X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=c88d8ebe4252a9a8079f5f2137adb0e8178f1491;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=2001338ce0bc244cf88df9d18b4cd602df2b5ced;hpb=b13f521553582ef2fbfd7815ae25e23284babdea;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 2001338..c88d8eb 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,221 +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 jalview.api.FeaturesDisplayedI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
+import jalview.bin.Cache;
 import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.BioJsAlignmentPojo;
-import jalview.json.binding.v1.BioJsFeaturePojo;
-import jalview.json.binding.v1.BioJsSeqPojo;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.gui.OOMWarning;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
 
-import java.awt.Color;
+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.ArrayList;
+import java.util.Objects;
+import java.util.TreeMap;
 
-import com.json.JSONException;
-
-public class BioJsHTMLOutput
+public class BioJsHTMLOutput extends HTMLOutput
 {
-  private AlignViewport av;
-
-  private jalview.api.FeatureRenderer fr;
+  private static File currentBJSTemplateFile;
 
-  private String globalColorScheme;
+  private static TreeMap<String, File> bioJsMSAVersions;
 
-  private FeaturesDisplayedI displayedFeatures;
+  public static final String DEFAULT_DIR = System.getProperty("user.home")
+          + File.separatorChar + ".biojs_templates" + File.separatorChar;
 
-  private String jalviewVersion;
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
+          .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+  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,
-          FeatureRenderer fr1)
+  public BioJsHTMLOutput(AlignmentPanel ap)
   {
-
-    jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
-    webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
-            "www.jalview.org", "http://www.jalview.org")
-            + "/services/launchApp";
-    if (ap != null)
-    {
-      this.av = ap.av;
-      this.globalColorScheme = ColourSchemeProperty.getColourName(av
-              .getGlobalColourScheme());
-      this.fr = ap.cloneFeatureRenderer();
-      displayedFeatures = av.getFeaturesDisplayed();
-    }
+    super(ap, "BioJS MSA");
   }
 
-  private void exportJalviewAlignmentAsBioJsHtmlFile()
+  public static void refreshVersionInfo(String dirName)
+          throws URISyntaxException
   {
-    try
-    {
-      String outputFile = getOutputFile();
-      String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
-              .getAlignment());
-      String bioJSTemplateString = getBioJsTemplateAsString(this);
-      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
-              .toString();
+    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>();
 
-      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)
+    for (File file : directory.listFiles())
     {
-      // do noting if no file was selected
-    } catch (Exception e)
+      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)
     {
-      e.printStackTrace();
+      setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
     }
+    setBioJsMSAVersions(versionFileMap);
   }
 
-  public String getOutputFile() throws NoFileSelectedException
+  public static void updateBioJS()
   {
-    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)
+    Thread updateThread = new Thread()
     {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
-              .getSelectedFile().getParent());
-      selectedFile = jvFileChooser.getSelectedFile().getPath();
-    }
-    else
-    {
-      throw new NoFileSelectedException("No file was selected.");
-    }
+      @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();
 
-    return selectedFile;
   }
 
-  public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
-          throws IOException, JSONException
+  public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
-    BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
+    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";
+      }
 
-    bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
-    bjsAlignment.setJalviewVersion(jalviewVersion);
-    bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
+      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;
+        }
+      }
 
-    int count = 0;
-    for (SequenceI seq : alignment.getSequences())
-    {
-      StringBuilder name = new StringBuilder();
-      name.append(seq.getName()).append("/").append(seq.getStart())
-              .append("-").append(seq.getEnd());
-
-      BioJsSeqPojo seqPojo = new BioJsSeqPojo();
-      seqPojo.setId(String.valueOf(++count));
-      seqPojo.setEnd(seq.getEnd());
-      seqPojo.setStart(seq.getStart());
-      seqPojo.setName(name.toString());
-      seqPojo.setSeq(seq.getSequenceAsString());
-
-      SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
-      if (seqFeatures != null)
+      File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+      if (!file.exists())
       {
-        ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
-        for (SequenceFeature sf : seqFeatures)
+
+        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 (displayedFeatures != null
-                  && displayedFeatures.isVisible(sf.getType()))
+          if (out != null)
           {
-
-            // TODO: translate graduated/complex colourschemes to biojs model
-            String featureColour = jalview.util.Format.getHexString(fr
-                    .findFeatureColour(Color.white, seq,
-                            seq.findIndex(sf.getBegin())));
-            BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
-            bjsFeature.setFillColor(featureColour);
-            bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
-            bjsFeature.setXend(seq.findIndex(sf.getEnd()));
-            bjsFeature.setText(sf.getType());
-            bjsSeqFeatures.add(bjsFeature);
+            out.flush();
+            out.close();
           }
         }
-        seqPojo.setFeatures(bjsSeqFeatures);
       }
-      bjsAlignment.getSeqs().add(seqPojo);
     }
 
-    return new com.json.JSONObject(bjsAlignment).toString()
-            .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
   }
 
-  public static String getBioJsTemplateAsString(Object currentObj)
-          throws IOException
+  public static String getURLContentAsString(String url)
+          throws OutOfMemoryError
   {
-    InputStreamReader isReader = null;
-    BufferedReader buffReader = null;
-    StringBuilder sb = new StringBuilder();
-    URL url = currentObj.getClass().getResource(
-            "/templates/BioJSTemplate.txt");
-    if (url != null)
+    StringBuilder responseStrBuilder = null;
+    InputStream is = null;
+    try
     {
-      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);
-        }
+      URL resourceUrl = new URL(url);
+      is = new BufferedInputStream(resourceUrl.openStream());
+      BufferedReader br = new BufferedReader(new InputStreamReader(is));
+      responseStrBuilder = new StringBuilder();
+      String lineContent;
 
-      } catch (Exception ex)
+      while ((lineContent = br.readLine()) != null)
       {
-        ex.printStackTrace();
-      } finally
+        responseStrBuilder.append(lineContent).append("\n");
+      }
+    } catch (OutOfMemoryError er)
+    {
+      er.printStackTrace();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    } finally
+    {
+      if (is != null)
       {
-        if (isReader != null)
+        try
         {
-          isReader.close();
-        }
-
-        if (buffReader != null)
+          is.close();
+        } catch (IOException e)
         {
-          buffReader.close();
+          e.printStackTrace();
         }
       }
     }
-    return sb.toString();
+    return responseStrBuilder == null ? null
+            : responseStrBuilder.toString();
+  }
+
+  public static File getCurrentBJSTemplateFile()
+  {
+    return currentBJSTemplateFile;
+  }
+
+  public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
+  {
+    BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
+  }
+
+  public static TreeMap<String, File> getBioJsMSAVersions()
+  {
+    return bioJsMSAVersions;
   }
 
-  public String getGlobalColorScheme()
+  public static void setBioJsMSAVersions(
+          TreeMap<String, File> bioJsMSAVersions)
   {
-    return globalColorScheme;
+    BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
   }
 
-  public void setGlobalColorScheme(String globalColorScheme)
+  @Override
+  public boolean isEmbedData()
   {
-    this.globalColorScheme = globalColorScheme;
+    return true;
+  }
+
+  @Override
+  public boolean isLaunchInBrowserAfterExport()
+  {
+    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();
+    }
+
   }
 
 }