Changeset 3221


Ignore:
Timestamp:
Apr 2, 2007, 12:58:49 PM (16 years ago)
Author:
Nicklas Nordborg
Message:

References #525: Write "Using the web client"

First draft completed.

File:
1 edited

Legend:

Unmodified
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  • trunk/doc/src/docbook/userdoc/webclient.xml

    r3214 r3221  
    180180            <imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"/></imageobject>
    181181            </inlinemediaobject>
    182             Refresh button
     182            Refresh page
    183183            </interface>
    184184          </term>
     
    215215            is configurable. If you, for example, work a lot with protocols, you may
    216216            add a link to the most recently viewed protocol.
    217             See <xref linkend="webclient.configuration.other"/>
     217            See <xref linkend="webclient.configuration.preferences.mostrecent"/>
    218218            </para>
    219219          </listitem>
     
    270270      <sect2 id="webclient.configuration.contact">
    271271        <title>Contact information</title>
     272       
     273        <para>
     274          Use the <menuchoice><guimenu>File</guimenu>
     275          <guimenuitem>Contact information</guimenuitem></menuchoice>
     276          menu to bring up the contact information dialog. It contains
     277          the following information:
     278        </para>
     279       
     280        <helptext external_id="userpreferences.contact" title="Contact information">
     281          <variablelist>
     282            <varlistentry>
     283              <term>
     284                <guilabel>Email</guilabel>
     285              </term>
     286              <listitem>
     287                Your email address (optional).
     288              </listitem>
     289            </varlistentry>
     290            <varlistentry>
     291              <term>
     292                <guilabel>Organisation</guilabel>
     293              </term>
     294              <listitem>
     295                The name of the organisation you work for or represent (optional).
     296              </listitem>
     297            </varlistentry>
     298            <varlistentry>
     299              <term>
     300                <guilabel>Address</guilabel>
     301              </term>
     302              <listitem>
     303                Your postal address as it should be printed on letters to you
     304                (optional).
     305              </listitem>
     306            </varlistentry>
     307            <varlistentry>
     308              <term>
     309                <guilabel>Phone</guilabel>
     310              </term>
     311              <listitem>
     312                Your phone number (optional). You may enter multiple phone numbers,
     313                for example your work phone number and a mobile number.
     314              </listitem>
     315            </varlistentry>
     316            <varlistentry>
     317              <term>
     318                <guilabel>Fax</guilabel>
     319              </term>
     320              <listitem>
     321                Your fax number (optional).
     322              </listitem>
     323            </varlistentry>
     324            <varlistentry>
     325              <term>
     326                <guilabel>Url</guilabel>
     327              </term>
     328              <listitem>
     329                An URL to your home page or your organisations home page (optional).
     330              </listitem>
     331            </varlistentry>
     332          </variablelist>
     333         
     334          <note>
     335            If you are using a multi-user account, for example a demo-account, you
     336            are not able to change theese settings.
     337          </note>
     338         
     339        </helptext>
    272340      </sect2>
    273341
    274342      <sect2 id="webclient.configuration.password">
    275343        <title>Changing password</title>
    276       </sect2>
    277 
    278       <sect2 id="webclient.configuration.other">
    279         <title>Other settings</title>
     344       
     345        <para>
     346          Use the <menuchoice><guimenu>File</guimenu>
     347          <guimenuitem>Change password</guimenuitem></menuchoice>
     348          menu to bring up the change password dialog.
     349        </para>
     350       
     351        <helptext external_id="userpreferences.password" title="Change password">
     352          <variablelist>
     353            <varlistentry>
     354              <term>
     355                <guilabel>New password</guilabel>
     356              </term>
     357              <listitem>
     358                Enter the new password.
     359              </listitem>
     360            </varlistentry>
     361            <varlistentry>
     362              <term>
     363                <guilabel>Retype password</guilabel>
     364              </term>
     365              <listitem>
     366                Retype the same password. You must do this to
     367                avoid spelling mistakes.
     368              </listitem>
     369            </varlistentry>
     370          </variablelist>
     371         
     372          <note>
     373            If you leave both fields empty the password will not be changed. It
     374            is not possible to have an empty password.
     375          </note>
     376         
     377          <note>
     378            If you are using a multi-user account, for example a demo-account, you
     379            are not able to change theese settings.
     380          </note>
     381         
     382        </helptext>
     383      </sect2>
     384
     385      <sect2 id="webclient.configuration.preferences">
     386        <title>Preferences</title>
     387       
     388        <para>
     389          Use the <menuchoice><guimenu>File</guimenu>
     390          <guimenuitem>Preferences</guimenuitem></menuchoice>
     391          menu to bring up the preferences dialog. It is divided into
     392          three tabs.
     393        </para>
     394       
     395        <sect3 id="webclient.configuration.preferences.appearance">
     396          <title>Appearance</title>
     397         
     398          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
     399         
     400          <para>
     401          This tab contains settings that affect the appearance of the
     402          web client.
     403          </para>
     404         
     405          <variablelist>
     406            <varlistentry>
     407              <term>
     408                <guilabel>Font size</guilabel>
     409              </term>
     410              <listitem>
     411                Select a basic font size. You can choose between
     412                five sizes: extra small (XS), small (S), medium (M),
     413                large (L) and extra large (XL). The default font size is
     414                medium.
     415              </listitem>
     416            </varlistentry>
     417            <varlistentry>
     418              <term>
     419                <guilabel>Scale factor</guilabel>
     420              </term>
     421              <listitem>
     422                The scale factor affects the size of popup windows.
     423                This setting exists because different browsers render
     424                pages differently. If you often find that popup windows
     425                are too small you can change this setting to make them
     426                bigger.
     427                <note>
     428                  The scale factor is automatically changed if the
     429                  font size is changed.
     430                </note>
     431              </listitem>
     432            </varlistentry>
     433            <varlistentry>
     434              <term>
     435                <guilabel>Toolbar</guilabel>
     436              </term>
     437              <listitem>
     438                You may choose if the toolbar buttons should
     439                have only images, only text or both images and text.
     440                The default is that they have both images and text.
     441              </listitem>
     442            </varlistentry>
     443            <varlistentry>
     444              <term>
     445                <guilabel>Recently used items</guilabel>
     446              </term>
     447              <listitem>
     448                The number of items to remember in the list
     449                of recently used items. This will make data input
     450                faster since fewer clicks are required to select
     451                items. The default is to remember 4 items.
     452              </listitem>
     453            </varlistentry>
     454            <varlistentry>
     455              <term>
     456                <guilabel>Ratio color range</guilabel>
     457              </term>
     458              <listitem>
     459                Select three colors to use when displaying
     460                data that is suitable for color coding, for
     461                example the intensity ratio in two-color
     462                experiments. The default setting is blue-black-yellow.
     463                The list of presets contains other useful color combinations
     464                (for example, the BASE 1 red-yellow-green) and the most
     465                recently used color combinations.
     466              </listitem>
     467            </varlistentry>
     468            <varlistentry>
     469              <term>
     470                <guilabel>Date format</guilabel>
     471              </term>
     472              <listitem>
     473                <para>
     474                A format string describing how dates should be displayed.
     475                We support all formatting options supported by the Java
     476                language. For more information see:
     477                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
     478                The most useful format patterns are:
     479                </para>
     480               
     481                <itemizedlist>
     482                  <listitem>yy: two-digit year</listitem>
     483                  <listitem>yyyy: four-digit year</listitem>
     484                  <listitem>MM: two-digit month</listitem>
     485                  <listitem>MMM: month name (short)</listitem>
     486                  <listitem>MMMM: month name (full)</listitem>
     487                  <listitem>dd: two-digit day in month</listitem>
     488                </itemizedlist>
     489               
     490                <para>
     491                The list of presets contains the most commonly/recently
     492                used date formats.
     493                </para>
     494               
     495              </listitem>
     496            </varlistentry>
     497           
     498            <varlistentry>
     499              <term>
     500                <guilabel>Date-time format</guilabel>
     501              </term>
     502              <listitem>
     503                <para>
     504                A format string describing how dates with times should be displayed.
     505                We support all formatting options supported by the Java
     506                language. For more information see:
     507                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
     508                The most useful time-format patterns are:
     509                </para>
     510               
     511                <itemizedlist>
     512                  <listitem>HH: two-digit hour (0-23)</listitem>
     513                  <listitem>hh: two-digit hour (1-12)</listitem>
     514                  <listitem>a: AM/PM marker</listitem>
     515                  <listitem>mm: two-digit minute</listitem>
     516                  <listitem>ss: two-digit second</listitem>
     517                </itemizedlist>
     518               
     519              </listitem>
     520            </varlistentry>
     521           
     522            <varlistentry>
     523              <term>
     524                <guilabel>Decimals</guilabel>
     525              </term>
     526              <listitem>
     527                The number of decimals to display for numeric values.
     528                The default is 2.
     529              </listitem>
     530            </varlistentry>
     531           
     532          </variablelist>
     533       
     534          </helptext>
     535       
     536        </sect3>
     537       
     538        <sect3 id="webclient.configuration.preferences.plugins">
     539          <title>Plugins</title>
     540         
     541          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
     542         
     543          <para>
     544            This tab contains settings that affect plugin execution.
     545          </para>
     546         
     547          <variablelist>
     548            <varlistentry>
     549              <term>
     550                <guilabel>Messages</guilabel>
     551              </term>
     552              <listitem>
     553                Mark the checkbox if you want to have a message sent
     554                to you when a plugin completes execution. This setting
     555                can be overridden each time you start a plugin.
     556              </listitem>
     557            </varlistentry>
     558          </variablelist>
     559          </helptext>
     560         
     561        </sect3>
     562       
     563        <sect3 id="webclient.configuration.preferences.mostrecent">
     564          <title>Most recent</title>
     565         
     566          <helptext external_id="userpreferences.mostrecent" title="Preferences - Most recent">
     567         
     568          <para>
     569            This tab contains settings that affect the <guilabel>Most
     570            recent</guilabel> menu. You can select which items should
     571            appear in the menu by moving them to the left list. Use
     572            the up and down arrows to change the order in which they appear.
     573          </para>
     574         
     575          <para>
     576            If the <guilabel>Load the names of all recent items</guilabel> checkbox
     577            is checked the name of the items will be displayed in the menu (for example,
     578            Experiment: My experiment). Otherwise only the type of the item is
     579            displayed (for example, Experiment).
     580          </para>
     581          </helptext>
     582         
     583        </sect3>
    280584      </sect2>
    281585 
     
    298602        menu to list samples and the
    299603        <menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
    300         menu to list experiments. A typical list
    301         page is shown below.
     604        menu to list experiments. An example of a list page that can list
     605        items of several types is the <link linkend="trashcan">Trashcan</link>.     
     606        A typical list page is shown below.
    302607      </para>
    303608     
     
    649954      <title>Working with items</title>
    650955     
     956      <para>
     957        No matter what you are doing in BASE some things works more
     958        or less in the same way. This section convers things that are
     959        common for most parts of BASE.
     960      </para>
     961             
    651962      <sect2 id="webclient.items.new">
    652         <title>Creating a new item</title>
     963        <title>Create a new item</title>
     964       
     965        <para>
     966          New items are mostly created from the list view. For example,
     967          to create a new experiment go to the
     968          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
     969          page. Here you will find a <guibutton>New&hellip;</guibutton> button in the
     970          toolbar. The button is disabled if you don't have permission to create new experiments.
     971          Otherwise, click on it and enter any required information in the popup dialog.
     972          Sometimes there are multiple tabs in this dialog. In the case of experiments
     973          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
     974          and <guilabel>Experimental factors</guilabel>.
     975         
     976          As a general rule, only the first tab has information that is required.
     977          The information in all other tabs are optional.
     978        </para>
     979       
     980        <para>
     981          Click on the <guibutton>Save</guibutton> button to save the new
     982          experiment to the database or on the <guibutton>Cancel</guibutton> button
     983          to abort.
     984        </para>
     985
     986        <note>
     987          <para>
     988          To speed up data entry when adding multiple new items there
     989          are a few tricks you can use to make the web client to enter
     990          default values for most properties. To find a default value
     991          the following checklist is used in this order.
     992          </para>
     993       
     994        <orderedlist>         
     995          <listitem>
     996            If the list have an active filter the filter values are
     997            used as default property values for the new item. For example,
     998            if you are listing experiments with <guilabel>Genepix</guilabel>
     999            raw data type the new experiment will automatically have
     1000            <guilabel>Genepix</guilabel> selected. This trick should work
     1001            for all properties except annotations.       
     1002          </listitem>
     1003         
     1004          <listitem>
     1005            When you link to other items the same item will be used the next time.
     1006            For example the extraction protocol used to create an extract from a sample
     1007            is remembered and the same protocol is used the next time you create an extract.
     1008            In fact, BASE will remember as many items as specified by
     1009            the <link linkend="webclient.configuration.preferences.appearance">
     1010            <guilabel>Recently used items</guilabel></link> setting (default is 4).
     1011          </listitem>
     1012         
     1013          <listitem>
     1014            If you have a project active and that project has specified default
     1015            values those values will be used for new items. A project can specify
     1016            defaults for protocols, hardware and software and a few other settings.
     1017          </listitem>
     1018         
     1019        </orderedlist>
     1020       
     1021        </note>
     1022       
    6531023      </sect2>
    6541024     
    6551025      <sect2 id="webclient.items.edit">
    656         <title>Editing an existing item</title>
     1026        <title>Edit an existing item</title>
     1027       
     1028        <para>
     1029          On all single-item views there is an <guibutton>Edit&hellip;</guibutton>
     1030          button in the toolbar that opens a popup dialog for editing the properties
     1031          of the item. This button is disabled if the logged in user doesn't have
     1032          write permission for the item.
     1033        </para>
     1034       
     1035        <para>
     1036          You don't have to go to the single-item view to edit an item.
     1037          Whenever an item appear in a list or another place and has a link
     1038          on it, you can use a shortcut to open it's edit popup. Press
     1039          and hold one of the <keycap>CTRL</keycap>,
     1040          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking on the
     1041          link. This will open the edit popup dialog for the item. If you don't
     1042          have write permission you will be taken to the single-item view of
     1043          that item instead.
     1044        </para>
     1045
     1046     
    6571047      </sect2>
    6581048
    6591049      <sect2 id="webclient.items.delete">
    660         <title>Delete an item</title>
     1050        <title>Delete items</title>
     1051
     1052        <para>
     1053          You can delete items either from the list view or from
     1054          a single-item view. In both cases, the item is only marked
     1055          as beeing removed. It is not deleted from the database. This allows
     1056          you to restore the item if you later find out that you need it again.
     1057          In fact, there is nothing special about a removed item. It can still be
     1058          used for the same things as any non-removed item can.
     1059        </para>
     1060
     1061        <important>
     1062          To really delete an item from the database you must use
     1063          the <link linkend="trashcan">trashcan</link>.
     1064        </important>
     1065       
     1066        <para>
     1067          To delete items from the list view you must first mark
     1068          the checkbox for each item you want to delete. Then, click on
     1069          the <guibutton>Delete</guibutton> button. The list should refresh iteself
     1070          automatically. If you want to confirm that the items have been removed
     1071          use the <guilabel>view / presets</guilabel> dropdown and select
     1072          the <guilabel>Removed</guilabel> option. The removed items should now
     1073          be displayed in the list with a small trashcan icon to indicate that
     1074          they have been removed.
     1075        </para>
     1076
     1077        <para>
     1078          To delete items from the single-item view you just click on the
     1079          <guibutton>Delete</guibutton> in the toolbar. The page will refresh
     1080          itself automatically and a small trashcan icon should be displayed.
     1081          If you don't have permission to delete the item the delete button
     1082          will be disabled.
     1083        </para>
     1084
    6611085      </sect2>
    6621086     
    6631087      <sect2 id="webclient.items.restore">
    664         <title>Restore a deleted item</title>
     1088        <title>Restore deleted items</title>
     1089       
     1090        <para>
     1091          You can restore deleted items either from the <link linkend="trashcan">trashcan</link>,
     1092          from the list view or from the single-item view. This section only covers the last two
     1093          cases. The trashcan has a chapter of it's own.
     1094        </para>
     1095
     1096        <para>
     1097          To delete items from the list view you must first make the deleted
     1098          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel>
     1099          dropdown and select the <guilabel>Removed</guilabel> option. This list should
     1100          refresh itself automatically. The removed items should now
     1101          be displayed in the list with a small trashcan icon to indicate that
     1102          they have been removed. Then, mark the checkbox for each item that you want
     1103          to restore and click the <guibutton>Restore</guibutton> button. The list should
     1104          refresh iteself automatically and the trashcan icon should be gone from the
     1105          restored items.
     1106        </para>
     1107       
     1108        <para>
     1109          To restore items from the single-item view you just click on the
     1110          <guibutton>Restore</guibutton> in the toolbar. The page will refresh
     1111          itself automatically and the small trashcan icon should be gone.
     1112          If you don't have permission to restore the item the restore button
     1113          will be disabled.
     1114        </para>
     1115
    6651116      </sect2>
    6661117
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