Changeset 1161

Timestamp:

Sep 16, 2009, 8:57:22 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

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

The installation now adds a "MeV analysis" configuration for the manual transform plug-in.

File:

• extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/install/Install.java (modified) (9 diffs)

extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/install/Install.java

@@ -27 +27 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.FileType;
+import net.sf.basedb.core.Group;
+import net.sf.basedb.core.GroupPermissions;
+import net.sf.basedb.core.Include;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemAlreadyExistsException;
+import net.sf.basedb.core.ItemKey;
 import net.sf.basedb.core.ItemNotFoundException;
+import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.Permission;
+import net.sf.basedb.core.PluginConfiguration;
+import net.sf.basedb.core.PluginConfigurationRequest;
 import net.sf.basedb.core.PluginDefinition;
 import net.sf.basedb.core.PluginParameter;
+import net.sf.basedb.core.PluginResponse;
 import net.sf.basedb.core.ProgressReporter;
 import net.sf.basedb.core.RequestInformation;
@@ -42 +50 @@
 import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.InteractivePlugin;
-import net.sf.basedb.core.plugin.Permissions;
 import net.sf.basedb.core.plugin.Plugin;
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
+import net.sf.basedb.core.plugin.Response.Status;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.mev.Mev;
+import net.sf.basedb.plugins.ManualTransformCreator;
 
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.EnumSet;
-import java.util.HashSet;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 /**
-
   Installation program for the MeV extension package. The installation
   will perform the following steps:
@@ -69 +80 @@
       <li>MeV CGH file
     </ul>
+  <li>Create a 'MeV analysis' configuration for the manual transform plug-in
   </ul>
   @since 1.5
@@ -94 +106 @@
   private RequestInformation configureJob = null;
   
-  private static final Set<Permissions> permissions = new HashSet<Permissions>();
-
   public Install()
   {}
@@ -108 +118 @@
   }
   @Override
-  public Collection<Permissions> getPermissions()
-  {
-    if (permissions.size() == 0)
-    {
-      permissions.add(new Permissions(Item.DATAFILETYPE, null, EnumSet.of(Permission.WRITE, Permission.CREATE)));
-      permissions.add(new Permissions(Item.FILETYPE, EnumSet.of(Permission.READ), null));
-    }
-    return permissions;
-  }
-  @Override
   public boolean supportsConfigurations()
   {
@@ -139 +139 @@
       try
       {
-        instalMevPackage(dc);
+        installMevPackage(dc);
         dc.commit();
       }
@@ -230 +230 @@
     Creates items that are required when working with the MeV package in BASE.
   */
-  public void instalMevPackage(DbControl dc)
+  public void installMevPackage(DbControl dc)
   {   
     FileType spotDataType = FileType.getById(dc, SystemItems.getId(net.sf.basedb.core.FileType.SPOT_DATA));
 
     //Data file types
-    createDataFileType(dc, Mev.ANALYSIS_FILE, "MeV analysis file", 
+    DataFileType mevAnalysisFile = createDataFileType(dc, Mev.ANALYSIS_FILE, "MeV analysis file", 
       "A MeV analysis file", 
       Item.BIOASSAYSET, "anl", spotDataType, null, null, null);
@@ -244 +244 @@
       "A MeV Tab-Delimited Multiple Sample file",
       Item.BIOASSAYSET, null, spotDataType, null, null, null);
-  }
-
+    ItemKey everyoneUse = getEveryoneUseKey(dc);
+    Map<String, Object> params = new HashMap<String, Object>();
+    params.put("fileTypes", mevAnalysisFile);
+    params.put("allowMoreFiles", true);
+    createPluginConfiguration(dc, ManualTransformCreator.class.getName(), 
+        "MeV analysis", 
+        "This manual transform represents work done " +
+        "in MeV. The resulting analysis file has been uploaded and attached " +
+        "to the bioassayset.", everyoneUse, params);
+  }
+
+  private PluginConfiguration createPluginConfiguration(DbControl dc,
+    String pluginClass, String name, String description, ItemKey key, 
+    Map<String, Object> parameters)
+  {
+    ItemQuery<PluginConfiguration> query = PluginConfiguration.getQuery();
+    query.include(Include.ALL);
+    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(name)));
+    query.restrict(Restrictions.eq(Hql.property("pluginDefinition.className"), 
+        Expressions.string(pluginClass)));
+    List<PluginConfiguration> list = query.list(dc);
+    PluginConfiguration config = null;
+    if (list.size() > 0)
+    {
+      config = list.get(0);
+    }
+    else
+    {
+      PluginDefinition plugin = PluginDefinition.getByClassName(dc, pluginClass);
+      config = plugin.newPluginConfiguration();
+      config.setName(name);
+      config.setDescription(description);
+      config.setItemKey(key);
+      dc.saveItem(config);
+      
+      PluginConfigurationRequest request = config.configure();
+      while (request != null)
+      {
+        RequestInformation ri = request.getRequestInformation();
+        for (PluginParameter<?> parameter : ri.getParameters())
+        {
+          String parameterName = parameter.getName();
+          Object value = parameters.get(parameterName);
+          request.setParameterValue(parameterName, value);
+        }
+        PluginResponse response = request.invoke();
+        Status status = response.getStatus();
+        if (status == Status.CONTINUE)
+        {
+          request = response.getNextRequest();
+        }
+        else if (status == Status.ERROR)
+        {
+          throw new BaseException(response.getMessage());
+        }
+        else
+        {
+          request = null;
+          response.saveParameters(dc);
+        }
+      }
+    }
+    return config;
+  }
+  
   private RequestInformation getConfigureJobParameters()
   {
@@ -301 +364 @@
     return dft;
   }
+  
+  private ItemKey getEveryoneUseKey(DbControl dc)
+  {
+    ItemKey everyoneUse = null;
+    try
+    {
+      Group everyone = Group.getById(dc, SystemItems.getId(Group.EVERYONE));
+      GroupPermissions gp = new GroupPermissions();
+      gp.addPermissions(everyone, EnumSet.of(Permission.USE));
+      everyoneUse = ItemKey.getNewOrExisting(dc, null, gp);
+    }
+    catch (Exception ex)
+    {}
+    return everyoneUse;
+  }
 }