Removed descriptions from and fixed the names of tissue type samples. Made the plugin report where it is in loading data.

Former-commit-id: d9fb8f5

Author: morgantaschuk

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

@@ -226,7 +226,7 @@ private int createLibrarySample(SampleInfo sample, int tissueTypeSampleAcc) thro
     private int retrieveTissueTypeSampleAccession(Integer parentSampleAcc, SampleInfo barcode) throws Exception {
         //get the tissue type sample if it exists, otherwise create it
         int tissueTypeSampleAcc = 0;
-        String name = barcode.getParentSample() + "_" + barcode.getTissueType();
+        String name = barcode.getParentSample() + "_" +barcode.getTissueOrigin()+"_"+ barcode.getTissueType();
         List<Sample> children = metadata.getChildSamplesFrom(parentSampleAcc);
         if (children != null) {
             for (Sample s : children) {
@@ -256,7 +256,7 @@ private Integer retrieveParentSampleAccession(List<Sample> parentSamples, Sample
             }
         }
         if (parentSampleAcc == null) {
-            parentSampleAcc = createSample(sample.getParentSample(), sample.getSampleDescription(),
+            parentSampleAcc = createSample(sample.getParentSample(), "",
                     experimentAccession, 0, sample.getOrganismId(), false);
         }
         names.put(parentSampleAcc, sample.getParentSample());

seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/batchmetadatainjection/CreateFromScratch.java

@@ -50,11 +50,12 @@ public RunInfo getRunInfo() {
         for (int i = 0; i < numLanes; i++) {
             LaneInfo lane = getLane(i);
             int numBarcodes = this.promptInteger("How many barcodes in lane " + lane.getLaneNumber() + "?", 1, null);
-            for (int j = 0; j < numBarcodes; j++) {
+            for (int j = 0; j < numBarcodes; j++) {                
                 try {
                     boolean done = false;
                     SampleInfo sample = null;
                     while (!done) {
+                        Log.stdout("-----For lane "+lane.getLaneNumber()+", barcode #"+(j+1)+"-----");
                         projectCode = ConsoleAdapter.getInstance().promptString("Project code (three or four letters)", projectCode);
                         String individualNumber = ConsoleAdapter.getInstance().promptString("Individual number (should be unique per project)", null);
                         sample = this.generateSampleInfo(projectCode + " " + individualNumber, projectCode, individualNumber,
@@ -80,7 +81,8 @@ private LaneInfo getLane(int i) {
         boolean doneLane = false;
         LaneInfo lane = null;
         while (!doneLane) {
-            int num = promptPositiveInteger("Lane number", (i+1), null, 1, Integer.MAX_VALUE);
+            Log.stdout("-----For lane #"+(i+1)+"-----");
+            int num = promptPositiveInteger("What is the lane number? ", (i+1), null, 1, Integer.MAX_VALUE);
             lane = this.generateLaneInfo(String.valueOf(num), -1);
             StringBuilder sb = new StringBuilder();
             printLaneInfo(lane, sb);