Changeset 3498

Timestamp:

Sep 18, 2015, 2:22:06 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #810: Gene report combiner plug-in should be able to combine to a zip file

The plug-in now has support for combining to a single PDF or to a ZIP file. Other formats should be relatively easy to implement.

Preparations for allowing the combiner to combine any report has been made. Actually, by manually changing the file name to something else (eg. pilotreport.pdf) it is already possible to do so. But this should probably be implemented as different configurations to make it easier to use.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• META-INF/extensions.xml (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/GeneReportsCombinerPlugin.java (modified) (13 diffs)

extensions/net.sf.basedb.reggie/trunk/META-INF/extensions.xml

@@ -125 +125 @@
     </settings>
   </plugin-definition>
-  <plugin-definition id="GeneReportsCombinerPlugin">
-    <about>
-      <name>Gene reports combiner</name>
+  <plugin-definition id="ReportsCombinerPlugin">
+    <about>
+      <name>Reports combiner</name>
       <description>
         Plug-in for combining multiple existing 
-        Gene reports to a single PDF and adding
+        reports to a single PDF/ZIP file and adding
         personal information about the patients.
       </description>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/GeneReportsCombinerPlugin.java

@@ -1 +1 @@
 package net.sf.basedb.reggie.plugins;
 
+import java.io.Closeable;
 import java.io.IOException;
 import java.io.InputStream;
@@ -8 +9 @@
 import java.util.List;
 import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 import net.sf.basedb.core.AnyToAny;
@@ -41 +44 @@
 import net.sf.basedb.reggie.r.GeneReport;
 import net.sf.basedb.util.Enumeration;
+import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.NameableComparator;
 
@@ -123 +127 @@
         storeValue(job, request, ri.getParameter("whichItems"));
         storeValue(job, request, ri.getParameter("filename"));
+        storeValue(job, request, ri.getParameter("format"));
 
         String whichItems = (String)request.getParameterValue("whichItems");
@@ -157 +162 @@
           job.setValues("rawBioAssays", new ItemParameterType<RawBioAssay>(RawBioAssay.class, null, true, 0, null), rawBioAssays);
           
-          response.setSuggestedJobName("Combine gene report for " + rawBioAssays.size() + " raw bioassays");
+          response.setSuggestedJobName("Combine reports for " + rawBioAssays.size() + " raw bioassays");
           response.setDownloadImmediately("The job configuration is complete", ExecutionTime.SHORTEST, true);
         }
@@ -196 +201 @@
       parameters.add(new PluginParameter<String>
         (
-          "whichItems", "Which raw bioassays", "The raw bioassays to create a combined Gene report for.", defaultWhich,
+          "whichItems", "Which raw bioassays", "The raw bioassays to create a combined report for.", defaultWhich,
           new StringParameterType(255, defaultWhich, true, 1, 0, 0, options)
         ));
       parameters.add(new PluginParameter<String>
         (
-          "filename", "Filename", "The filename to look for when searching for existing gene reporter.", GeneReport.DEFAULT_PDF_NAME,
+          "filename", "Report filename", "The filename to look for when searching for existing reports.", GeneReport.DEFAULT_PDF_NAME,
           new StringParameterType(255, GeneReport.DEFAULT_PDF_NAME, true)
         ));
+      
+      String defaultCombine = "PDF";
+      Enumeration<String, String> combineOptions = new Enumeration<String, String>();
+      combineOptions.add("PDF", "PDF");
+      combineOptions.add("ZIP", "ZIP");
+      parameters.add(new PluginParameter<String>
+      (
+        "format", "Format", "Select the output format for the combined reports\n\n"
+            + "PDF = Creates a single PDF with one page for each report\n"
+            + "ZIP = Creates a ZIP file with one file for each report", defaultCombine,
+        new StringParameterType(255, defaultCombine, true, 1, 0, 0, combineOptions)
+      ));     
       
       configureJob = new RequestInformation
       (
         Request.COMMAND_CONFIGURE_JOB, 
-        "Gene report options", 
-        "Set options for combining the Gene report PDF:s", 
+        "Report options", 
+        "Set options for combining the report PDF:s", 
         parameters
       );
@@ -248 +265 @@
       filename = Reggie.getConfig().getConfig("rscript/gene-report/pdf-name", null, GeneReport.DEFAULT_PDF_NAME);
     }
-    out.setFilename(filename);
-    out.setMimeType("application/pdf");
     
     List<RawBioAssay> rawBioAssays = (List<RawBioAssay>)job.getValues("rawBioAssays");
@@ -256 +271 @@
     ItemSubtype specimenType = Subtype.SPECIMEN.get(dc);
     ItemSubtype patientType = Subtype.PATIENT.get(dc);
-    PdfUtil pdf = new PdfUtil("Combined gene report: " + rawBioAssays.size() + " pages", null);
+    
+    String format = (String)job.getValue("format");
+    PdfCombiner combiner = null;
+    
     try
     {
-      pdf.open(out);
+      if ("ZIP".equals(format))
+      {
+        combiner = new PdfToZipCombiner(filename, out);
+      }
+      else
+      {
+        combiner = new PdfToPdfCombiner(filename, out);
+      }
       
       int total = rawBioAssays.size();
@@ -276 +301 @@
         // Get existing PDF
         InputStream existingPdf = null;
+        File file = null;
         try
         {
@@ -281 +307 @@
           if (link.getToType() == Item.FILE)
           {
-            File f = (File)link.getTo();
-            existingPdf = f.getDownloadStream(0);
+            file = (File)link.getTo();
+            existingPdf = file.getDownloadStream(0);
           }
         }
@@ -288 +314 @@
         {}
         
-        if (existingPdf == null)
-        {
+        try
+        {
+          if (existingPdf != null && combiner.addFile(rba, file, existingPdf))
+          {
+            combined++;
+          }
+          else
+          {
+            skipped++;
+          }
+        }
+        catch (IOException ex)
+        {
+          ex.printStackTrace(System.out);
           skipped++;
         }
-        else
-        {
-          // Load existing PDF
-          pdf.importPdf(existingPdf, 0, 0, 1, 1);
-          pdf.getDocument().newPage();
-          combined++;
-        }
       }
       
       if (progress != null)
       {
-        String msg = "Combined gene reports for " + combined + " raw bioassays.";
+        String msg = "Combined reports for " + combined + " raw bioassays.";
         if (skipped > 0) msg += " Skipped " + skipped + " that was not found.";
         progress.display(100, msg);
@@ -310 +341 @@
     finally
     {
+      FileUtil.close(combiner);
       out.flush();
-      if (pdf != null) pdf.close();
     }
   }
@@ -324 +355 @@
   protected String getSuccessMessage()
   {
-    String msg = "Combined gene reports for " + combined + " raw bioassays.";
+    String msg = "Combined reports for " + combined + " raw bioassays.";
     if (skipped > 0) msg += " Skipped " + skipped + " that was not found.";
     return msg;
   }
 
-  
-  
+  /**
+    Abstract base class for combining multiple PDF:s into a single file.
+  */
+  static abstract class PdfCombiner
+    implements Closeable
+  {
+    
+    /**
+      Add a PDF file to the combined file.
+      @param raw The raw bioassay that the pdf file is related to
+      @param file The file item representing the pdf file
+      @param pdf The input stream reading the pdf file.
+      @return TRUE if the file was added, FALSE if not
+      @throws IOException
+    */
+    abstract boolean addFile(RawBioAssay raw, File file, InputStream pdf)
+      throws IOException;
+    
+  }
+  
+  /**
+    Combine PDF files info a ZIP archive. The file names in the ZIP 
+    are set from the raw bioassay.
+  */
+  static class PdfToZipCombiner
+    extends PdfCombiner
+  {
+
+    private ZipOutputStream zip;
+    
+    PdfToZipCombiner(String filename, ExportOutputStream out) 
+    {
+      out.setFilename(filename.substring(0, filename.lastIndexOf("."))+".zip");
+      out.setMimeType("application/zip");
+      zip = new ZipOutputStream(out);
+      zip.setMethod(ZipOutputStream.DEFLATED);
+    }
+    
+    @Override
+    public void close() 
+      throws IOException
+    {
+      zip.flush();
+      zip.close();
+      zip = null;
+    }
+
+    @Override
+    boolean addFile(RawBioAssay raw, File file, InputStream pdf) 
+      throws IOException
+    {
+      ZipEntry entry = new ZipEntry(raw.getName()+".pdf");
+      entry.setSize(file.getSize());
+      if (file.getLastUpdate() != null)
+      {
+        entry.setTime(file.getLastUpdate().getTime());
+      }
+      zip.putNextEntry(entry);
+      
+      FileUtil.copy(pdf, zip);
+      zip.flush();
+      zip.closeEntry();
+      return true;
+    }
+    
+  }
+  
+  /**
+    Combine PDF files into another PDF file.
+  */
+  static class PdfToPdfCombiner
+    extends PdfCombiner
+  {
+    private PdfUtil pdfOut;
+    
+    PdfToPdfCombiner(String filename, ExportOutputStream out) 
+    {
+      out.setFilename(filename);
+      out.setMimeType("application/pdf");
+      pdfOut = new PdfUtil("Combined report ", null);
+      pdfOut.open(out);
+    }
+    
+    @Override
+    public void close() 
+      throws IOException
+    {
+      pdfOut.close();
+      pdfOut = null;
+    }
+    
+    @Override
+    boolean addFile(RawBioAssay raw, File file, InputStream pdfIn) 
+      throws IOException
+    {
+      pdfOut.importPdf(pdfIn, 0, 0, 1, 1);
+      pdfOut.getDocument().newPage();
+      return true;
+    }
+    
+  }
 }