X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=52ce845cb4a373c23a7e70221e5b5efcaf8b14f9;hb=6e0685c38078ddcf959db75d001f8c92b114c8ae;hp=9c159911ea93920f05a887ae6804bcb6875ae8ac;hpb=64fb69927bb37d8773a75b684a3e7ab3f0c5c212;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 9c15991..52ce845 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,15 +1,37 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.exceptions.NoFileSelectedException;
-import jalview.ftp.FtpClient;
-import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
+import jalview.gui.OOMWarning;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
 
+import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import java.net.URISyntaxException;
@@ -17,151 +39,59 @@ import java.net.URL;
 import java.util.Objects;
 import java.util.TreeMap;
 
-import org.apache.commons.net.ftp.FTP;
-import org.apache.commons.net.ftp.FTPClient;
-import org.apache.commons.net.ftp.FTPFile;
-
-
-public class BioJsHTMLOutput
+public class BioJsHTMLOutput extends HTMLOutput
 {
-  private AlignViewport av;
 
   private static File currentBJSTemplateFile;
 
   private static TreeMap<String, File> bioJsMSAVersions;
 
-  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
-          .getDefault("biojs_template_directory", "/biojs_templates/");
-
-  public static final String BJS_FTP_USER = jalview.bin.Cache.getDefault(
-          "biojs_ftp_user", "test");
+  public static final String DEFAULT_DIR = System.getProperty("user.home")
+          + File.separatorChar + ".biojs_templates" + File.separatorChar;
 
-  public static final String BJS_FTP_PWD = jalview.bin.Cache.getDefault(
-          "biojs_ftp_pwd", "test");
-
-  public static final String BJS_FTP_PORT = jalview.bin.Cache.getDefault(
-          "biojs_ftp_port", "22");
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+          .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  public static final String BJS_FTP_SERVER = jalview.bin.Cache.getDefault(
-          "biojs_ftp_server", "localhost");
+  public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
+          .getDefault("biojs_template_git_repo",
+                  "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
-  public BioJsHTMLOutput(AlignmentPanel ap,
-          FeatureRenderer fr1)
+  public BioJsHTMLOutput(AlignmentPanel ap)
   {
-
-    if (ap != null)
-    {
-
-      this.av = ap.av;
-      av.setFeatureRenderer(new FeatureRenderer(ap));
-    }
-
+    super(ap);
   }
 
-  public void exportJalviewAlignmentAsBioJsHtmlFile()
+  @Override
+  public void exportHTML(String outputFile)
   {
+    exportStarted();
     try
     {
-      String outputFile = getOutputFile();
-      String jalviewAlignmentJson = JSONFile.getJSONData(av);
-      String bioJSTemplateString = getBioJsTemplateAsString();
-      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
-              .toString();
-
-      PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-              outputFile));
-      out.print(generatedBioJsWithJalviewAlignmentAsJson);
-      out.flush();
-      out.close();
-      jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
-    } catch (NoFileSelectedException ex)
+      if (outputFile == null)
+      {
+        outputFile = getOutputFile();
+      }
+      generatedFile = new File(outputFile);
+    } catch (NoFileSelectedException e)
     {
-      // do noting if no file was selected
+      setProgressMessage(MessageManager.formatMessage(
+              "status.cancelled_image_export_operation", "BioJS MSA"));
+      return;
     } catch (Exception e)
     {
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", "BioJS MSA"));
       e.printStackTrace();
+      return;
     }
-  }
-
-  public String getOutputFile() throws NoFileSelectedException
-  {
-    String selectedFile = null;
-    JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
-    jvFileChooser.setFileView(new JalviewFileView());
-
-    // TODO uncomment when supported by MassageManager
-    jvFileChooser.setDialogTitle(MessageManager
-            .getString("label.save_as_biojs_html"));
-    jvFileChooser.setDialogTitle("save as BioJs HTML");
-    jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
-
-    int fileChooserOpt = jvFileChooser.showSaveDialog(null);
-    if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
-    {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
-              .getSelectedFile().getParent());
-      selectedFile = jvFileChooser.getSelectedFile().getPath();
-    }
-    else
-    {
-      throw new NoFileSelectedException("No file was selected.");
-    }
-    return selectedFile;
-  }
+    new Thread(this).start();
 
-
-  public static String getBioJsTemplateAsString()
-          throws IOException
-  {
-    InputStreamReader isReader = null;
-    BufferedReader buffReader = null;
-    StringBuilder sb = new StringBuilder();
-    Objects.requireNonNull(getCurrentBJSTemplateFile(),
-            "BioJsTemplate File not initialized!");
-    @SuppressWarnings("deprecation")
-    URL url = getCurrentBJSTemplateFile().toURL();
-    if (url != null)
-    {
-      try
-      {
-        isReader = new InputStreamReader(url.openStream());
-        buffReader = new BufferedReader(isReader);
-        String line;
-        String lineSeparator = System.getProperty("line.separator");
-        while ((line = buffReader.readLine()) != null)
-        {
-          sb.append(line).append(lineSeparator);
-        }
-
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      } finally
-      {
-        if (isReader != null)
-        {
-          isReader.close();
-        }
-
-        if (buffReader != null)
-        {
-          buffReader.close();
-        }
-      }
-    }
-    return sb.toString();
   }
 
-  public TreeMap<String, File> updateBioJSVersionsInfo(String dirName)
+  public static void refreshVersionInfo(String dirName)
           throws URISyntaxException
   {
-    URL url = getClass().getResource(dirName);
-    File directory = new File(url.toURI());
+    File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
     Objects.requireNonNull(dirName, "dirName MUST not be null!");
     Objects.requireNonNull(directory, "directory MUST not be null!");
     TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
@@ -188,54 +118,124 @@ public class BioJsHTMLOutput
     {
       setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
     }
-    return versionFileMap;
+    setBioJsMSAVersions(versionFileMap);
   }
 
-  public void updateBioJS()
+  public static void updateBioJS()
   {
-    TreeMap<String, File> versionLists = null;
-    try
+    Thread updateThread = new Thread()
     {
-      // downlaodNewBioJsTemplates(BJS_TEMPLATES_LOCAL_DIRECTORY);
-      versionLists = updateBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
-      setBioJsMSAVersions(versionLists);
-    } catch (URISyntaxException e)
-    {
-      e.printStackTrace();
-    }
+      @Override
+      public void run()
+      {
+        try
+        {
+          String gitRepoPkgJson = getURLContentAsString(
+                  BJS_TEMPLATE_GIT_REPO);
+          if (gitRepoPkgJson != null)
+          {
+            BioJSRepositoryPojo release = new BioJSRepositoryPojo(
+                    gitRepoPkgJson);
+            syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+            refreshVersionInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+          }
+        } catch (URISyntaxException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    };
+    updateThread.start();
+
   }
 
-  public void downlaodNewBioJsTemplates(String localDirectory)
+  public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
-    FTPClient client = FtpClient.getFtpClient(BJS_FTP_SERVER);
-    if (FtpClient.authenticateUser(client, BJS_FTP_USER, BJS_FTP_PWD))
+    for (BioJSReleasePojo bjsRelease : repo.getReleases())
     {
-      client.enterLocalPassiveMode();
-      try
+      String releaseUrl = bjsRelease.getUrl();
+      String releaseVersion = bjsRelease.getVersion();
+      String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
+      if (releaseVersion.equals(repo.getLatestReleaseVersion()))
       {
-        client.setFileType(FTP.BINARY_FILE_TYPE);
-        for (FTPFile fFile : client.listFiles())
+        releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
+      }
+
+      File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
+      if (!biojsDirectory.exists())
+      {
+        if (!biojsDirectory.mkdirs())
         {
-          String localFileName = BJS_TEMPLATES_LOCAL_DIRECTORY
-                  + fFile.getName();
-          String remoteFileName = fFile.getName();
-          FtpClient.downloadFile(client, remoteFileName, localFileName);
+          System.out.println("Couldn't create local directory : "
+                  + BJS_TEMPLATES_LOCAL_DIRECTORY);
+          return;
         }
-      } catch (IOException e)
+      }
+
+      File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+      if (!file.exists())
       {
-        e.printStackTrace();
+
+        PrintWriter out = null;
+        try
+        {
+          out = new java.io.PrintWriter(new java.io.FileWriter(file));
+          out.print(getURLContentAsString(releaseUrl));
+        } catch (IOException e)
+        {
+          e.printStackTrace();
+        } finally
+        {
+          if (out != null)
+          {
+            out.flush();
+            out.close();
+          }
+        }
       }
     }
+
   }
 
-  // public static void main(String[] args) throws IOException
-  // {
-  // Document doc = Jsoup.connect("http://howto.unixdev.net").get();
-  // for (Element file : doc.select("td.right td a"))
-  // {
-  // System.out.println(file.attr("href"));
-  // }
-  // }
+  public static String getURLContentAsString(String url)
+          throws OutOfMemoryError
+  {
+    StringBuilder responseStrBuilder = null;
+    InputStream is = null;
+    try
+    {
+      URL resourceUrl = new URL(url);
+      is = new BufferedInputStream(resourceUrl.openStream());
+      BufferedReader br = new BufferedReader(new InputStreamReader(is));
+      responseStrBuilder = new StringBuilder();
+      String lineContent;
+
+      while ((lineContent = br.readLine()) != null)
+      {
+        responseStrBuilder.append(lineContent).append("\n");
+      }
+    } catch (OutOfMemoryError er)
+    {
+      er.printStackTrace();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    } finally
+    {
+      if (is != null)
+      {
+        try
+        {
+          is.close();
+        } catch (IOException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+    return responseStrBuilder == null ? null
+            : responseStrBuilder.toString();
+  }
 
   public static File getCurrentBJSTemplateFile()
   {
@@ -258,5 +258,56 @@ public class BioJsHTMLOutput
     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
   }
 
+  @Override
+  public boolean isEmbedData()
+  {
+    return true;
+  }
+
+  @Override
+  public boolean isLaunchInBrowserAfterExport()
+  {
+    return true;
+  }
+
+  @Override
+  public File getExportedFile()
+  {
+    return generatedFile;
+  }
+
+  @Override
+  public void run()
+  {
+    try
+    {
+      String bioJSON = getBioJSONData();
+      String bioJSTemplateString = HTMLOutput
+              .readFileAsString(getCurrentBJSTemplateFile());
+      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
+              .replaceAll("#sequenceData#", bioJSON).toString();
+
+      PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(generatedFile));
+      out.print(generatedBioJsWithJalviewAlignmentAsJson);
+      out.flush();
+      out.close();
+      setProgressMessage(MessageManager
+              .formatMessage("status.export_complete", "BioJS"));
+      exportCompleted();
+
+    } catch (OutOfMemoryError err)
+    {
+      System.out.println("########################\n" + "OUT OF MEMORY "
+              + generatedFile + "\n" + "########################");
+      new OOMWarning("Creating Image for " + generatedFile, err);
+    } catch (Exception e)
+    {
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", "HTML"));
+      e.printStackTrace();
+    }
+
+  }
 
 }