Changeset 6958

Timestamp:

Sep 30, 2015, 2:55:14 PM (6 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Updated test program to set experimental factor values on root raw bioassays instead of raw bioassays.

Noted that the "Item overview validation" now complains about missing experimental factors, probably because it has not been updated and still check the raw bioassays and not the root raw bioassays.

Location:

trunk

Files:

• doc/test/roles/index.html (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Experiment.java (modified) (1 diff)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (8 diffs)

trunk/doc/test/roles/index.html

@@ -2127 +2127 @@
   </li>
   
-  <li><a name="inheritannotations"></a>
-    Inherit the annotations from the scans, extracts, samples and biosource for each raw bioassay.
-    Use the <i>auto-inherit</i> function that exists on the experiment properties
-    tab. Make sure that all experimental factors are selected by the check boxes,
-    then click on the <i>Auto-inherit</i> link in the column header. <br>
-    <b>Note!</b> The <i>Dye swap</i>
-    annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
-    data set is missing biomaterial parents with annotations.<br>
-    <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
-    annotations. Fix this by manually removing the annotations that are inherited from
-    the <i>Extract A.ref.qc</i> extract. 
-    <p>
-
-  </li>
-  
   <li>
     Import raw data to the Genepix and Cufflinks raw bioassays. 
@@ -2242 +2227 @@
     
   </li>
+  
+  <li><a name="inheritannotations"></a>
+    Inherit the annotations from the scans, extracts, samples and biosource for each root raw bioassay.
+    Use the <i>auto-inherit</i> function that exists on the experiment properties
+    tab. Make sure that all experimental factors are selected by the check boxes,
+    then click on the <i>Auto-inherit</i> link in the column header. Use the <b>Inherit</b> 
+    option for some annotations and <b>Clone</b> option for some. Uncheck the <b>No duplicates</b>
+    option for the <i>RIN</i> annotation (see note 2 below).
+    <br>
+    <b>Note!</b> The <i>Affymetrix raw A.3</i>
+    data set is missing biomaterial parents with annotations.<br>
+    <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
+    annotations. Verify and fix this by manually removing the annotations that are inherited 
+    from the <i>Extract A.ref.qc</i> extract (value=9.2). 
+    <p>
+
+  </li>
+  
   
   <li>

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -1431 +1431 @@
       //  oldItem.getAnnotationSet() : null;
       AnnotationSet newAs = newItem.getAnnotationSet();
-      /*if (oldItem == newItem)
+      if (oldItem == newItem)
       {
         // The items were not loaded in separate sessions, the protocol has to be 
@@ -1438 +1438 @@
         if (p != null) dc.reattachItem(p, false);
       }
-      */
       
       for (int entryNo = 0; entryNo < jsonModified.size(); entryNo++)

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

@@ -733 +733 @@
 
   /**
+    Get the root raw bioassay that represents the given raw bioassay
+    in this experiment. 
+    @return A root raw bioassay object or null if the given
+      raw bioassay is not part of the experiment
+    @since 3.6
+  */
+  public RootRawBioAssay getRootRawBioAssay(RawBioAssay raw)
+  {
+    RootRawBioAssayData root = getData().getRootRawBioAssays().get(raw.getData());
+    return getDbControl().getItem(RootRawBioAssay.class, root);
+  }
+  
+  /**
     Create a new root transformation for this experiment.
     @param job The job that executed the transformation

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

@@ -23 +23 @@
 
 import net.sf.basedb.core.Annotatable;
-import net.sf.basedb.core.Annotation;
 import net.sf.basedb.core.AnnotationSet;
 import net.sf.basedb.core.AnnotationType;
@@ -57 +56 @@
 import net.sf.basedb.core.RawDataType;
 import net.sf.basedb.core.RawDataTypes;
+import net.sf.basedb.core.RootRawBioAssay;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.Software;
@@ -359 +359 @@
       seqRaw2 = Util.findRawBioAssay(dc, "SeqRaw A.24h");
       
-      inheritAnnotations(dc, rba1, s1, e1Qc, bioSource, sc1);
-      inheritAnnotations(dc, rba2, s2, e2Qc, bioSource, sc2);
-      inheritAnnotations(dc, rba1DyeSwap, s1, e1Qc, bioSource, sc1DyeSwap);
-      inheritAnnotations(dc, rba2DyeSwap, s2, e2Qc, bioSource, sc2DyeSwap);
-      
-      // Affymetrix
-      inheritAnnotations(dc, affyRaw1, s1, e1Qc, bioSource, affyScan1);
-      inheritAnnotations(dc, affyRaw2, s2, e2Qc, bioSource, affyScan2);
-      inheritAnnotations(dc, affyRaw3, sRef, eRefQc, affyScan3);
-      
-      // Sequence
-      inheritAnnotations(dc, seqRaw1, s1, e1Qc, bioSource);
-      inheritAnnotations(dc, seqRaw2, s2, e2Qc, bioSource);
-      
       PluginConfiguration rawDataImporter = Util.findPluginConfiguration(dc, "Raw data for project A");
       PluginConfiguration rawDataImporterDyeSwap = Util.findPluginConfiguration(dc, "Raw data for project A (dye-swap)");
@@ -386 +372 @@
       importRawData(seqRawImporter, seqData1, seqRaw1);
       importRawData(seqRawImporter, seqData2, seqRaw2);
-  
+        
       // Experiment
       dc = TestUtil.getDbControl();
-      Experiment exp1 = createExperiment(dc, "Experiment A", 
-        RawDataTypes.getSafeRawDataType("genepix"), rba1, rba2, rba1DyeSwap, rba2DyeSwap);
-      Experiment affyExperiment = createExperiment(dc, "Affymetrix A", 
-        affymetrixPlatform.getRawDataType(), affyRaw1, affyRaw2, affyRaw3);
-      Experiment seqExperiment = createExperiment(dc, "Sequence A", 
-        RawDataTypes.getSafeRawDataType("cufflinks"), seqRaw1, seqRaw2);
+      AnnotationType drugResistance = Util.findAnnotationType(dc, "Drug resistance", Item.BIOSOURCE);
+      AnnotationType dyeSwap = Util.findAnnotationType(dc, "Dye swap", Item.RAWBIOASSAY);
+      AnnotationType pmtGain = Util.findAnnotationType(dc, "PMT gain", Item.DERIVEDBIOASSAY);
+      AnnotationType rin = Util.findAnnotationType(dc, "RIN", Item.EXTRACT);
+      AnnotationType timeAnnotation = Util.findAnnotationType(dc, "Time", Item.SAMPLE);
+      
+      Experiment exp1 = createExperiment(dc, "Experiment A", RawDataTypes.getSafeRawDataType("genepix"), 
+        rawBioAssays(rba1, rba2, rba1DyeSwap, rba2DyeSwap),
+        experimentalFactors(drugResistance, dyeSwap, pmtGain, rin, timeAnnotation)
+        );
+      Experiment affyExperiment = createExperiment(dc, "Affymetrix A", affymetrixPlatform.getRawDataType(), 
+        rawBioAssays(affyRaw1, affyRaw2, affyRaw3),
+        experimentalFactors(drugResistance, pmtGain, rin, timeAnnotation)
+        );
+      Experiment seqExperiment = createExperiment(dc, "Sequence A", RawDataTypes.getSafeRawDataType("cufflinks"), 
+        rawBioAssays(seqRaw1, seqRaw2),
+        experimentalFactors(drugResistance, rin, timeAnnotation)
+        );
+      dc.commit();
+      
+      // Experimental factors
+      // Experiment A
+      dc = TestUtil.getDbControl();
+      inheritExperimentalFactors(dc, exp1, rba1, s1, e1Qc, bioSource, sc1);
+      inheritExperimentalFactors(dc, exp1, rba2, s2, e2Qc, bioSource, sc2);
+      inheritExperimentalFactors(dc, exp1, rba1DyeSwap, s1, e1Qc, bioSource, sc1DyeSwap);
+      inheritExperimentalFactors(dc, exp1, rba2DyeSwap, s2, e2Qc, bioSource, sc2DyeSwap);
+      
+      // Affymetrix
+      inheritExperimentalFactors(dc, affyExperiment, affyRaw1, s1, e1Qc, bioSource, affyScan1);
+      inheritExperimentalFactors(dc, affyExperiment, affyRaw2, s2, e2Qc, bioSource, affyScan2);
+      inheritExperimentalFactors(dc, affyExperiment, affyRaw3, sRef, eRefQc, affyScan3);
+      
+      // Sequence
+      inheritExperimentalFactors(dc, seqExperiment, seqRaw1, s1, e1Qc, bioSource);
+      inheritExperimentalFactors(dc, seqExperiment, seqRaw2, s2, e2Qc, bioSource);
       dc.commit();
       
@@ -415 +431 @@
   }
 
+  public static RawBioAssay[] rawBioAssays(RawBioAssay... rba)
+  {
+    return rba;
+  }
+  
+  public static AnnotationType[] experimentalFactors(AnnotationType... annotationTypes)
+  {
+    return annotationTypes;
+  }
+  
   /**
     Create a biosource.
@@ -679 +705 @@
   
   /**
-    Inherit all annotations from the parent.
-  */
-  public static void inheritAnnotations(DbControl dc, Annotatable item, Annotatable... parents)
-  {
-    AnnotationSet as = item.getAnnotationSet();
+    Inherit all annotations to the root raw bioassay from the 
+    raw bioassay and other parents.
+  */
+  public static void inheritExperimentalFactors(DbControl dc, Experiment experiment, RawBioAssay raw, Annotatable... parents)
+  {
+    experiment = Experiment.getById(dc, experiment.getId());
+    raw = RawBioAssay.getById(dc, raw.getId());
+    RootRawBioAssay root = experiment.getRootRawBioAssay(raw);
+    AnnotationSet as = root.getAnnotationSet();
+    if (raw.isAnnotated()) as.inheritAll(raw.getAnnotationSet(), false);
     for (Annotatable parent : parents)
     {
@@ -726 +757 @@
     Create an experiment.
   */
-  public static Experiment createExperiment(DbControl dc, String name, RawDataType rawDataType, RawBioAssay... rawBioAssays)
+  public static Experiment createExperiment(DbControl dc, String name, RawDataType rawDataType, RawBioAssay[] rawBioAssays, AnnotationType[] experimentalFactors)
   {
     TestUtil.write("--Creating experiment: " + name + "\n");
@@ -732 +763 @@
     experiment.setName(name);
     
-    for (RawBioAssay rba : rawBioAssays)
-    {
-      rba = RawBioAssay.getById(dc, rba.getId()); // To get the latest information
-      experiment.addRawBioAssay(rba);
-      
-      AnnotationSet as = rba.getAnnotationSet();
-      for (Annotation a : as.getAnnotations(null).list(dc))
+    if (rawBioAssays != null)
+    {
+      for (RawBioAssay rba : rawBioAssays)
       {
-        experiment.addExperimentalFactor(a.getAnnotationType());
+        experiment.addRawBioAssay(rba);
+      }
+    }
+    
+    if (experimentalFactors != null)
+    {
+      for (AnnotationType at : experimentalFactors)
+      {
+        experiment.addExperimentalFactor(at);
       }
     }