Changeset 7003

Timestamp:

Nov 6, 2015, 2:08:14 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1960 and #1958: Inherit annotations from Hardware, Software and Protocol

Fixed in the items listed and added Kit:s to the list of items to inherit from.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/ArrayBatch.java (modified) (1 diff)
• src/core/net/sf/basedb/core/BioPlate.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/DerivedBioAssay.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Extract.java (modified) (1 diff)
• src/core/net/sf/basedb/core/MeasuredBioMaterial.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/PhysicalBioAssay.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (1 diff)
• www/biomaterials/bioplates/bioplates.js (modified) (2 diffs)
• www/biomaterials/extracts/extracts.js (modified) (1 diff)
• www/biomaterials/samples/samples.js (modified) (1 diff)
• www/common/annotations/inherit.jsp (modified) (1 diff)
• www/lims/arraybatches/batches.js (modified) (1 diff)
• www/views/derivedbioassays/bioassays.js (modified) (1 diff)
• www/views/physicalbioassays/bioassays.js (modified) (1 diff)
• www/views/rawbioassays/bioassays.js (modified) (1 diff)

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

@@ -139 +139 @@
     
     addAnnotatableParents(getDbControl(), annotatable, 
-      data.getArrayDesign()
+      data.getArrayDesign(),
+      data.getProtocol(),
+      data.getPrintRobot()
     );
     return annotatable;

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

@@ -32 +32 @@
 
 import java.util.Date;
+import java.util.HashSet;
 import java.util.Set;
 
@@ -148 +149 @@
   
   /**
-    Gets parent plates, always returns null
+    Get the freezer.
    */
   @Override
@@ -154 +155 @@
     throws BaseException
   {
-    return null;
+    Set<Annotatable> annotatable = new HashSet<Annotatable>();
+    BioPlateData data = getData();
+    
+    addAnnotatableParents(getDbControl(), annotatable, 
+      data.getFreezer()
+    );
+    return annotatable;
   }
 

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

@@ -377 +377 @@
       data.getExtract(),
       data.getHardware(),
-      data.getSoftware()
+      data.getSoftware(),
+      data.getProtocol(),
+      data.getKit()
     );
     

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

@@ -374 +374 @@
   {
     Set<Annotatable> annotatable = super.getAnnotatableParents();
-    try
-    {
-      if (getData().getTag() != null) annotatable.add(getTag());
-    }
-    catch (PermissionDeniedException ex)
-    {}
+    ExtractData data = getData();
+    addAnnotatableParents(getDbControl(), annotatable,
+      data.getTag()
+    );
     return annotatable;
   }

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

@@ -32 +32 @@
 import java.util.WeakHashMap;
 
+import net.sf.basedb.core.data.BioMaterialEventData;
 import net.sf.basedb.core.data.BioPlateData;
 import net.sf.basedb.core.data.BioPlateTypeData;
@@ -214 +215 @@
   {
     Set<Annotatable> annotatable = super.getAnnotatableParents();
+    DbControl dc = getDbControl();
     
     MeasuredBioMaterialData data = getData();
-    DbControl dc = getDbControl();
-
+    BioMaterialEvent event = getCreationEvent();
+    BioMaterialEventData eventData = event.getData();
+
+    addAnnotatableParents(dc, annotatable, 
+      eventData.getHardware(),
+      eventData.getProtocol(),
+      eventData.getKit()
+    );
+    
     if (data.getBioWell() != null)
     {
@@ -231 +240 @@
     {
       // Multiple parent items
-      ItemQuery<? extends BioMaterial> query = getCreationEvent().getSources();
+      ItemQuery<? extends BioMaterial> query = event.getSources();
       query.include(Include.ALL);
       if (parents != null && parents.size() > 0)

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

@@ -338 +338 @@
     addAnnotatableParents(dc, annotatable, 
       data.getArraySlide(),
-      eventData.getHardware()
+      eventData.getHardware(),
+      eventData.getProtocol(),
+      eventData.getKit()
     );
 

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

@@ -247 +247 @@
       data.getParentBioAssay(),
       data.getParentExtract(),
-      data.getSoftware()
+      data.getSoftware(),
+      data.getProtocol()
     );
     return annotatable;

trunk/www/biomaterials/bioplates/bioplates.js

@@ -40 +40 @@
       
       // Tab validation
-      TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
+      TabControl.addTabActivateListener('settings.annotations', bioplates.loadAnnotationsFrame);
       TabControl.addTabValidator('settings.info', bioplates.validateBioPlate);
 
@@ -125 +125 @@
   }
 
+  bioplates.loadAnnotationsFrame = function()
+  {
+    Annotations.autoLoadEditFrame(null, null, bioplates.getParents());
+  }
+  
+  bioplates.getParents = function()
+  {
+    var frm = document.forms['bioplate'];
+    var parents = new Array();
+    var storageId = Math.abs(parseInt(frm.storage_id.value));
+    if (storageId > 0) parents[parents.length] = 'HARDWARE:'+storageId;
+    return parents;
+  }
+
   
   bioplates.viewWells = function()

trunk/www/biomaterials/extracts/extracts.js

@@ -291 +291 @@
   {
     var frm = document.forms['extract'];
-    var url = '../tags/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
     var url = '&resetTemporary=1';
     url += ItemSubtype.createRelatedFilter('subtype_id', 'TAG');

trunk/www/biomaterials/samples/samples.js

@@ -291 +291 @@
       }
     }
+    var protocolId = Math.abs(parseInt(frm.protocol_id.value));
+    if (protocolId > 0) parents[parents.length] = 'PROTOCOL:'+protocolId;
+    var kitId = Math.abs(parseInt(frm.kit_id.value));
+    if (kitId > 0) parents[parents.length] = 'KIT:'+kitId;
+
     return parents;
   }

trunk/www/common/annotations/inherit.jsp

@@ -221 +221 @@
   // Parent items may have been submitted by caller
   String[] parents = request.getParameterValues("parents");
-  parents = null;
   // Each parameter is ITEMTYPE:ID:ID:...
   if (parents != null)

trunk/www/lims/arraybatches/batches.js

@@ -176 +176 @@
       if (arrayDesignId > 0) parents[parents.length] = 'ARRAYDESIGN:'+arrayDesignId;
     }
+    var protocolId = Math.abs(parseInt(frm.protocol_id.value));
+    if (protocolId > 0) parents[parents.length] = 'PROTOCOL:'+protocolId;
+    var printRobotId = Math.abs(parseInt(frm.printrobot_id.value));
+    if (printRobotId > 0) parents[parents.length] = 'HARDWARE:'+printRobotId;
     return parents;
   }

trunk/www/views/derivedbioassays/bioassays.js

@@ -249 +249 @@
     var softwareId = Math.abs(parseInt(frm.software_id.value));
     if (softwareId > 0) parents[parents.length] = 'SOFTWARE:'+softwareId;
+    var kitId = Math.abs(parseInt(frm.kit_id.value));
+    if (kitId > 0) parents[parents.length] = 'KIT:'+kitId;
     return parents;
   }

trunk/www/views/physicalbioassays/bioassays.js

@@ -207 +207 @@
     var hardwareId = Math.abs(parseInt(frm.hardware_id.value));
     if (hardwareId > 0) parents[parents.length] = 'HARDWARE:'+hardwareId;
+    var protocolId = Math.abs(parseInt(frm.protocol_id.value));
+    if (protocolId > 0) parents[parents.length] = 'PROTOCOL:'+protocolId;
+    var kitId = Math.abs(parseInt(frm.kit_id.value));
+    if (kitId > 0) parents[parents.length] = 'KIT:'+kitId;
 
     var ids = Link.getIdsInList(frm.extracts, 'EXTRACT');

trunk/www/views/rawbioassays/bioassays.js

@@ -204 +204 @@
     var softwareId = Math.abs(parseInt(frm.software_id.value));
     if (softwareId > 0) parents[parents.length] = 'SOFTWARE:'+softwareId;
+    var protocolId = Math.abs(parseInt(frm.protocol_id.value));
+    if (protocolId > 0) parents[parents.length] = 'PROTOCOL:'+protocolId;
     if (frm.arraydesign_id)
     {