Merge pull request #49 from SeqWare/feature/BatchInjectTakeTwo

Feature/batch inject take two

Former-commit-id: a170204

Author: denis-yuen

seqware-common/src/main/java/net/sourceforge/seqware/common/factory/DBAccess.java

@@ -105,6 +105,7 @@ public synchronized static void close() {
             metadataDBWrapper.set(null);
             //db = null;
         }
+        metadataDBWrapper.remove();
     }
 
     private DBAccess() {

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

@@ -1955,7 +1955,7 @@ public void annotateWorkflowRun(int workflowSWID, Set<WorkflowRunAttribute> atts
     // TODO Auto-generated method stub
   }
 
-  public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip) {
+  public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip, String filePath) {
     throw new NotImplementedException("This method is not supported through the direct MetaDB connection!");
   }
 

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

@@ -94,7 +94,7 @@ public ReturnValue addStudy(String title, String description, String accession,
    * @param title a {@link java.lang.String} object.
    * @return a {@link net.sourceforge.seqware.common.module.ReturnValue} object.
    */
-  public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip);
+  public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip, String filePath);
 
     /**
    * <p>addSample.</p>

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

@@ -94,7 +94,7 @@ public ReturnValue addSample(Integer experimentAccession, Integer parentSampleAc
     return (new ReturnValue(ReturnValue.SUCCESS));
     }
 
-    public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip) {
+    public ReturnValue addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip, String filePath) {
         logger.info("No metadata connection");
         return (new ReturnValue(ReturnValue.SUCCESS));
     }

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

@@ -43,7 +43,8 @@ public int compareTo(LibrarySelection that) {
 
     @Override
     public String toString() {
-        return "LibrarySelection{" + "librarySelectionId=" + librarySelectionId + ", name=" + name + ", description=" + description + '}';
+        return new StringBuilder().append("LibrarySelection ").append(librarySelectionId)
+                .append(":\t").append(name).append("\t").append(description).toString();
     }
 
 

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

@@ -43,7 +43,8 @@ public int compareTo(LibrarySource that) {
 
     @Override
     public String toString() {
-        return "LibrarySource{" + "librarySourceId=" + librarySourceId + ", name=" + name + ", description=" + description + '}';
+        return new StringBuilder().append("LibrarySource ").append(librarySourceId)
+                .append(":\t").append(name).append("\t").append(description).toString();
     }
 
 

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

@@ -43,7 +43,8 @@ public int compareTo(LibraryStrategy that) {
 
     @Override
     public String toString() {
-        return "LibraryStrategy{" + "libraryStrategyId=" + libraryStrategyId + ", name=" + name + ", description=" + description + '}';
+        return new StringBuffer().append("LibraryStrategy ").append(libraryStrategyId)
+                .append(":\t").append(name).append("\t").append(description).toString();
     }
 
 

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

@@ -56,7 +56,8 @@ public boolean equals(Object other) {
 
     @Override
     public String toString() {
-        return "Organism{" + "organismId=" + organismId + ", name=" + name + ", code=" + code + ", accession=" + accession + ", ncbiTaxId=" + ncbiTaxId + '}';
+        return new StringBuilder().append("Organism ").append(organismId)
+                .append(":\t").append(name).toString();
     }
 
 	/**

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

@@ -43,7 +43,8 @@ public int compareTo(Platform that) {
 
     @Override
     public String toString() {
-        return "Platform{" + "platformId=" + platformId + ", name=" + name + ", description=" + description + ", instrumentModel=" + instrumentModel + '}';
+        return new StringBuilder().append("Platform ").append(platformId)
+                .append(":\t").append(name).append("\t").append(instrumentModel).append("\t").append(description).toString();
     }
 
     /** {@inheritDoc} */