Removed 'isRoot' field from Sample; added in experiment accession for every Sample in BatchMetadataInjection; Added in null parents for samples.

Former-commit-id: c742f59

Author: morgantaschuk

seqware-common/src/main/java/net/sourceforge/seqware/common/metadata/MetadataWS.java

@@ -296,12 +296,14 @@ public ReturnValue addSample(Integer experimentAccession, Integer parentSampleAc
                 Experiment e = ll.findExperiment("/" + experimentAccession.toString());
                 s.setExperiment(e);
             }
+            Set<Sample> parents = new HashSet<Sample>();
             if (parentSampleAccession != 0) {
                 Sample parentSample = ll.findSample("/"+parentSampleAccession);
-                Set<Sample> parents = new HashSet<Sample>();
                 parents.add(parentSample);
-                s.setParents(parents);
+            } else{
+                parents.add(null);
             }
+            s.setParents(parents);
             s.setOrganism(o);
             s.setTitle(title);
             s.setName(title);

seqware-common/src/main/java/net/sourceforge/seqware/common/model/Sample.java

@@ -81,7 +81,6 @@ public int compare(Sample t, Sample t1) {
     private Set<SampleLink> sampleLinks = new TreeSet<SampleLink>();
     // non-persisted field to store organism_id
     private Integer organismId;
-    private boolean isRoot;
 
     /**
      * <p>Constructor for Sample.</p>
@@ -928,13 +927,6 @@ public void setSampleLinks(Set<SampleLink> sampleLinks) {
         this.sampleLinks = sampleLinks;
     }
 
-    public boolean isIsRoot() {
-        return isRoot;
-    }
-
-    public void setIsRoot(boolean isRoot) {
-        this.isRoot = isRoot;
-    }
 
     /**
      * {@inheritDoc}

seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/BatchMetadataInjection.java

@@ -187,11 +187,11 @@ private ReturnValue inject(RunInfo run) throws Exception {
 
                 Log.debug("lane: " + laneAccession + " parent sample: " + parentSampleAcc);
 
-                int tissueTypeSampleAcc = retrieveTissueTypeSampleAccession(parentSampleAcc, barcode);
+                int tissueTypeSampleAcc = retrieveTissueTypeSampleAccession(parentSampleAcc, barcode, experimentAccession);
 
                 Log.debug("tissue type sample: " + tissueTypeSampleAcc);
 
-                int librarySampleNameAcc = createLibrarySample(barcode, tissueTypeSampleAcc);
+                int librarySampleNameAcc = createLibrarySample(barcode, tissueTypeSampleAcc, experimentAccession);
 
                 int barcodeAcc = createIUS(barcode, laneAccession, librarySampleNameAcc);
 
@@ -200,11 +200,11 @@ private ReturnValue inject(RunInfo run) throws Exception {
         return ret;
     }
 
-    private int createLibrarySample(SampleInfo sample, int tissueTypeSampleAcc) throws Exception {
+    private int createLibrarySample(SampleInfo sample, int tissueTypeSampleAcc, int experimentAccession) throws Exception {
 
         //get the library sample
         int librarySampleNameAcc = createSample(sample.getName(), sample.getSampleDescription(),
-                0, tissueTypeSampleAcc, sample.getOrganismId(), true);
+                experimentAccession, tissueTypeSampleAcc, sample.getOrganismId(), true);
 
         List<Sample> children = metadata.getChildSamplesFrom(tissueTypeSampleAcc);
         for (Sample s : children) {
@@ -223,7 +223,7 @@ private int createLibrarySample(SampleInfo sample, int tissueTypeSampleAcc) thro
         return librarySampleNameAcc;
     }
 
-    private int retrieveTissueTypeSampleAccession(Integer parentSampleAcc, SampleInfo barcode) throws Exception {
+    private int retrieveTissueTypeSampleAccession(Integer parentSampleAcc, SampleInfo barcode, int experimentAccession) throws Exception {
         //get the tissue type sample if it exists, otherwise create it
         int tissueTypeSampleAcc = 0;
         String name = barcode.getParentSample() + "_" +barcode.getTissueOrigin()+"_"+ barcode.getTissueType();
@@ -236,7 +236,7 @@ private int retrieveTissueTypeSampleAccession(Integer parentSampleAcc, SampleInf
             }
         }
         if (tissueTypeSampleAcc == 0) {
-            tissueTypeSampleAcc = createSample(name, "", 0,
+            tissueTypeSampleAcc = createSample(name, "", experimentAccession,
                     parentSampleAcc, barcode.getOrganismId(), false);
         }
         names.put(tissueTypeSampleAcc, name);