src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.api.AlignmentViewPanel;
   4 import jalview.datamodel.AlignmentExportData;
   5 import jalview.exceptions.NoFileSelectedException;
   6 import jalview.json.binding.biojs.BioJSReleasePojo;
   7 import jalview.json.binding.biojs.BioJSRepositoryPojo;
   8 import jalview.util.MessageManager;
   9
  10 import java.io.BufferedInputStream;
  11 import java.io.BufferedReader;
  12 import java.io.File;
  13 import java.io.IOException;
  14 import java.io.InputStream;
  15 import java.io.InputStreamReader;
  16 import java.io.PrintWriter;
  17 import java.net.URISyntaxException;
  18 import java.net.URL;
  19 import java.util.Objects;
  20 import java.util.TreeMap;
  21
  22
  23 public class BioJsHTMLOutput
  24 {
  25   private AlignmentViewPanel ap;
  26
  27   private static File currentBJSTemplateFile;
  28
  29   private static TreeMap<String, File> bioJsMSAVersions;
  30
  31   public static final String DEFAULT_DIR = System.getProperty("user.home")
  32           + File.separatorChar + ".biojs_templates" + File.separatorChar;
  33
  34   public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
  35           .getDefault("biojs_template_directory", DEFAULT_DIR);
  36
  37   public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
  38           .getDefault(
  39                   "biojs_template_git_repo",
  40                   "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
  41
  42   public BioJsHTMLOutput(AlignmentViewPanel ap)
  43   {
  44     if (ap != null)
  45     {
  46       this.ap = ap;
  47     }
  48   }
  49
  50   public void exportJalviewAlignmentAsBioJsHtmlFile()
  51   {
  52     try
  53     {
  54       String outputFile = getOutputFile();
  55       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
  56       AlignmentExportData exportData = jalview.gui.AlignFrame
  57               .getAlignmentForExport(
  58               JSONFile.FILE_DESC, ap.getAlignViewport());
  59       if (exportData.getSettings().isCancelled())
  60       {
  61         return;
  62       }
  63       String jalviewAlignmentJson = new FormatAdapter(ap,
  64               exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
  65               exportData.getAlignment(), exportData.getOmitHidden(),
  66               exportData.getStartEndPostions(), ap.getAlignViewport()
  67                       .getColumnSelection());
  68
  69       String bioJSTemplateString = getBioJsTemplateAsString();
  70       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
  71               .replaceAll(
  72 "#sequenceData#", jalviewAlignmentJson)
  73               .toString();
  74
  75       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  76               outputFile));
  77       out.print(generatedBioJsWithJalviewAlignmentAsJson);
  78       out.flush();
  79       out.close();
  80       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
  81     } catch (NoFileSelectedException ex)
  82     {
  83       // do noting if no file was selected
  84     } catch (Exception e)
  85     {
  86       e.printStackTrace();
  87     }
  88   }
  89
  90   public String getOutputFile() throws NoFileSelectedException
  91   {
  92     String selectedFile = null;
  93     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
  94             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  95             { "html" }, new String[]
  96             { "HTML files" }, "HTML files");
  97     jvFileChooser.setFileView(new JalviewFileView());
  98
  99     jvFileChooser.setDialogTitle(MessageManager
 100             .getString("label.save_as_biojs_html"));
 101     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 102
 103     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 104     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 105     {
 106       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 107               .getSelectedFile().getParent());
 108       selectedFile = jvFileChooser.getSelectedFile().getPath();
 109     }
 110     else
 111     {
 112       throw new NoFileSelectedException("No file was selected.");
 113     }
 114     return selectedFile;
 115   }
 116
 117
 118   public static String getBioJsTemplateAsString()
 119           throws IOException
 120   {
 121     InputStreamReader isReader = null;
 122     BufferedReader buffReader = null;
 123     StringBuilder sb = new StringBuilder();
 124     Objects.requireNonNull(getCurrentBJSTemplateFile(),
 125             "BioJsTemplate File not initialized!");
 126     @SuppressWarnings("deprecation")
 127     URL url = getCurrentBJSTemplateFile().toURL();
 128     if (url != null)
 129     {
 130       try
 131       {
 132         isReader = new InputStreamReader(url.openStream());
 133         buffReader = new BufferedReader(isReader);
 134         String line;
 135         String lineSeparator = System.getProperty("line.separator");
 136         while ((line = buffReader.readLine()) != null)
 137         {
 138           sb.append(line).append(lineSeparator);
 139         }
 140
 141       } catch (Exception ex)
 142       {
 143         ex.printStackTrace();
 144       } finally
 145       {
 146         if (isReader != null)
 147         {
 148           isReader.close();
 149         }
 150
 151         if (buffReader != null)
 152         {
 153           buffReader.close();
 154         }
 155       }
 156     }
 157     return sb.toString();
 158   }
 159
 160   public static void refreshBioJSVersionsInfo(String dirName)
 161           throws URISyntaxException
 162   {
 163     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
 164     Objects.requireNonNull(dirName, "dirName MUST not be null!");
 165     Objects.requireNonNull(directory, "directory MUST not be null!");
 166     TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
 167
 168     for (File file : directory.listFiles())
 169     {
 170       if (file.isFile())
 171       {
 172         String fileName = file.getName().substring(0,
 173                 file.getName().lastIndexOf("."));
 174         String fileMeta[] = fileName.split("_");
 175         if (fileMeta.length > 2)
 176         {
 177           setCurrentBJSTemplateFile(file);
 178           versionFileMap.put(fileMeta[2], file);
 179         }
 180         else if (fileMeta.length > 1)
 181         {
 182           versionFileMap.put(fileMeta[1], file);
 183         }
 184       }
 185     }
 186     if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
 187     {
 188       setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
 189     }
 190     setBioJsMSAVersions(versionFileMap);
 191   }
 192
 193   public static void updateBioJS()
 194   {
 195     Thread updateThread = new Thread()
 196     {
 197       public void run()
 198       {
 199         try
 200         {
 201           String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
 202           if (gitRepoPkgJson != null)
 203           {
 204             BioJSRepositoryPojo release = new BioJSRepositoryPojo(
 205                     gitRepoPkgJson);
 206             syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
 207             refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
 208           }
 209         } catch (URISyntaxException e)
 210         {
 211           e.printStackTrace();
 212         }
 213       }
 214     };
 215     updateThread.start();
 216
 217   }
 218
 219
 220   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
 221   {
 222     for (BioJSReleasePojo bjsRelease : repo.getReleases())
 223     {
 224       String releaseUrl = bjsRelease.getUrl();
 225       String releaseVersion = bjsRelease.getVersion();
 226       String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
 227       if (releaseVersion.equals(repo.getLatestReleaseVersion()))
 228       {
 229         releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
 230       }
 231
 232       File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
 233       if (!biojsDirectory.exists())
 234       {
 235         if (!biojsDirectory.mkdirs())
 236         {
 237           System.out.println("Couldn't create local directory : "
 238                   + BJS_TEMPLATES_LOCAL_DIRECTORY);
 239           return;
 240         }
 241       }
 242
 243       File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
 244       if (!file.exists())
 245       {
 246
 247         PrintWriter out = null;
 248         try
 249         {
 250           out = new java.io.PrintWriter(new java.io.FileWriter(file));
 251           out.print(getURLContentAsString(releaseUrl));
 252         } catch (IOException e)
 253         {
 254           e.printStackTrace();
 255         } finally
 256         {
 257           if (out != null)
 258           {
 259             out.flush();
 260             out.close();
 261           }
 262         }
 263       }
 264     }
 265
 266   }
 267
 268   public static String getURLContentAsString(String url)
 269           throws OutOfMemoryError
 270   {
 271     StringBuilder responseStrBuilder = null;
 272     InputStream is = null;
 273     try
 274     {
 275       URL resourceUrl = new URL(url);
 276       is = new BufferedInputStream(resourceUrl.openStream());
 277       BufferedReader br = new BufferedReader(new InputStreamReader(is));
 278       responseStrBuilder = new StringBuilder();
 279       String lineContent;
 280
 281       while ((lineContent = br.readLine()) != null)
 282       {
 283         responseStrBuilder.append(lineContent).append("\n");
 284       }
 285     } catch (OutOfMemoryError er)
 286     {
 287       er.printStackTrace();
 288     } catch (Exception ex)
 289     {
 290       ex.printStackTrace();
 291     } finally
 292     {
 293       if (is != null)
 294       {
 295         try
 296         {
 297           is.close();
 298         } catch (IOException e)
 299         {
 300           e.printStackTrace();
 301         }
 302       }
 303     }
 304     return responseStrBuilder == null ? null : responseStrBuilder
 305             .toString();
 306   }
 307
 308   public static File getCurrentBJSTemplateFile()
 309   {
 310     return currentBJSTemplateFile;
 311   }
 312
 313   public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
 314   {
 315     BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
 316   }
 317
 318   public static TreeMap<String, File> getBioJsMSAVersions()
 319   {
 320     return bioJsMSAVersions;
 321   }
 322
 323   public static void setBioJsMSAVersions(
 324           TreeMap<String, File> bioJsMSAVersions)
 325   {
 326     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
 327   }
 328
 329 }