Allow ReadData to store/report expected reads

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/ReadData.java

@@ -56,6 +56,8 @@ public interface ReadData extends Serializable
 
     public Integer getModifiedBy();
 
+    public Integer getTotalReads();
+
     public String getSra_accession();
 
     public boolean isArchived();

SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java

@@ -1,14 +1,21 @@
 package org.labkey.sequenceanalysis;
 
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.Transient;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.pipeline.PipelineJobService;
+import org.labkey.api.query.FieldKey;
 import org.labkey.api.sequenceanalysis.model.ReadData;
+import org.labkey.api.util.PageFlowUtil;
 
 import java.io.File;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -32,6 +39,7 @@ public class ReadDataImpl implements ReadData
     private Integer _runId;
     private boolean _archived = false;
     private String sra_accession;
+    private Integer _totalReads;
 
     private Map<Integer, File> _cachedFiles = new HashMap<>();
 
@@ -197,6 +205,44 @@ public void setFile(File f, int fileIdx)
         _cachedFiles.put(fileIdx, f);
     }
 
+    @Override
+    public Integer getTotalReads()
+    {
+        if (getFileId1() == null)
+        {
+            return null;
+        }
+
+        if (_totalReads == null)
+        {
+            if (PipelineJobService.get().getLocationType() != PipelineJobService.LocationType.WebServer)
+            {
+                throw new IllegalStateException("Cannot call getTotalReads() on the remote server unless this value has been cached");
+            }
+
+            SimpleFilter filter = new SimpleFilter(FieldKey.fromString("dataid"), getFileId1());
+            filter.addCondition(FieldKey.fromString("readset"), getReadset(), CompareType.EQUAL);
+            filter.addCondition(FieldKey.fromString("metricvalue"), "Total Reads", CompareType.EQUAL);
+            TableSelector ts = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_QUALITY_METRICS), PageFlowUtil.set("metricvalue"), filter, new Sort("-rowid"));
+            List<Double> values = ts.getArrayList(Double.class);
+            if (!values.isEmpty())
+            {
+                _totalReads = values.get(0).intValue();
+            }
+            else
+            {
+                _totalReads = 0;
+            }
+        }
+
+        return _totalReads;
+    }
+
+    public void setTotalReads(Integer totalReads)
+    {
+        _totalReads = totalReads;
+    }
+
     @Transient
     private File getFile(int fileIdx, Integer fileId)
     {
@@ -242,6 +288,8 @@ public void cacheForRemoteServer()
             getFile1();
             getFile2();
         }
+
+        getTotalReads();
     }
 
     @Transient

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java

@@ -786,7 +786,7 @@ private void doConsolidate(JobContext ctx, File workingDestinationWorkspaceFolde
         {
             File contigFolder = new File(workingDestinationWorkspaceFolder, getFolderNameFromInterval(i));
             ctx.getLogger().info("Consolidating contig folder: " + contigFolder);
-            ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Consolidating contig folder: " + contigFolder);
+            ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Consolidating contig folder: " + contigFolder.getName());
 
             List<String> toRun = new ArrayList<>(baseArgs);
             toRun.add("-a");