Changeset 1068


Ignore:
Timestamp:
May 15, 2009, 11:01:50 AM (14 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #214: Move TDMS export to this extension

Location:
extensions/net.sf.basedb.mev/trunk
Files:
5 added
1 deleted
6 edited

Legend:

Unmodified
Added
Removed

  • extensions/net.sf.basedb.mev/trunk/META-INF/extensions.xml

    r1061 r1068  
    6666    </action-factory>
    6767  </extension>
    68     <extension
    69     id="net.sf.basedb.mev.testlaunchexport"
    70     extends="net.sf.basedb.clients.web.bioassayset.list.tools"
    71     >
    72     <index>3</index>
    73     <about>
    74       <name>Test - MeV TDMS Export</name>
    75       <description>
    76         Adds an action to the "Tools" column that exports data to a
    77         MeV TDMS file. For debug only.
    78       </description>
    79     </about>
    80     <action-factory>
    81       <factory-class>
    82         net.sf.basedb.mev.factory.MevButtonFactory
    83       </factory-class>
    84       <parameters>
    85         <requireSpotData>true</requireSpotData>
    86         <title>Test MeV TDMS file</title>
    87         <tooltip>Immediately creates a MeV TDMS file from the data in this bioassay set</tooltip>
    88         <onClick>MeV.testTDMS($ID$)</onClick>
    89         <icon>~/images/tm4_export.png</icon>
    90         <script>~/scripts/mev.jsp</script>
    91       </parameters>
    92     </action-factory>
    93   </extension>
    94  
    9568  <extension
    9669    id="net.sf.basedb.mev.options"

  • extensions/net.sf.basedb.mev/trunk/README

    r1061 r1068  
    2424    installation. Otherwise, just wait a bit and the automatic installation will
    2525    find and install the new extension.
    26  5. Done. The MeV Launcher appears as an action in the "Tools" column when
    27     viewing bioassay sets of an experiment. Some (per-user) options can be
    28     specified by opening the 'Extensions -> MeV Launcher options' menu.
     26 5. Run the plug-in installation wizard by clicking the 'New' button on the
     27    'Administration -> Plugins -> Definitions' page. Make sure the option for
     28    the 'Extensions directory' is selected. Install all plug-ins found in
     29    the mev-launcher.jar file.
     30 6. Done.
     31 
     32 The MeV Launcher appears as an action in the "Tools" column when
     33 viewing bioassay sets of an experiment. Some (per-user) options can be
     34 specified by opening the 'Extensions -> MeV Launcher options' menu.
     35
     36The MeV export plug-ins appears in the 'Export' dialog when viewing
     37bioassay sets of an experiment.
    2938
    3039== Known issues ==

  • extensions/net.sf.basedb.mev/trunk/RELEASE

    r697 r1068  
    1515    * In build.xml: <property name="version" value="A.B" />
    1616    * In META-INF/extensions.xml: <version>A.B</version>
     17    * In src/net/sf/basedb/mev/MeV.java: public ... String VERSION = "A.B"
    1718
    1819 3. Make sure that the code compiles and can be packaged.

  • extensions/net.sf.basedb.mev/trunk/build.xml

    r1061 r1068  
    6969    description="Creates the extension JAR file"
    7070    >
     71    <copy todir="${build}">
     72      <fileset dir="." includes="META-INF/*" />
     73    </copy>
     74    <replace token="%%plugins.jar%%" value="${jar.name}" file="${build}/META-INF/base-plugins.xml" />
    7175    <jar
    7276      jarfile="${jar.name}"
    7377      >
    7478      <fileset dir="${build}" />
    75       <fileset dir="." includes="META-INF/**" />
    7679      <fileset dir="." includes="resources/**" />
    7780    </jar>

  • extensions/net.sf.basedb.mev/trunk/resources/launch_export.jsp

    r1061 r1068  
    5050DbControl dc = null;
    5151String defaultPath = "/";
    52 String defaultFileName = "mev.txt";
     52String defaultFileName = "";
    5353String jobName = "Create MeV TDMS file";
    5454try
    … …  
    5858  ItemContext cc = sc.getCurrentContext(Item.BIOASSAYSET);
    5959  cc.setId(bioAssaySetId);
    60   defaultFileName = Path.makeSafeFilename(bas.getName() + ".mev.txt", "");
     60  defaultFileName = Path.makeSafeFilename(bas.getName() + ".tdms.txt", "");
    6161  jobName += " for " + bas.getName();
    6262  try
    … …  
    8989  {
    9090    var url = getRoot()+'common/plugin/index.jsp?ID='+getSessionId();
    91     url += '&cmd=NewJob&plugin_class=net.sf.basedb.plugins.BioAssaySetExporter';
     91    url += '&cmd=NewJob&plugin_class=net.sf.basedb.mev.plugin.TdmsExporterPlugin';
    9292    url += '&item_type=BIOASSAYSET&context_type=ITEM';
    9393    url += '&job_name=' + encodeURIComponent('<%=jobName%>');
    94     url += '&parameter:fileformat=mev.tdms';
    9594    url += '&parameter:saveAs='+encodeURIComponent('<%=HTML.javaScriptEncode(defaultPath+defaultFileName)%>');
    9695    url += '&parameter:attachToBioAssaySet=true';
    … …  
    104103  <base:note type="question" title="<%=title%>">
    105104  The selected bioassay is not associated with a MeV TDMS file.
    106   Do you wish to create one with the BioAssaySetExporter plug-in?
     105  Do you wish to create one with the MeV TDMS exporter plug-in?
    107106  <br><br>
    108   <a href="test.xjsp?ID=<%=ID%>&bioassayset_id=<%=bioAssaySetId%>">Test new export</a>
    109107  </base:note>
    110108  <p>

  • extensions/net.sf.basedb.mev/trunk/src/net/sf/basedb/mev/export/TdmsExporter.java

    r1061 r1068  
    1919import net.sf.basedb.util.Values;
    2020import net.sf.basedb.util.export.TableWriter;
    21 import net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter;
    2221import net.sf.basedb.util.export.spotdata.AssayField;
    2322import net.sf.basedb.util.export.spotdata.DynamicField;
    … …  
    5251 
    5352  @author nicklas
    54   @version 1.3
     53  @since 1.3 
    5554*/
    5655public class TdmsExporter
    57   extends AbstractBioAssaySetExporter
     56  extends MevExporter
    5857{
    5958
    … …  
    6766  {}
    6867 
    69   /*
    70     Configuration properties
    71     ------------------------
    72   */
    73   /**
    74     Set the stream were the exported data should be written.
    75     It is expected that the given writer is a fresh writer and
    76     that no data has been written to it yet.
    77   */
    78   public void setWriter(TableWriter out)
    79   {
    80     this.out = out;
    81   }
    82   // --------------------------
    83 
    8468  /**
    8569    From AbstractBioAssaySetExporter class
    … …  
    9478  {
    9579    super.beginExport();
     80    out = getTableWriter();
    9681    addExperimentalFactorsAsAssayFields();
    9782    addReporterFields();
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