Changeset 3535

Timestamp:

Oct 8, 2015, 2:09:21 PM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #812: Pilot report wizard

Parse the *.txt files containing the score for each plot. The score is converted to text (Låg/Hög?, Negativ/Positiv?) depending on if the score is lower or higher than 0. If no txt file is available N/A is written instead.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/pdf/PilotReportWorker.java (modified) (4 diffs)

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

@@ -1 +1 @@
 package net.sf.basedb.reggie.pdf;
 
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -23 +25 @@
 import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.Sample;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.Site;
@@ -211 +214 @@
       
       // Plots
-      float y = PLOT_START_Y;
+      float yPlot = PLOT_START_Y;
       float yText = PLOT_TEXT_START_Y;
       String[] plots = { "GGI", "ESR1", "PGR", "ERBB2", "MKI67" };
       String[] lowHigh = { "Låg", "Hög" };
-      String[] positiveNegative = { "Negativ", "Positiv" };
+      String[] negativePositive = { "Negativ", "Positiv" };
       for (int plotNo = 0; plotNo < plots.length; plotNo++)
       {
-        // TODO - the text is from a random number!
-        String[] options = plotNo == 0 || plotNo == 4 ? lowHigh : positiveNegative;
-        pdfUtil.addText(options[Math.random() > 0.5 ? 0 : 1], 14, Element.ALIGN_LEFT, PLOT_TEXT_X, yText);
+        String plot = plots[plotNo];
+        File plotTxt = new File(workDir, plot+".txt");
+        float plotScore = parsePlotScore(plotTxt);
+        String[] options = plotNo == 0 || plotNo == 4 ? lowHigh : negativePositive;
+        pdfUtil.addText(Float.isNaN(plotScore) ? "N/A" : options[plotScore < 0 ? 0 : 1], 14, Element.ALIGN_LEFT, PLOT_TEXT_X, yText);
         yText -= PLOT_DELTA_Y;
 
-        String plot = plots[plotNo];
-        File f2 = new File(workDir, plot+".pdf");
-        if (f2.exists())
+        File plotPdf = new File(workDir, plot+".pdf");
+        if (plotPdf.exists())
         {
-          pdfUtil.importPdf(new FileInputStream(f2), PLOT_X, y, 1.0f, 1.0f);
-          y -= PLOT_DELTA_Y;
+          pdfUtil.importPdf(new FileInputStream(plotPdf), PLOT_X, yPlot, 1.0f, 1.0f);
         }
+        yPlot -= PLOT_DELTA_Y;
       }
       
@@ -291 +295 @@
   }
   
+  private float parsePlotScore(File plotScore)
+    throws IOException
+  {
+    BufferedReader reader = null;
+    float score = Float.NaN;
+    if (plotScore.exists())
+    {
+      try
+      {
+        reader = new BufferedReader(new FileReader(plotScore));
+        score = (float)Type.FLOAT.parseString(reader.readLine());
+      }
+      finally
+      {
+        FileUtil.close(reader);
+      }
+    }
+    return score;
+  }
+  
   /**
     Add personal information to the pilot report.