Changeset 5729

Timestamp:

Sep 8, 2011, 3:35:22 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1620: Implement a 'Manual derived bioassay creator' plug-in

The plug-in can be used and it is possible to put restrictions on the parent bioassay subtype. There are no parameters for setting protocol, hardware or software... This might be needed, but I don't know if it should be on the configuration or in the job wizard. This could be an enhancement for a later BASE version.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/DerivedBioAssay.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java (modified) (7 diffs)
• src/plugins/core/core-plugins.xml (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/ManualDerivedBioAssayCreator.java (added)
• src/plugins/core/net/sf/basedb/plugins/batchimport/DerivedBioAssayImporter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java (modified) (1 diff)
• src/test/TestDerivedBioAssay.java (modified) (2 diffs)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (3 diffs)
• www/views/derivedbioassays/index.jsp (modified) (2 diffs)
• www/views/derivedbioassays/view_bioassay.jsp (modified) (1 diff)

trunk/src/core/net/sf/basedb/core/DerivedBioAssay.java

@@ -102 +102 @@
       permission checking and database access
     @param bioAssay The parent physical bioassay
+    @param job The job that created the new bioassay
     @return A new DerivedBioAssay item
   */
-  public static DerivedBioAssay getNew(DbControl dc, PhysicalBioAssay bioAssay)
+  public static DerivedBioAssay getNew(DbControl dc, PhysicalBioAssay bioAssay, Job job)
   {
     if (bioAssay == null) throw new InvalidUseOfNullException("bioAssay");
@@ -113 +114 @@
     dbas.getData().setPhysicalBioAssay(bioAssay.getData());
     dbas.getData().setEntryDate(new Date());
+    dbas.getData().setJob(job == null ? null : job.getData());
     return dbas;
   }
@@ -121 +123 @@
       permission checking and database access
     @param parent The parent bioassay 
+    @param job The job that created the new bioassay
     @return A new DerivedBioAssay item
   */
-  public static DerivedBioAssay getNew(DbControl dc, DerivedBioAssay parent)
+  public static DerivedBioAssay getNew(DbControl dc, DerivedBioAssay parent, Job job)
   {
     if (parent == null) throw new InvalidUseOfNullException("parent");
@@ -134 +137 @@
     dbas.getData().setExtract(parent.getData().getExtract());
     dbas.getData().setEntryDate(new Date());
+    dbas.getData().setJob(job == null ? null : job.getData());
     return dbas;
   }

trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

@@ -30 +30 @@
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.DerivedBioAssay;
 import net.sf.basedb.core.DynamicSpotQuery;
 import net.sf.basedb.core.Experiment;
@@ -75 +76 @@
   
   /**
+    GuiContext = [Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM]
+    @since 3.0
+  */
+  protected static final GuiContext CONTEXT_DERIVEDBIOASSAY =
+    new GuiContext(Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM);
+  
+  /**
     The default gui contexts where it makes sense to use an analysis plugin. 
     Override for the {@link InteractivePlugin#getGuiContexts()} method to
@@ -108 +116 @@
   
   /**
-    The source parameter.
+    The source parameter for bioassay set.
     @see #getSourceBioAssaySetParameter(String, String)
   */
-  private PluginParameter<BioAssaySet> sourceParameter = null;
+  private PluginParameter<BioAssaySet> sourceBioAssaySetParameter = null;
+
+
+  /**
+    The parameter type for the source derived bioassay.
+    @since 3.0
+  */
+  private static final ItemParameterType<DerivedBioAssay> sourceDerivedBioAssayType = 
+    new ItemParameterType<DerivedBioAssay>(DerivedBioAssay.class, null, true, 1, null);
+  
+
+  /**
+    The source parameter for derived bioassay.
+    @see #getSourceDerivedBioAssayParameter(String, String)
+    @since 3.0
+  */
+  private PluginParameter<DerivedBioAssay> sourceDerivedBioAssayParameter = null;
+
   
   /**
@@ -148 +173 @@
   }
   /**
-    Check that the item is a bioassayset and that the logged in user has 
-    permission to use the current experiment.
+    Check that the item is a bioassayset/derived bioassay and that the 
+    logged in user has permission to use the current item.
       @param context Current guicontext 
       @param item The item to check.
-    @return null if the item is a bioassayset, an error message otherwise
+    @return null if the item is a valid item, an error message otherwise
     @throws net.sf.basedb.core.PermissionDeniedException If the logged in user dosen't have
       permission to use the Experiment
@@ -176 +201 @@
       }
     }
+    else if (context.equals(CONTEXT_DERIVEDBIOASSAY))
+    {
+      if (item == null)
+      {
+        message = "The object is null";
+      }
+      else if (!(item instanceof DerivedBioAssay))
+      {
+        message = "The object is not a DerivedBioAssay: " + item;
+      }
+      else
+      {
+        DerivedBioAssay dba = (DerivedBioAssay)item;
+        dba.checkPermission(Permission.USE);
+      }
+    }
     else
     {
@@ -206 +247 @@
   protected PluginParameter<BioAssaySet> getSourceBioAssaySetParameter(String label, String description)
   {
-    if (sourceParameter == null)
+    if (sourceBioAssaySetParameter == null)
     {
       if (label == null) label = "Source bioassay set";
       if (description == null) description = "The bioassay set that is used as the data source for this job.";
-      sourceParameter = new PluginParameter<BioAssaySet>
+      sourceBioAssaySetParameter = new PluginParameter<BioAssaySet>
         (
           SOURCE_BIOASSAYSET, label, description, sourceBioAssaySetType
         );
     }
-    return sourceParameter;
-  }
+    return sourceBioAssaySetParameter;
+  }
+  
+  protected static final String SOURCE_DERIVEDBIOASSAY = "source";
+  
+  /**
+    Get a plugin parameter that asks for a derived bioassay to use as data source for
+    the plugin. Calling this method multiple times return the same plugin parameter object.
+    The label and description for the first call is always used.
+    
+    @param label The parameter label, or null to use the default (Source bioassay)
+    @param description The parameter description, or null to use the default 
+      (The derived bioassay that is used as the data source for this job.)
+  */
+  protected PluginParameter<DerivedBioAssay> getSourceDerivedBioAssayParameter(String label, String description)
+  {
+    if (sourceDerivedBioAssayParameter == null)
+    {
+      if (label == null) label = "Source bioassay";
+      if (description == null) description = "The derived  bioassay set that is used as the data source for this job.";
+      sourceDerivedBioAssayParameter = new PluginParameter<DerivedBioAssay>
+        (
+            SOURCE_DERIVEDBIOASSAY, label, description, sourceDerivedBioAssayType
+        );
+    }
+    return sourceDerivedBioAssayParameter;
+  }
+
   
   protected static final String SOURCE_BIOASSAYS = "bioAssays";
@@ -398 +465 @@
   
   /**
+    Get the current source derived bioassay. We first check the job's parameter
+    values with the {@link #getSourceDerivedBioAssay(DbControl)} method. If this
+    returns null we check the information in the current context:
+    <code>SessionControl.getCurrentContext(Item.DERIVEDBIOASSAY)</code>. Note
+    that this information is normally only available during the configuration
+    phase of a plugin, not during the execution phase.
+    
+    @param dc The DbControl to use for database access
+    @return The current derived bioassay or null
+    @see #getSourceBioAssaySet(DbControl)
+    @since 3.0
+  */
+  protected DerivedBioAssay getCurrentDerivedBioAssay(DbControl dc)
+  {
+    DerivedBioAssay current = getSourceDerivedBioAssay(dc);
+    if (current == null)
+    {
+      int currentId = sc.getCurrentContext(Item.DERIVEDBIOASSAY).getId();
+      if (currentId != 0) current = DerivedBioAssay.getById(dc, currentId);
+    }
+    return current;
+  }
+  
+  /**
+    Get the derived bioassay that is used as the source for the plugin. 
+    The source bioassay is only available in the execution phase
+    if the plugin has saved it as a job parameter during the configuration
+    of a job.
+    
+    @return The source derived bioassay or null
+    @see #getSourceDerivedBioAssayParameter(String, String)
+    @since 3.0
+  */
+  protected DerivedBioAssay getSourceDerivedBioAssay(DbControl dc)
+  {
+    DerivedBioAssay source = (DerivedBioAssay)job.getValue(SOURCE_DERIVEDBIOASSAY);
+    if (source != null) source = DerivedBioAssay.getById(dc, source.getId());
+    return source;
+  }
+
+  
+  /**
     Generate a name for the transformation based on the plugin and it's
     configuration. The name is created by taking the name of the plugin from the

trunk/src/plugins/core/core-plugins.xml

@@ -483 +483 @@
   </plugin-definition>
 
+  <plugin-definition id="ManualDerivedBioAssayCreator">
+    <about>
+      <name>Manual derived bioassay creator</name>
+      <description>
+        This plug-in allows a user to manually register an external 
+        analysis procedure that has happened outside of BASE and to 
+        register the parameters used and the output files that was 
+        generated. Before this plug-in can be used a configuration 
+        that represents the external tool must be created. The 
+        configuration will be used to register possible parameters 
+        and output files.
+      </description>
+    </about>
+    <plugin-class>net.sf.basedb.plugins.ManualDerivedBioAssayCreator</plugin-class>
+    <settings>
+      <property name="everyone-use">1</property>
+      <property name="immediate-execution">1</property>
+    </settings>
+  </plugin-definition>
+
   <plugin-definition id="BioSourceImporter">
     <about>

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/DerivedBioAssayImporter.java

@@ -306 +306 @@
     {
       DerivedBioAssay parent = findDerivedBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, parentSubtype);
-      bioAssay = DerivedBioAssay.getNew(dc, parent);
+      bioAssay = DerivedBioAssay.getNew(dc, parent, job.getJob());
     }
     else
     {
       PhysicalBioAssay pba = findPhysicalBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, parentSubtype);
-      bioAssay = DerivedBioAssay.getNew(dc, pba);
+      bioAssay = DerivedBioAssay.getNew(dc, pba, job.getJob());
     }
     

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java

@@ -213 +213 @@
       hyb = findHybridization(dc, FallbackIdMethod.NAME_OR_ID, hybridizationMapper.getValue(data));
     }
-    DerivedBioAssay scan = DerivedBioAssay.getNew(dc, hyb);
+    DerivedBioAssay scan = DerivedBioAssay.getNew(dc, hyb, job.getJob());
     scan.setItemSubtype(ItemSubtype.getById(dc, SystemItems.getId(DerivedBioAssay.SCAN)));
     updateItem(dc, scan, data);

trunk/src/test/TestDerivedBioAssay.java

@@ -92 +92 @@
     {
       dc = TestUtil.getDbControl();
-      DerivedBioAssay dbas = DerivedBioAssay.getNew(dc, PhysicalBioAssay.getById(dc, bioAssayId));
+      DerivedBioAssay dbas = DerivedBioAssay.getNew(dc, PhysicalBioAssay.getById(dc, bioAssayId), null);
       dbas.setName(name);
       dbas.setDescription("Added at "+new Date());
@@ -140 +140 @@
     {
       dc = TestUtil.getDbControl();
-      DerivedBioAssay dbas = DerivedBioAssay.getNew(dc, DerivedBioAssay.getById(dc, parentId));
+      DerivedBioAssay dbas = DerivedBioAssay.getNew(dc, DerivedBioAssay.getById(dc, parentId), null);
       dbas.setName(name);
       dbas.setDescription("Added at "+new Date());

trunk/src/test/net/sf/basedb/test/roles/UserTest.java

@@ -547 +547 @@
   {
     TestUtil.write("--Creating scan: " + name + "\n");
-    DerivedBioAssay scan = DerivedBioAssay.getNew(dc, hyb);
+    DerivedBioAssay scan = DerivedBioAssay.getNew(dc, hyb, null);
     scan.setItemSubtype(ItemSubtype.getById(dc, SystemItems.getId(DerivedBioAssay.SCAN)));
     scan.setName(name);
@@ -570 +570 @@
   {
     TestUtil.write("--Creating root bioassay: " + name + "\n");
-    DerivedBioAssay bioAssay = DerivedBioAssay.getNew(dc, parent);
+    DerivedBioAssay bioAssay = DerivedBioAssay.getNew(dc, parent, null);
     bioAssay.setItemSubtype(ItemSubtype.getById(dc, SystemItems.getId(subtype)));
     bioAssay.setName(name);
@@ -587 +587 @@
   {
     TestUtil.write("--Creating derived bioassay: " + name + "\n");
-    DerivedBioAssay bioAssay = DerivedBioAssay.getNew(dc, parent);
+    DerivedBioAssay bioAssay = DerivedBioAssay.getNew(dc, parent, null);
     bioAssay.setItemSubtype(ItemSubtype.getById(dc, SystemItems.getId(subtype)));
     bioAssay.setName(name);

trunk/www/views/derivedbioassays/index.jsp

@@ -182 +182 @@
       {
         PhysicalBioAssay bioAssay = PhysicalBioAssay.getById(dc, physicalBioAssayId);
-        bas = DerivedBioAssay.getNew(dc, bioAssay);
+        bas = DerivedBioAssay.getNew(dc, bioAssay, null);
         cc.setRecent(bioAssay, maxRecent);
       }
@@ -188 +188 @@
       {
         DerivedBioAssay parent = DerivedBioAssay.getById(dc, parentId);
-        bas = DerivedBioAssay.getNew(dc, parent);
+        bas = DerivedBioAssay.getNew(dc, parent, null);
         cc.setRecent(parent, maxRecent);
       }

trunk/www/views/derivedbioassays/view_bioassay.jsp

@@ -610 +610 @@
         <jsp:param name="item_type" value="<%=itemType.name()%>" />
         <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="title" value="Other items related to this bioassay set" />
+        <jsp:param name="title" value="Other items related to this bioassay" />
       </jsp:include>
       </div>