src/jalview/io/BioJsHTMLOutput.java

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