From e58c9b0c6d453c75810eb08cb2651769fccf7f8a Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 18 Aug 2015 13:22:36 +0100
Subject: [PATCH] JAL-1835 made BioJSON embedding to html exports
 configurable, and trapped import of html files without
 BioJSON

---
 src/jalview/io/AppletFormatAdapter.java |    6 ++++-
 src/jalview/io/HtmlFile.java            |   42 ++++++++++++++++++-------------
 src/jalview/io/HtmlSvgOutput.java       |   12 +++++----
 3 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 02de02e..7dc263b 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignmentView;
 import jalview.util.MessageManager;
 
 import java.io.File;
+import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 
@@ -343,7 +344,10 @@ public class AppletFormatAdapter
           ex.printStackTrace();
         }
       }
-
+      if (format.equalsIgnoreCase("HTML"))
+      {
+        throw new IOException(e.getMessage());
+      }
       // If we get to this stage, the format was not supported
       throw new java.io.IOException(SUPPORTED_FORMATS);
     }
diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 0f5cd55..4805b8e 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -68,26 +68,33 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
   @Override
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
-      Element content = null;
-      Document doc = null;
-      try {
-    	  StringBuilder htmlData = new StringBuilder();
-          String currentLine;
-          while ((currentLine = nextLine()) != null)
-          {
-            htmlData.append(currentLine);
-          }
-
-          doc = Jsoup.parse(htmlData.toString());
-      } catch (OutOfMemoryError oom) {
-    	  errormessage = "Not enough memory to process HTML document";
-    	  throw new IOException(errormessage);
+      StringBuilder htmlData = new StringBuilder();
+      String currentLine;
+      while ((currentLine = nextLine()) != null)
+      {
+        htmlData.append(currentLine);
       }
+      doc = Jsoup.parse(htmlData.toString());
+    } catch (OutOfMemoryError oom)
+    {
+      errormessage = "Not enough memory to process HTML document";
+      throw new IOException(errormessage);
+    }
+
+    try
+    {
       content = doc.getElementById("seqData");
-      
-      JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
+      if (content == null)
+      {
+        errormessage = "The html document is not embedded with BioJSON data";
+        throw new IOException(errormessage);
+      }
+      JSONFile jsonFile = new JSONFile().parse(new StringReader(content
+              .val()));
       this.seqs = jsonFile.getSeqs();
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
@@ -98,8 +105,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
       this.displayedFeatures = jsonFile.getDisplayedFeatures();
     } catch (Exception e)
     {
-      errormessage = "Failed to extract data from HTML document.";
-      throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
+      throw e;
     }
   }
 
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 1eb86b7..7fcf629 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -97,22 +97,24 @@ public class HtmlSvgOutput
 
       String titleSvgData = g1.getSVGDocument();
       String alignSvgData = g2.getSVGDocument();
-
+      String jsonData = null;
+      boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
+              .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+      if (isEmbbedBioJSON)
+      {
       AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
               JSONFile.FILE_DESC, av);
       if (exportData.getSettings().isCancelled())
       {
         return;
       }
-      String jsonData = new FormatAdapter(ap, exportData.getSettings())
+        jsonData = new FormatAdapter(ap, exportData.getSettings())
               .formatSequences(JSONFile.FILE_DESC, exportData
                       .getAlignment(), exportData.getOmitHidden(),
                       exportData.getStartEndPostions(), ap
                               .getAlignViewport().getColumnSelection());
-
-      // String jsonData = JSONFile.getJSONData(ap);
+      }
       String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
-
       FileOutputStream out = new FileOutputStream(file);
       out.write(htmlData.getBytes());
       out.flush();
-- 
1.7.10.2