src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.api.AlignmentViewPanel;
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.AlignmentExportData;
   6 import jalview.exceptions.NoFileSelectedException;
   7 import jalview.gui.AlignFrame;
   8 import jalview.json.binding.v1.BioJSReleasePojo;
   9 import jalview.json.binding.v1.BioJSRepositoryPojo;
  10 import jalview.util.BrowserLauncher;
  11 import jalview.util.MessageManager;
  12
  13 import java.io.BufferedInputStream;
  14 import java.io.BufferedReader;
  15 import java.io.File;
  16 import java.io.IOException;
  17 import java.io.InputStream;
  18 import java.io.InputStreamReader;
  19 import java.io.PrintWriter;
  20 import java.net.URISyntaxException;
  21 import java.net.URL;
  22 import java.util.Objects;
  23 import java.util.TreeMap;
  24
  25
  26 public class BioJsHTMLOutput
  27 {
  28   private AlignmentViewPanel ap;
  29
  30   private static File currentBJSTemplateFile;
  31
  32   private static TreeMap<String, File> bioJsMSAVersions;
  33
  34   public static final String DEFAULT_DIR = System.getProperty("user.home")
  35           + File.separatorChar + ".biojs_templates" + File.separatorChar;
  36
  37   public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
  38           .getDefault("biojs_template_directory", DEFAULT_DIR);
  39
  40   public static final String BJS_TEMPLATE_GIT_REPO = Cache
  41           .getDefault(
  42                   "biojs_template_git_repo",
  43                   "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
  44
  45   public BioJsHTMLOutput(AlignmentViewPanel ap)
  46   {
  47     if (ap != null)
  48     {
  49       this.ap = ap;
  50     }
  51   }
  52
  53   public void exportJalviewAlignmentAsBioJsHtmlFile()
  54   {
  55     try
  56     {
  57       String outputFile = getOutputFile();
  58       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
  59       AlignmentExportData exportData = AlignFrame
  60               .getAlignmentForExport(
  61               JSONFile.FILE_DESC, ap.getAlignViewport());
  62       if (exportData.getSettings().isCancelled())
  63       {
  64         return;
  65       }
  66       String jalviewAlignmentJson = new FormatAdapter(ap,
  67               exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
  68               exportData.getAlignment(), exportData.getOmitHidden(),
  69               exportData.getStartEndPostions(), ap.getAlignViewport()
  70                       .getColumnSelection());
  71
  72       String bioJSTemplateString = getBioJsTemplateAsString();
  73       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
  74               .replaceAll(
  75 "#sequenceData#", jalviewAlignmentJson)
  76               .toString();
  77
  78       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  79               outputFile));
  80       out.print(generatedBioJsWithJalviewAlignmentAsJson);
  81       out.flush();
  82       out.close();
  83       BrowserLauncher.openURL("file:///" + outputFile);
  84     } catch (NoFileSelectedException ex)
  85     {
  86       // do noting if no file was selected
  87     } catch (Exception e)
  88     {
  89       e.printStackTrace();
  90     }
  91   }
  92
  93   public String getOutputFile() throws NoFileSelectedException
  94   {
  95     String selectedFile = null;
  96     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
  97             Cache.getProperty("LAST_DIRECTORY"), new String[]
  98             { "html" }, new String[]
  99             { "HTML files" }, "HTML files");
 100     jvFileChooser.setFileView(new JalviewFileView());
 101
 102     jvFileChooser.setDialogTitle(MessageManager
 103             .getString("label.save_as_biojs_html"));
 104     jvFileChooser.setDialogTitle("save as BioJs HTML");
 105     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 106
 107     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 108     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 109     {
 110       Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 111               .getSelectedFile().getParent());
 112       selectedFile = jvFileChooser.getSelectedFile().getPath();
 113     }
 114     else
 115     {
 116       throw new NoFileSelectedException("No file was selected.");
 117     }
 118     return selectedFile;
 119   }
 120
 121
 122   public static String getBioJsTemplateAsString()
 123           throws IOException
 124   {
 125     InputStreamReader isReader = null;
 126     BufferedReader buffReader = null;
 127     StringBuilder sb = new StringBuilder();
 128     Objects.requireNonNull(getCurrentBJSTemplateFile(),
 129             "BioJsTemplate File not initialized!");
 130     @SuppressWarnings("deprecation")
 131     URL url = getCurrentBJSTemplateFile().toURL();
 132     if (url != null)
 133     {
 134       try
 135       {
 136         isReader = new InputStreamReader(url.openStream());
 137         buffReader = new BufferedReader(isReader);
 138         String line;
 139         String lineSeparator = System.getProperty("line.separator");
 140         while ((line = buffReader.readLine()) != null)
 141         {
 142           sb.append(line).append(lineSeparator);
 143         }
 144
 145       } catch (Exception ex)
 146       {
 147         ex.printStackTrace();
 148       } finally
 149       {
 150         if (isReader != null)
 151         {
 152           isReader.close();
 153         }
 154
 155         if (buffReader != null)
 156         {
 157           buffReader.close();
 158         }
 159       }
 160     }
 161     return sb.toString();
 162   }
 163
 164   public static void refreshBioJSVersionsInfo(String dirName)
 165           throws URISyntaxException
 166   {
 167     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
 168     Objects.requireNonNull(dirName, "dirName MUST not be null!");
 169     Objects.requireNonNull(directory, "directory MUST not be null!");
 170     TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
 171
 172     for (File file : directory.listFiles())
 173     {
 174       if (file.isFile())
 175       {
 176         String fileName = file.getName().substring(0,
 177                 file.getName().lastIndexOf("."));
 178         String fileMeta[] = fileName.split("_");
 179         if (fileMeta.length > 2)
 180         {
 181           setCurrentBJSTemplateFile(file);
 182           versionFileMap.put(fileMeta[2], file);
 183         }
 184         else if (fileMeta.length > 1)
 185         {
 186           versionFileMap.put(fileMeta[1], file);
 187         }
 188       }
 189     }
 190     if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
 191     {
 192       setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
 193     }
 194     setBioJsMSAVersions(versionFileMap);
 195   }
 196
 197   public static void updateBioJS()
 198   {
 199     Thread updateThread = new Thread()
 200     {
 201       public void run()
 202       {
 203         try
 204         {
 205           String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
 206           if (gitRepoPkgJson != null)
 207           {
 208             BioJSRepositoryPojo release = new BioJSRepositoryPojo(
 209                     gitRepoPkgJson);
 210             syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
 211             refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
 212           }
 213         } catch (URISyntaxException e)
 214         {
 215           e.printStackTrace();
 216         }
 217       }
 218     };
 219     updateThread.start();
 220
 221   }
 222
 223
 224   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
 225   {
 226     for (BioJSReleasePojo bjsRelease : repo.getReleases())
 227     {
 228       String releaseUrl = bjsRelease.getUrl();
 229       String releaseVersion = bjsRelease.getVersion();
 230       String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
 231       if (releaseVersion.equals(repo.getLatestReleaseVersion()))
 232       {
 233         releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
 234       }
 235
 236       File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
 237       if (!biojsDirectory.exists())
 238       {
 239         if (!biojsDirectory.mkdirs())
 240         {
 241           System.out.println("Couldn't create local directory : "
 242                   + BJS_TEMPLATES_LOCAL_DIRECTORY);
 243           return;
 244         }
 245       }
 246
 247       File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
 248       if (!file.exists())
 249       {
 250
 251         PrintWriter out = null;
 252         try
 253         {
 254           out = new java.io.PrintWriter(new java.io.FileWriter(file));
 255           out.print(getURLContentAsString(releaseUrl));
 256         } catch (IOException e)
 257         {
 258           e.printStackTrace();
 259         } finally
 260         {
 261           if (out != null)
 262           {
 263             out.flush();
 264             out.close();
 265           }
 266         }
 267       }
 268     }
 269
 270   }
 271
 272   public static String getURLContentAsString(String url)
 273           throws OutOfMemoryError
 274   {
 275     StringBuilder responseStrBuilder = null;
 276     InputStream is = null;
 277     try
 278     {
 279       URL resourceUrl = new URL(url);
 280       is = new BufferedInputStream(resourceUrl.openStream());
 281       BufferedReader br = new BufferedReader(new InputStreamReader(is));
 282       responseStrBuilder = new StringBuilder();
 283       String lineContent;
 284
 285       while ((lineContent = br.readLine()) != null)
 286       {
 287         responseStrBuilder.append(lineContent).append("\n");
 288       }
 289     } catch (OutOfMemoryError er)
 290     {
 291       er.printStackTrace();
 292     } catch (Exception ex)
 293     {
 294       ex.printStackTrace();
 295     } finally
 296     {
 297       if (is != null)
 298       {
 299         try
 300         {
 301           is.close();
 302         } catch (IOException e)
 303         {
 304           e.printStackTrace();
 305         }
 306       }
 307     }
 308     return responseStrBuilder == null ? null : responseStrBuilder
 309             .toString();
 310   }
 311
 312   public static File getCurrentBJSTemplateFile()
 313   {
 314     return currentBJSTemplateFile;
 315   }
 316
 317   public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
 318   {
 319     BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
 320   }
 321
 322   public static TreeMap<String, File> getBioJsMSAVersions()
 323   {
 324     return bioJsMSAVersions;
 325   }
 326
 327   public static void setBioJsMSAVersions(
 328           TreeMap<String, File> bioJsMSAVersions)
 329   {
 330     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
 331   }
 332
 333 }