JAL-1641 updated json schema to make it more generic in order to accomodate more...

[jalview.git] / src / jalview / io / BioJsHTMLOutput.java

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 9c15991..ff55400 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,15 +1,18 @@
 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.json.binding.v1.BioJSReleasePojo;
+import jalview.json.binding.v1.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;
@@ -17,10 +20,6 @@ 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
 {
@@ -33,29 +32,19 @@ public class BioJsHTMLOutput
   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 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_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/tcofoegbu/bjs-template/master/package.json");
 
   public BioJsHTMLOutput(AlignmentPanel ap,
           FeatureRenderer fr1)
   {
-
     if (ap != null)
     {
-
       this.av = ap.av;
       av.setFeatureRenderer(new FeatureRenderer(ap));
     }
-
   }
 
   public void exportJalviewAlignmentAsBioJsHtmlFile()
@@ -157,7 +146,7 @@ public class BioJsHTMLOutput
     return sb.toString();
   }
 
-  public TreeMap<String, File> updateBioJSVersionsInfo(String dirName)
+  public void refreshBioJSVersionsInfo(String dirName)
           throws URISyntaxException
   {
     URL url = getClass().getResource(dirName);
@@ -188,54 +177,113 @@ public class BioJsHTMLOutput
     {
       setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
     }
-    return versionFileMap;
+    setBioJsMSAVersions(versionFileMap);
   }
 
   public void updateBioJS()
   {
-    TreeMap<String, File> versionLists = null;
     try
     {
-      // downlaodNewBioJsTemplates(BJS_TEMPLATES_LOCAL_DIRECTORY);
-      versionLists = updateBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
-      setBioJsMSAVersions(versionLists);
+      String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
+      BioJSRepositoryPojo release = new BioJSRepositoryPojo(gitRepoPkgJson);
+      syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+      refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
     } catch (URISyntaxException e)
     {
       e.printStackTrace();
     }
   }
 
-  public void downlaodNewBioJsTemplates(String localDirectory)
+
+  public void syncUpdates(String localDir, BioJSRepositoryPojo repo)
+          throws URISyntaxException
   {
-    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 file = null;
+      URL url = getClass().getResource(
+              BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+      if (url == null)
+      {
+        String path = getClass().getResource(BJS_TEMPLATES_LOCAL_DIRECTORY)
+                .getPath();
+        System.out.println("------> " + path);
+        file = new File(path + releaseFile);
+      }
+      else
+      {
+        file = new File(url.toURI());
+      }
+
+      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
         {
-          String localFileName = BJS_TEMPLATES_LOCAL_DIRECTORY
-                  + fFile.getName();
-          String remoteFileName = fFile.getName();
-          FtpClient.downloadFile(client, remoteFileName, localFileName);
+          if (out != null)
+          {
+            out.flush();
+            out.close();
+          }
         }
-      } catch (IOException e)
-      {
-        e.printStackTrace();
       }
     }
+
   }
 
-  // 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 +306,4 @@ public class BioJsHTMLOutput
     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
   }
 
-
 }