Ignore:
Timestamp:
Nov 10, 2008, 4:35:27 PM (15 years ago)
Author:
Martin Svensson
Message:

Fixes #1151 User role-test can now test batch importers. Documentation is updated(still in old format). Also updated build.xml to copy the test/role-directory when creating dist, links from wiki will work after next release.

File:
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/test/roles/index.html

    r4626 r4633  
    2424  <head>
    2525    <title>BASE - Test procedures for predefined roles</title>
    26   <link rel=stylesheet type="text/css" href="../../styles.css">
     26  <link rel=stylesheet type="text/css" href="../../historical/styles.css">
    2727  </head>
    2828<body>
    … …  
    158158    <li>Change to the <code>build/test/</code> directory.</li>
    159159
    160     <li>Run test programs: <code>./test.sh roles &lt;cmds&gt;</code> where
     160    <li>Run test programs: <code>./test.sh roles [OPTION] &lt;cmds&gt;</code> where
    161161      <code>&lt;cmds&gt;</code> is one or more of the following:
    162162      <ul>
    … …  
    167167      <li><code>user</code>: run the regular user tests</li>
    168168      <li><code>guest</code>: run the guest user tests</li>
     169      </ul>
     170      and <code>OPTION</code> can be none or more of:
     171      <ul>
     172      <li><code>-b</code>: if the batch importers should be tested</li>
     173      <li><code>-w</code>: if the test program should wait for ENTER before emptying the database.</li>
    169174      </ul>
    170175    </li>
    … …  
    10761081    </table>
    10771082    <p>
     1083    Or
     1084    <p>
     1085    Import array designs with the ArrayDesignImporter plug-in.
     1086    <ol>
     1087      <li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li>
     1088      <li>Click on the <code>Import</code> button on the array design list page.</li>
     1089      <li>Choose ArrayDesignImporter in the plug-in drop-down list.</li>
     1090      <li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set
     1091        the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
     1092        tab.</li>
     1093      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>     
     1094    </ol>
     1095    <p>
    10781096  </li>
    10791097 
    … …  
    11871205    </table>
    11881206    <p>
     1207    Or
     1208    <p>
     1209    Import array batches with the ArrayBatchImporter plug-in.
     1210    <ol>
     1211      <li>Click on the <code>Import</code> button on the array batch list page.</li>
     1212      <li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li>
     1213      <li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set  the parsing parameters
     1214        with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
     1215        tab.</li>
     1216      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>     
     1217    </ol>
     1218    <p>   
    11891219  </li>
    11901220
    … …  
    12101240    </tr>
    12111241    </table>
     1242    <p>
     1243    Or
     1244    <p>
     1245    Import array slides with the ArraySlideImporter plug-in.
     1246    <ol>
     1247      <li>Click on the <code>Import</code> button on the array slide list page.</li>
     1248      <li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li>
     1249      <li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set  the parsing parameters
     1250        with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
     1251        tab.</li>
     1252      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>     
     1253    </ol>
    12121254    <p>
    12131255  </li>
    … …  
    12191261    The user is a typical worker in the project. The user does the actual experimentation in the
    12201262    lab, which includes collecting samples, doing extraction, labeling and hybridizations.
    1221     The user also scans and analyses the raw data resulting from the images.
     1263    The user also scans and analyses the raw data resulting from the images. Inserting items can be
     1264    done in two different ways, .
    12221265  </p>
    12231266 
    1224   <ol>
    1225   <li>
    1226     Activate the <code>Project A</code> project<p></li>
    1227    
     1267  <p>
     1268    First activate the <code>Project A</code> project and then do one of following proceedures.
     1269  </p>
     1270  <p>
     1271    Use the batch importers for each item type.
     1272    <ol>
     1273      <li>Click on the <code>Import</code> button on the list page.</li>
     1274      <li>Select &lt;itemtype&gt;Importer in the plug-in drop-down list and click <code>Next</code></li>
     1275      <li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters
     1276        by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab.
     1277        <table class="listing" cellspacing="0" cellpadding="2" border="0">
     1278        <tr>
     1279          <th>Itemtype</th>
     1280          <th>File</th>
     1281        </tr>
     1282        <tr>
     1283          <td>Biosource</td>
     1284          <td>biosource_out.txt</td>       
     1285        </tr>
     1286        <tr>
     1287          <td>Samples</td>
     1288          <td>sample_out.txt</td>
     1289        </tr>
     1290        <tr>
     1291          <td>Extracts</td>
     1292          <td>extract_out.txt</td>
     1293        </tr>
     1294        <tr>
     1295          <td>Labeled extracts</td>
     1296          <td>labeledextract_out.txt</td>
     1297        </tr>
     1298        <tr>
     1299          <td>Hybridizations</td>
     1300          <td>hybridization_out.txt</td>
     1301        </tr>
     1302        <tr>
     1303          <td>Scans</td>
     1304          <td>scan_out.txt</td>
     1305        </tr>
     1306        <tr>
     1307          <td>Raw bioassays</td>
     1308          <td>rawbioassay_out.txt</td>
     1309        </tr>
     1310        </table>
     1311        The files listed for biosource and samples also contains annotations
     1312        for the items and these files should also be used with the annotation importer.
     1313        The procedure is the same as for batch importers except that only <code>\\Name\\</code>
     1314        is needed in the column mapping. The annotation column should be selected by default in
     1315        the second wizzard-step.       
     1316      </li>
     1317      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
     1318      <li>Then <a href="#inheritannotations">go to the step</a> in the next list where inherited annotations are set to the raw data
     1319        and proceed from there.</li>     
     1320    </ol>
     1321  </p>
     1322  <p>
     1323  Inserting each item manually
     1324  <ol> 
    12281325  <li>
    12291326    Create a biosource:
    … …  
    15931690  </li>
    15941691 
    1595   <li>
     1692  <li><a name="inheritannotations"></a>
    15961693    Inherit the annotations from the samples and biosource for each raw bioassay.
    15971694    <p>
    … …  
    17041801  </li>
    17051802 
     1803  </ol>
     1804  </li>
    17061805  </ol>
    17071806
Note: See TracChangeset for help on using the changeset viewer.