Changeset 1159

Timestamp:

Sep 15, 2009, 1:22:43 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #241: Add MeV Analysis file as a file type for bioassay sets

Added an "Installation" plug-in that is used to register data file types needed by the MeV package. Updated the installation instructions. This should complete this ticket, but I want to do some more tests.

Location:

extensions/net.sf.basedb.mev/trunk

Files:

• META-INF/base-plugins.xml (modified) (1 diff)
• README (modified) (2 diffs)
• src/server/net/sf/basedb/mev/install (added)
• src/server/net/sf/basedb/mev/install/Install.java (added)
• src/server/net/sf/basedb/mev/plugin/CghExporterPlugin.java (modified) (6 diffs)

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

@@ -10 +10 @@
     <hasconfigurations/>
   </pluginclass>
+  <pluginclass classname="net.sf.basedb.mev.install.Install">
+    <minbaseversion>2.12</minbaseversion>
+    <hasconfigurations/>
+  </pluginclass>
 </plugins>

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

@@ -28 +28 @@
     the 'Extensions directory' is selected. Install all plug-ins found in 
     the mev-launcher.jar file.
- 6. The 'MeV CGH exporter' requires that an admin configures the reporter
-    annotations that corresponds to the CGH file columns. Go to the
+ 6. Run the 'MeV package installer' plug-in. Find this plug-in on the 
+    'Administrate -> Plugins -> Definitions' page, click on it, and then
+    on the 'Run plugin' button. Complete the installation wizard. This will
+    install required items, eg. data file types, that are required by MeV.
+ 7. The 'MeV CGH exporter' plug-in requires that an admin configures the 
+    reporter annotations that corresponds to the CGH file columns. Go to the
     'Administrate -> Plugins -> Definitions' page and click on the 
     'MeV CGH exporter' plug-in. Click on 'New configuration...' and 
@@ -35 +39 @@
     configure' and select the corresponding reporter annotation columns
     for the four CGH file columns (chromosome, start, end and description).
-    Finish the configuration. Note! This step will also register a file
-    type for CGH. Make sure the logged in user has enough permissions to
-    create new file types.
- 7. Done. 
+    Finish the configuration.
+ 8. Done. 
  
  The MeV Launcher appears as an action in the "Tools" column when

extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/plugin/CghExporterPlugin.java

@@ -14 +14 @@
 import net.sf.basedb.core.BooleanParameterType;
 import net.sf.basedb.core.Config;
-import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.ExtendedProperties;
@@ -21 +20 @@
 import net.sf.basedb.core.FileSetMember;
 import net.sf.basedb.core.FileStoreUtil;
-import net.sf.basedb.core.FileType;
 import net.sf.basedb.core.Item;
-import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.ItemParameterType;
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.Path;
-import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.PluginDefinition;
 import net.sf.basedb.core.PluginParameter;
@@ -33 +29 @@
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.StringParameterType;
-import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
@@ -361 +356 @@
           Config.getCharset()));
       parameters.add(getOverwriteParameter(null, null));
-      if (checkCghFileType(dc) != null)
-      {
-        parameters.add(new PluginParameter<Boolean>(
-            "attachToBioAssaySet",
-            "Attach file to bioassay set",
-            "Deselect this option if you don't want the generated file to " +
-            "become attached to the current bioassay set. This option is ignored " +
-            "if the file isn't saved in the BASE file system.",
-            new BooleanParameterType(true, false)
-          ));
-      }
+      parameters.add(new PluginParameter<Boolean>(
+          "attachToBioAssaySet",
+          "Attach file to bioassay set",
+          "Deselect this option if you don't want the generated file to " +
+          "become attached to the current bioassay set. This option is ignored " +
+          "if the file isn't saved in the BASE file system.",
+          new BooleanParameterType(true, false)
+        ));
       dc.commit();
 
@@ -391 +383 @@
   private RequestInformation getConfigurePluginParameters(GuiContext context)
   {
-    if (configurePlugin != null) return configurePlugin;
-    
-    // Check/create MeV CGH file type
-    DbControl dc = null;
-    try
-    {
-      dc = sc.newDbControl();
-      checkCghFileType(dc);
-      dc.commit();
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-    
+    if (configurePlugin != null) return configurePlugin;    
     List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
 
@@ -467 +445 @@
     return configurePlugin;
   }
-
-  public DataFileType checkCghFileType(DbControl dc)
-  {
-    DataFileType cgh = null;
-    try
-    {
-      cgh = DataFileType.getByExternalId(dc, Mev.CGH_FILE);
-    }
-    catch (ItemNotFoundException ex)
-    {
-      if (dc.getSessionControl().hasPermission(Permission.CREATE, Item.DATAFILETYPE))
-      {
-        cgh = DataFileType.getNew(dc, Mev.CGH_FILE, Item.BIOASSAYSET);
-        cgh.setName("MeV CGH");
-        cgh.setDescription("A MeV Comparative Genomic Hybridization file");
-        cgh.setGenericType(FileType.getById(dc, SystemItems.getId(FileType.SPOT_DATA)));
-        dc.saveItem(cgh);
-      }
-    }
-    catch (Exception ex)
-    {}
-    return cgh;
-  }
-  
 }