Examples with Release org.cytoscape.app.internal.net.WebApp.Release used on opensource projects

Example 1 with Release

use of org.cytoscape.app.internal.net.WebApp.Release in project cytoscape-impl by cytoscape.

the class WebQuerier method downloadApp.

/**
 * Given the unique app name used by the app store, query the app store for the
 * download URL and download the app to the given directory.
 *
 * If a file with the same name exists in the directory, it is overwritten.
 *
 * @param appName The unique app name used by the app store
 * @param version The desired version, or <code>null</code> to obtain the latest release
 * @param directory The directory used to store the downloaded file
 * @param taskMonitor
 */
public File downloadApp(WebApp webApp, String version, File directory, DownloadStatus status) throws AppDownloadException {
    List<WebApp.Release> compatibleReleases = getCompatibleReleases(webApp);
    if (compatibleReleases.size() > 0) {
        WebApp.Release releaseToDownload = null;
        if (version != null) {
            for (WebApp.Release compatibleRelease : compatibleReleases) {
                // Check if the desired version is found in the list of available versions
                if (compatibleRelease.getReleaseVersion().matches("(^\\s*|.*,)\\s*" + version + "\\s*(\\s*$|,.*)")) {
                    releaseToDownload = compatibleRelease;
                }
            }
            if (releaseToDownload == null) {
                throw new AppDownloadException("No release with the requested version " + version + " was found for the requested app " + webApp.getFullName());
            }
        } else {
            releaseToDownload = compatibleReleases.get(compatibleReleases.size() - 1);
        }
        URL downloadUrl = null;
        try {
            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());
        }
        if (downloadUrl != null) {
            try {
                // Prepare to download
                URLConnection connection = streamUtil.getURLConnection(downloadUrl);
                InputStream inputStream = connection.getInputStream();
                long contentLength = connection.getContentLength();
                ReadableByteChannel readableByteChannel = Channels.newChannel(inputStream);
                File outputFile;
                try {
                    // Replace spaces with underscores
                    String outputFileBasename = webApp.getName().replaceAll("\\s", "_");
                    // Append version information
                    outputFileBasename += "-v" + releaseToDownload.getReleaseVersion();
                    // Strip disallowed characters
                    outputFileBasename = OUTPUT_FILENAME_DISALLOWED_CHARACTERS.matcher(outputFileBasename).replaceAll("");
                    // Append extension
                    outputFileBasename += ".jar";
                    // Output file has same name as app, but spaces and slashes are replaced with hyphens
                    outputFile = new File(directory.getCanonicalPath() + File.separator + outputFileBasename);
                    if (outputFile.exists()) {
                        outputFile.delete();
                    }
                    outputFile.createNewFile();
                    FileOutputStream fileOutputStream = new FileOutputStream(outputFile);
                    try {
                        FileChannel fileChannel = fileOutputStream.getChannel();
                        long currentDownloadPosition = 0;
                        long bytesTransferred;
                        TaskMonitor taskMonitor = status.getTaskMonitor();
                        do {
                            bytesTransferred = fileChannel.transferFrom(readableByteChannel, currentDownloadPosition, 1 << 14);
                            if (status.isCanceled()) {
                                outputFile.delete();
                                return null;
                            }
                            currentDownloadPosition += bytesTransferred;
                            if (contentLength > 0) {
                                double progress = (double) currentDownloadPosition / contentLength;
                                taskMonitor.setProgress(progress);
                            }
                        } while (bytesTransferred > 0);
                    } finally {
                        fileOutputStream.close();
                    }
                } finally {
                    readableByteChannel.close();
                }
                return outputFile;
            } catch (IOException e) {
                throw new AppDownloadException("Error while downloading app " + webApp.getFullName() + ", " + e.getMessage());
            }
        }
    } else {
        throw new AppDownloadException("No available releases were found for the app " + webApp.getFullName() + ".");
    }
    return null;
}

Example 2 with Release

use of org.cytoscape.app.internal.net.WebApp.Release in project cytoscape-impl by cytoscape.

the class WebQuerier method checkForUpdate.

private Update checkForUpdate(App app, String url, AppManager appManager) {
    Set<WebApp> urlApps = appsByUrl.get(url);
    if (urlApps != null) {
        // Look for an app with same name
        for (WebApp webApp : urlApps) {
            if (webApp.getName().equalsIgnoreCase(app.getAppName())) {
                WebApp.Release highestVersionRelease = null;
                for (WebApp.Release release : webApp.getReleases()) {
                    if (highestVersionRelease == null || compareVersions(highestVersionRelease.getReleaseVersion(), release.getReleaseVersion()) > 0) {
                        highestVersionRelease = release;
                    }
                }
                if (highestVersionRelease != null && compareVersions(highestVersionRelease.getReleaseVersion(), app.getVersion()) < 0) {
                    Update update = new Update();
                    update.setUpdateVersion(highestVersionRelease.getReleaseVersion());
                    update.setApp(app);
                    update.setWebApp(webApp);
                    update.setRelease(highestVersionRelease);
                    return update;
                }
            }
        }
    }
    return null;
}

Example 3 with Release

use of org.cytoscape.app.internal.net.WebApp.Release in project cytoscape-impl by cytoscape.

the class WebQuerier method findAppDescriptions.

public void findAppDescriptions(Set<App> apps) {
    if (appsByUrl.get(DEFAULT_APP_STORE_URL) == null) {
        return;
    }
    // Find the set of all available apps
    Set<WebApp> allWebApps = new HashSet<WebApp>(appsByUrl.get(DEFAULT_APP_STORE_URL).size());
    for (String url : appsByUrl.keySet()) {
        Set<WebApp> urlApps = appsByUrl.get(url);
        for (WebApp webApp : urlApps) {
            allWebApps.add(webApp);
        }
    }
    // Find set of all app releases
    Map<Release, WebApp> allReleases = new HashMap<Release, WebApp>(appsByUrl.get(DEFAULT_APP_STORE_URL).size());
    List<Release> appReleases = null;
    for (WebApp webApp : allWebApps) {
        appReleases = webApp.getReleases();
        for (Release appRelease : appReleases) {
            allReleases.put(appRelease, webApp);
        }
    }
    // Find matching app hashes
    for (Release release : allReleases.keySet()) {
        for (App app : apps) {
            String checksum = app.getSha512Checksum().toLowerCase();
            // in cases where multiple stores give the same hash.
            if (checksum.indexOf(release.getSha512Checksum().toLowerCase()) != -1 && app.getDescription() == null) {
                // WebQuerier obtains app information from app store because no description metadata is required
                // in the app zip file itself. This was to allow better App-Bundle interchangeability, not
                // imposing unneeded restrictions on OSGi bundles (from past discussion on mailing list, some time in 2012)
                // System.out.println("Found description: " + allReleases.get(release).getDescription());
                app.setDescription(allReleases.get(release).getDescription());
            }
        }
    }
}

Example 4 with Release

use of org.cytoscape.app.internal.net.WebApp.Release in project cytoscape-impl by cytoscape.

the class ResolveAppDependenciesTask method resolveAppDependencies.

private void resolveAppDependencies(App appToInstall) throws Exception {
    CyVersion version = appManager.getCyVersion();
    if (!appToInstall.isCompatible(version))
        throw new Exception("Unable to install " + appToInstall.getAppName() + ".\nIt is incompatible with this version of Cytoscape (" + version.getVersion() + ").");
    taskMonitor.setStatusMessage("Resolving dependencies for " + appToInstall.getAppName() + "...");
    for (App installedApp : appManager.getInstalledApps()) {
        if (installedApp.getAppName().equals(appToInstall.getAppName())) {
            appsToReplace.put(appToInstall, installedApp);
            break;
        }
    }
    dependencyStack.push(appToInstall.getAppName());
    if (appToInstall.getDependencies() != null)
        for (App.Dependency dep : appToInstall.getDependencies()) {
            if (dependencyStack.contains(dep.getName()))
                throw new Exception("Invalid circular dependency: " + dep.getName());
            else if (findAppForDep(dep, appsToInstall) != null)
                continue;
            else if (findAppForDep(dep, appManager.getInstalledApps()) != null)
                continue;
            else {
                App dependencyApp = findAppForDep(dep, appQueue);
                if (dependencyApp != null) {
                    appQueue.remove(dependencyApp);
                } else {
                    Set<WebApp> webApps = appManager.getWebQuerier().getAllApps();
                    if (webApps == null)
                        throw new Exception("Cannot access the App Store to resolve dependencies. Please check your internet connection.");
                    WebApp webApp = findWebAppForDep(dep, webApps);
                    if (webApp == null)
                        throw new Exception("Cannot find dependency: " + dependencyStack.firstElement() + " requires " + dep.getName() + ", which is not available in the App Store");
                    List<Release> releases = webApp.getReleases();
                    Release latestRelease = releases.get(releases.size() - 1);
                    if (WebQuerier.compareVersions(dep.getVersion(), latestRelease.getReleaseVersion()) >= 0) {
                        taskMonitor.setStatusMessage("Downloading dependency for " + dependencyStack.firstElement() + ": " + webApp.getFullName());
                        File appFile = appManager.getWebQuerier().downloadApp(webApp, null, new File(appManager.getDownloadedAppsPath()), status);
                        dependencyApp = appManager.getAppParser().parseApp(appFile);
                    } else
                        throw new Exception("Cannot find dependency: " + dependencyStack.firstElement() + " requires " + dep.getName() + " " + dep.getVersion() + " or later, latest release in App Store is " + latestRelease.getReleaseVersion());
                }
                resolveAppDependencies(dependencyApp);
            }
        }
    dependencyStack.pop();
    appsToInstall.add(appToInstall);
}

Example 5 with Release

use of org.cytoscape.app.internal.net.WebApp.Release in project cytoscape-impl by cytoscape.

the class WebQuerier method getAllApps.

public Set<WebApp> getAllApps() {
    // If we have a cached result from the previous query, use that one
    if (this.appsByUrl.get(currentAppStoreUrl) != null) {
        return this.appsByUrl.get(currentAppStoreUrl);
    }
    DebugHelper.print("Obtaining apps from app store..");
    Set<WebApp> result = new HashSet<WebApp>();
    String jsonResult = null;
    try {
        // Obtain information about the app from the website
        jsonResult = query(currentAppStoreUrl + "backend/all_apps");
        if (appManager != null && appManager.getAppManagerDialog() != null) {
            appManager.getAppManagerDialog().hideNetworkError();
        }
        // Parse the JSON result
        JSONArray jsonArray = new JSONArray(jsonResult);
        JSONObject jsonObject = null;
        String keyName;
        for (int index = 0; index < jsonArray.length(); index++) {
            jsonObject = jsonArray.getJSONObject(index);
            WebApp webApp = new WebApp();
            keyName = "fullname";
            if (jsonObject.has(keyName)) {
                webApp.setName(jsonObject.get(keyName).toString());
                webApp.setFullName(jsonObject.get(keyName).toString());
            } else {
                continue;
            }
            keyName = "icon_url";
            if (jsonObject.has(keyName)) {
                webApp.setIconUrl(jsonObject.get(keyName).toString());
            }
            keyName = "page_url";
            if (jsonObject.has(keyName)) {
                webApp.setPageUrl(currentAppStoreUrl.substring(0, currentAppStoreUrl.length() - 1) + jsonObject.get(keyName).toString());
            }
            keyName = "description";
            if (jsonObject.has(keyName)) {
                webApp.setDescription(jsonObject.get(keyName).toString());
            }
            keyName = "downloads";
            if (jsonObject.has(keyName)) {
                try {
                    webApp.setDownloadCount(Integer.parseInt(jsonObject.get(keyName).toString()));
                } catch (NumberFormatException e) {
                }
            }
            keyName = "stars_percentage";
            if (jsonObject.has(keyName)) {
                try {
                    webApp.setStarsPercentage(Integer.parseInt(jsonObject.get(keyName).toString()));
                } catch (NumberFormatException e) {
                }
            }
            keyName = "votes";
            if (jsonObject.has(keyName)) {
                try {
                    webApp.setVotes(Integer.parseInt(jsonObject.get(keyName).toString()));
                } catch (NumberFormatException e) {
                }
            }
            keyName = "citation";
            if (jsonObject.has(keyName)) {
                webApp.setCitation(jsonObject.get(keyName).toString());
            }
            try {
                List<WebApp.Release> releases = new LinkedList<WebApp.Release>();
                if (jsonObject.has("releases")) {
                    JSONArray jsonReleases = jsonObject.getJSONArray("releases");
                    JSONObject jsonRelease;
                    boolean isCompatible = true;
                    for (int releaseIndex = 0; releaseIndex < jsonReleases.length(); releaseIndex++) {
                        jsonRelease = jsonReleases.getJSONObject(releaseIndex);
                        WebApp.Release release = new WebApp.Release();
                        release.setBaseUrl(currentAppStoreUrl);
                        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)) {
                            release.setCompatibleCytoscapeVersions(jsonRelease.get(keyName).toString());
                            isCompatible = release.isCompatible(cyVersion);
                        }
                        if (isCompatible)
                            releases.add(release);
                    }
                    // Sort releases by version number
                    Collections.sort(releases, new Comparator<WebApp.Release>() {

                        @Override
                        public int compare(Release first, Release second) {
                            return compareVersions(second.getReleaseVersion(), first.getReleaseVersion());
                        }
                    });
                }
                webApp.setReleases(releases);
            } catch (JSONException e) {
                logger.warn("Error obtaining releases for app: " + webApp.getFullName() + ", " + e.getMessage());
            }
            // DebugHelper.print("Obtaining ImageIcon: " + iconUrlPrefix + webApp.getIconUrl());
            // webApp.setImageIcon(new ImageIcon(new URL(iconUrlPrefix + webApp.getIconUrl())));
            // Check the app for compatible releases
            List<WebApp.Release> compatibleReleases = getCompatibleReleases(webApp);
            // Only add this app if it has compatible releases
            if (compatibleReleases.size() > 0) {
                // Obtain tags associated with this app
                processAppTags(webApp, jsonObject);
                result.add(webApp);
            }
        }
    } catch (final IOException e) {
        if (appManager != null && appManager.getAppManagerDialog() != null) {
            appManager.getAppManagerDialog().showNetworkError();
        }
        e.printStackTrace();
        result = null;
    } catch (JSONException e) {
        // TODO Auto-generated catch block
        DebugHelper.print("Error parsing JSON: " + e.getMessage());
        e.printStackTrace();
    }
    // DebugHelper.print(result.size() + " apps found from web store.");
    // Cache the result of this query
    this.appsByUrl.put(currentAppStoreUrl, result);
    return result;
}