Changeset 3295


Ignore:
Timestamp:
May 7, 2007, 12:25:09 PM (14 years ago)
Author:
Nicklas Nordborg
Message:

References #525: Write "Using the web client"

Now ready for reading.

File:
1 edited

Legend:

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

    r3276 r3295  
    369369            <varlistentry>
    370370              <term>
    371                 <userinput>Full name</userinput>
     371                <guilabel>Full name</guilabel>
    372372              </term>
    373373              <listitem>
     
    381381            <varlistentry>
    382382              <term>
    383                 <userinput>Email</userinput>
     383                <guilabel>Email</guilabel>
    384384              </term>
    385385              <listitem>
     
    391391            <varlistentry>
    392392              <term>
    393                 <userinput>Organisation</userinput>
     393                <guilabel>Organisation</guilabel>
    394394              </term>
    395395              <listitem>
     
    401401            <varlistentry>
    402402              <term>
    403                 <userinput>Address</userinput>
     403                <guilabel>Address</guilabel>
    404404              </term>
    405405              <listitem>
     
    412412            <varlistentry>
    413413              <term>
    414                 <userinput>Phone</userinput>
     414                <guilabel>Phone</guilabel>
    415415              </term>
    416416              <listitem>
     
    423423            <varlistentry>
    424424              <term>
    425                 <userinput>Fax</userinput>
     425                <guilabel>Fax</guilabel>
    426426              </term>
    427427              <listitem>
     
    433433            <varlistentry>
    434434              <term>
    435                 <userinput>Url</userinput>
     435                <guilabel>Url</guilabel>
    436436              </term>
    437437              <listitem>
     
    475475            <varlistentry>
    476476              <term>
    477                 <userinput>New password</userinput>
     477                <guilabel>New password</guilabel>
    478478              </term>
    479479              <listitem>
     
    485485            <varlistentry>
    486486              <term>
    487                 <userinput>Retype password</userinput>
     487                <guilabel>Retype password</guilabel>
    488488              </term>
    489489              <listitem>
     
    540540            <varlistentry>
    541541              <term>
    542                 <userinput>Font size</userinput>
     542                <guilabel>Font size</guilabel>
    543543              </term>
    544544              <listitem>
     
    553553            <varlistentry>
    554554              <term>
    555                 <userinput>Scale factor</userinput>
     555                <guilabel>Scale factor</guilabel>
    556556              </term>
    557557              <listitem>
     
    571571            <varlistentry>
    572572              <term>
    573                 <userinput>Toolbar</userinput>
     573                <guilabel>Toolbar</guilabel>
    574574              </term>
    575575              <listitem>
     
    583583            <varlistentry>
    584584              <term>
    585                 <userinput>Recently used items</userinput>
     585                <guilabel>Recently used items</guilabel>
    586586              </term>
    587587              <listitem>
     
    595595            <varlistentry>
    596596              <term>
    597                 <userinput>Ratio color range</userinput>
     597                <guilabel>Ratio color range</guilabel>
    598598              </term>
    599599              <listitem>
     
    611611            <varlistentry>
    612612              <term>
    613                 <userinput>Date format</userinput>
     613                <guilabel>Date format</guilabel>
    614614              </term>
    615615              <listitem>
     
    641641            <varlistentry>
    642642              <term>
    643                 <userinput>Date-time format</userinput>
     643                <guilabel>Date-time format</guilabel>
    644644              </term>
    645645              <listitem>
     
    665665            <varlistentry>
    666666              <term>
    667                 <userinput>Decimals</userinput>
     667                <guilabel>Decimals</guilabel>
    668668              </term>
    669669              <listitem>
     
    693693            <varlistentry>
    694694              <term>
    695                 <userinput>Messages</userinput>
     695                <guilabel>Messages</guilabel>
    696696              </term>
    697697              <listitem>
     
    721721         
    722722          <para>
    723             If the <userinput>Load the names of all recent items</userinput> checkbox
     723            If the <guilabel>Load the names of all recent items</guilabel> checkbox
    724724            is checked the name of the items will be displayed in the menu (for example,
    725725            Experiment: My experiment). Otherwise only the type of the item is
     
    731731      </sect2>
    732732 
     733    </sect1>
     734   
     735    <sect1 id="webclient.items">
     736      <title>Working with items</title>
     737     
     738      <para>
     739        No matter what you are doing in BASE some things works more
     740        or less in the same way. This section convers things that are
     741        common for most parts of BASE.
     742      </para>
     743     
     744      <para>
     745        You mostly work with a single type of item at a time. This is
     746        reflected in the menu system. For example, use <guimenu>View</guimenu>
     747        <guimenuitem>Samples</guimenuitem> to work with samples, and
     748        <guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem> to
     749        work with experiments. In most cases the list view for that type
     750        of item is displayed. The list view, as the name says,
     751        is used to list all items. There are two more standard views, the
     752        single-item view and the edit view.
     753      </para>
     754     
     755      <variablelist>
     756        <varlistentry>
     757          <term>List view</term>
     758          <listitem>
     759            <para>
     760            This view lists all items of a certain type. Gives you
     761            an overview of your items. The view allows you to search
     762            and it is possible to configure which information to show
     763            for each item. It also contains functions that
     764            can be used on multiple items at the same time, for example,
     765            delete, share and export.
     766            </para>
     767          </listitem>
     768        </varlistentry>
     769     
     770        <varlistentry>
     771          <term>Single-item view</term>
     772          <listitem>
     773            <para>
     774            Displays information about a single item. Sometimes it is very little,
     775            sometimes it is very much and the information may be divided
     776            into multiple tabs.
     777            </para>
     778          </listitem>
     779        </varlistentry>
     780     
     781        <varlistentry>
     782          <term>Edit view</term>
     783          <listitem>
     784            <para>
     785            This view is used for editing the information
     786            about a single item. It is always displayed as a popup window.
     787            </para>
     788          </listitem>
     789        </varlistentry>
     790      </variablelist>
     791             
     792      <sect2 id="webclient.items.new">
     793        <title>Create a new item</title>
     794       
     795        <para>
     796          New items are mostly created from the list view. For example,
     797          to create a new experiment go to the
     798          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
     799          page. Here you will find a <guibutton>New&hellip;</guibutton> button in the
     800          toolbar. The button is disabled if you don't have permission to create new experiments.
     801          Otherwise, click on it and enter any required information in the popup dialog.
     802          Sometimes there are multiple tabs in this dialog. In the case of experiments
     803          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
     804          and <guilabel>Experimental factors</guilabel>.
     805         
     806          As a general rule, only the first tab has information that is required.
     807          The information in all other tabs are optional.
     808        </para>
     809       
     810        <para>
     811          In some places you will also find actions that create items
     812          directly in the list. For example in the list of samples or on
     813          the single-item view for a sample you can create an extract using that
     814          sample as the parent. If you use such links the parent
     815          item will in most cases be selected automatically, which saves
     816          you a few clicks when creating new items.
     817        </para>
     818       
     819        <para>
     820          Click on the <guibutton>Save</guibutton> button to save the new
     821          item to the database or on the <guibutton>Cancel</guibutton> button
     822          to abort.
     823        </para>
     824
     825        <note>
     826          <para>
     827          To speed up data entry when adding multiple new items there
     828          are a few tricks you can use to make the web client supply
     829          default values for most properties. To find a default value
     830          the following checklist is used in this order:
     831          </para>
     832       
     833        <orderedlist>         
     834          <listitem>
     835            <para>
     836            If the list have an active filter the filter values are
     837            used as default property values for the new item. For example,
     838            if you are listing experiments with <guilabel>Genepix</guilabel>
     839            raw data type the new experiment will automatically have
     840            <guilabel>Genepix</guilabel> selected. This trick should work
     841            for all properties except annotations, if it doesn't
     842            report it as a bug to the development team.
     843            </para>
     844          </listitem>
     845         
     846          <listitem>
     847            <para>
     848            When you link to other items the same item will be used the next time.
     849            For example, if you create an extract and selects an extraction protocol
     850            the same protocol is used the next time you create another extract.
     851            In fact, BASE will remember as many items as specified by
     852            the <link linkend="webclient.configuration.preferences.appearance">
     853            <guilabel>Recently used items</guilabel></link> setting (default is 4),
     854            allowing you to quickly select one of those protocols.
     855            </para>
     856          </listitem>
     857         
     858          <listitem>
     859            <para>
     860            If you have a project active and that project has specified default
     861            values those values will be used for new items. A project can specify
     862            defaults for protocols, hardware and software and a few other settings.
     863            </para>
     864          </listitem>
     865         
     866        </orderedlist>
     867       
     868        </note>
     869       
     870      </sect2>
     871     
     872      <sect2 id="webclient.items.edit">
     873        <title>Edit an existing item</title>
     874       
     875        <para>
     876          On all single-item views there is an <guibutton>Edit&hellip;</guibutton>
     877          button in the toolbar that opens a popup dialog for editing the properties
     878          of the item. This button is disabled if the logged in user doesn't have
     879          write permission for the item.
     880        </para>
     881       
     882        <para>
     883          You can also open the edit popup in most other places where
     884          the item appears, for example, in lists or the single-item view
     885          of a related item. Press and hold one of the <keycap>CTRL</keycap>,
     886          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
     887          on the link and the edit window will open in a popup.
     888          If you don't have write permission
     889          on the item there is no meaning to open the edit popup and you will
     890          be taken to the single-item view page instead.
     891        </para>
     892
     893        <para>
     894          Click on the <guibutton>Save</guibutton> button to save the changes
     895          to the database or on the <guibutton>Cancel</guibutton> button
     896          to abort.
     897        </para>
     898     
     899      </sect2>
     900
     901      <sect2 id="webclient.items.delete">
     902        <title>Delete items</title>
     903
     904        <para>
     905          You can delete items either from the list view or from
     906          a single-item view. In both cases, the item is only moved to
     907          the trashcan. No information is deleted from the database. This allows
     908          you to restore the item if you later find out that you need it again.
     909          In fact, there is nothing special about a removed item. It can still be
     910          used for the same things as any non-removed item can.
     911        </para>
     912
     913        <important>
     914          To really delete an item from the database you must use
     915          the trashcan. See <xref linkend="trashcan"/>
     916        </important>
     917       
     918        <para>
     919          To delete items from the list view you must first mark
     920          the checkbox for each item you want to delete. Then, click on
     921          the <guibutton>Delete</guibutton> button. The list should refresh itself
     922          automatically. If you want to confirm that the items have been removed
     923          use the <guilabel>view / presets</guilabel> dropdown and select
     924          the <guilabel>Removed</guilabel> option. The removed items should now
     925          be displayed in the list with a small trashcan icon to indicate that
     926          they are located in the trashcan.
     927        </para>
     928
     929        <para>
     930          To delete items from the single-item view, click on the
     931          <guibutton>Delete</guibutton> button in the toolbar. The page will refresh
     932          itself automatically and a small trashcan icon should be displayed.
     933          If you don't have permission to delete the item the delete button
     934          is disabled.
     935        </para>
     936
     937      </sect2>
     938     
     939      <sect2 id="webclient.items.restore">
     940        <title>Restore deleted items</title>
     941       
     942        <para>
     943          You can restore deleted items either from the trashcan,
     944          from the list view or from the single-item view. This section only covers the last two
     945          cases. The trashcan has a <link linkend="trashcan">chapter of it's own</link>.
     946        </para>
     947
     948        <para>
     949          To delete items from the list view you must first make the deleted
     950          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel>
     951          dropdown and select the <guilabel>Removed</guilabel> option. The list should
     952          refresh itself automatically. The removed items are
     953          displayed in the list with a small trashcan icon to indicate that
     954          they are located in the trashcan. Then, mark the checkbox for each item that you want
     955          to restore and click the <guibutton>Restore</guibutton> button. The list should
     956          refresh itself automatically and the trashcan icon should be gone from the
     957          restored items.
     958        </para>
     959       
     960        <para>
     961          To restore items from the single-item view, click on the
     962          <guibutton>Restore</guibutton> button in the toolbar. The page will refresh
     963          itself automatically and the small trashcan icon should be gone.
     964          If you don't have permission to restore the item the restore button
     965          is disabled.
     966        </para>
     967
     968      </sect2>
     969
     970      <sect2 id="webclient.items.share">
     971        <title>Share items to other users</title>
     972        <para>
     973          Sharing data with other users is an important feature
     974          of BASE, which allows you cooperate in teams. If you have
     975          followed the instructions in <xref linkend="project_permission" />
     976          you will find that you almost never have to share items manually
     977          to other users. This is because whenever you work with an active
     978          project each new item you create will automatically be shared
     979          to that project. In most cases, this is all you need.
     980        </para>
     981       
     982        <para>
     983          If you still need to manually share your data with other users,
     984          here is how to do it.
     985        </para>
     986       
     987        <para>
     988          From a list view, mark the checkbox for each item you want to share.
     989          Then, click on the <guibutton>Share&hellip;</guibutton> button.
     990          If you are on a single-item page, click on the <guibutton>Share&hellip;</guibutton>
     991          button on that page. In both cases, this will open the
     992          <guilabel>Set access permissions</guilabel>
     993          dialog window.
     994        </para>
     995       
     996        <figure id="webclient.items.share.set_permissions">
     997          <title>Sharing items to other users</title>
     998          <screenshot>
     999          <mediaobject>
     1000            <imageobject>
     1001              <imagedata fileref="figures/set_permissions.png" format="PNG"/>
     1002            </imageobject>
     1003          </mediaobject>
     1004          </screenshot>
     1005        </figure>
     1006       
     1007        <helptext external_id="share.setpermissions" title="Set access permissions">
     1008          <variablelist>
     1009            <varlistentry>
     1010              <term><guilabel>Members</guilabel></term>
     1011              <listitem>
     1012                <para>
     1013                The list displays the users, groups and projects
     1014                that already has acess to the items you selected.
     1015                The list shows the name and the permission level.
     1016                The permission level uses a one-letter code as follows:
     1017                </para>
     1018               
     1019                <itemizedlist>
     1020                <listitem><guilabel>R</guilabel> = Read</listitem>
     1021                <listitem><guilabel>U</guilabel> = Use</listitem>
     1022                <listitem><guilabel>W</guilabel> = Write</listitem>
     1023                <listitem><guilabel>D</guilabel> = Delete</listitem>
     1024                <listitem><guilabel>O</guilabel> = Take ownership</listitem>
     1025                <listitem><guilabel>P</guilabel> = Set permission</listitem>
     1026                </itemizedlist>
     1027               
     1028                <para>
     1029                  Instead of a permission code, the word <guilabel>varying</guilabel>
     1030                  may be displayed. This happens if the items you selected have been
     1031                  shared with different permission.
     1032                </para>
     1033               
     1034              </listitem>
     1035            </varlistentry>
     1036           
     1037            <varlistentry>
     1038              <term><guilabel>Permissions</guilabel></term>
     1039              <listitem>
     1040                <para>
     1041                When you select a user, group or project in the
     1042                list, the checkboxes will display the current permission.
     1043                The exception is if the permissions are varying, in which
     1044                case no checkboxes are checked.
     1045                To change the permissions just check the permissions you want to
     1046                grant or uncheck the permissions you want to revoke.
     1047                You can select more than one user, group or project
     1048                and change the permissions for all of them at once.
     1049                </para>
     1050              </listitem>
     1051            </varlistentry>           
     1052
     1053            <varlistentry>
     1054              <term><guibutton>Add users</guibutton></term>
     1055              <listitem>
     1056                <para>
     1057                Opens a popup window that allows you to select
     1058                users to share the items to. In the popup window, mark
     1059                one or more users and click on the <guibutton>Ok</guibutton>
     1060                button. Unless you are an administrator, the popup window
     1061                will only list users that are members of at least one of the
     1062                groups where you also are a member. It will not list users that
     1063                already have access to the items.
     1064                </para>
     1065              </listitem>
     1066            </varlistentry>
     1067
     1068            <varlistentry>
     1069              <term><guibutton>Add groups</guibutton></term>
     1070              <listitem>
     1071                <para>
     1072                Opens a popup window that allows you to select
     1073                groups to share the items to. In the popup window, mark
     1074                one or more groups and click on the <guibutton>Ok</guibutton>
     1075                button. Unless you are an administrator, the popup window
     1076                will only list groups where you are a member. It will not list
     1077                groups that already have access to the items.
     1078                </para>
     1079              </listitem>
     1080            </varlistentry>
     1081           
     1082            <varlistentry>
     1083              <term><guibutton>Add projects</guibutton></term>
     1084              <listitem>
     1085                <para>
     1086                Opens a popup window that allows you to select
     1087                projects to share the items to. In the popup window, mark
     1088                one or more projects and click on the <guibutton>Ok</guibutton>
     1089                button. Unless you are an administrator, the popup window
     1090                will only list projects where you are a member. It will not list
     1091                projects that already have access to the items.
     1092                </para>
     1093              </listitem>
     1094            </varlistentry>
     1095
     1096            <varlistentry>
     1097              <term><guibutton>Remove</guibutton></term>
     1098              <listitem>
     1099                <para>
     1100                Click on this button to revoke access permissions from
     1101                the selected users, groups and projects.
     1102                </para>
     1103              </listitem>   
     1104            </varlistentry>
     1105          </variablelist>
     1106       
     1107          <para>
     1108            Use the <guibutton>Save</guibutton> button to save your
     1109            changes or the <guibutton>Cancel</guibutton> button to
     1110            close the popup without saving.
     1111          </para>
     1112        </helptext>
     1113
     1114      </sect2>
     1115
     1116      <sect2 id="webclient.items.takeownership">
     1117        <title>Take ownership of items</title>
     1118        <para>
     1119          Sometime it maybe necessary to change the owner of an item.
     1120          As a user you can't give the ownership of your items to another
     1121          user. It is instead the other user that must take the ownership
     1122          of your items. For this to work, you must first give the other user
     1123          permission to do so. That it, you must share your items with
     1124          <guilabel>Take ownership</guilabel> permission to other user.
     1125          See <xref linkend="webclient.items.share" />.
     1126        </para>
     1127       
     1128        <para>
     1129          When the items have been shared the other user go to the
     1130          list view (or the single-item view), mark the checkboxes for
     1131          the items, and click in the <guibutton>Take ownership</guibutton>
     1132          button. A warning message about not beeing able to undo the action
     1133          is displayed. Click on <guibutton>Ok</guibutton> to continue or
     1134          <guibutton>Cancel</guibutton> to abort.
     1135        </para>
     1136       
     1137        <note>
     1138          The original owner may not have access permissions to the items
     1139          any longer. If that is desired, the new owner must share the items
     1140          to the original owner.
     1141        </note>
     1142       
     1143      </sect2>
     1144     
     1145      <sect2 id="webclient.items.export">
     1146        <title>Export items</title>
     1147        <para>
     1148          This has a chapter of it's own. See <xref linkend="import_export_data.export"/>.
     1149        </para>
     1150      </sect2>
     1151
    7331152    </sect1>
    7341153   
     
    7881207            <para>
    7891208            If there are many items the list will be divided into
    790             pages showin a limited number of items at the same time.
     1209            pages, each one showing a limited number of items.
    7911210            The navigation bar allows you to
    7921211            move to other pages and specify how many items each page
     
    8021221          <listitem>
    8031222            <para>
    804             A list with preconfigured settings allowing you to
     1223            A list with preconfigured settings which allows you to
    8051224            quickly switch between different layouts (sort order, visible
    8061225            columns, filter settings, etc).
     
    8491268          column is used for sub-sorting the list. The procedure can be
    8501269          repeated with more columns if you need to sort on three or more
    851           columns. To revert to sort by only one column again click the
     1270          columns. To revert to sort by only one column again click a
    8521271          column header without holding down any key.
    8531272        </para>
     
    9401359        </figure>
    9411360       
    942         <para>
    943           Use the left/right arrow buttons to move columns between
    944           the <guilabel>Visible columns</guilabel> list and the
    945           <guilabel>Hidden columns</guilabel> list. Use the up/down arrow
    946           buttons to arrange the order of the visible columns. The topmost column
    947           will be shown to the left.
    948         </para>
    949        
    950         <para>
    951           Columns marked with an <guilabel>×</guilabel> are required
    952           and can't be hidden. In mosts lists the <guilabel>Name</guilabel> column
    953           is the only column that is required.
    954         </para>
    955        
    956         <para>
    957           The <guilabel>Presets</guilabel> dropdown list allows you to
    958           select a set of preconfigured columns. You may also create
    959           your own preset if you often need to switch between different
    960           configurations. The list of presets is the same as the one
    961           described <link linkend="webclient.itemlist.presets">below</link>,
    962           but if used from this dialog the presets doesn't affect filters,
    963           sort order, etc.
    964         </para>
    965        
    966        
     1361        <helptext external_id="columns.configure"
     1362          title="Set column order and visiblity">
     1363       
     1364        <variablelist>
     1365        <varlistentry>
     1366          <term><guilabel>Visible columns</guilabel></term>
     1367          <listitem>
     1368            <para>
     1369              Shows the columns that are currently visible.
     1370              Use the up/down arrow buttons to arrange the order of the
     1371              visible columns. The topmost column is shown to the left.
     1372              Use the right arrow button to move columns from this list
     1373              to the hidden columns list. Columns marked with an <guilabel>×</guilabel>
     1374              are required
     1375              and can't be hidden. In mosts lists the <guilabel>Name</guilabel> column
     1376              is the only column that is required.
     1377            </para>
     1378          </listitem>
     1379        </varlistentry>
     1380         
     1381        <varlistentry>
     1382          <term><guilabel>Hidden columns</guilabel></term>
     1383          <listitem>
     1384            <para>
     1385              Shows columns that are not currently visible in the
     1386              list. Use the left arrow button to move columns from
     1387              this list to the visible columns list.
     1388            </para>
     1389          </listitem>
     1390        </varlistentry>
     1391       
     1392       
     1393        <varlistentry>
     1394          <term><guilabel>Presets</guilabel></term>
     1395          <listitem>
     1396            <para>
     1397              A dropdown list that allows you to
     1398              select a set of preconfigured columns. You may also create
     1399              your own preset if you often need to switch between different
     1400              configurations. The list of presets is the same as the one
     1401              described <link linkend="webclient.itemlist.presets">below</link>,
     1402              but if used from this dialog the presets doesn't affect filters,
     1403              sort order, etc.
     1404            </para>
     1405          </listitem>
     1406        </varlistentry>
     1407        </variablelist>
     1408       
     1409          <para>
     1410            Use the <guibutton>Save</guibutton> button to apply your
     1411            changes or the <guibutton>Cancel</guibutton> button to
     1412            close the popup without saving.
     1413          </para>
     1414
     1415        </helptext>
     1416
    9671417      </sect2>
    9681418     
     
    10331483              <listitem>
    10341484                <para><guilabel>Removed</guilabel> - If checked, items that have been
    1035                 marked for deletion are shown, otherwise they are hidden.</para>
     1485                moved to the trashcan are shown, otherwise they are hidden.</para>
    10361486              </listitem>
    10371487              <listitem>
     
    10601510           
    10611511            <para>
    1062               The default options are to only display items that the current
    1063               user owns and, if a project is active, items in that project.
     1512              The default is to display item that the current user
     1513              owns and, if a project is active, items in that project.
    10641514            </para>
    10651515           
     
    10871537                use the dropdown list for this.</para>
    10881538              </listitem>
    1089              
    10901539            </itemizedlist>
    1091          
    1092          
    1093           </listitem>
    1094 
     1540          </listitem>
    10951541        </orderedlist>
    1096       </sect2>
    1097      
     1542       
     1543        <sect3 id="webclient.itemlist.presets.saveas">
     1544          <title>Save a preset</title>
     1545         
     1546          <para>
     1547            If you select the <guilabel>Save as&hellip;</guilabel>
     1548            option from the <guilabel>view / presets</guilabel> dropdown
     1549            the <guilabel>Save preset as</guilabel> dialog is opened.
     1550          </para>
     1551         
     1552          <figure id="webclient.figures.savepresetas">
     1553            <title>Save preset as</title>
     1554            <screenshot>
     1555              <mediaobject>
     1556                <imageobject><imagedata fileref="figures/save_preset.png" format="PNG" /></imageobject>
     1557              </mediaobject>
     1558            </screenshot>
     1559          </figure>
     1560         
     1561          <helptext external_id="contexts.saveas" title="Save preset as">
     1562         
     1563          <variablelist>
     1564          <varlistentry>
     1565            <term><guilabel>For item</guilabel></term>
     1566            <listitem>
     1567              <para>
     1568              The type of item the preset is saved for.
     1569              </para>
     1570            </listitem>
     1571          </varlistentry>
     1572          <varlistentry>
     1573            <term><guilabel >Name</guilabel></term>
     1574            <listitem>
     1575              <para>
     1576              The name of the preset. The name must be unique.
     1577              </para>
     1578            </listitem>
     1579          </varlistentry>
     1580          <varlistentry>
     1581            <term><guilabel>Overwrite existing</guilabel></term>
     1582            <listitem>
     1583              <para>
     1584              If a preset with the same name already exists, it is
     1585              overwritten if this checkbox is checked.
     1586              </para>
     1587            </listitem>
     1588          </varlistentry>
     1589          <varlistentry>
     1590            <term><guilabel>Public</guilabel></term>
     1591            <listitem>
     1592              <para>
     1593              This options is only available for users
     1594              which has the <emphasis>SHARE_TO_EVERYONE</emphasis>
     1595              permission. If checked the preset is visible to
     1596              all users.
     1597              </para>
     1598            </listitem>
     1599          </varlistentry>
     1600          </variablelist>
     1601         
     1602          <para>
     1603            Use the <guibutton>Ok</guibutton> button to save the preset
     1604            or the <guibutton>Cancel</guibutton> button to
     1605            close the popup without saving.
     1606          </para>
     1607         
     1608         
     1609          </helptext>
     1610         
     1611        </sect3>
     1612       
     1613        <sect3 id="webclient.itemlist.presets.manage">
     1614          <title>Manage presets</title>
     1615         
     1616          <para>
     1617            If you select the <guilabel>Manage&hellip;</guilabel>
     1618            option from the <guilabel>view / presets</guilabel> dropdown
     1619            the <guilabel>Manage presets</guilabel> dialog is opened.
     1620          </para>
     1621         
     1622          <figure id="webclient.figures.managepresets">
     1623            <title>Manage presets</title>
     1624            <screenshot>
     1625              <mediaobject>
     1626                <imageobject><imagedata fileref="figures/manage_presets.png" format="PNG" /></imageobject>
     1627              </mediaobject>
     1628            </screenshot>
     1629          </figure>
     1630         
     1631          <helptext external_id="contexts.manage" title="Manage presets">
     1632         
     1633          <para>
     1634            From this dialog you can delete or load presets.
     1635          </para>
     1636         
     1637          <para>
     1638            To delete presets, first mark the checkbox in front of
     1639            each preset you want to delete. Then, click on the
     1640            <guibutton>Delete&hellip;</guibutton> button. You will get
     1641            a warning about that the action can't be undone. Unlike other
     1642            items, the presets are not moved to the trashcan. Click on
     1643            <guibutton>Ok</guibutton> to delete the preset.
     1644          </para>
     1645         
     1646          <note>
     1647            <title>Edit a preset</title>
     1648            It is not possible to edit a preset directly. To change an
     1649            existing preset you must:
     1650           
     1651            <orderedlist>
     1652            <listitem>Load the preset.</listitem>
     1653            <listitem>Use the interface to change column settings, filter,
     1654              sort order, etc.</listitem>
     1655            <listitem>Save the preset with the same name.</listitem>
     1656            </orderedlist>
     1657           
     1658          </note>
     1659         
     1660          <para>
     1661            Use the <guibutton>Close</guibutton> button to
     1662            close the popup.
     1663          </para>
     1664         
     1665         
     1666          </helptext>
     1667         
     1668        </sect3>
     1669       
     1670      </sect2>
    10981671    </sect1>
    10991672   
    1100     <sect1 id="webclient.items">
    1101       <title>Working with items</title>
    1102      
    1103       <para>
    1104         No matter what you are doing in BASE some things works more
    1105         or less in the same way. This section convers things that are
    1106         common for most parts of BASE.
    1107       </para>
    1108              
    1109       <sect2 id="webclient.items.new">
    1110         <title>Create a new item</title>
    1111        
    1112         <para>
    1113           New items are mostly created from the list view. For example,
    1114           to create a new experiment go to the
    1115           <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
    1116           page. Here you will find a <guibutton>New&hellip;</guibutton> button in the
    1117           toolbar. The button is disabled if you don't have permission to create new experiments.
    1118           Otherwise, click on it and enter any required information in the popup dialog.
    1119           Sometimes there are multiple tabs in this dialog. In the case of experiments
    1120           there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
    1121           and <guilabel>Experimental factors</guilabel>.
    1122          
    1123           As a general rule, only the first tab has information that is required.
    1124           The information in all other tabs are optional.
    1125         </para>
    1126        
    1127         <para>
    1128           In some places you will also find actions that create items
    1129           directly in the list. For example in the list of samples or on
    1130           the single-item view you can create an extract using that
    1131           sample as the parent. If you use such links the parent
    1132           item will in most cases be selected automatically, which saves
    1133           you a few clicks when creating new items.
    1134         </para>
    1135        
    1136         <para>
    1137           Click on the <guibutton>Save</guibutton> button to save the new
    1138           item to the database or on the <guibutton>Cancel</guibutton> button
    1139           to abort.
    1140         </para>
    1141 
    1142         <note>
    1143           <para>
    1144           To speed up data entry when adding multiple new items there
    1145           are a few tricks you can use to make the web client to enter
    1146           default values for most properties. To find a default value
    1147           the following checklist is used in this order.
    1148           </para>
    1149        
    1150         <orderedlist>         
    1151           <listitem>
    1152             <para>
    1153             If the list have an active filter the filter values are
    1154             used as default property values for the new item. For example,
    1155             if you are listing experiments with <guilabel>Genepix</guilabel>
    1156             raw data type the new experiment will automatically have
    1157             <guilabel>Genepix</guilabel> selected. This trick should work
    1158             for all properties except annotations, if it doesn't
    1159             report it as a bug to the development team.
    1160             </para>
    1161           </listitem>
    1162          
    1163           <listitem>
    1164             <para>
    1165             When you link to other items the same item will be used the next time.
    1166             For example, if you create an extract and selects an extraction protocol
    1167             the same protocol is used the next time you create another extract.
    1168             In fact, BASE will remember as many items as specified by
    1169             the <link linkend="webclient.configuration.preferences.appearance">
    1170             <guilabel>Recently used items</guilabel></link> setting (default is 4),
    1171             allowing you to quickly select one of those protocols.
    1172             </para>
    1173           </listitem>
    1174          
    1175           <listitem>
    1176             <para>
    1177             If you have a project active and that project has specified default
    1178             values those values will be used for new items. A project can specify
    1179             defaults for protocols, hardware and software and a few other settings.
    1180             </para>
    1181           </listitem>
    1182          
    1183         </orderedlist>
    1184        
    1185         </note>
    1186        
    1187       </sect2>
    1188      
    1189       <sect2 id="webclient.items.edit">
    1190         <title>Edit an existing item</title>
    1191        
    1192         <para>
    1193           On all single-item views there is an <guibutton>Edit&hellip;</guibutton>
    1194           button in the toolbar that opens a popup dialog for editing the properties
    1195           of the item. This button is disabled if the logged in user doesn't have
    1196           write permission for the item.
    1197         </para>
    1198        
    1199         <para>
    1200           You can also open the edit popup in most other places where
    1201           the item appears, for example, in lists or the single-item view
    1202           of a related item. If you just click on the link you will be taken
    1203           to the single-item view page of the item, but if you also
    1204           hold down one of the <keycap>CTRL</keycap>,
    1205           <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking on the
    1206           link the edit dialog will open instead. If you don't have write permission
    1207           on the item there is no meaning to open the edit popup and you will
    1208           be taken to the single-item view page.
    1209         </para>
    1210 
    1211      
    1212       </sect2>
    1213 
    1214       <sect2 id="webclient.items.delete">
    1215         <title>Delete items</title>
    1216 
    1217         <para>
    1218           You can delete items either from the list view or from
    1219           a single-item view. In both cases, the item is only put into
    1220           the trashcan. It is not deleted from the database. This allows
    1221           you to restore the item if you later find out that you need it again.
    1222           In fact, there is nothing special about a removed item. It can still be
    1223           used for the same things as any non-removed item can.
    1224         </para>
    1225 
    1226         <important>
    1227           To really delete an item from the database you must use
    1228           the <link linkend="trashcan">trashcan</link>.
    1229         </important>
    1230        
    1231         <para>
    1232           To delete items from the list view you must first mark
    1233           the checkbox for each item you want to delete. Then, click on
    1234           the <guibutton>Delete</guibutton> button. The list should refresh iteself
    1235           automatically. If you want to confirm that the items have been removed
    1236           use the <guilabel>view / presets</guilabel> dropdown and select
    1237           the <guilabel>Removed</guilabel> option. The removed items should now
    1238           be displayed in the list with a small trashcan icon to indicate that
    1239           they are located in the trashcan.
    1240         </para>
    1241 
    1242         <para>
    1243           To delete items from the single-item view you just click on the
    1244           <guibutton>Delete</guibutton> in the toolbar. The page will refresh
    1245           itself automatically and a small trashcan icon should be displayed.
    1246           If you don't have permission to delete the item the delete button
    1247           is disabled.
    1248         </para>
    1249 
    1250       </sect2>
    1251      
    1252       <sect2 id="webclient.items.restore">
    1253         <title>Restore deleted items</title>
    1254        
    1255         <para>
    1256           You can restore deleted items either from the trashcan,
    1257           from the list view or from the single-item view. This section only covers the last two
    1258           cases. The trashcan has a <link linkend="trashcan">chapter of it's own</link>.
    1259         </para>
    1260 
    1261         <para>
    1262           To delete items from the list view you must first make the deleted
    1263           items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel>
    1264           dropdown and select the <guilabel>Removed</guilabel> option. The list should
    1265           refresh itself automatically. The removed items should now
    1266           be displayed in the list with a small trashcan icon to indicate that
    1267           they are located in the trashcan. Then, mark the checkbox for each item that you want
    1268           to restore and click the <guibutton>Restore</guibutton> button. The list should
    1269           refresh iteself automatically and the trashcan icon should be gone from the
    1270           restored items.
    1271         </para>
    1272        
    1273         <para>
    1274           To restore items from the single-item view you just click on the
    1275           <guibutton>Restore</guibutton> in the toolbar. The page will refresh
    1276           itself automatically and the small trashcan icon should be gone.
    1277           If you don't have permission to restore the item the restore button
    1278           is disabled.
    1279         </para>
    1280 
    1281       </sect2>
    1282 
    1283       <sect2 id="webclient.items.share">
    1284         <title>Share items to other users</title>
    1285         <para>
    1286           Sharing data with other users is an important feature
    1287           of BASE, which allows you cooperate in teams. If you have
    1288           followed the instructions in <xref linkend="project_permission" />
    1289           you will find that you almost never have to share items manually
    1290           to other users. This is because whenever you work with an active
    1291           project each new item you create will automatically be shared
    1292           to that project.
    1293         </para>
    1294        
    1295         <para>
    1296           If you still need to manually share your data with other users,
    1297           here is how to do it.
    1298         </para>
    1299        
    1300         <para>
    1301           From a list view, mark the checkbox for each item you want to share.
    1302           Then, click on the <guibutton>Share&hellip;</guibutton> button.
    1303           If you are on a single-item page you just have
    1304           to click on the <guibutton>Share&hellip;</guibutton> button on that
    1305           page. In both cases, this will open the <guilabel>Set access permissions</guilabel>
    1306           dialog window.
    1307         </para>
    1308        
    1309         <figure id="webclient.items.share.set_permissions">
    1310           <title>Sharing items to other users</title>
    1311           <screenshot>
    1312           <mediaobject>
    1313             <imageobject>
    1314               <imagedata fileref="figures/set_permissions.png" format="PNG"/>
    1315             </imageobject>
    1316           </mediaobject>
    1317           </screenshot>
    1318         </figure>
    1319        
    1320         <helptext external_id="share.setpermissions" title="Set access permissions">
    1321           <variablelist>
    1322             <varlistentry>
    1323               <term><userinput>Members</userinput></term>
    1324               <listitem>
    1325                 <para>
    1326                 The list displays the user, groups and project
    1327                 that already has acess to the items you selected.
    1328                 The list shows the name and the permission level.
    1329                 The permission level uses a one-letter code as follows:
    1330                 </para>
    1331                
    1332                 <itemizedlist>
    1333                 <listitem><guilabel>R</guilabel> = Read</listitem>
    1334                 <listitem><guilabel>U</guilabel> = Use</listitem>
    1335                 <listitem><guilabel>W</guilabel> = Write</listitem>
    1336                 <listitem><guilabel>D</guilabel> = Delete</listitem>
    1337                 <listitem><guilabel>O</guilabel> = Take ownership</listitem>
    1338                 <listitem><guilabel>P</guilabel> = Set permission</listitem>
    1339                 </itemizedlist>
    1340                
    1341                 <para>
    1342                   Instead of a permission code, the word <guilabel>varying</guilabel>
    1343                   may be displayed. This happens if the items you selected have been
    1344                   shared with different permission
    1345                 </para>
    1346                
    1347               </listitem>
    1348             </varlistentry>
    1349            
    1350             <varlistentry>
    1351               <term><userinput>Permissions</userinput></term>
    1352               <listitem>
    1353                 <para>
    1354                 When you select a user, group or project in the
    1355                 list the checkboxes will display the current permission,
    1356                 except if the permissions are varying. In this case no
    1357                 checkboxes are checked.
    1358                
    1359                 To change the permissions just check the permissions you want to
    1360                 grant or uncheck the permissions you want to revoke.
    1361                 You can select more than one user, group or project
    1362                 and change the permissions for all of them at once.
    1363                 </para>
    1364               </listitem>
    1365             </varlistentry>           
    1366 
    1367             <varlistentry>
    1368               <term><guibutton>Add users</guibutton></term>
    1369               <listitem>
    1370                 <para>
    1371                 Opens a popup window that allows you to select
    1372                 users to share the items to. In the popup window, mark
    1373                 one or more users and click on the <guibutton>Ok</guibutton>
    1374                 button. Unless you are an administrator, the popup window
    1375                 will only list users that are members of at least one of the
    1376                 groups where you also are a member. It will not list users that
    1377                 already have access to the items.
    1378                 </para>
    1379               </listitem>
    1380             </varlistentry>
    1381 
    1382             <varlistentry>
    1383               <term><guibutton>Add groups</guibutton></term>
    1384               <listitem>
    1385                 <para>
    1386                 Opens a popup window that allows you to select
    1387                 groups to share the items to. In the popup window, mark
    1388                 one or more groups and click on the <guibutton>Ok</guibutton>
    1389                 button. Unless you are an administrator, the popup window
    1390                 will only list groups where you are a member. It will not list
    1391                 groups that already have access to the items.
    1392                 </para>
    1393               </listitem>
    1394             </varlistentry>
    1395            
    1396             <varlistentry>
    1397               <term><guibutton>Add projects</guibutton></term>
    1398               <listitem>
    1399                 <para>
    1400                 Opens a popup window that allows you to select
    1401                 projects to share the items to. In the popup window, mark
    1402                 one or more projects and click on the <guibutton>Ok</guibutton>
    1403                 button. Unless you are an administrator, the popup window
    1404                 will only list projects where you are a member. It will not list
    1405                 projects that already have access to the items.
    1406                 </para>
    1407               </listitem>
    1408             </varlistentry>
    1409 
    1410             <varlistentry>
    1411               <term><guibutton>Remove</guibutton></term>
    1412               <listitem>
    1413                 <para>
    1414                 Click on this button to revoke access permissions from
    1415                 the selected users, groups and projects.
    1416                 </para>
    1417               </listitem>   
    1418             </varlistentry>
    1419           </variablelist>
    1420        
    1421           <para>
    1422             Use the <guibutton>Save</guibutton> button to save your
    1423             changes or the <guibutton>Cancel</guibutton> button to
    1424             clost the popup without saving.
    1425           </para>
    1426         </helptext>
    1427 
    1428       </sect2>
    1429 
    1430       <sect2 id="webclient.items.takeownership">
    1431         <title>Take ownership of items</title>
    1432         <para>
    1433           TODO
    1434         </para>
    1435       </sect2>
    1436      
    1437       <sect2 id="webclient.items.export">
    1438         <title>Export items</title>
    1439         <para>
    1440           TODO - see other chapter/section.
    1441         </para>
    1442       </sect2>
    1443 
    1444     </sect1>
    1445    
    1446    
    14471673</chapter>
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