src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.exceptions.NoFileSelectedException;
   4 import jalview.gui.AlignViewport;
   5 import jalview.gui.AlignmentPanel;
   6 import jalview.gui.FeatureRenderer;
   7 import jalview.json.binding.v1.BioJSReleasePojo;
   8 import jalview.json.binding.v1.BioJSRepositoryPojo;
   9 import jalview.util.MessageManager;
  10
  11 import java.io.BufferedInputStream;
  12 import java.io.BufferedReader;
  13 import java.io.File;
  14 import java.io.IOException;
  15 import java.io.InputStream;
  16 import java.io.InputStreamReader;
  17 import java.io.PrintWriter;
  18 import java.net.URISyntaxException;
  19 import java.net.URL;
  20 import java.util.Objects;
  21 import java.util.TreeMap;
  22
  23
  24 public class BioJsHTMLOutput
  25 {
  26   private AlignViewport av;
  27
  28   private static File currentBJSTemplateFile;
  29
  30   private static TreeMap<String, File> bioJsMSAVersions;
  31
  32   public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
  33           .getDefault("biojs_template_directory", "/biojs_templates/");
  34
  35   public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
  36           .getDefault(
  37                   "biojs_template_git_repo",
  38                   "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
  39
  40   public BioJsHTMLOutput(AlignmentPanel ap,
  41           FeatureRenderer fr1)
  42   {
  43     if (ap != null)
  44     {
  45       this.av = ap.av;
  46       av.setFeatureRenderer(new FeatureRenderer(ap));
  47     }
  48   }
  49
  50   public void exportJalviewAlignmentAsBioJsHtmlFile()
  51   {
  52     try
  53     {
  54       String outputFile = getOutputFile();
  55       String jalviewAlignmentJson = JSONFile.getJSONData(av);
  56       String bioJSTemplateString = getBioJsTemplateAsString();
  57       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
  58               .replaceAll(
  59 "#sequenceData#", jalviewAlignmentJson)
  60               .toString();
  61
  62       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  63               outputFile));
  64       out.print(generatedBioJsWithJalviewAlignmentAsJson);
  65       out.flush();
  66       out.close();
  67       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
  68     } catch (NoFileSelectedException ex)
  69     {
  70       // do noting if no file was selected
  71     } catch (Exception e)
  72     {
  73       e.printStackTrace();
  74     }
  75   }
  76
  77   public String getOutputFile() throws NoFileSelectedException
  78   {
  79     String selectedFile = null;
  80     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
  81             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  82             { "html" }, new String[]
  83             { "HTML files" }, "HTML files");
  84     jvFileChooser.setFileView(new JalviewFileView());
  85
  86     // TODO uncomment when supported by MassageManager
  87     jvFileChooser.setDialogTitle(MessageManager
  88             .getString("label.save_as_biojs_html"));
  89     jvFileChooser.setDialogTitle("save as BioJs HTML");
  90     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
  91
  92     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  93     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
  94     {
  95       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
  96               .getSelectedFile().getParent());
  97       selectedFile = jvFileChooser.getSelectedFile().getPath();
  98     }
  99     else
 100     {
 101       throw new NoFileSelectedException("No file was selected.");
 102     }
 103     return selectedFile;
 104   }
 105
 106
 107   public static String getBioJsTemplateAsString()
 108           throws IOException
 109   {
 110     InputStreamReader isReader = null;
 111     BufferedReader buffReader = null;
 112     StringBuilder sb = new StringBuilder();
 113     Objects.requireNonNull(getCurrentBJSTemplateFile(),
 114             "BioJsTemplate File not initialized!");
 115     @SuppressWarnings("deprecation")
 116     URL url = getCurrentBJSTemplateFile().toURL();
 117     if (url != null)
 118     {
 119       try
 120       {
 121         isReader = new InputStreamReader(url.openStream());
 122         buffReader = new BufferedReader(isReader);
 123         String line;
 124         String lineSeparator = System.getProperty("line.separator");
 125         while ((line = buffReader.readLine()) != null)
 126         {
 127           sb.append(line).append(lineSeparator);
 128         }
 129
 130       } catch (Exception ex)
 131       {
 132         ex.printStackTrace();
 133       } finally
 134       {
 135         if (isReader != null)
 136         {
 137           isReader.close();
 138         }
 139
 140         if (buffReader != null)
 141         {
 142           buffReader.close();
 143         }
 144       }
 145     }
 146     return sb.toString();
 147   }
 148
 149   public void refreshBioJSVersionsInfo(String dirName)
 150           throws URISyntaxException
 151   {
 152     URL url = getClass().getResource(dirName);
 153     File directory = new File(url.toURI());
 154     Objects.requireNonNull(dirName, "dirName MUST not be null!");
 155     Objects.requireNonNull(directory, "directory MUST not be null!");
 156     TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
 157
 158     for (File file : directory.listFiles())
 159     {
 160       if (file.isFile())
 161       {
 162         String fileName = file.getName().substring(0,
 163                 file.getName().lastIndexOf("."));
 164         String fileMeta[] = fileName.split("_");
 165         if (fileMeta.length > 2)
 166         {
 167           setCurrentBJSTemplateFile(file);
 168           versionFileMap.put(fileMeta[2], file);
 169         }
 170         else if (fileMeta.length > 1)
 171         {
 172           versionFileMap.put(fileMeta[1], file);
 173         }
 174       }
 175     }
 176     if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
 177     {
 178       setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
 179     }
 180     setBioJsMSAVersions(versionFileMap);
 181   }
 182
 183   public void updateBioJS()
 184   {
 185     try
 186     {
 187       String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
 188       BioJSRepositoryPojo release = new BioJSRepositoryPojo(gitRepoPkgJson);
 189       syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
 190       refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
 191     } catch (URISyntaxException e)
 192     {
 193       e.printStackTrace();
 194     }
 195   }
 196
 197
 198   public void syncUpdates(String localDir, BioJSRepositoryPojo repo)
 199           throws URISyntaxException
 200   {
 201     for (BioJSReleasePojo bjsRelease : repo.getReleases())
 202     {
 203       String releaseUrl = bjsRelease.getUrl();
 204       String releaseVersion = bjsRelease.getVersion();
 205       String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
 206       if (releaseVersion.equals(repo.getLatestReleaseVersion()))
 207       {
 208         releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
 209       }
 210       File file = null;
 211       URL url = getClass().getResource(
 212               BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
 213       if (url == null)
 214       {
 215         String path = getClass().getResource(BJS_TEMPLATES_LOCAL_DIRECTORY)
 216                 .getPath();
 217         System.out.println("------> " + path);
 218         file = new File(path + releaseFile);
 219       }
 220       else
 221       {
 222         file = new File(url.toURI());
 223       }
 224
 225       if (!file.exists())
 226       {
 227         PrintWriter out = null;
 228         try
 229         {
 230           out = new java.io.PrintWriter(new java.io.FileWriter(file));
 231           out.print(getURLContentAsString(releaseUrl));
 232         } catch (IOException e)
 233         {
 234           e.printStackTrace();
 235         } finally
 236         {
 237           if (out != null)
 238           {
 239             out.flush();
 240             out.close();
 241           }
 242         }
 243       }
 244     }
 245
 246   }
 247
 248   public static String getURLContentAsString(String url)
 249           throws OutOfMemoryError
 250   {
 251     StringBuilder responseStrBuilder = null;
 252     InputStream is = null;
 253     try
 254     {
 255       URL resourceUrl = new URL(url);
 256       is = new BufferedInputStream(resourceUrl.openStream());
 257       BufferedReader br = new BufferedReader(new InputStreamReader(is));
 258       responseStrBuilder = new StringBuilder();
 259       String lineContent;
 260
 261       while ((lineContent = br.readLine()) != null)
 262       {
 263         responseStrBuilder.append(lineContent).append("\n");
 264       }
 265     } catch (OutOfMemoryError er)
 266     {
 267       er.printStackTrace();
 268     } catch (Exception ex)
 269     {
 270       ex.printStackTrace();
 271     } finally
 272     {
 273       if (is != null)
 274       {
 275         try
 276         {
 277           is.close();
 278         } catch (IOException e)
 279         {
 280           e.printStackTrace();
 281         }
 282       }
 283     }
 284     return responseStrBuilder == null ? null : responseStrBuilder
 285             .toString();
 286   }
 287
 288   public static File getCurrentBJSTemplateFile()
 289   {
 290     return currentBJSTemplateFile;
 291   }
 292
 293   public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
 294   {
 295     BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
 296   }
 297
 298   public static TreeMap<String, File> getBioJsMSAVersions()
 299   {
 300     return bioJsMSAVersions;
 301   }
 302
 303   public static void setBioJsMSAVersions(
 304           TreeMap<String, File> bioJsMSAVersions)
 305   {
 306     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
 307   }
 308
 309 }