Author: paperwing Date: 2012-08-03 16:02:32 -0700 (Fri, 03 Aug 2012) New Revision: 30099
Modified: core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/App.java core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebApp.java core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallFromStorePanel.java Log: refs #1272 Download site combo box keeps track of entered URLs until Cytoscape exits, can now switch between the 2 current app store sites: http://apps3.nrnb.org/ and http://apps.cytoscape.org, though they have identical app databases. Added method to compute SHA-512 digest for vertification before install and update, started method to check a given app store url for app updates. Modified: core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/App.java =================================================================== --- core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/App.java 2012-08-03 22:54:29 UTC (rev 30098) +++ core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/App.java 2012-08-03 23:02:32 UTC (rev 30099) @@ -72,6 +72,11 @@ */ private boolean officialNameObtained; + /** + * The SHA-512 checksum of the app file, in format sha512:0a516c.. + */ + private String sha512Checksum; + private AppStatus status; /** @@ -551,6 +556,10 @@ return compatibleVersions; } + public String getSha512Checksum() { + return sha512Checksum; + } + public URL getAppStoreUrl() { return appStoreUrl; } @@ -603,6 +612,10 @@ this.compatibleVersions = compatibleVersions; } + public void setSha512Checksum(String sha512Checksum) { + this.sha512Checksum = sha512Checksum; + } + public void setAppStoreUrl(URL appStoreURL) { this.appStoreUrl = appStoreURL; } Modified: core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java =================================================================== --- core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java 2012-08-03 22:54:29 UTC (rev 30098) +++ core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java 2012-08-03 23:02:32 UTC (rev 30099) @@ -2,7 +2,14 @@ import java.io.File; import java.io.FileFilter; +import java.io.FileInputStream; +import java.io.FileNotFoundException; import java.io.IOException; +import java.io.InputStream; +import java.nio.ByteBuffer; +import java.security.DigestInputStream; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; import java.util.Collection; import java.util.HashSet; import java.util.Set; @@ -520,6 +527,12 @@ public void installApp(App app) throws AppInstallException { try { + System.out.println(getChecksum(app.getAppFile())); + } catch (ChecksumException e) { + System.out.println(e.getMessage()); + } + + try { app.moveAppFile(this, new File(getInstalledAppsPath())); } catch (IOException e) { throw new AppInstallException("Unable to move app file, " + e.getMessage()); @@ -883,14 +896,67 @@ appListeners.add(appListener); } - public void removeAppListener(AppsChangedListener appListener) { + public void removeAppListener(AppsChangedListener appListener) { appListeners.remove(appListener); } + public class ChecksumException extends Exception { + private static final long serialVersionUID = 7022699404764909882L; + + public ChecksumException(String text) { + super(text); + } + } + /** - * Install apps from the local storage directory containing previously installed apps. + * Obtain the SHA-512 checksum of a file, in the following format: sha512:3c1c.. + * @param file The file to find the checksum + * @return The SHA-512 checksum, in format: sha512:e1.. + * @throws ChecksumException If unable to obtain SHA-512 algorithm implementation, + * file does not exist, or IO error while reading */ - public void installAppsFromDirectory() { - installAppsInDirectory(new File(getInstalledAppsPath()), false); + public String getChecksum(File file) throws ChecksumException { + MessageDigest messageDigest; + + try { + messageDigest = MessageDigest.getInstance("SHA-512"); + } catch (NoSuchAlgorithmException e) { + throw new ChecksumException("Unable to obtain SHA-512 algorithm implementation"); + } + + InputStream inputStream; + try { + inputStream = new FileInputStream(file); + } catch (FileNotFoundException e) { + throw new ChecksumException("File " + file.getAbsolutePath() + " does not exist."); + } + + try { + inputStream = new DigestInputStream(inputStream, messageDigest); + + byte[] byteBuffer = new byte[128]; + + while (inputStream.available() != 0) { + inputStream.read(byteBuffer); + } + } catch (IOException e) { + throw new ChecksumException("Error reading from file " + file + ", " + e.getMessage()); + } finally { + try { + inputStream.close(); + } catch (IOException e) { + logger.warn("Failed to close input stream on file " + file.getAbsolutePath() + ", " + e.getMessage()); + } + } + + byte[] digest = messageDigest.digest(); + + String result = ""; + for (int i = 0; i < digest.length; i++) { + // Convert each byte to a 2-digit hex number, adding 0x100 to obtain the 0 if the byte is 0E + result += Integer.toString((digest[i] & 0xff) + 0x100, 16).substring(1); + } + + return "sha512:" + result; } } Modified: core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebApp.java =================================================================== --- core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebApp.java 2012-08-03 22:54:29 UTC (rev 30098) +++ core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebApp.java 2012-08-03 23:02:32 UTC (rev 30099) @@ -56,6 +56,7 @@ private String releaseDate; private String releaseVersion; private String compatibleCytoscapeVersions; + private String sha512Checksum; @Override public int compareTo(Release other) { @@ -78,6 +79,9 @@ return compatibleCytoscapeVersions; } + public String getSha512Checksum() { + return sha512Checksum; + } public void setRelativeUrl(String relativeUrl) { this.relativeUrl = relativeUrl; @@ -94,6 +98,10 @@ public void setCompatibleCytoscapeVersions(String compatibleCytoscapeVersions) { this.compatibleCytoscapeVersions = compatibleCytoscapeVersions; } + + public void setSha512Checksum(String checksum) { + this.sha512Checksum = checksum; + } } Modified: core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java =================================================================== --- core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java 2012-08-03 22:54:29 UTC (rev 30098) +++ core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/net/WebQuerier.java 2012-08-03 23:02:32 UTC (rev 30099) @@ -21,6 +21,7 @@ import org.apache.commons.io.IOUtils; import org.cytoscape.app.internal.exception.AppDownloadException; +import org.cytoscape.app.internal.manager.App; import org.cytoscape.app.internal.manager.AppManager; import org.cytoscape.app.internal.net.WebQuerier.AppTag; import org.cytoscape.app.internal.util.DebugHelper; @@ -61,7 +62,7 @@ // private Map<String, AppTag> appTags; /** - * A reference to the result obtained by the last successful query for all available apps + * A reference to the result obtained by the last successful query for all available apps * to this app store URL. */ private Map<String, Set<WebApp>> appsByUrl; @@ -192,7 +193,7 @@ return DEFAULT_APP_STORE_URL; } - public String getCurrentAppStoreUrl(String url) { + public String getCurrentAppStoreUrl() { return currentAppStoreUrl; } @@ -259,7 +260,7 @@ String jsonResult = null; try { // Obtain information about the app from the website - jsonResult = query(DEFAULT_APP_STORE_URL + "backend/all_apps"); + jsonResult = query(currentAppStoreUrl + "backend/all_apps"); // Parse the JSON result JSONArray jsonArray = new JSONArray(jsonResult); @@ -331,9 +332,10 @@ WebApp.Release release = new WebApp.Release(); - release.setRelativeUrl(jsonRelease.get("release_download_url").toString()); - release.setReleaseDate(jsonRelease.get("created_iso").toString()); - release.setReleaseVersion(jsonRelease.get("version").toString()); + release.setRelativeUrl(jsonRelease.optString("release_download_url")); + release.setReleaseDate(jsonRelease.optString("created_iso")); + release.setReleaseVersion(jsonRelease.optString("version")); + release.setSha512Checksum(jsonRelease.optString("hexchecksum")); keyName = "works_with"; if (jsonRelease.has(keyName)) { @@ -466,7 +468,7 @@ URL downloadUrl = null; try { - downloadUrl = new URL(DEFAULT_APP_STORE_URL + releaseToDownload.getRelativeUrl()); + downloadUrl = new URL(currentAppStoreUrl + releaseToDownload.getRelativeUrl()); } catch (MalformedURLException e) { throw new AppDownloadException("Unable to obtain URL for version " + version + " of the release for " + webApp.getFullName()); @@ -524,11 +526,30 @@ return compatibleReleases; } - public Set<WebApp> getAppsByTag(String tagName) { // Query for apps (which includes tag information) if not done so Set<WebApp> webApps = getAllApps(); return appsByTagNameByUrl.get(currentAppStoreUrl).get(tagName); } + + public Set<Update> checkForUpdates(Set<App> apps) { + Set<Update> updates = new HashSet<Update>(); + + for (App app : apps) { + + } + + return updates; + } + + private Update checkForUpdate(App app, String url) { + Set<WebApp> urlApps = appsByUrl.get(url); + + if (urlApps != null) { + + } + + return null; + } } Modified: core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallFromStorePanel.java =================================================================== --- core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallFromStorePanel.java 2012-08-03 22:54:29 UTC (rev 30098) +++ core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/ui/InstallFromStorePanel.java 2012-08-03 23:02:32 UTC (rev 30099) @@ -4,6 +4,9 @@ import java.awt.Container; import java.awt.Desktop; import java.awt.Font; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; import java.io.File; import java.io.IOException; import java.net.URISyntaxException; @@ -15,6 +18,8 @@ import java.util.List; import java.util.Set; +import javax.swing.ComboBoxEditor; +import javax.swing.DefaultComboBoxModel; import javax.swing.JFileChooser; import javax.swing.JTree; import javax.swing.SwingUtilities; @@ -106,15 +111,20 @@ setupTextFieldListener(); - taskManager.execute(new TaskIterator(new Task() { + queryForApps(); + } + + // Queries the currently set app store url for available apps. + private void queryForApps() { + taskManager.execute(new TaskIterator(new Task() { // Obtain information for all available apps, then append tag information @Override public void run(TaskMonitor taskMonitor) throws Exception { - taskMonitor.setTitle("Obtaining Apps from App Store"); - WebQuerier webQuerier = appManager.getWebQuerier(); + taskMonitor.setTitle("Obtaining apps from: " + webQuerier.getCurrentAppStoreUrl()); + taskMonitor.setStatusMessage("Getting available apps"); Set<WebApp> availableApps = webQuerier.getAllApps(); @@ -233,7 +243,22 @@ downloadSiteLabel.setText("Download Site:"); downloadSiteComboBox.setEditable(true); - downloadSiteComboBox.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "http://apps3.nrnb.org/"; })); + downloadSiteComboBox.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "http://apps3.nrnb.org/";, "http://apps.cytoscape.org/"; })); + downloadSiteComboBox.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(java.awt.event.ItemEvent evt) { + downloadSiteComboBoxItemStateChanged(evt); + } + }); + downloadSiteComboBox.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(java.awt.event.ActionEvent evt) { + downloadSiteComboBoxActionPerformed(evt); + } + }); + downloadSiteComboBox.addKeyListener(new java.awt.event.KeyAdapter() { + public void keyPressed(java.awt.event.KeyEvent evt) { + downloadSiteComboBoxKeyPressed(evt); + } + }); closeButton.setText("Close"); closeButton.addActionListener(new java.awt.event.ActionListener() { @@ -293,6 +318,57 @@ .addContainerGap()) ); + // Add a key listener to the download site combo box to listen for the enter key event + final WebQuerier webQuerier = this.appManager.getWebQuerier(); + + downloadSiteComboBox.getEditor().getEditorComponent().addKeyListener(new KeyAdapter() { + + @Override + public void keyPressed(KeyEvent e) { + final ComboBoxEditor editor = downloadSiteComboBox.getEditor(); + final Object selectedValue = editor.getItem(); + + if (e.isActionKey() || e.getKeyCode() == KeyEvent.VK_ENTER) { + + if (downloadSiteComboBox.getModel() instanceof DefaultComboBoxModel + && selectedValue != null) { + final DefaultComboBoxModel comboBoxModel = (DefaultComboBoxModel) downloadSiteComboBox.getModel(); + + SwingUtilities.invokeLater(new Runnable() { + + @Override + public void run() { + boolean selectedAlreadyInList = false; + + for (int i = 0; i < comboBoxModel.getSize(); i++) { + Object listElement = comboBoxModel.getElementAt(i); + + if (listElement.equals(selectedValue)) { + selectedAlreadyInList = true; + + break; + } + } + + if (!selectedAlreadyInList) { + comboBoxModel.insertElementAt(selectedValue, 1); + + editor.setItem(selectedValue); + } + } + + }); + } + + if (webQuerier.getCurrentAppStoreUrl() != selectedValue.toString()) { + webQuerier.setCurrentAppStoreUrl(selectedValue.toString()); + + queryForApps(); + } + } + } + }); + // Make the JTextPane render HTML using the default UI font Font font = UIManager.getFont("Label.font"); String bodyRule = "body { font-family: " + font.getFamily() + "; " + @@ -623,4 +699,57 @@ private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) { ((javax.swing.JDialog)InstallFromStorePanel.this.parent).dispose(); } + + private void downloadSiteComboBoxItemStateChanged(java.awt.event.ItemEvent evt) { + } + + private void downloadSiteComboBoxActionPerformed(java.awt.event.ActionEvent evt) { + + final Object selected = downloadSiteComboBox.getSelectedItem(); + + if (downloadSiteComboBox.getModel() instanceof DefaultComboBoxModel + && selected != null) { + final DefaultComboBoxModel comboBoxModel = (DefaultComboBoxModel) downloadSiteComboBox.getModel(); + + SwingUtilities.invokeLater(new Runnable() { + + @Override + public void run() { + boolean selectedAlreadyInList = false; + + for (int i = 0; i < comboBoxModel.getSize(); i++) { + Object listElement = comboBoxModel.getElementAt(i); + + if (listElement.equals(selected)) { + selectedAlreadyInList = true; + + if (i > 0) { + // comboBoxModel.removeElementAt(i); + // comboBoxModel.insertElementAt(listElement, 1); + } + + break; + } + } + + if (!selectedAlreadyInList) { + comboBoxModel.insertElementAt(selected, 1); + } + } + + }); + + if (appManager.getWebQuerier().getCurrentAppStoreUrl() != selected.toString()) { + appManager.getWebQuerier().setCurrentAppStoreUrl(selected.toString()); + + queryForApps(); + } + } + + + + } + + private void downloadSiteComboBoxKeyPressed(java.awt.event.KeyEvent evt) { + } } -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
