Changeset 5795


Ignore:
Timestamp:
Oct 10, 2011, 12:08:12 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

New and updated screenshots for chapter 8-14.

Location:
trunk
Files:
6 added
25 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/user/annotations.xml

    r5782 r5795  
    5959      <emphasis>Protocols</emphasis>
    6060      and
    61       <emphasis>Bioassay sets</emphasis>
     61      <emphasis>Bioassay sets</emphasis>.
    6262    </para>
    6363
     
    138138    <para>
    139139      The <guilabel>Edit annotation type</guilabel> window is opened in a
    140       pop-up. It contains four different tabs.
     140      pop-up. It contains several tabs.
    141141    </para>
    142142 
     
    176176            database. This value can be used by tools that
    177177            need to update annotation types in BASE from external
    178             sources. The value does not have to be unique.
     178            sources. The value does not have to be unique and is not
     179            used by BASE.
    179180            </para>
    180181          </listitem>
     
    224225          <listitem>
    225226            <para>
    226               A short textual description of the
     227              A short textual description
    227228              to clarify the usage.
    228229            </para>
     
    405406          <para>
    406407          If the annotation type has been marked as a
    407           <guilabel>Protocol</guilabel> parameter, these settings are
     408          <guilabel>Protocol parameter</guilabel>, these settings are
    408409          ignored, with one exception. If you wish to view parameter
    409410          values in the list view for a specific item type you must select
     
    516517      <title>Categories</title>
    517518   
     519      <figure
     520        id="annotations.figures.annotationtype.categories">
     521        <title>Annotation type categories</title>
     522        <screenshot>
     523          <mediaobject>
     524            <imageobject>
     525              <imagedata
     526                fileref="figures/annotationtype_categories.png" format="PNG" />
     527            </imageobject>
     528          </mediaobject>
     529        </screenshot>
     530      </figure>
     531     
    518532      <helptext external_id="annotationtype.edit.categories"
    519533        title="Categories">
     
    534548          button to remove the selected categories.
    535549        </para>
    536          
     550       
     551        <tip>
     552          <title>Create categories with the same name as item subtypes</title>
     553          <para>
     554            If you, for example, have defined multiple subtypes of extracts
     555            (see <xref linkend="subtypes" />),
     556            it usually so that some annotation types are only intended for
     557            one subtype while some other annotation types are only intended
     558            for the other subtype. If you create categories with the same name
     559            as the item subtypes, BASE will automatically select the corresponding
     560            category when annotating an extract with a subtype. This makes the interface
     561            cleaner and easier to use since irrelevant annotation types are hidden.
     562            Note that it is possible for annotations to be part of more than one
     563            category so it is also possible to define annotation types that are
     564            intended for all types of extracts by including them in both categories.
     565          </para>
     566        </tip>
     567       
    537568        <seeother>
    538569          <other external_id="annotationtype.edit">Properties</other>
     
    544575  </sect1>
    545576 
    546   <sect1 id="annotations.categories">
    547     <?dbhtml filename="categories.html" ?>
    548     <title>Annotation type categories</title>
    549    
    550     <para>
    551       <guilabel>Annotation Type Categories</guilabel>
    552       allow grouping of related Annotation Types, based on
    553       users requirements.
    554     </para>
    555    
    556     <para>
    557       For managing categories go to
    558       <menuchoice>
    559         <guimenu>Administrate</guimenu>
    560         <guimenuitem>Types</guimenuitem>
    561           <guisubmenu>Annotation Type categories</guisubmenu>
    562         </menuchoice>.
    563     </para>
    564 
    565     <example id="annotation_types.example.atcategory">
    566       <title>Annotation category examples</title>
    567      
    568       <para>
    569         <itemizedlist>
    570         <listitem>
    571           <para>
    572           A category <userinput>Hematology Descriptors</userinput>
    573           could be created to group together annotation types such as
    574           <userinput>Lymphocyte count</userinput> and
    575           <userinput>Hematocrite</userinput>
    576           </para>
    577         </listitem>
    578        
    579         <listitem>
    580           <para>
    581           A category <userinput>Plasma Clinical Descriptors</userinput>
    582           could be created to group together annotation types such as
    583           <userinput>ALT activity (UI/mL)</userinput> and
    584           <userinput>LDH activity (UI/mL)</userinput>
    585           </para>
    586         </listitem>
    587         </itemizedlist>
    588       </para>
    589     </example>
    590    
    591     <tip>
    592       <para>
    593       If you use the same name for a category as for an item subtype (see <xref linkend="subtypes" />)
    594       the annotations in this category will be selected by default when editing an item item
    595       by that subtype. This can be useful when you have two or more subtypes of the same
    596       main item type and a different set of annotations that should be used on each subtype.
    597       For example, <emphasis>Labeled extract</emphasis> and <emphasis>Library</emphasis>
    598       are subtypes of <emphasis>Extract</emphasis>, which probably have different annotation
    599       types.
    600       </para>
    601     </tip>
    602    
    603   </sect1>
    604 
    605577  <sect1 id="annotations.annotating">
    606578    <?dbhtml filename="annotating.html" ?>
  • trunk/doc/src/docbook/user/jobs.xml

    r5738 r5795  
    4444  </para>
    4545
    46 
    47   <sect1 id="jobs.properties">
    48     <title>Properties</title>
     46  <para>
    4947    Click on
    5048    <menuchoice>
     
    5250      <guimenuitem>Jobs</guimenuitem>
    5351    </menuchoice>
    54     to list your jobs.
    55     <para>
     52      to list your jobs.
    5653      Details of a single job is displayed in a pop-up window. This window opens either if you
    5754      click on a job's name from the list page of jobs or when a job configuration is
     
    6663      </para>
    6764    </helptext>
     65   
     66    <figure id="jobs.figures.properties">
     67      <title>Job properties</title>
     68      <screenshot>
     69        <mediaobject>
     70          <imageobject>
     71            <imagedata fileref="figures/job_properties.png" format="PNG" />
     72          </imageobject>
     73        </mediaobject>
     74      </screenshot>
     75    </figure>
     76   
    6877    <helptext external_id="job.view.properties" title="Job properties">
    6978      <para>
     
    115124          <varlistentry>
    116125            <term>
    117               <optional>
    118126                <guilabel>Description</guilabel>
    119               </optional>
    120127            </term>
    121128            <listitem>
     
    123130                A description of the job. Like the name-property it can be set in
    124131                the job configuration.
    125               </para>
    126             </listitem>
    127           </varlistentry>
    128           <varlistentry>
    129             <term>
    130               <guilabel>Type</guilabel>
    131             </term>
    132             <listitem>
    133               <para>
    134                 The type of job, which is depending on the plug-in that is used. It
    135                 can be one of these five:
    136                 <itemizedlist>
    137                   <listitem>Export</listitem>
    138                   <listitem>Import</listitem>
    139                   <listitem>Analysis</listitem>
    140                   <listitem>Intensity</listitem>
    141                   <listitem>Other</listitem>
    142                 </itemizedlist>
    143132              </para>
    144133            </listitem>
     
    175164                  <listitem>
    176165                    <para>
     166                      <emphasis>Preparing</emphasis>
     167                      - The job queue is preparing to executed the job.
     168                    </para>
     169                  </listitem>
     170                  <listitem>
     171                    <para>
    177172                      <emphasis>Executing</emphasis>
    178173                      - The job is being executed.
     
    191186                    </para>
    192187                  </listitem>
    193                   <listitem>
    194                     <para>
    195                       <emphasis>Preparing</emphasis>
    196                       - The job queue is preparing to executed the job.
    197                     </para>
    198                   </listitem>
    199                   <listitem>
     188c               <listitem>
    200189                    <para>
    201190                      <emphasis>Aborting</emphasis>
     
    205194                  </listitem>
    206195                </itemizedlist>
    207               </para>
    208             </listitem>
    209           </varlistentry>
    210           <varlistentry>
    211             <term>
    212               <guilabel>Status message</guilabel>
    213             </term>
    214             <listitem>
    215               <para>
    216                 A message, given by the plug-in, with more information about the
    217                 status.
     196               
     197                This field will also display any messages from the plug-in while it
     198                is running and the final message after it's completion.
    218199              </para>
    219200            </listitem>
     
    344325        <listitem>
    345326          <para>
    346           Retry a failed job with different. This feeture is supported by most but not
     327          Retry a failed job with different parameters. This feeture is supported by most but not
    347328          all plug-ins. It is very useful when the failure is due to a misconfiguration
    348329          and the job may succeed if it was configured differently.
     
    374355     
    375356    </helptext>
    376   </sect1>
    377357</chapter>
  • trunk/doc/src/docbook/user/platforms.xml

    r5783 r5795  
    3737      Affymetrix platform (as defined in BASE) uses CEL files for
    3838      raw data and CDF files for array design information.
    39     </para>
    40    
    41     <para>
    4239      The concept of a platform is also tightly coupled to the
    4340      ability to keep data in files instead of importing it to
     
    4845   
    4946    <para>
    50       BASE comes pre-installed with two platforms; A generic platform
    51       and the Affymetrix platform. Other platforms, such as Illumina,
     47      BASE comes pre-installed with three platforms.
     48    </para>
     49   
     50    <itemizedlist>
     51      <listitem>
     52        <para>
     53        A generic platform that can be used with almost any
     54        type of data that can be imported into the database from
     55        simple column-based text files.
     56        </para>
     57      </listitem>
     58   
     59      <listitem>
     60        <para>
     61        The Affymetrix platform which keep data in CEL and CDF files
     62        instead of importing into the database.
     63        </para>
     64      </listitem>
     65     
     66      <listitem>
     67        <para>
     68        A sequencing platform which uses GTF files to define array designs
     69        and FPKM counts as raw data.
     70        </para>
     71      </listitem>
     72   
     73    </itemizedlist>
     74     
     75    <para>
     76      Other platforms, such as Illumina,
    5277      are available as non-core plug-in packages, see
    5378      <xref linkend="resources.plugins" />. An administrator may
     
    6085    </seeother>
    6186    </helptext>
    62 
    63 
    6487
    6588    <para>
     
    189212        <listitem>
    190213          <para>
    191             This checkbox will modify the required flag for the
    192             selected file types.
     214            Mark this checkbox to indicate that the file is required for
     215            the platform.
    193216          </para>
    194217         
    195218          <note>
    196219            <para>
    197             The requried flag is not a hard requirement. It is only
    198             used for generating warnings when validating an experiment.
     220            The requried flag is not enforced when creating items. It is
     221            used for generating warnings when validating an experiment and
     222            can be checked by plug-ins that may need the file in order
     223            to run.
    199224            </para>
    200225          </note>
    201226         
     227        </listitem>
     228      </varlistentry>
     229      <varlistentry>
     230        <term><guilabel>Allow multiple files</guilabel></term>
     231        <listitem>
     232          <para>
     233            Mark this checkbox if it is possible to have more than one
     234            file of the given type. In most cases, a single file is used,
     235            but some platforms (for example Illumina) may split data into
     236            multiple files.
     237          </para>
    202238        </listitem>
    203239      </varlistentry>
     
    285321        Make it possible to validate and extract metadata from attached files.
    286322        This is done by extensions. Currently, BASE ships
    287         with extensions for CEL and CDF files, but the administrator may have installed
     323        with extensions for CEL, CDF and GTF files, but the administrator may have installed
    288324        extensions for other file types. See <xref linkend="extensions_developer.fileset_validator"/>
    289325        for more information about creating extensions.
  • trunk/doc/src/docbook/user/protocols.xml

    r5738 r5795  
    124124        <seeother>
    125125          <other external_id="protocol.edit.parameters">Protocol parameters</other>
     126          <other external_id="annotations.edit">Annotations</other>
    126127        </seeother>
    127128      </helptext>
     
    191192        <seeother>
    192193          <other external_id="protocol.edit">Edit protocol</other>
    193           <other external_id="annotations.edit">Annotations &amp; parameters</other>
     194          <other external_id="annotations.edit">Annotations</other>
    194195        </seeother>
    195196     
    196197      </helptext>
     198     
     199      <para>
     200        The <guilabel>Annotations</guilabel> tab allows BASE users to use
     201        annotation types to refine protocol description. More about annotating items
     202        can be read in <xref linkend="annotations.annotating" />.
     203      </para>
    197204  </sect1>
    198205</chapter>
  • trunk/doc/src/docbook/user/reporters.xml

    r5738 r5795  
    2727<chapter id="reporters" chunked="0">
    2828  <title>Reporters</title>
    29   <sect1 id="reporters.introduction">
    30     <title>Introduction</title>
     29 
    3130    <helptext external_id="reporter.view.properties"
    3231      title="About reporters">
     
    4544    </para>
    4645    </helptext>
    47   </sect1>
    4846 
    4947  <sect1 id="reportertypes">
     
    5755      and qualification defined during the array design
    5856      specification.
    59     </para>
    60     </helptext>
    61    
    62     <para>
     57      <nohelp>
    6358      You can manage the reporter types by going to
    6459      <menuchoice>
     
    6762        <guisubmenu>Reporter types</guisubmenu>
    6863      </menuchoice>.
     64      </nohelp>
    6965    </para>
     66    </helptext>
    7067   
    7168    <figure
     
    122119      <menuchoice>
    123120        <guimenu>View</guimenu>
    124         <guimenuitem>Reporter</guimenuitem>
     121        <guimenuitem>Reporters</guimenuitem>
    125122      </menuchoice> to view and manage the reporters.
    126123    </para>
     
    178175      </para>
    179176     
    180       <sect3 id="reporters.properties">
    181         <title>Reporter properties</title>
    182        
    183177        <figure id="reporters.figures.properties">
    184178          <title>Reporter properties</title>
     
    245239          </seeother>
    246240        </helptext>
    247       </sect3>
    248      
    249       <sect3 id="reporters.extended_properties">
    250         <title>Extended properties</title>
    251        
     241
    252242        <figure id="reporters.figures.extended_properties">
    253243          <title>Extended reporter properties</title>
     
    295285          </seeother>
    296286        </helptext>
    297       </sect3>
    298287    </sect2>
    299288 
     
    302291      <title>Deleting reporters</title>
    303292     
    304       <important>
     293      <caution>
    305294        <title>Deleted reporters cannot be restored</title>
    306295        <para>
     
    313302          confirm before the reporters are deleted.
    314303        </para>
    315       </important>
     304      </caution>
    316305     
    317306      <para>
     
    463452            should be included in the list. This option is only available
    464453            when creating a new reporter list, not when editing an existing
    465             list.
     454            list. The default is to create a list with <emphasis>all</emphasis>
     455            reporters that are in the current list.
    466456            </para>
    467457          </listitem>
     
    490480      </helptext>
    491481
     482
     483    <sect2 id="reporterlists.merge">
     484      <title>Merging reporter lists</title>
     485
     486      <para>
     487        It is possible to modify a reporter list by merging it with other reporter
     488        lists. Go to the single-item view page for a reporter list. There should be
     489        three buttons in the toolbar corresponding to three main merge variants:
     490      </para>
     491     
     492      <itemizedlist>
     493        <listitem>
     494          <para>
     495            <guilabel>Union:</guilabel> Add all reporters from
     496            the source lists to the destination list.
     497          </para>
     498        </listitem>
     499        <listitem>
     500          <para>
     501            <guilabel>Intersection:</guilabel> Keep only reporters
     502            that are present in all selected lists.
     503          </para>
     504        </listitem>
     505        <listitem>
     506          <para>
     507            <guilabel>Complement:</guilabel> Keep only reporters that
     508            are unique for the destination list.
     509          </para>
     510        </listitem>
     511      </itemizedlist>
     512     
     513      <para>
     514        All three buttons open up the same dialog with different default selections.
     515      </para>
     516
     517      <figure
     518        id="reporterlists.figures.merge">
     519        <title>Merge reporter lists</title>
     520        <screenshot>
     521          <mediaobject>
     522            <imageobject>
     523              <imagedata fileref="figures/reporterlist-merge.png" format="PNG" />
     524            </imageobject>
     525          </mediaobject>
     526        </screenshot>
     527      </figure>
     528
     529      <helptext external_id="reporterlist.merge"
     530        title="Merge reporter lists">
     531     
     532       
     533        <variablelist>
     534          <varlistentry>
     535            <term><guilabel>This list</guilabel></term>
     536            <listitem>
     537              <para>Shows the name of the current reporter list.</para>
     538            </listitem>
     539          </varlistentry>
     540          <varlistentry>
     541            <term><guilabel>What to do</guilabel></term>
     542            <listitem>
     543              <para>
     544                In this drop-down list you can select if you want to
     545                <emphasis>add</emphasis>, <emphasis>keep</emphasis>
     546                or <emphasis>remove</emphasis> reporters from the
     547                selected list based on if a reporter is present in one
     548                or all of some other reporter lists (selected below).
     549                The image to the right gives an overview what will
     550                happen for the currently selected alternatives. The
     551                red-colored areas indicate which reporters that are
     552                included in the final list. The white-colored areas
     553                indicate reporters that doesn't pass the filter and
     554                are excluded from the final list.
     555              </para>
     556            </listitem>
     557          </varlistentry>
     558          <varlistentry>
     559            <term><guilabel>Reporter lists</guilabel></term>
     560            <listitem>
     561              <para>
     562                You will need to select at least one more list
     563                to merge with.
     564              </para>
     565            </listitem>
     566          </varlistentry>
     567       
     568        </variablelist>
     569     
     570
     571      </helptext>
     572    </sect2>
     573
     574
     575
    492576  </sect1>
    493577</chapter>
  • trunk/doc/src/docbook/user/subtypes.xml

    r5738 r5795  
    5353      This feature can be a real time-saver when used together with project default items
    5454      (see <xref linkend="project_permissions.project.defaults" />).
    55       When creating new items (eg a biomaterial) BASE will search among the
     55      When creating new items (eg. a biomaterial) BASE will search among the
    5656      default items in the active project for protocols, hardware, software,
    5757      etc. and automatically select the best match based on the subtype of the new
     
    123123          the current subtype. The possible options depend on the which the
    124124          main item type is. For example, for <emphasis>biosource</emphasis>
    125           there are no other related subtypes, but <emphasis>physical bioassay</emphasis>
    126           can have a related protocol and hardware subtype as well as a
    127           related extract subtype.
     125          there are no other related subtypes, but a <emphasis>derived bioassay</emphasis>
     126          can have a related physical bioassay and extract as well as protocol, hardware and
     127          software subtypes.
    128128          </para>
    129129        </listitem>
     
    157157    <helptext external_id="itemsubtype.filetypes" title="File types">
    158158      <para>
    159         If the main item type for a subtype is a <emphasis>physical bioassay</emphasis>
    160         or <emphasis>derived bioassay</emphasis> (which has support for linking
    161         of data files) it is possible to select data file types
     159        If the main item type for a subtype is a <emphasis>derived bioassay</emphasis>
     160        (which has support for linking of data files) it is possible to select data file types
    162161        <nohelp>(see <xref linkend="platforms.datafiletypes"/>)</nohelp>
    163162        that can be used for items of the given subtype. This is very similar to how
     
    176175        </listitem>
    177176      </varlistentry>
     177      <varlistentry>
     178        <term><guilabel>Required</guilabel></term>
     179        <listitem>
     180          <para>
     181            Mark this checkbox to indicate that the file is required for
     182            all items of the given subtype.
     183          </para>
     184         
     185          <note>
     186            <para>
     187            The requried flag is not enforced when creating items. It is
     188            used for generating warnings when validating an experiment and
     189            can be checked by plug-ins that may need the file in order
     190            to run.
     191            </para>
     192          </note>
     193         
     194        </listitem>
     195      </varlistentry>
     196      <varlistentry>
     197        <term><guilabel>Allow multiple files</guilabel></term>
     198        <listitem>
     199          <para>
     200            Mark this checkbox if it is possible to have more than one
     201            file of the given type. In most cases, a single file is used,
     202            but some subtypes, for example Scan, may generate multiple images.
     203          </para>
     204        </listitem>
     205      </varlistentry>
    178206     
    179207      <varlistentry>
  • trunk/doc/src/docbook/user/wares.xml

    r5738 r5795  
    104104   
    105105    <para>
    106       A hardware is used in BASE to represent the software that is used to
     106      A software item is used in BASE to represent the software that is used to
    107107      process and analyze data outside of BASE. Analysis that is done inside
    108108      BASE is usually represented as plug-ins.
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