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.v1.BioJSReleasePojo;
   7 import jalview.json.binding.v1.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.setDialogTitle("save as BioJs HTML");
 102     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 103
 104     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 105     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 106     {
 107       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 108               .getSelectedFile().getParent());
 109       selectedFile = jvFileChooser.getSelectedFile().getPath();
 110     }
 111     else
 112     {
 113       throw new NoFileSelectedException("No file was selected.");
 114     }
 115     return selectedFile;
 116   }
 117
 118
 119   public static String getBioJsTemplateAsString()
 120           throws IOException
 121   {
 122     InputStreamReader isReader = null;
 123     BufferedReader buffReader = null;
 124     StringBuilder sb = new StringBuilder();
 125     Objects.requireNonNull(getCurrentBJSTemplateFile(),
 126             "BioJsTemplate File not initialized!");
 127     @SuppressWarnings("deprecation")
 128     URL url = getCurrentBJSTemplateFile().toURL();
 129     if (url != null)
 130     {
 131       try
 132       {
 133         isReader = new InputStreamReader(url.openStream());
 134         buffReader = new BufferedReader(isReader);
 135         String line;
 136         String lineSeparator = System.getProperty("line.separator");
 137         while ((line = buffReader.readLine()) != null)
 138         {
 139           sb.append(line).append(lineSeparator);
 140         }
 141
 142       } catch (Exception ex)
 143       {
 144         ex.printStackTrace();
 145       } finally
 146       {
 147         if (isReader != null)
 148         {
 149           isReader.close();
 150         }
 151
 152         if (buffReader != null)
 153         {
 154           buffReader.close();
 155         }
 156       }
 157     }
 158     return sb.toString();
 159   }
 160
 161   public static void refreshBioJSVersionsInfo(String dirName)
 162           throws URISyntaxException
 163   {
 164     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
 165     Objects.requireNonNull(dirName, "dirName MUST not be null!");
 166     Objects.requireNonNull(directory, "directory MUST not be null!");
 167     TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
 168
 169     for (File file : directory.listFiles())
 170     {
 171       if (file.isFile())
 172       {
 173         String fileName = file.getName().substring(0,
 174                 file.getName().lastIndexOf("."));
 175         String fileMeta[] = fileName.split("_");
 176         if (fileMeta.length > 2)
 177         {
 178           setCurrentBJSTemplateFile(file);
 179           versionFileMap.put(fileMeta[2], file);
 180         }
 181         else if (fileMeta.length > 1)
 182         {
 183           versionFileMap.put(fileMeta[1], file);
 184         }
 185       }
 186     }
 187     if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
 188     {
 189       setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
 190     }
 191     setBioJsMSAVersions(versionFileMap);
 192   }
 193
 194   public static void updateBioJS()
 195   {
 196     Thread updateThread = new Thread()
 197     {
 198       public void run()
 199       {
 200         try
 201         {
 202           String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
 203           if (gitRepoPkgJson != null)
 204           {
 205             BioJSRepositoryPojo release = new BioJSRepositoryPojo(
 206                     gitRepoPkgJson);
 207             syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
 208             refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
 209           }
 210         } catch (URISyntaxException e)
 211         {
 212           e.printStackTrace();
 213         }
 214       }
 215     };
 216     updateThread.start();
 217
 218   }
 219
 220
 221   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
 222   {
 223     for (BioJSReleasePojo bjsRelease : repo.getReleases())
 224     {
 225       String releaseUrl = bjsRelease.getUrl();
 226       String releaseVersion = bjsRelease.getVersion();
 227       String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
 228       if (releaseVersion.equals(repo.getLatestReleaseVersion()))
 229       {
 230         releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
 231       }
 232
 233       File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
 234       if (!biojsDirectory.exists())
 235       {
 236         if (!biojsDirectory.mkdirs())
 237         {
 238           System.out.println("Couldn't create local directory : "
 239                   + BJS_TEMPLATES_LOCAL_DIRECTORY);
 240           return;
 241         }
 242       }
 243
 244       File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
 245       if (!file.exists())
 246       {
 247
 248         PrintWriter out = null;
 249         try
 250         {
 251           out = new java.io.PrintWriter(new java.io.FileWriter(file));
 252           out.print(getURLContentAsString(releaseUrl));
 253         } catch (IOException e)
 254         {
 255           e.printStackTrace();
 256         } finally
 257         {
 258           if (out != null)
 259           {
 260             out.flush();
 261             out.close();
 262           }
 263         }
 264       }
 265     }
 266
 267   }
 268
 269   public static String getURLContentAsString(String url)
 270           throws OutOfMemoryError
 271   {
 272     StringBuilder responseStrBuilder = null;
 273     InputStream is = null;
 274     try
 275     {
 276       URL resourceUrl = new URL(url);
 277       is = new BufferedInputStream(resourceUrl.openStream());
 278       BufferedReader br = new BufferedReader(new InputStreamReader(is));
 279       responseStrBuilder = new StringBuilder();
 280       String lineContent;
 281
 282       while ((lineContent = br.readLine()) != null)
 283       {
 284         responseStrBuilder.append(lineContent).append("\n");
 285       }
 286     } catch (OutOfMemoryError er)
 287     {
 288       er.printStackTrace();
 289     } catch (Exception ex)
 290     {
 291       ex.printStackTrace();
 292     } finally
 293     {
 294       if (is != null)
 295       {
 296         try
 297         {
 298           is.close();
 299         } catch (IOException e)
 300         {
 301           e.printStackTrace();
 302         }
 303       }
 304     }
 305     return responseStrBuilder == null ? null : responseStrBuilder
 306             .toString();
 307   }
 308
 309   public static File getCurrentBJSTemplateFile()
 310   {
 311     return currentBJSTemplateFile;
 312   }
 313
 314   public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
 315   {
 316     BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
 317   }
 318
 319   public static TreeMap<String, File> getBioJsMSAVersions()
 320   {
 321     return bioJsMSAVersions;
 322   }
 323
 324   public static void setBioJsMSAVersions(
 325           TreeMap<String, File> bioJsMSAVersions)
 326   {
 327     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
 328   }
 329
 330 }