Changeset 1540

Timestamp:

Feb 22, 2012, 9:31:59 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #361: MeV TDMS exporter should only include reporter fields that are present in the experiment

Location:

extensions/net.sf.basedb.mev/trunk

Files:

• .classpath (modified) (1 diff)
• META-INF/extensions.xml (modified) (2 diffs)
• README (modified) (1 diff)
• build.xml (modified) (2 diffs)
• lib/compile (modified) (1 prop)
• src/server/net/sf/basedb/mev/Mev.java (modified) (1 diff)
• src/server/net/sf/basedb/mev/export/TdmsExporter.java (modified) (2 diffs)

extensions/net.sf.basedb.mev/trunk/.classpath

@@ -8 +8 @@
   <classpathentry kind="lib" path="resources/jar/mev-gui-impl.jar" sourcepath="/mev-4.4.1/source"/>
   <classpathentry kind="lib" path="resources/jar/HTTPClient.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-core-3.0.0.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-coreplugins-3.0.0.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-webclient-3.0.0.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-webservices-client-3.0.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-core-3.1.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-coreplugins-3.1.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-webclient-3.1.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-webservices-client-3.1.0.jar"/>
   <classpathentry kind="output" path="bin"/>
 </classpath>

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

@@ -8 +8 @@
       it import data from the current bioassay set.
     </description>
-    <version>1.8</version>
+    <version>1.9-dev</version>
     <copyright>BASE development team</copyright>
     <email>basedb-users@lists.sourceforge.net</email>
     <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev</url>
-    <min-base-version>3.0.0</min-base-version>    
+    <min-base-version>3.1.0</min-base-version>    
   </about>
   <plugin-definition id="PackageInstaller">
@@ -103 +103 @@
         <title>MeV Launcher options&amp;hellip;</title>
         <tooltip>Specify options for the MeV Launcher</tooltip>
-        <onClick>Main.openPopup('$HOME$/options.jsp?ID='+getSessionId(), 'MeVLauncherOptions', 500, 400)</onClick>
+        <onClick>Main.openPopup('$HOME$/options.jsp?ID='+getSessionId(), 'MeVLauncherOptions', 450, 300)</onClick>
         <icon>~/images/tm4.png</icon>
       </parameters>

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

@@ -1 +1 @@
 == Requirements ==
 
- 1. BASE 3.0 or later.
+ 1. BASE 3.1 or later.
  
 == Introduction ==

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

@@ -10 +10 @@
   <!-- variables used -->
   <property name="name" value="mev-launcher" />
-  <property name="version" value="1.8" />
+  <property name="version" value="1.9-dev" />
   <property name="src" location="src" description="Location of source files" />
   <property name="build" location="build" description="Location of compiled files" />
@@ -24 +24 @@
   <property name="javac.encoding" value="UTF-8" />
   <property name="depend.base-version" 
-    value="3.0.0" 
+    value="3.1.0" 
     description="The BASE version that this project depends on."
   />

extensions/net.sf.basedb.mev/trunk/lib/compile

@@ -1 @@
-BASE2*.jar
-base-core-3.0.0.jar
-base-coreplugins-3.0.0.jar
-base-webclient-3.0.0.jar
-base-webservices-client-3.0.0.jar
+base-*.jar
+

@@ -1 @@
-BASE2*.jar
-base-core-3.0.0.jar
-base-coreplugins-3.0.0.jar
-base-webclient-3.0.0.jar
-base-webservices-client-3.0.0.jar
+base-*.jar
+

extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/Mev.java

@@ -36 +36 @@
     The current version of this plug-in package.
   */
-  public static final String VERSION = "1.8";
+  public static final String VERSION = "1.9-dev";
 
   /**

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

@@ -31 +31 @@
 import net.sf.basedb.core.BioAssay;
 import net.sf.basedb.core.BioAssaySet;
+import net.sf.basedb.core.ClonableProperty;
 import net.sf.basedb.core.DatabaseException;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DynamicResultIterator;
 import net.sf.basedb.core.DynamicSpotQuery;
-import net.sf.basedb.core.ExtendedProperties;
-import net.sf.basedb.core.ExtendedProperty;
 import net.sf.basedb.core.Formula;
 import net.sf.basedb.core.IntensityTransform;
+import net.sf.basedb.core.ReporterCloneTemplate;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.SqlResult;
@@ -280 +280 @@
   /**
     Adds position, externalId, symbol, plus all admin-defined extended 
-    properties as reporter fields.
+    properties as reporter fields. If the experiment has cloned reporter annotations
+    only fields that are present in the copy are exported.
   */
   protected void addReporterFields()
   {
     addReporterField(ExportableFieldFactory.jep("pos()", "id", Type.INT, Formula.AverageMethod.NONE, null));
-    addReporterField(ExportableFieldFactory.reporter("externalId", null, Type.STRING, null, null));
-    addReporterField(ExportableFieldFactory.reporter("symbol", null, Type.STRING, null, null));
-    for (ExtendedProperty ep : ExtendedProperties.getProperties("ReporterData"))
-    {
-      addReporterField(ExportableFieldFactory.reporter(ep, null, null));
+    ReporterCloneTemplate template = getSource().getExperiment().getVirtualDb().getReporterCloneTemplate();
+    
+    if (template.hasClonableProperty(ClonableProperty.EXTERNAL_ID))
+    {
+      addReporterField(ExportableFieldFactory.reporter(template.getClonableProperty(ClonableProperty.EXTERNAL_ID), null, null));
+    }
+
+    if (template.hasClonableProperty(ClonableProperty.SYMBOL))
+    {
+      addReporterField(ExportableFieldFactory.reporter(template.getClonableProperty(ClonableProperty.SYMBOL), null, null));
+    }
+    
+    List<ClonableProperty> properties = template == null ? 
+        ClonableProperty.getAll() : template.getClonableProperties();
+    for (ClonableProperty ep : properties)
+    {
+      if (ep.isExtendedProperty())
+      {
+        addReporterField(ExportableFieldFactory.reporter(ep, null, null));
+      }
     }
   }

@@ -1 @@
-BASE2*.jar
-base-core-3.0.0.jar
-base-coreplugins-3.0.0.jar
-base-webclient-3.0.0.jar
-base-webservices-client-3.0.0.jar
+base-*.jar
+