+/*
+ * 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;
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()
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));
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();
}
}
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);
}
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;
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>();
{
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()
{
BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
}
-
}
git://source.jalview.org / jalview.git / blobdiff