove reporters to the list use the
     483          <guilabel>Reporters</guilabel> tab on the single-item
     484          view page of a reporter list. This tab lists all
     485          reporters in the list and there are functions for
     486          removing, adding and importing reporters to the list.
     487          </para>
     488        </tip>
     489
     490
    476491      </helptext>
    477492
  • trunk/doc/src/docbook/userdoc/wares.xml

    r5693 r5706  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <chapter id="hardware">
    27   <?dbhtml dir="hardware"?>
    28   <title>Hardware</title>
    29   <para>
    30     Information about laboratory equipment can be tracked in
    31     BASE using two structures, the use of which is detailed in
    32     the following sections.
    33   </para>
    34   <sect1 id="hardware.hardwaretypes">
    35     <title>Hardware types</title>
     26<chapter id="wares" chunked="0">
     27  <?dbhtml dir="wares"?>
     28  <title>Hardware and software</title>
    3629
    37     <helptext external_id="hardwaretype.view.properties"
    38       title="Hardware types">
    39 
    40       <para>
    41         <guilabel>Hardware Type</guilabel>
    42         allows classification of hardware based on their usage
    43         and purpose in the laboratory workflow. By default, BASE
    44         creates the 3 main hardware types and
    45         those correspond to the main hardware families
    46         identified by
    47         <ulink
    48           url="http://www.mged.org/Workgroups/MIAME/miame.html">
    49           MIAME requirements</ulink>.
    50         These 3 hardware types are
    51         <guilabel>Print Robot</guilabel>,
    52         <guilabel>Scanner</guilabel>,
    53         and
    54         <guilabel>Hybridization station</guilabel>.
    55       </para>
    56       <para>
    57         In case those built-in types are not enough, it
    58         is possible to create new ones.
    59       </para>
    60     </helptext>
    61 
    62     <para>
    63       You can manage the hardware types by going to
    64       <menuchoice>
    65         <guimenu>Administrate</guimenu>
    66         <guimenuitem>Types</guimenuitem>
    67         <guisubmenu>Hardware types</guisubmenu>
    68       </menuchoice>.
    69     </para>
    70    
    71     <figure
    72       id="hardware.figures.hardwaretype">
    73       <title>Hardware type properties</title>
    74       <screenshot>
    75         <mediaobject>
    76           <imageobject>
    77             <imagedata
    78               fileref="figures/edit_hardwaretype.png" format="PNG" />
    79           </imageobject>
    80         </mediaobject>
    81       </screenshot>
    82     </figure>
    83 
    84     <helptext external_id="hardwaretype.edit"
    85       title="Edit hardware type">
    86    
    87       <variablelist>
    88       <varlistentry>
    89         <term><guilabel>Name</guilabel></term>
    90         <listitem>
    91           <para>
    92             The name of the hardware type.
    93             <tip>
    94               <para>
    95                 It is advised to define the name
    96                 so that it is compatible with the MIAME
    97                 requirements and recommendations issues by
    98                 microarray data repositories.
    99               </para>
    100             </tip>
    101           </para>
    102         </listitem>
    103       </varlistentry>
    104       <varlistentry>
    105         <term><guilabel>Description</guilabel></term>
    106         <listitem>
    107           <para>
    108             A description of the hardware type.
    109           </para>
    110         </listitem>
    111       </varlistentry>
    112       </variablelist>
    113     </helptext>
    114   </sect1>
    115  
    116   <sect1 id="hardware.hardware">
     30  <sect1 id="wares.hardware">
    11731    <title>Hardware</title>
    11832   
    11933    <para>
    120       In BASE, hardware can be created by two routes. Either
    121       from the single-item view of a hardware type or from the
    122       list view of hardware.
     34      A hardware is used in BASE to represent a piece of equipment in the lab
     35      that is used in the experiments.
     36      Information about hardware is typically added to a BASE server by an administrator
     37      and can be managed from <menuchoice>
     38        <guimenu>Administrate</guimenu>
     39        <guimenuitem>Hardware</guimenuitem>
     40      </menuchoice>.
    12341    </para>
    12442   
     
    14866      </varlistentry>
    14967      <varlistentry>
    150         <term><guilabel>Version</guilabel></term>
    151         <listitem>
    152           <para>
    153           The version number or model of the hardware.
    154           </para>
    155         </listitem>
    156       </varlistentry>
    157       <varlistentry>
    15868        <term><guilabel>Type</guilabel></term>
    15969        <listitem>
     
    16171          The hardware type of the hardware. The list
    16272          may evolve depending on additions by the server
    163           administrator.
     73          administrator. Selecting the proper hardware type
     74          is important and enables BASE to automatically guess
     75          the most likely hardware when creating new items.
     76          <nohelp>
     77            See <xref linkend="subtypes" /> for more information.
     78          </nohelp>
     79          </para>
     80        </listitem>
     81      </varlistentry>
     82      <varlistentry>
     83        <term><guilabel>Version</guilabel></term>
     84        <listitem>
     85          <para>
     86          The version number or model of the hardware.
    16487          </para>
    16588        </listitem>
     
    177100   
    178101  </sect1>
     102 
     103  <sect1 id="wares.software">
     104    <title>Software</title>
     105   
     106    <para>
     107      A hardware is used in BASE to represent the software that is used to
     108      process and analyze data outside of BASE. Analysis that is done inside
     109      BASE is usually represented as plug-ins.
     110      Information about software is typically added to a BASE server by an administrator
     111      and can be managed from <menuchoice>
     112        <guimenu>Administrate</guimenu>
     113        <guimenuitem>Software</guimenuitem>
     114      </menuchoice>.
     115    </para>
     116   
     117    <figure
     118      id="software.figures.edit_softwware">
     119      <title>Software properties</title>
     120      <screenshot>
     121        <mediaobject>
     122          <imageobject>
     123            <imagedata
     124              fileref="figures/edit_software.png" format="PNG" />
     125          </imageobject>
     126        </mediaobject>
     127      </screenshot>
     128    </figure>
     129         
     130    <helptext external_id="software.edit"
     131      title="Edit software">
     132      <variablelist>
     133      <varlistentry>
     134        <term><guilabel>Name</guilabel></term>
     135        <listitem>
     136          <para>
     137          The name of the software.
     138          </para>
     139        </listitem>
     140      </varlistentry>
     141      <varlistentry>
     142        <term><guilabel>Type</guilabel></term>
     143        <listitem>
     144          <para>
     145          The software type of the software. The list
     146          may evolve depending on additions by the server
     147          administrator. Selecting the proper software type
     148          is important and enables BASE to automatically guess
     149          the most likely software when creating new items.
     150          <nohelp>
     151            See <xref linkend="subtypes" /> for more information.
     152          </nohelp>
     153          </para>
     154        </listitem>
     155      </varlistentry>
     156      <varlistentry>
     157        <term><guilabel>Version</guilabel></term>
     158        <listitem>
     159          <para>
     160          The version number of the software.
     161          </para>
     162        </listitem>
     163      </varlistentry>
     164      <varlistentry>
     165        <term><guilabel>Description</guilabel></term>
     166        <listitem>
     167          <para>
     168          A description of the software.
     169          </para>
     170        </listitem>
     171      </varlistentry>
     172      </variablelist>
     173    </helptext>
     174 
     175  </sect1>
     176 
    179177</chapter>
  • trunk/www/admin/annotationtypes/edit_annotationtype.jsp

    r5657 r5706  
    917917      <tr>
    918918        <td>
    919           <select name="usableUnits" size="5" multiple style="width: 15em;" ondblclick="removeFromUsableUnits()">
     919          <select name="usableUnits" size="10" multiple style="width: 18em;" ondblclick="removeFromUsableUnits()">
    920920          </select>
    921921        </td>
    922         <td>
    923            <br>
     922        <td valign="middle">
    924923          <base:button
    925924            onclick="addToUsableUnits()"
    926             title="<img src='../../images/move_left.gif' alt='' style='vertical-align: middle;'>"
     925            image="move_left.gif"
     926            title=""
    927927            tooltip="Enable the annotation type for the selected unit(s)"
    928928          /><p>
    929929          <base:button
    930930            onclick="removeFromUsableUnits()"
    931             title="<img src='../../images/move_right.gif' alt='' style='vertical-align: middle;'>"
     931            image="move_right.gif"
     932            title=""
    932933            tooltip="Disable the annotation type for the selected unit(s)"
    933934          />
    934           <br>
    935935        </td>
    936936        <td>
    937           <select name="allUnits" size="5" multiple style="width: 15em;" ondblclick="addToUsableUnits()">
     937          <select name="allUnits" size="10" multiple style="width: 18em;" ondblclick="addToUsableUnits()">
    938938          </select>
    939939          <input type="hidden" name="removeUsableUnits" value="">
  • trunk/www/admin/annotationtypes/list_annotationtypes.jsp

    r5590 r5706  
    6666  import="java.util.Map"
    6767  import="java.util.Set"
     68  import="java.util.EnumSet"
    6869%>
    6970<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
     
    135136      style="display: none;">
    136137      <%
     138      Set<Type> separator = EnumSet.of(Type.DOUBLE, Type.TEXT, Type.BOOLEAN);
    137139      for (Type valueType : Type.values())
    138140      {
     
    143145        />
    144146        <%
     147        if (separator.contains(valueType))
     148        {
     149          %>
     150          <m:menuseparator />
     151          <%
     152        }
    145153      }
    146154      %>
  • trunk/www/admin/itemsubtypes/edit_subtype.jsp

    r5698 r5706  
    348348    <t:tab
    349349      id="filetypes"
    350       title="File types">
     350      title="File types"
     351      helpid="itemsubtype.filetypes">
    351352      <div id="filetypes.enabled">
    352353      <table class="form" cellspacing=0>
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