X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=c88d8ebe4252a9a8079f5f2137adb0e8178f1491;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=6869292e97a02345e7d07b42a99ceb8f8d187200;hpb=9e5effcac65476958e619298a1a939254f77bc4b;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 6869292..c88d8eb 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,111 +1,279 @@
+/*
+ * 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 static java.nio.file.Files.readAllBytes;
-import static java.nio.file.Paths.get;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
+import jalview.bin.Cache;
 import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.json.binding.v1.BioJsAlignmentPojo;
-import jalview.json.binding.v1.BioJsSeqPojo;
+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;
+import java.net.URL;
+import java.util.Objects;
+import java.util.TreeMap;
 
-import org.jsoup.Jsoup;
-import org.jsoup.nodes.Document;
-import org.jsoup.nodes.Element;
+public class BioJsHTMLOutput extends HTMLOutput
+{
+  private static File currentBJSTemplateFile;
 
-import com.json.JSONException;
-import com.json.JSONObject;
+  private static TreeMap<String, File> bioJsMSAVersions;
 
-public class BioJsHTMLOutput
-{
-  private AlignViewport av;
-  private FeatureRenderer fr;
+  public static final String DEFAULT_DIR = System.getProperty("user.home")
+          + File.separatorChar + ".biojs_templates" + File.separatorChar;
+
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
+          .getDefault("biojs_template_directory", DEFAULT_DIR);
+
+  public static final String BJS_TEMPLATE_GIT_REPO = Cache.getDefault(
+          "biojs_template_git_repo",
+          "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
+
+  public BioJsHTMLOutput(AlignmentPanel ap)
+  {
+    super(ap, "BioJS MSA");
+  }
+
+  public static void refreshVersionInfo(String dirName)
+          throws URISyntaxException
+  {
+    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>();
+
+    for (File file : directory.listFiles())
+    {
+      if (file.isFile())
+      {
+        String fileName = file.getName().substring(0,
+                file.getName().lastIndexOf("."));
+        String fileMeta[] = fileName.split("_");
+        if (fileMeta.length > 2)
+        {
+          setCurrentBJSTemplateFile(file);
+          versionFileMap.put(fileMeta[2], file);
+        }
+        else if (fileMeta.length > 1)
+        {
+          versionFileMap.put(fileMeta[1], file);
+        }
+      }
+    }
+    if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
+    {
+      setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
+    }
+    setBioJsMSAVersions(versionFileMap);
+  }
 
-  public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
-          FeatureRenderer fr1)
+  public static void updateBioJS()
   {
-    this.av = ap.av;
+    Thread updateThread = new Thread()
+    {
+      @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();
 
-    this.fr = new FeatureRenderer(ap);
-    fr.transferSettings(fr1);
-    exportAsBioJsHtml();
   }
 
-  private void exportAsBioJsHtml()
+  public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
+    for (BioJSReleasePojo bjsRelease : repo.getReleases())
+    {
+      String releaseUrl = bjsRelease.getUrl();
+      String releaseVersion = bjsRelease.getVersion();
+      String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
+      if (releaseVersion.equals(repo.getLatestReleaseVersion()))
+      {
+        releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
+      }
+
+      File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
+      if (!biojsDirectory.exists())
+      {
+        if (!biojsDirectory.mkdirs())
+        {
+          System.out.println("Couldn't create local directory : "
+                  + BJS_TEMPLATES_LOCAL_DIRECTORY);
+          return;
+        }
+      }
+
+      File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+      if (!file.exists())
+      {
+
+        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 String getURLContentAsString(String url)
+          throws OutOfMemoryError
+  {
+    StringBuilder responseStrBuilder = null;
+    InputStream is = null;
     try
     {
-      JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
-      int fileChooserOpt = jvFileChooser.showSaveDialog(null);
-      if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
+      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)
       {
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
-                .getSelectedFile().getParent());
-        String selectedFile = jvFileChooser.getSelectedFile().getPath();
-        String generartedBioJs = generateBioJsAlignmentData(av
-                .getAlignment());
-        PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-                selectedFile));
-        out.print(generartedBioJs);
-        out.close();
-        jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
+        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();
   }
 
-  private JalviewFileChooser getJalviewFileChooserOption()
+  public static File getCurrentBJSTemplateFile()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
-
-    chooser.setFileView(new JalviewFileView());
-    // TODO uncomment when supported by MassageManager
-    // chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html"));
-    chooser.setDialogTitle("save as BioJs HTML");
-    chooser.setToolTipText(MessageManager.getString("action.save"));
-
-    return chooser;
+    return currentBJSTemplateFile;
   }
 
-  private String generateBioJsAlignmentData(AlignmentI alignment)
-          throws IOException, JSONException
+  public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
   {
-    BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
+    BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
+  }
 
-    int count = 0;
-    for (SequenceI seq : alignment.getSequences())
-    {
-      bjsAlignment.getSeqs().add(
-              new BioJsSeqPojo(String.valueOf(++count), seq.getName(), seq
-                      .getSequenceAsString()));
-    }
+  public static TreeMap<String, File> getBioJsMSAVersions()
+  {
+    return bioJsMSAVersions;
+  }
 
-    String seqs = new JSONObject(bjsAlignment).getString("seqs");
-    String bioJSTemplate = new String(
-            readAllBytes(get("resources/templates/BioJSTemplate.txt")));
+  public static void setBioJsMSAVersions(
+          TreeMap<String, File> bioJsMSAVersions)
+  {
+    BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
+  }
 
-    return bioJSTemplate.replaceAll("#sequenceData#", seqs);
+  @Override
+  public boolean isEmbedData()
+  {
+    return true;
   }
 
-  public static void main(String[] args) throws IOException
+  @Override
+  public boolean isLaunchInBrowserAfterExport()
   {
-    Document doc = Jsoup.parse(new String(
-            readAllBytes(get("resources/templates/BioJSTemplate.txt"))));
+    return true;
+  }
+
+  @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", getDescription()));
+      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", getDescription()));
+      e.printStackTrace();
+    }
 
-    Element content = doc.getElementById("seqData");
-    System.out.println(content.val());
   }
 
 }
-