X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=9454cae12b65f3adba5f5fead6759bd7e2430758;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=9c159911ea93920f05a887ae6804bcb6875ae8ac;hpb=64fb69927bb37d8773a75b684a3e7ab3f0c5c212;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 9c15991..9454cae 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,15 +1,39 @@
+/*
+ * 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.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
-import jalview.ftp.FtpClient;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
+import jalview.gui.IProgressIndicator;
+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;
@@ -17,45 +41,42 @@ 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
 {
-  private AlignViewport av;
+  private AlignmentViewPanel ap;
 
-  private static File currentBJSTemplateFile;
+  private long pSessionId;
 
-  private static TreeMap<String, File> bioJsMSAVersions;
+  private IProgressIndicator pIndicator;
 
-  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
-          .getDefault("biojs_template_directory", "/biojs_templates/");
+  private boolean headless;
 
-  public static final String BJS_FTP_USER = jalview.bin.Cache.getDefault(
-          "biojs_ftp_user", "test");
+  private static File currentBJSTemplateFile;
 
-  public static final String BJS_FTP_PWD = jalview.bin.Cache.getDefault(
-          "biojs_ftp_pwd", "test");
+  private static TreeMap<String, File> bioJsMSAVersions;
 
-  public static final String BJS_FTP_PORT = jalview.bin.Cache.getDefault(
-          "biojs_ftp_port", "22");
+  public static final String DEFAULT_DIR = System.getProperty("user.home")
+          + File.separatorChar + ".biojs_templates" + File.separatorChar;
 
-  public static final String BJS_FTP_SERVER = jalview.bin.Cache.getDefault(
-          "biojs_ftp_server", "localhost");
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+          .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  public BioJsHTMLOutput(AlignmentPanel ap,
-          FeatureRenderer fr1)
-  {
+  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(AlignmentViewPanel ap,
+          IProgressIndicator pIndicator)
+  {
     if (ap != null)
     {
-
-      this.av = ap.av;
-      av.setFeatureRenderer(new FeatureRenderer(ap));
+      this.ap = ap;
+      this.pSessionId = System.currentTimeMillis();
+      this.pIndicator = pIndicator;
+      this.headless = (System.getProperty("java.awt.headless") != null && System
+              .getProperty("java.awt.headless").equals("true"));
     }
-
   }
 
   public void exportJalviewAlignmentAsBioJsHtmlFile()
@@ -63,12 +84,58 @@ public class BioJsHTMLOutput
     try
     {
       String outputFile = getOutputFile();
-      String jalviewAlignmentJson = JSONFile.getJSONData(av);
+      // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      AlignExportSettingI exportSettings = new AlignExportSettingI()
+      {
+        @Override
+        public boolean isExportHiddenSequences()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportHiddenColumns()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportAnnotations()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportFeatures()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportGroups()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isCancelled()
+        {
+          return false;
+        }
+
+      };
+      AlignmentExportData exportData = jalview.gui.AlignFrame
+              .getAlignmentForExport(JSONFile.FILE_DESC,
+                      ap.getAlignViewport(), exportSettings);
+      String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+              .formatSequences(JSONFile.FILE_DESC, exportData
+                      .getAlignment(), exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(), ap
+                              .getAlignViewport().getColumnSelection());
+
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
-              .toString();
+              .replaceAll("#sequenceData#", bioJSON).toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
               outputFile));
@@ -76,11 +143,18 @@ public class BioJsHTMLOutput
       out.flush();
       out.close();
       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+      if (pIndicator != null && !headless)
+      {
+        pIndicator.setProgressBar(MessageManager.formatMessage(
+                "status.export_complete", "BioJS"), pSessionId);
+      }
     } catch (NoFileSelectedException ex)
     {
       // do noting if no file was selected
     } catch (Exception e)
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"), pSessionId);
       e.printStackTrace();
     }
   }
@@ -88,16 +162,21 @@ public class BioJsHTMLOutput
   public String getOutputFile() throws NoFileSelectedException
   {
     String selectedFile = null;
+    if (pIndicator != null && !headless)
+    {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "status.waiting_for_user_to_select_output_file", "HTML"),
+              pSessionId);
+    }
+
     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
+            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);
@@ -109,14 +188,15 @@ public class BioJsHTMLOutput
     }
     else
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "status.cancelled_image_export_operation", "BioJS"),
+              pSessionId);
       throw new NoFileSelectedException("No file was selected.");
     }
     return selectedFile;
   }
 
-
-  public static String getBioJsTemplateAsString()
-          throws IOException
+  public static String getBioJsTemplateAsString() throws IOException
   {
     InputStreamReader isReader = null;
     BufferedReader buffReader = null;
@@ -157,11 +237,10 @@ public class BioJsHTMLOutput
     return sb.toString();
   }
 
-  public TreeMap<String, File> updateBioJSVersionsInfo(String dirName)
+  public static void refreshBioJSVersionsInfo(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 +267,123 @@ 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);
+            refreshBioJSVersionsInfo(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 +406,4 @@ public class BioJsHTMLOutput
     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
   }
 
-
 }