Changeset 5724


Ignore:
Timestamp:
Sep 8, 2011, 9:12:06 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Added section about bioplate events in the biomaterials chapter. No screenshots yet.

Location:
trunk
Files:
5 edited

Legend:

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

    r5708 r5724  
    925925        to select a biomaterial. The same dialog can also be accessed from
    926926        the <guilabel>Wells</guilabel> tab. Assigning a biomaterial to a
    927         biowell can also be done when editing a sample or extract.
     927        biowell can also be done when editing a sample or extract, or
     928        by using the <link linkend="biomaterials.placeonplate">Place-on-plate
     929        wizard</link>.
    928930      </para>
    929931     
     
    10921094   
    10931095      <para>
    1094         TODO
     1096        Certain actions can be applied collectively to the biomaterial on a bioplate,
     1097        either as a whole or a subset that is picked by the user.
     1098        A list of the available actions can be found on the list page
     1099        <menuchoice>
     1100          <guimenu>Biomaterial LIMS</guimenu>
     1101          <guimenuitem>Bioplate event types</guimenuitem>
     1102        </menuchoice>.
     1103       
     1104        Although it is possible to create more event types here there is usually no
     1105        meaning to do so, since each event needs a specailized GUI wizard to take
     1106        care of it. The possibility to add more event types should be seen as an
     1107        opportunity for extension development.
    10951108      </para>
    1096    
     1109     
     1110      <sect3 id="biomaterials.placeonplate">
     1111        <title>The place-on-plate event</title>
     1112     
     1113        <figure id="biomaterials.figures.placeonplate">
     1114          <title>Place on plate wizard</title>
     1115          <screenshot>
     1116            <mediaobject>
     1117              <imageobject>
     1118                <imagedata
     1119                  fileref="figures/place_on_plate.png" format="PNG" />
     1120              </imageobject>
     1121            </mediaobject>
     1122          </screenshot>
     1123        </figure>
     1124     
     1125        <helptext external_id="bioplateevent.place-on-plate" title="Place on plate">
     1126        <para>
     1127          This event is available on the sample and extract list pages and can be used
     1128          to place multiple biomaterial on a bioplate in one go. Click on
     1129          the <guibutton>Place on plate</guibutton> button to start the wizard.
     1130          The wizard will automatically use the selected biomaterials or, if none
     1131          are selected, all listed biomaterials that aren't alredy located on a
     1132          plate.
     1133
     1134          <variablelist>
     1135            <varlistentry>
     1136              <term><guilabel>Event name</guilabel></term>
     1137              <listitem>
     1138                <para>
     1139                  Give a name to the event, or keep the suggested name.
     1140                </para>
     1141              </listitem>
     1142            </varlistentry>
     1143            <varlistentry>
     1144              <term><guilabel>Event date</guilabel></term>
     1145              <listitem>
     1146                <para>
     1147                  The date of the event.
     1148                </para>
     1149              </listitem>
     1150            </varlistentry>
     1151            <varlistentry>
     1152              <term><guilabel>Protocol</guilabel></term>
     1153              <listitem>
     1154                <para>
     1155                  The protocol used in the event, if any.
     1156                </para>
     1157              </listitem>
     1158            </varlistentry>
     1159            <varlistentry>
     1160              <term><guilabel>Hardware</guilabel></term>
     1161              <listitem>
     1162                <para>
     1163                  The hardware item used in the event, if any.
     1164                </para>
     1165              </listitem>
     1166            </varlistentry>
     1167            <varlistentry>
     1168              <term><guilabel>Description</guilabel></term>
     1169              <listitem>
     1170                <para>
     1171                  Other comments about the event.
     1172                </para>
     1173              </listitem>
     1174            </varlistentry>
     1175            <varlistentry>
     1176              <term><guilabel>Select plate...</guilabel></term>
     1177              <listitem>
     1178                <para>
     1179                  You need to select an existing plate on which the
     1180                  biomaterial should be placed. It is only possible to
     1181                  use one plate in each event. If you want to place biomaterial
     1182                  on more than one plate, the wizard must be repeated for
     1183                  each destination plate.
     1184                </para>
     1185              </listitem>
     1186            </varlistentry>
     1187            <varlistentry>
     1188              <term><guilabel>Clear</guilabel></term>
     1189              <listitem>
     1190                <para>
     1191                  Clear all current placement.
     1192                </para>
     1193              </listitem>
     1194            </varlistentry>
     1195            <varlistentry>
     1196              <term><guilabel>Place by row/column</guilabel></term>
     1197              <listitem>
     1198                <para>
     1199                  Automatically place the remaining biomaterial by filling empty wells,
     1200                  starting with rows or columns.
     1201                </para>
     1202              </listitem>
     1203            </varlistentry>
     1204            <varlistentry>
     1205              <term><guilabel>Items to place</guilabel></term>
     1206              <listitem>
     1207                <para>
     1208                  This column contains the biomaterial that should be placed on the plate.
     1209                  When a destination plate has been selected, it is displayed as a grid to
     1210                  the right. To place a biomaterial either use the <guibutton>Plate by row</guibutton>
     1211                  or <guibutton>Place by column</guibutton> buttons, or select an item in this
     1212                  list. When an item has been selected, click on the destination well on the
     1213                  plate. The coordinate of the well is displayed in the gray area before the
     1214                  biomaterial name and a line is drawn between it and the destination well.
     1215                  The destination well is also marked with an icon.
     1216                  If the <guilabel>Auto-select next unmapped item</guilabel> is selected
     1217                  the selection is automatically moved to the next biomaterial which can then
     1218                  be placed by selecting another destination well. If a mistake is made it is
     1219                  easy to correct. Simply re-select the item and then click on the correct well.
     1220                </para>
     1221              </listitem>
     1222            </varlistentry>
     1223
     1224          </variablelist>
     1225         
     1226          When the biomaterial has been placed on the plate (it is not neccessary to place all of them)
     1227          click on <guibutton>Save</guibutton> to store everything. BASE will create a plate event
     1228          for the selected destination plate and "other"-type events for each biomaterial that was
     1229          placed on it.
     1230        </para>
     1231        </helptext>
     1232      </sect3>
     1233
     1234      <sect3 id="biomaterials.move">
     1235        <title>The move biomaterials event</title>
     1236     
     1237        <figure id="biomaterials.figures.move">
     1238          <title>Move biomaterials wizard</title>
     1239          <screenshot>
     1240            <mediaobject>
     1241              <imageobject>
     1242                <imagedata
     1243                  fileref="figures/move_biomaterials.png" format="PNG" />
     1244              </imageobject>
     1245            </mediaobject>
     1246          </screenshot>
     1247        </figure>
     1248     
     1249        <helptext external_id="bioplateevent.move" title="Move biomaterials">
     1250        <para>
     1251          This event is available on the single-item view page of a bioplate
     1252          and can be used to move biomaterial from one plate to another. Click on
     1253          the <guibutton>Move biomaterial</guibutton> button to start the wizard.
     1254          <variablelist>
     1255            <varlistentry>
     1256              <term><guilabel>Event name</guilabel></term>
     1257              <listitem>
     1258                <para>
     1259                  Give a name to the event, or keep the suggested name.
     1260                </para>
     1261              </listitem>
     1262            </varlistentry>
     1263            <varlistentry>
     1264              <term><guilabel>Event date</guilabel></term>
     1265              <listitem>
     1266                <para>
     1267                  The date of the event.
     1268                </para>
     1269              </listitem>
     1270            </varlistentry>
     1271            <varlistentry>
     1272              <term><guilabel>Protocol</guilabel></term>
     1273              <listitem>
     1274                <para>
     1275                  The protocol used in the event, if any.
     1276                </para>
     1277              </listitem>
     1278            </varlistentry>
     1279            <varlistentry>
     1280              <term><guilabel>Hardware</guilabel></term>
     1281              <listitem>
     1282                <para>
     1283                  The hardware item used in the event, if any.
     1284                </para>
     1285              </listitem>
     1286            </varlistentry>
     1287            <varlistentry>
     1288              <term><guilabel>Description</guilabel></term>
     1289              <listitem>
     1290                <para>
     1291                  Other comments about the event.
     1292                </para>
     1293              </listitem>
     1294            </varlistentry>
     1295            <varlistentry>
     1296              <term><guilabel>Select plate...</guilabel></term>
     1297              <listitem>
     1298                <para>
     1299                  You need to select an existing plate to which the
     1300                  biomaterial should be moved. It is only possible to
     1301                  use one plate in each event. If you want to move biomaterial
     1302                  to more than one plate, the wizard must be repeated for
     1303                  each destination plate.
     1304                </para>
     1305              </listitem>
     1306            </varlistentry>
     1307            <varlistentry>
     1308              <term><guilabel>Clear</guilabel></term>
     1309              <listitem>
     1310                <para>
     1311                  Clear all current mapping between the source and destination plates.
     1312                </para>
     1313              </listitem>
     1314            </varlistentry>
     1315            <varlistentry>
     1316              <term><guilabel>Place by row/column</guilabel></term>
     1317              <listitem>
     1318                <para>
     1319                  Automatically move the remaining biomaterial by filling empty wells,
     1320                  starting with rows or columns.
     1321                </para>
     1322              </listitem>
     1323            </varlistentry>
     1324            <varlistentry>
     1325              <term><guilabel>Predefined mapping</guilabel></term>
     1326              <listitem>
     1327                <para>
     1328                  Use this button to select a predefined mapping between source
     1329                  and destination wells. The biomaterial will be moved according
     1330                  to the mapping.
     1331                </para>
     1332              </listitem>
     1333            </varlistentry>
     1334            <varlistentry>
     1335              <term><guilabel>Source plate</guilabel></term>
     1336              <listitem>
     1337                <para>
     1338                  This displays the source plate as a grid with icons that indicate
     1339                  filled and movable wells.
     1340                 
     1341                  When a destination plate has been selected, it is displayed as a similar grid to
     1342                  the right. To move a biomaterial either use the <guibutton>Place by row</guibutton>,
     1343                  <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
     1344                  buttons, or select a well on the source plate. When a source well has been selected,
     1345                  click on a well on the destination plate. A line is drawn between the source and
     1346                  destination wells and the icons are updated to show what is going on. The
     1347                  wells on the destination plate will also show the coordinate of the mapped
     1348                  source well unless the <guilabel>Show source coordinates</guilabel>
     1349                  checkbox is deselected. If a mistake is made it is
     1350                  easy to correct. Simply re-select the source well and then click on the correct
     1351                  destination well.
     1352                   
     1353                </para>
     1354              </listitem>
     1355            </varlistentry>
     1356          </variablelist>
     1357
     1358          When the biomaterial has been mapped between the source and destination plates
     1359          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton> to store everything.
     1360          BASE will create a plate event for the selected plates and "other"-type events for each
     1361          biomaterial that was moved.
     1362
     1363        </para>
     1364        </helptext>
     1365      </sect3>
     1366     
     1367      <sect3 id="biomaterials.create_child">
     1368        <title>The create child plate event</title>
     1369     
     1370        <figure id="biomaterials.figures.create_child_1">
     1371          <title>Create child plate wizard - step 1</title>
     1372          <screenshot>
     1373            <mediaobject>
     1374              <imageobject>
     1375                <imagedata
     1376                  fileref="figures/create_child_plate_1.png" format="PNG" />
     1377              </imageobject>
     1378            </mediaobject>
     1379          </screenshot>
     1380        </figure>
     1381     
     1382        <helptext external_id="bioplateevent.create-child-1" title="Create child plate - step 1">
     1383        <para>
     1384          This event is available on the single-item view page of a bioplate
     1385          when the bioplate is limited to a single type of biomaterial (eg.
     1386          only samples or only extracts). The event is used to create either
     1387          a child bioplate with biomaterial that is derived from the biomaterial
     1388          on the parent plate or to create one or more physical bioassays. Click on
     1389          the <guibutton>Create child bioplate</guibutton> button to start the wizard.
     1390        </para>
     1391       
     1392        <para>
     1393          The wizard has two steps. In the first step you set properties that
     1394          are related to the event and to the creation of child plates and
     1395          biomaterial. The first step is divied into three main sections.
     1396        </para>
     1397       
     1398       
     1399        <bridgehead>Event</bridgehead>
     1400       
     1401        <variablelist>
     1402          <varlistentry>
     1403            <term><guilabel>Event name</guilabel></term>
     1404            <listitem>
     1405              <para>
     1406                Give a name to the event, or keep the suggested name.
     1407              </para>
     1408            </listitem>
     1409          </varlistentry>
     1410          <varlistentry>
     1411            <term><guilabel>Event date</guilabel></term>
     1412            <listitem>
     1413              <para>
     1414                The date of the event.
     1415              </para>
     1416            </listitem>
     1417          </varlistentry>
     1418          <varlistentry>
     1419            <term><guilabel>Protocol</guilabel></term>
     1420            <listitem>
     1421              <para>
     1422                The protocol used in the event, if any.
     1423              </para>
     1424            </listitem>
     1425          </varlistentry>
     1426          <varlistentry>
     1427            <term><guilabel>Hardware</guilabel></term>
     1428            <listitem>
     1429              <para>
     1430                The hardware item used in the event, if any.
     1431              </para>
     1432            </listitem>
     1433          </varlistentry>
     1434          <varlistentry>
     1435            <term><guilabel>Description</guilabel></term>
     1436            <listitem>
     1437              <para>
     1438                Other comments about the event.
     1439              </para>
     1440            </listitem>
     1441          </varlistentry>
     1442        </variablelist>
     1443         
     1444        <bridgehead>Child biomaterial</bridgehead>
     1445        <variablelist>
     1446          <varlistentry>
     1447            <term><guilabel>Type</guilabel></term>
     1448            <listitem>
     1449              <para>
     1450                The type of child items to create. If the source plate
     1451                contains samples, you can select between sample and
     1452                extract and if the source plate contains extract you
     1453                can select between extract and physical bioassay.
     1454              </para>
     1455            </listitem>
     1456          </varlistentry>
     1457          <varlistentry>
     1458            <term><guilabel>Subtype</guilabel></term>
     1459            <listitem>
     1460              <para>
     1461                The subtype to assign to the newly created biomaterial
     1462                (or physical bioassay). The list of options is automatically
     1463                updated based on the selection in the <guilabel>Type</guilabel>
     1464                list.
     1465              </para>
     1466            </listitem>
     1467          </varlistentry>
     1468          <varlistentry>
     1469            <term><guilabel>Tag</guilabel></term>
     1470            <listitem>
     1471              <para>
     1472                Visible when creating child extracts only. Select the tag to
     1473                assign to the new extract. If no tag is selected and the
     1474                source biomaterial is also extracts, the children will get the
     1475                same tag as their parents.
     1476              </para>
     1477            </listitem>
     1478          </varlistentry>
     1479          <varlistentry>
     1480            <term><guilabel>Original quantity</guilabel></term>
     1481            <listitem>
     1482              <para>
     1483                The original quantity of the new biomaterial. Not visible when
     1484                creating a physical bioassay.
     1485              </para>
     1486            </listitem>
     1487          </varlistentry>
     1488          <varlistentry>
     1489            <term><guilabel>Used quantity</guilabel></term>
     1490            <listitem>
     1491              <para>
     1492                The quantity that was used from the parent biomaterial
     1493                in the process of creating child biomaterial.
     1494              </para>
     1495            </listitem>
     1496          </varlistentry>
     1497          <varlistentry>
     1498            <term><guilabel>Description</guilabel></term>
     1499            <listitem>
     1500              <para>
     1501                Other comments about the new biomaterial.
     1502              </para>
     1503            </listitem>
     1504          </varlistentry>
     1505        </variablelist>
     1506       
     1507       
     1508        <bridgehead>Child plates</bridgehead>
     1509        <variablelist>
     1510          <varlistentry>
     1511            <term><guilabel>No. of plates</guilabel></term>
     1512            <listitem>
     1513              <para>
     1514                The number of child plates to create. The default value is 1.
     1515              </para>
     1516            </listitem>
     1517          </varlistentry>
     1518          <varlistentry>
     1519            <term><guilabel>Name prefix</guilabel></term>
     1520            <listitem>
     1521              <para>
     1522                The child plates will be named using the prefix plus a running number
     1523                starting with 0. Eg. New plate.0.
     1524              </para>
     1525            </listitem>
     1526          </varlistentry>
     1527          <varlistentry>
     1528            <term><guilabel>Geometry</guilabel></term>
     1529            <listitem>
     1530              <para>
     1531                The geometry of the child plates. The default is the same
     1532                geometry as the parent plate. This option is replaced with
     1533                <guilabel>Size of bioassay</guilabel> when creating a
     1534                physical bioassay.
     1535              </para>
     1536            </listitem>
     1537          </varlistentry>
     1538          <varlistentry>
     1539            <term><guilabel>Plate type</guilabel></term>
     1540            <listitem>
     1541              <para>
     1542                The plate type of the child plates. Not used when creating a
     1543                physical bioassay.
     1544              </para>
     1545            </listitem>
     1546          </varlistentry>
     1547          <varlistentry>
     1548            <term><guilabel>Freezer</guilabel></term>
     1549            <listitem>
     1550              <para>
     1551                The freezer in which the new child plates are located. Not used
     1552                when creating a physical bioassay.
     1553              </para>
     1554            </listitem>
     1555          </varlistentry>
     1556          <varlistentry>
     1557            <term><guilabel>Description</guilabel></term>
     1558            <listitem>
     1559              <para>
     1560                Other comments about the new child plates.
     1561              </para>
     1562            </listitem>
     1563          </varlistentry>
     1564        </variablelist>
     1565       
     1566        <seeother>
     1567          <other external_id="bioplateevent.create-child-2">Create child plate - step 2</other>
     1568        </seeother>
     1569        </helptext>
     1570
     1571        <figure id="biomaterials.figures.create_child_2">
     1572          <title>Create child plate wizard - step 2</title>
     1573          <screenshot>
     1574            <mediaobject>
     1575              <imageobject>
     1576                <imagedata
     1577                  fileref="figures/create_child_plate_2.png" format="PNG" />
     1578              </imageobject>
     1579            </mediaobject>
     1580          </screenshot>
     1581        </figure>
     1582     
     1583        <helptext external_id="bioplateevent.create-child-2" title="Create child plate - step 2">
     1584        <para>
     1585          The second step display the source plate and new child plates as a grid.
     1586          To create child biomaterial either use the <guibutton>Place by row</guibutton>,
     1587          <guibutton>Place by column</guibutton> or <guibutton>Predefined mapping</guibutton>
     1588          buttons, or select a well on the source plate. When a source well has been selected,
     1589          click on a well on the destination plate. A line is drawn between the source and
     1590          destination wells and the icons are updated to show what is going on. The
     1591          wells on the destination plate will also show the coordinate of the mapped
     1592          source well unless the <guilabel>Show source coordinates</guilabel>
     1593          checkbox is deselected. If a mistake is made it is
     1594          easy to correct. Simply re-select the source well and then click on the correct
     1595          destination well.
     1596        </para>
     1597       
     1598        <para>
     1599          When a child biomaterial is selected you have the option to override the
     1600          automatially generated name. It is also possible to change the name
     1601          and barcode of the child plate.
     1602        </para>
     1603       
     1604        <note>
     1605          The principle is the same when creating physical bioassays, except that no
     1606          new child biomaterial is created.
     1607        </note>
     1608       
     1609        <para>
     1610          When the biomaterial has been mapped between the source and destination plates
     1611          (it is not neccessary to map all of them) click on <guibutton>Save</guibutton>
     1612          to store everything. BASE will create a plate event for the selected plates
     1613          and "create" or "bioassay"-type events for each biomaterial that was used.
     1614        </para>
     1615       
     1616        <seeother>
     1617          <other external_id="bioplateevent.create-child-1">Create child plate - step 1</other>
     1618        </seeother>
     1619       
     1620        </helptext>
     1621      </sect3>
    10971622    </sect2>
    10981623   
  • trunk/lib/docbook/preprocess/webclient_helptext.xsl

    r5635 r5724  
    8585    <lbl><xsl:apply-templates /></lbl>
    8686  </xsl:template>
     87 
     88  <xsl:template match="bridgehead">
     89    <h4><xsl:apply-templates /></h4>
     90  </xsl:template>
    8791
    8892</xsl:stylesheet>
  • trunk/www/biomaterials/wizards/create_child_bioplate_step2.jsp

    r5723 r5724  
    696696  <base:body onload="init()">
    697697    <div id="canvas"></div>
    698     <h3>Create child bioplate - step 2/2</h3>
     698    <h3>Create child bioplate - step 2/2 <base:help helpid="bioplateevent.create-child-2" /></h3>
    699699    <div class="boxedbottom" style="height: <%=(int)(scale*500)%>px; padding: 0px;">
    700700      <form name="main" action="index.jsp" method="post">
  • trunk/www/biomaterials/wizards/place_on_plate.jsp

    r5710 r5724  
    5151<%
    5252final Item itemType = Item.valueOf(request.getParameter("itemType"));
    53 //final String subContext = Values.getString(request.getParameter("subcontext"), "");
    5453final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
    55 //final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, null, null);
    5654final ItemContext cc = sc.getCurrentContext(Item.BIOPLATEEVENT, BioPlateEventType.PLACE_ON_PLATE);
    5755final String ID = sc.getId();
     
    632630  <base:body onload="init()">
    633631    <div id="canvas"></div>
    634     <h3>Place biomaterial on plate</h3>
     632    <h3>Place biomaterial on plate <base:help helpid="bioplateevent.place-on-plate" /></h3>
    635633    <div class="boxedbottom" style="height: <%=(int)(scale*500)%>px; padding: 0px;">
    636634      <form name="main" action="index.jsp" method="post">
  • trunk/www/include/styles/help.css

    r5426 r5724  
    114114
    115115.variablelist {
    116   border-top: 1px solid #cccccc;
    117   border-bottom: 1px solid #cccccc;
    118116}
    119117
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