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