Changeset 3531

Timestamp:

Oct 5, 2015, 1:27:26 PM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #812: Pilot report wizard

Prepared the script for sending the FPKM file as input to the pilot report R script.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• dao/Rawbioassay.java (modified) (2 diffs)
• pdf/PilotReportWorker.java (modified) (3 diffs)
• r/PilotReport.java (modified) (6 diffs)
• r/RResult.java (modified) (2 diffs)
• r/RScriptDefinition.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Rawbioassay.java

@@ -14 +14 @@
 import net.sf.basedb.core.DynamicRawDataQuery;
 import net.sf.basedb.core.DynamicResultIterator;
+import net.sf.basedb.core.File;
+import net.sf.basedb.core.FileSetMember;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.RawBioAssay;
@@ -126 +128 @@
   
   /**
+    Get the file of the given type.
+    @since 3.7
+  */
+  public File getFile(DbControl dc, Datafiletype fileType)
+  {
+    RawBioAssay item = getItem();
+    File f = null;
+    if (item.hasFileSet())
+    {
+      FileSetMember member = item.getFileSet().getMember(fileType.load(dc));
+      if (member != null) f = member.getFile();
+    }
+    return f;
+  }
+  
+  /**
     Calculate sum of fpkm values for the given genes.
     @return A map with key=gene and value=sum of fpkm

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/pdf/PilotReportWorker.java

@@ -196 +196 @@
       String[] subtypeNames = { "LumA", "LumB", "HER2", "Basal", "Normal" };
       float[] subtypeScore = new float[5];
-      float maxVal = Float.NEGATIVE_INFINITY;
+      int maxIndex = 0;
       for (int i = 0; i < 5; i++)
       {
         subtypeScore[i] = (float)(Math.random()*2-1);
-        if (subtypeScore[i] > maxVal) maxVal = subtypeScore[i];
+        if (subtypeScore[i] > subtypeScore[maxIndex]) maxIndex = i;
       }
+      
       for (int i = 0; i < 5; i++)
       {
-        if (Float.compare(maxVal, subtypeScore[i]) == 0)
+        if (i == maxIndex)
         {
           pdfUtil.addBoldText(twoDecimals.format(subtypeScore[i]), 12, Element.ALIGN_LEFT, SUBTYPE_X2+i*SUBTYPE_XX, SUBTYPE_Y2);
@@ -215 +216 @@
       }
       
-      
       // Plots
       float y = PLOT_START_Y;
@@ -221 +221 @@
       File workDir = result.getWorkDir();
       String[] lowHigh = { "Låg", "Hög" };
-      String[] positiveNegative = { "Negative", "Positive" };
+      String[] positiveNegative = { "Negativ", "Positiv" };
       
       for (int plotNo = 0; plotNo < 5; plotNo++)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/r/PilotReport.java

@@ -1 +1 @@
 package net.sf.basedb.reggie.r;
 
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -7 +10 @@
 import java.util.Map;
 
-
+import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.File;
+import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.XmlConfig;
+import net.sf.basedb.reggie.dao.Datafiletype;
 import net.sf.basedb.reggie.dao.Rawbioassay;
 import net.sf.basedb.reggie.pdf.PdfUtil;
+import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.Values;
 
@@ -102 +109 @@
   public Result run(DbControl dc, Rawbioassay raw)
   {
+    File fpkmFile = raw.getFile(dc, Datafiletype.FPKM);
+    if (fpkmFile == null)
+    {
+      throw new ItemNotFoundException(Datafiletype.FPKM.getName() + " for raw bioassay " + raw.getName());
+    }
         
     // Calculate sum(fpkm) for given genes
@@ -115 +127 @@
     String values = Values.getString(v, ",", true);
     String caseName = checkValidScriptParameter(raw.getName());
+    
     scanB.setParameter("value", "c(" + values + ")");
     scanB.setParameter("case", "'"+caseName+"'");
-
-    Result result = run(new Result(raw, genes));
+    scanB.setParameter("fpkm", "'${workdir}/"+fpkmFile.getName()+"'");
+    
+    Result result = run(new Result(raw, fpkmFile, genes));
     return result;
   }
@@ -126 +140 @@
   {
     public final Rawbioassay raw;
+    public final File fpkmFile;
     public final List<String> genes;
     
@@ -131 +146 @@
       Creates a new result object for the given raw bioassay.
     */
-    public Result(Rawbioassay raw, List<String> genes) 
+    public Result(Rawbioassay raw, File fpkmFile, List<String> genes) 
     {
       super();
       this.raw = raw;
+      this.fpkmFile = fpkmFile;
       this.genes = genes;
+    }
+
+    @Override
+    protected void loadFilesToWorkDir() 
+      throws IOException 
+    {
+      InputStream in = null;
+      OutputStream out = null;
+      try
+      {
+        in = fpkmFile.getDownloadStream(0);
+        out = new FileOutputStream(new java.io.File(getWorkDir(), fpkmFile.getName()));
+        FileUtil.copy(in, out);
+      }
+      finally
+      {
+        FileUtil.close(in);
+        FileUtil.close(out);
+      }
     }
     

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/r/RResult.java

@@ -2 +2 @@
 
 import java.io.File;
+import java.io.IOException;
 
 import net.sf.basedb.util.FileUtil;
@@ -78 +79 @@
     }
   }
+  
+  /**
+    Called before the script is started and allows the
+    result object to upload files that are needed by
+    the script to the working directory.
+  */
+  protected void loadFilesToWorkDir()
+    throws IOException
+  {}
   
   void setExitStatus(int exitStatus)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/r/RScriptDefinition.java

@@ -128 +128 @@
     }
     
-    if (logger.isDebugEnabled())
-    {
-      logger.debug("Running R: " + rCmd.toString());
-    }
-    
     String rscript_path = Reggie.getConfig().getRequiredConfig("rscript/path", null);
-    ProcessBuilder builder = new ProcessBuilder(
-      rscript_path,
-      "-e",
-      rCmd.toString()
-    );
 
-    System.out.println("Calling: " + rCmd.toString());
-    
     try
     {
@@ -157 +145 @@
         isGenerated = true;
       }
+      
+      // Replace ${workdir} with current working directory
+      String cmd = rCmd.toString().replace("${workdir}", dir.getAbsolutePath().replace('\\', '/'));
       if (logger.isDebugEnabled())
       {
+        logger.debug("Running R: " + cmd);
         logger.debug("Working directory: " + dir);
       }
-
+      
+      ProcessBuilder builder = new ProcessBuilder(rscript_path, "-e", cmd);
       builder.directory(dir);
       result.setWorkDir(dir, isGenerated);
+      result.loadFilesToWorkDir();
       
       Process proc = builder.start();