+/*
+ * 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.bin.Cache;
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;
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 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 BioJsHTMLOutput(AlignmentPanel ap,
- FeatureRenderer fr1)
- {
-
- if (ap != null)
- {
-
- this.av = ap.av;
- av.setFeatureRenderer(new FeatureRenderer(ap));
- }
-
- }
-
- public void exportJalviewAlignmentAsBioJsHtmlFile()
- {
- 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)
- {
- // do noting if no file was selected
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
-
- 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());
+ public static final String DEFAULT_DIR = System.getProperty("user.home")
+ + File.separatorChar + ".biojs_templates" + File.separatorChar;
- // 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;
- }
+ 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 static String getBioJsTemplateAsString()
- throws IOException
+ public BioJsHTMLOutput(AlignmentPanel ap)
{
- 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();
+ super(ap, "BioJS MSA");
}
- 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>();
{
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()))
+ {
+ releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
+ }
+
+ File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
+ if (!biojsDirectory.exists())
{
- client.setFileType(FTP.BINARY_FILE_TYPE);
- for (FTPFile fFile : client.listFiles())
+ 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()
{
BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
}
+ @Override
+ public boolean isEmbedData()
+ {
+ 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();
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff