Changeset 3528

Timestamp:

Oct 5, 2015, 11:03:44 AM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #812: Pilot report wizard

Print out molecular subtype scores and other values. The values are currently randomly generated.

Location:

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

Files:

• PdfUtil.java (modified) (5 diffs)
• PilotReportWorker.java (modified) (9 diffs)

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

@@ -108 +108 @@
   
   private BaseFont defaultFont;
+  private BaseFont boldFont;
   
   /**
@@ -119 +120 @@
     this.reader = null;
     this.defaultFont = getDefaultFont();
+    this.boldFont = getBoldFont();
   }
   
@@ -136 +138 @@
     this.creator = info.get("Creator");
     this.defaultFont = getDefaultFont();
+    this.boldFont = getBoldFont();
   }
   
@@ -214 +217 @@
   
   /**
+    Create a bold font for text elements.
+    @see BaseFont for pre-defined font names
+  */
+  public BaseFont getBoldFont()
+  {
+    if (boldFont == null)
+    {
+      try
+      {
+        URL openSans = PdfUtil.class.getResource("/META-INF/fonts/OpenSans-Bold.ttf");
+        return BaseFont.createFont("jar:"+openSans.getPath(), BaseFont.IDENTITY_H, true);
+      }
+      catch (IOException | DocumentException ex)
+      {
+        throw new RuntimeException(ex);
+      }
+    }
+    return boldFont;
+  }
+  
+  /**
     Add text to the document.
     
@@ -233 +257 @@
   
   /**
+    Add bold text to the document.
+    
+    @param canvas The document canvas
+    @param text The text to add
+    @param fontSize Font size to use
+    @param align Alignment
+    @param x X coordinate in points
+    @param y Y coordinate in points
+  */
+  public void addBoldText(String text, float fontSize, int align, float x, float y)
+  {
+    if (text == null || text.equals("")) return;
+    canvas.beginText();
+    canvas.setFontAndSize(boldFont, fontSize); 
+    canvas.showTextAligned(align, text, x, y, 0);
+    canvas.endText();
+  }
+  
+  /**
     Draw grid line around the page. Major grid is 50pt, with minor at every 10pt and
     ticks at every 2pt.

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

@@ -14 +14 @@
 import java.util.Map;
 
-import com.itextpdf.text.BaseColor;
 import com.itextpdf.text.Element;
-import com.itextpdf.text.pdf.PdfContentByte;
-import com.itextpdf.text.pdf.StringUtils;
 
 import net.sf.basedb.core.BioMaterial;
@@ -24 +21 @@
 import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.Sample;
-import net.sf.basedb.core.StringUtil;
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.Site;
@@ -33 +29 @@
 import net.sf.basedb.reggie.dao.RnaQc;
 import net.sf.basedb.reggie.dao.Subtype;
-import net.sf.basedb.reggie.logo.Logo;
 import net.sf.basedb.reggie.r.PilotReport;
 import net.sf.basedb.reggie.r.RResult;
 import net.sf.basedb.util.MD5;
-import net.sf.basedb.util.NumberFormatUtil;
-import net.sf.basedb.util.Values;
-import net.sf.basedb.util.formatter.NumberFormatter;
 
 /**
@@ -45 +37 @@
   generates a PDF document with the plots and other information.
   
-  TODO - this is currently a partial copy of the GeneReport.
+  TODO - this is currently a mix of data from the Gene report (plots),
+  random values (molecular subtype) and actual information from the
+  database (header section).
 
   @author nicklas
@@ -65 +59 @@
   private static final float MARGIN_LEFT = 14;
   
-  /* PLOT POSITIONS */
-  // Left X of plots
-  private static final float PLOT_X = 355; //309;
-  // Bottom Y of first plot
-  private static final float PLOT_START_Y = 474.5f; //588;
-  // Distance between plots
-  private static final float PLOT_DELTA_Y = 89.5f; //124;
-  // Size of plots
-  private static final float PLOT_WIDTH = 160; //270;
-  private static final float PLOT_HEIGHT = 80; //97;
-
   /* TEXT POSITIONS */
   // Left X of text columns
@@ -90 +73 @@
   private static final float TEXT_Y4 = 718;
   private static final float TEXT_Y5 = 690;
-      
+  
+  // Molecular subtype box
+  private static final float SUBTYPE_Y1 = 616;
+  private static final float SUBTYPE_Y2 = 608;
+  private static final float SUBTYPE_X1 = 156;
+  private static final float SUBTYPE_X2 = 330;
+  private static final float SUBTYPE_XX = 50;
+  
+  /* PLOT POSITIONS */
+  // Left X of plots
+  private static final float PLOT_X = 355;
+  // Bottom Y of first plot
+  private static final float PLOT_START_Y = 474.5f;
+  // Distance between plots
+  private static final float PLOT_DELTA_Y = 89.5f;
+  // Size of plots
+  private static final float PLOT_WIDTH = 160;
+  private static final float PLOT_HEIGHT = 80;
+  // Text releated to plot
+  private static final float PLOT_TEXT_X = 214;
+  private static final float PLOT_TEXT_START_Y = 510;
+  
   private PilotReport script;
   private String config;
@@ -142 +146 @@
     Site site = Site.findByCaseName(raw.getName());
     
+    
+    
     PdfUtil pdfUtil = null;
     try
@@ -150 +156 @@
       pdfUtil.importPdf(new FileInputStream(pdfTemplatePath), 0, 0,  1.0f, 1.0f);
       //pdfUtil.drawGrid();
-      
-      float y = PLOT_START_Y;
-      File workDir = result.getWorkDir();
-      for (String gene : result.genes)
-      {
-        File f2 = new File(workDir, "scanb_"+gene+".pdf");
-        if (f2.exists())
-        {
-          pdfUtil.importPdf(new FileInputStream(f2), PLOT_X, y, 1.0f, 1.0f);
-          y -= PLOT_DELTA_Y;
-        }
-      }
-      
       
       // Patient and sample information
@@ -200 +193 @@
       if (site != Site.UNKNOWN) pdfUtil.addText(site.getName(), 12, Element.ALIGN_LEFT, TEXT_X5, TEXT_Y5);
       
+      // Molecular subtype
+      String[] subtypeNames = { "LumA", "LumB", "HER2", "Basal", "Normal" };
+      float[] subtypeScore = new float[5];
+      float maxVal = Float.NEGATIVE_INFINITY;
+      for (int i = 0; i < 5; i++)
+      {
+        subtypeScore[i] = (float)(Math.random()*2-1);
+        if (subtypeScore[i] > maxVal) maxVal = subtypeScore[i];
+      }
+      for (int i = 0; i < 5; i++)
+      {
+        if (Float.compare(maxVal, subtypeScore[i]) == 0)
+        {
+          pdfUtil.addBoldText(twoDecimals.format(subtypeScore[i]), 12, Element.ALIGN_LEFT, SUBTYPE_X2+i*SUBTYPE_XX, SUBTYPE_Y2);
+          pdfUtil.addText(subtypeNames[i], 14, Element.ALIGN_LEFT, SUBTYPE_X1, SUBTYPE_Y1);
+        }
+        else
+        {
+          pdfUtil.addText(twoDecimals.format(subtypeScore[i]), 12, Element.ALIGN_LEFT, SUBTYPE_X2+i*SUBTYPE_XX, SUBTYPE_Y2);
+        }
+      }
+      
+      
+      // Plots
+      float y = PLOT_START_Y;
+      float yText = PLOT_TEXT_START_Y;
+      File workDir = result.getWorkDir();
+      String[] lowHigh = { "Låg", "Hög" };
+      String[] positiveNegative = { "Negative", "Positive" };
+      
+      for (int plotNo = 0; plotNo < 5; plotNo++)
+      {
+        String[] options = plotNo == 0 || plotNo == 4 ? lowHigh : positiveNegative;
+        pdfUtil.addText(options[subtypeScore[plotNo] < 0 ? 0 : 1], 14, Element.ALIGN_LEFT, PLOT_TEXT_X, yText);
+        yText -= PLOT_DELTA_Y;
+
+        if (result.genes.size() > plotNo)
+        {
+          String gene = result.genes.get(plotNo);
+          File f2 = new File(workDir, "scanb_"+gene+".pdf");
+          if (f2.exists())
+          {
+            pdfUtil.importPdf(new FileInputStream(f2), PLOT_X, y, 1.0f, 1.0f);
+            y -= PLOT_DELTA_Y;
+          }
+        }
+      }
+      
       // Extra info at bottom
       pdfUtil.addText(raw.getName(), 8, Element.ALIGN_RIGHT, MARGIN_RIGHT, 10);