Changeset 5784


Ignore:
Timestamp:
Oct 5, 2011, 2:52:42 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Import and export of data.

Location:
trunk/doc/src/docbook/user
Files:
2 edited

Legend:

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

    r5738 r5784  
    3838-->
    3939<chapter id="export_data" chunked="0">
     40
    4041  <title>Export of data</title>
    4142  <para>
     
    5960    <menuchoice>
    6061      <guimenu>Administrate</guimenu>
    61       <guimenuitem>Plugins</guimenuitem>
    62       <guisubmenu>Definitions</guisubmenu>
     62      <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
     63      <guisubmenu>Plug-in definitions</guisubmenu>
    6364    </menuchoice>
    6465    to check which plug-ins are installed on your BASE server. When
     
    6869  </para>
    6970  <note>
    70     <title>Missing/unavailable button</title>
     71    <title>No "Export" button?</title>
    7172    <para>
    7273      If the export button is missing from a page were you would expect
     
    369370        <varlistentry>
    370371          <term>
     372            <guilabel>Units</guilabel>
     373          </term>
     374          <listitem>
     375            <para>
     376              If the export includes annotation with units, the exporter normally
     377              uses the same unit that was used when annotating each item. This can be
     378              different from item to item. Select this option to force all annotation
     379              values to use the same unit (=the default unit for the annotation type).
     380            </para>
     381          </listitem>
     382        </varlistentry>
     383        <varlistentry>
     384          <term>
     385            <guilabel>Column prefix</guilabel>
     386          </term>
     387          <listitem>
     388            <para>
     389              Adds a prefix to each column header. This is useful for keeping
     390              column names unique when combining multiple files outside of
     391              BASE.
     392            </para>
     393          </listitem>
     394        </varlistentry>
     395        <varlistentry>
     396          <term>
    371397            <guilabel>Save as</guilabel>
    372398          </term>
  • trunk/doc/src/docbook/user/import_data.xml

    r5738 r5784  
    4545    to enter by hand due to the large number of data items. There is
    4646    also convenience batch importers for importing other items such as
    47     biosources, samples, and extracts. The batch importers are
     47    biosources, samples, and annotations. The batch importers are
    4848    described later in this chapter after the general import
    4949    description.
     
    5353    configuration, for example, the import plug-ins need some
    5454    information about how to find headers and data lines in
    55     files. BASE ships with a number of export plug-ins as a part of
     55    files. BASE ships with a number of import plug-ins as a part of
    5656    the core plug-ins package, cf. <xref linkend="coreplugins.import"
    5757    />. The core plug-in section links to configuration examples for
     
    5959    <menuchoice>
    6060      <guimenu>Administrate</guimenu>
    61       <guimenuitem>Plugins</guimenuitem>
    62       <guisubmenu>Definitions</guisubmenu>
     61      <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
     62      <guisubmenu>Plug-in definitions</guisubmenu>
    6363    </menuchoice>
    6464    to check which plug-ins are installed on your BASE server. When
     
    6868  </para>
    6969    <note>
    70     <title>Missing/unavailable button</title>
     70    <title>No "Import" button?</title>
    7171    <para>
    7272      If the import button is missing from a page were you would expect
     
    170170                <menuchoice>
    171171                  <guimenu>Administrate</guimenu>
    172                   <guimenuitem>Plugins</guimenuitem>
    173                   <guisubmenu>Definitions</guisubmenu>
     172                  <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
     173                  <guisubmenu>Plug-in definitions</guisubmenu>
    174174                </menuchoice>
    175175                and
    176176                <menuchoice>
    177177                  <guimenu>Administrate</guimenu>
    178                   <guimenuitem>Plugins</guimenuitem>
    179                   <guisubmenu>Configurations</guisubmenu>
    180                 </menuchoice>.
     178                  <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
     179                  <guisubmenu>Plug-in configuration</guisubmenu>
     180                </menuchoice>
    181181              </para>
    182182              <note>
     
    302302          <para>
    303303            Click on the &gbNext; button
    304             to start the auto detection.
     304            to start the auto detection. There are three possible outcomes:
    305305          </para>
    306306
    307           <para>
    308             If the auto detection finds a exactly one plug-in and file format
    309             the next step is to configure any additional parameters needed
    310             by the plug-in. This is the same step as if you had selected
    311             the same plug-in and file format in the first step.
    312             If no plug-in can be found an error message is displayed.
    313           </para>
    314 
    315           <note>
    316             <title>More then one compatible plug-in/file format</title>
    317             <para>
    318               If more than one matching plug-in or file format is used
     307          <itemizedlist>
     308            <listitem>
     309              <para>
     310              Exactly one matching plug-in and file format is found. The next step is
     311              to configure any additional parameters needed
     312              by the plug-in. This is the same step as if you had selected
     313              the same plug-in and file format in the first step.
     314              </para>
     315            </listitem>
     316            <listitem>
     317              <para>
     318              If no matching plug-in and file format is found an error message
     319              is displayed. If logged in with enough permissions to do so there
     320              is an option to create a new file format/configuration.
     321              </para>
     322            </listitem>
     323            <listitem>
     324              <para>
     325              If multiple matching plug-ins and file formats are found
    319326              you will be taken back to the first step. This time
    320327              the lists will only include the matching plug-ins/file formats
    321328              and the auto detect option is not present.
    322             </para>
    323           </note>
     329              </para>
     330            </listitem>
     331          </itemizedlist>
    324332
    325333          <seeother>
     
    383391              A section which contains different options how to
    384392              handle errors when parsing the file. Normally you can
    385               select if the import should fail as a while or if
    386               the line with the error should be skipped.
     393              select if the import should fail as a whole or if
     394              only the line with the error should be skipped.
    387395            </para>
    388396          </listitem>
     
    506514            <para>
    507515              Multi-item references are references to several other
    508               items of the same type. The labeled extracts of a
    509               hybridization or pooled samples are two examples of
    510               items that refer to several other items; a hybridization
    511               may contain several labeled extracts and a sample may be
     516              items of the same type. The extracts of a
     517              physical bioassay or pooled samples are two examples of
     518              items that refer to several other items; a physical bioassay
     519              may contain several extracts and a sample may be
    512520              a pool of several samples. In some cases a multi-item
    513521              reference is bundled with simple
    514522              values, <emphasis>eg.</emphasis>, used quantity of a
    515               source biomaterial, the array index a labeled extract is
     523              source biomaterial, the position an extract is
    516524              used on, etc. Multi-item references are never removed by
    517525              the importer, only added or updated. Removing an item
     
    522530        </itemizedlist>
    523531        The batch importers do not set values for annotations since
    524         this is handled by the already existing annotation importer
     532        this is handled by the annotation importer
    525533        plug-in (<xref linkend="annotations.massimport" />). However,
    526534        the annotation importer and batch item importers have similar
     
    530538
    531539      <para>
    532         The importer only works one item type at each use and can be
     540        The importer only works with one type of items at each use and can be
    533541        used in a <emphasis>dry-run</emphasis> mode where everything
    534542        is performed as if a real import is taking place, but the work
     
    547555          For proper and efficient use of the batch importers users
    548556          need to understand how the files to be imported should be
    549           formatted. For users who wishes to get a hands-on
    550           experience there is
    551           an <ulink url="http://base.thep.lu.se/attachment/wiki/DocBookSupport/batchimport_sample.ods?format=raw">OpenOffice
    552           spreadsheet with sample sheets that work with the batch
    553           importers</ulink> available for download. This file can be
    554           used to import a set of data from the biosource level down
    555           to hybridizations with proper associations and properties
    556           simply by using the batch importers.
    557         </para>
    558 
    559         <para>
    560           The input file must be organised into columns separated by a
     557          formatted. The input file must be organised into columns separated by a
    561558          specified character such as a tab or comma character. The
    562559          data header line contains the column headers which defines
     
    650647          parameters. The list below comments on some of the
    651648          parameters available.
     649        </para>
     650       
    652651          <variablelist>
    653652            <varlistentry>
     
    672671            <varlistentry>
    673672              <term>
     673                <guilabel>Data directory</guilabel>
     674              </term>
     675              <listitem>
     676                <para>
     677                  This option is only available for items that has support for
     678                  attaching files (eg. array design, derived bioassay, etc.).
     679                  This setting is used to resolve file references that doesn't
     680                  include a complete absolute path.
     681                </para>
     682              </listitem>
     683            </varlistentry>
     684            <varlistentry>
     685              <term>
    674686                <guilabel>Identification method</guilabel>
    675687              </term>
     
    682694                  the user must be mapped to a column in the file. If
    683695                  it is not set there is obviously no way for the
    684                   plug-in to identify if an item already exists .
     696                  plug-in to identify if an item already exists.
     697                </para>
     698              </listitem>
     699            </varlistentry>
     700            <varlistentry>
     701              <term>
     702                <guilabel>Item subtypes</guilabel>
     703              </term>
     704              <listitem>
     705                <para>
     706                  Only look for existing items among the selected subtypes. If no subtype
     707                  is selected all items are searched. If exactly one subtype is selected
     708                  new items are automatically created with this subtype (unless it is overridden
     709                  by specific subtype values in the import file).
    685710                </para>
    686711              </listitem>
     
    722747                </para>
    723748                <para>
    724                   When creating pooled items,
    725                   the <property>pooled</property> property is used to
    726                   tell the plug-in that an item is pooled. Pooled in
    727                   BASE language really means that the item parent is
    728                   of the same type as the item itself. If an item is
    729                   not pooled then the parent is of another type
    730                   following a predefined hierarchy in BASE. In
    731                   ascending order the BASE ordering
     749                  When working with biomaterial items, the
     750                  <guilabel>Parent type</guilabel> property is used to
     751                  tell the plug-in how to find parent items. This only
     752                  has to be set if the parent item is of the same type
     753                  as the biomaterial being imported since the default
     754                  is to look for the nearest parent type in the predefined hierarchy.
     755                  In ascending order the BASE ordering
    732756                  of <emphasis>parent - child - grandchild -
    733757                  ...</emphasis> item relation is <emphasis>biosource
    734                   - sample - extract - labeled extract</emphasis>.
    735                 </para>
    736                 <para>
    737                   The values accepted for <property>pooled</property>
    738                   are <constant>empty (' ')</constant>,
    739                   <constant>0</constant>, <constant>1</constant>,
    740                   <constant>no</constant>, <constant>yes</constant>,
    741                   <constant>false</constant>,
    742                   and <constant>true</constant>. Any other string is
    743                   interpreted as the item is pooled.  Sometimes all
    744                   items in a file to be imported are pooled but there
    745                   is no column that marks the pooled status. This can
     758                  - sample - extract</emphasis>.
     759                </para>
     760                <para>
     761                  The values accepted for <guilabel>Parent type</guilabel>
     762                  are <constant>BIOSOURCE</constant>,
     763                  <constant>SAMPLE</constant> or <constant>EXTRACT</constant>.
     764                  Sometimes all items in a file to be imported have the same parent
     765                  type but there is no column with this information. This can
    746766                  be resolved by setting
    747                   the <property>pooled</property> mapping to a
    748                   constant string
    749                   <constant>'1'</constant> which make all items to be
    750                   treated as pooled in the import (no backslash '\'
    751                   character, compare with column header mapping
    752                   strings that contain backslash characters
    753                   like <constant>'\pool column\'</constant>).
     767                  the <guilabel>Parent type</guilabel> mapping to a
     768                  constant string (eg. no backslash '\' character).
     769                </para>
     770              </listitem>
     771            </varlistentry>
     772            <varlistentry>
     773              <term>
     774                <guilabel>Permissions</guilabel>
     775              </term>
     776              <listitem>
     777                <para>
     778                  This is a column mapping that can be used to update the permissions
     779                  set on items. Normally, new items are only shared to the active project
     780                  (if any). By naming a permission template, new items are shared using
     781                  the permissions from that template instead. Permissions on already existing
     782                  items are merged with the permission from the template.
    754783                </para>
    755784              </listitem>
    756785            </varlistentry>
    757786          </variablelist>
     787         
     788          <para>
    758789          After setting the parameters,
    759790          select <guilabel>Next</guilabel>. Another parameter dialog
    760791          will appear where error handling options can be set among
    761792          with
     793          </para>
     794         
    762795          <variablelist>
    763796            <varlistentry>
     
    792825            </varlistentry>
    793826          </variablelist>
    794         </para>
     827
    795828
    796829        <para>
     
    798831          referenced on each line. There are three outcomes of this
    799832          item search
     833        </para>
     834       
    800835          <itemizedlist>
    801836            <listitem>
     
    816851                More than one item is found. Depending on parameter
    817852                settings this may abort the plug-in or the plug-in may
    818                 ignored the line.
     853                ignore the line.
    819854              </para>
    820855            </listitem>
    821856          </itemizedlist>
    822         </para>
    823857
    824858      </sect2>
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