List of usage examples for java.lang String equals
public boolean equals(Object anObject)
From source file:com.adobe.aem.demo.communities.Loader.java
public static void main(String[] args) { String hostname = null;/*from w w w .ja va 2s .c o m*/ String port = null; String altport = null; String csvfile = null; String location = null; String language = "en"; String analytics = null; String adminPassword = "admin"; String[] url = new String[10]; // Handling 10 levels maximum for nested comments boolean reset = false; boolean configure = false; int urlLevel = 0; int row = 0; HashMap<String, ArrayList<String>> learningpaths = new HashMap<String, ArrayList<String>>(); // Command line options for this tool Options options = new Options(); options.addOption("h", true, "Hostname"); options.addOption("p", true, "Port"); options.addOption("a", true, "Alternate Port"); options.addOption("f", true, "CSV file"); options.addOption("r", false, "Reset"); options.addOption("u", true, "Admin Password"); options.addOption("c", false, "Configure"); options.addOption("s", true, "Analytics Endpoint"); options.addOption("t", false, "Analytics Tracking"); CommandLineParser parser = new BasicParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { hostname = cmd.getOptionValue("h"); } if (cmd.hasOption("p")) { port = cmd.getOptionValue("p"); } if (cmd.hasOption("a")) { altport = cmd.getOptionValue("a"); } if (cmd.hasOption("f")) { csvfile = cmd.getOptionValue("f"); } if (cmd.hasOption("u")) { adminPassword = cmd.getOptionValue("u"); } if (cmd.hasOption("t")) { if (cmd.hasOption("s")) { analytics = cmd.getOptionValue("s"); } } if (cmd.hasOption("r")) { reset = true; } if (cmd.hasOption("c")) { configure = true; } if (csvfile == null || port == null || hostname == null) { System.out.println( "Request parameters: -h hostname -p port -a alternateport -u adminPassword -f path_to_CSV_file -r (true|false, delete content before import) -c (true|false, post additional properties)"); System.exit(-1); } } catch (ParseException ex) { logger.error(ex.getMessage()); } String componentType = null; try { logger.debug("AEM Demo Loader: Processing file " + csvfile); // Reading the CSV file, line by line Reader in = new FileReader(csvfile); Iterable<CSVRecord> records = CSVFormat.EXCEL.parse(in); for (CSVRecord record : records) { row = row + 1; logger.info("Row: " + row + ", new record: " + record.get(0)); // Let's see if we deal with a comment if (record.get(0).startsWith("#")) { // We can ignore the comment line and move on continue; } // Let's see if we need to terminate this process if (record.get(0).equals(KILL)) { System.exit(1); } // Let's see if we need to create a new Community site if (record.get(0).equals(SITE)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody(":operation", "social:createSite", ContentType.create("text/plain", MIME.UTF8_CHARSET)); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); String urlName = null; for (int i = 2; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); if (value.equals("TRUE")) { value = "true"; } if (value.equals("FALSE")) { value = "false"; } if (name.equals("urlName")) { urlName = value; } if (name.equals(LANGUAGE)) { language = value; } if (name.equals(BANNER)) { File attachment = new File( csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + value); builder.addBinaryBody(BANNER, attachment, ContentType.MULTIPART_FORM_DATA, attachment.getName()); } else if (name.equals(THUMBNAIL)) { File attachment = new File( csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + value); builder.addBinaryBody(THUMBNAIL, attachment, ContentType.MULTIPART_FORM_DATA, attachment.getName()); } else { builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } } // Site creation String siteId = doPost(hostname, port, "/content.social.json", "admin", adminPassword, builder.build(), "response/siteId"); // Site publishing, if there's a publish instance to publish to if (!port.equals(altport)) { List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); nameValuePairs.add(new BasicNameValuePair("id", "nobot")); nameValuePairs.add(new BasicNameValuePair(":operation", "social:publishSite")); nameValuePairs .add(new BasicNameValuePair("path", "/content/sites/" + urlName + "/" + language)); doPost(hostname, port, "/communities/sites.html", "admin", adminPassword, new UrlEncodedFormEntity(nameValuePairs), null); // Wait for site to be available on Publish doWait(hostname, altport, "admin", adminPassword, (siteId != null ? siteId : urlName) + "-groupadministrators"); } continue; } // Let's see if we need to create a new Tag if (record.get(0).equals(TAG)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); for (int i = 1; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0 && record.get(i + 1).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } // Tag creation doPost(hostname, port, "/bin/tagcommand", "admin", adminPassword, builder.build(), null); continue; } // Let's see if we need to create a new Community site template, and if we can do it (script run against author instance) if (record.get(0).equals(SITETEMPLATE)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody(":operation", "social:createSiteTemplate", ContentType.create("text/plain", MIME.UTF8_CHARSET)); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); for (int i = 2; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } // Site template creation doPost(hostname, port, "/content.social.json", "admin", adminPassword, builder.build(), null); continue; } // Let's see if we need to create a new Community group if (record.get(0).equals(GROUP)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody(":operation", "social:createCommunityGroup", ContentType.create("text/plain", MIME.UTF8_CHARSET)); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); for (int i = 3; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); if (value.equals("TRUE")) { value = "true"; } if (value.equals("FALSE")) { value = "false"; } if (name.equals(IMAGE)) { File attachment = new File( csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + value); builder.addBinaryBody(IMAGE, attachment, ContentType.MULTIPART_FORM_DATA, attachment.getName()); } else { builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } } // Group creation String memberGroupId = doPost(hostname, port, record.get(1), getUserName(record.get(2)), getPassword(record.get(2), adminPassword), builder.build(), "response/memberGroupId"); // Wait for group to be available on Publish, if available logger.debug("Waiting for completion of Community Group creation"); doWait(hostname, port, "admin", adminPassword, memberGroupId); continue; } // Let's see if it's simple Sling Delete request if (record.get(0).equals(SLINGDELETE)) { doDelete(hostname, port, record.get(1), "admin", adminPassword); continue; } // Let's see if we need to add users to an AEM Group if ((record.get(0).equals(GROUPMEMBERS) || record.get(0).equals(SITEMEMBERS)) && record.get(GROUP_INDEX_NAME) != null) { // Checking if we have a member group for this site String groupName = record.get(GROUP_INDEX_NAME); if (record.get(0).equals(SITEMEMBERS)) { // Let's fetch the siteId for this Community Site Url String siteConfig = doGet(hostname, port, groupName, "admin", adminPassword, null); try { String siteId = new JSONObject(siteConfig).getString("siteId"); if (siteId != null) groupName = "community-" + siteId + "-members"; logger.debug("Member group name is " + groupName); } catch (Exception e) { logger.error(e.getMessage()); } } // Pause until the group can found doWait(hostname, port, "admin", adminPassword, groupName); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); nameValuePairs.add(new BasicNameValuePair("filter", "[{\"operation\":\"like\",\"rep:principalName\":\"" + groupName + "\"}]")); nameValuePairs.add(new BasicNameValuePair("type", "groups")); String groupList = doGet(hostname, port, "/libs/social/console/content/content/userlist.social.0.10.json", "admin", adminPassword, nameValuePairs); logger.debug("List of groups" + groupList); if (groupList.indexOf(groupName) > 0) { logger.debug("Group was found on " + port); try { JSONArray jsonArray = new JSONObject(groupList).getJSONArray("items"); if (jsonArray.length() == 1) { JSONObject jsonObject = jsonArray.getJSONObject(0); String groupPath = jsonObject.getString("path"); logger.debug("Group path is " + groupPath); // Constructing a multi-part POST for group membership MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.setMode(HttpMultipartMode.BROWSER_COMPATIBLE); List<NameValuePair> groupNameValuePairs = buildNVP(record, 2); for (NameValuePair nameValuePair : groupNameValuePairs) { builder.addTextBody(nameValuePair.getName(), nameValuePair.getValue(), ContentType.create("text/plain", MIME.UTF8_CHARSET)); } // Adding the list of group members doPost(hostname, port, groupPath + ".rw.userprops.html", "admin", adminPassword, builder.build(), null); } else { logger.info("We have more than one match for a group with this name!"); } } catch (Exception e) { logger.error(e.getMessage()); } } continue; } // Let's see if it's user related if (record.get(0).equals(USERS)) { //First we need to get the path to the user node String json = doGet(hostname, port, "/libs/granite/security/currentuser.json", getUserName(record.get(1)), getPassword(record.get(1), adminPassword), null); if (json != null) { try { // Fetching the home property String home = new JSONObject(json).getString("home"); if (record.get(2).equals(PREFERENCES)) { home = home + "/preferences"; } else { home = home + "/profile"; } logger.debug(home); // Now we can post all the preferences or the profile List<NameValuePair> nameValuePairs = buildNVP(record, 3); doPost(hostname, port, home, "admin", adminPassword, new UrlEncodedFormEntity(nameValuePairs), null); } catch (Exception e) { logger.error(e.getMessage()); } } continue; } // Let's see if we deal with a new block of content or just a new entry if (record.get(0).equals(CALENDAR) || record.get(0).equals(SLINGPOST) || record.get(0).equals(RATINGS) || record.get(0).equals(BLOG) || record.get(0).equals(JOURNAL) || record.get(0).equals(COMMENTS) || record.get(0).equals(REVIEWS) || record.get(0).equals(FILES) || record.get(0).equals(SUMMARY) || record.get(0).equals(ACTIVITIES) || record.get(0).equals(JOIN) || record.get(0).equals(FOLLOW) || record.get(0).equals(MESSAGE) || record.get(0).equals(ASSET) || record.get(0).equals(AVATAR) || record.get(0).equals(RESOURCE) || record.get(0).equals(LEARNING) || record.get(0).equals(QNA) || record.get(0).equals(FORUM)) { // New block of content, we need to reset the processing to first Level componentType = record.get(0); url[0] = record.get(1); urlLevel = 0; if (!componentType.equals(SLINGPOST) && reset) { int pos = record.get(1).indexOf("/jcr:content"); if (pos > 0) doDelete(hostname, port, "/content/usergenerated" + record.get(1).substring(0, pos), "admin", adminPassword); } // If the Configure command line flag is set, we try to configure the component with all options enabled if (componentType.equals(SLINGPOST) || configure) { String configurePath = getConfigurePath(record.get(1)); List<NameValuePair> nameValuePairs = buildNVP(record, 2); if (nameValuePairs.size() > 2) // Only do this when really have configuration settings doPost(hostname, port, configurePath, "admin", adminPassword, new UrlEncodedFormEntity(nameValuePairs), null); } // We're done with this line, moving on to the next line in the CSV file continue; } // Let's see if we need to indent the list, if it's a reply or a reply to a reply if (record.get(1).length() != 1) continue; // We need a valid level indicator if (Integer.parseInt(record.get(1)) > urlLevel) { url[++urlLevel] = location; logger.debug("Incremented urlLevel to: " + urlLevel + ", with a new location:" + location); } else if (Integer.parseInt(record.get(1)) < urlLevel) { urlLevel = Integer.parseInt(record.get(1)); logger.debug("Decremented urlLevel to: " + urlLevel); } // Get the credentials or fall back to password String password = getPassword(record.get(0), adminPassword); String userName = getUserName(record.get(0)); // Adding the generic properties for all POST requests List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); if (!componentType.equals(RESOURCE)) nameValuePairs.add(new BasicNameValuePair("id", "nobot")); nameValuePairs.add(new BasicNameValuePair("_charset_", "UTF-8")); // Setting some specific fields depending on the content type if (componentType.equals(COMMENTS)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createComment")); nameValuePairs.add(new BasicNameValuePair("message", record.get(2))); } // Creates a forum post (or reply) if (componentType.equals(FORUM)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createForumPost")); nameValuePairs.add(new BasicNameValuePair("subject", record.get(2))); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } // Follows a user (followedId) for the user posting the request if (componentType.equals(FOLLOW)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:follow")); nameValuePairs.add(new BasicNameValuePair("userId", "/social/authors/" + userName)); nameValuePairs.add(new BasicNameValuePair("followedId", "/social/authors/" + record.get(2))); } // Uploading Avatar picture if (componentType.equals(AVATAR)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:changeAvatar")); } // Joins a user (posting the request) to a Community Group (path) if (componentType.equals(JOIN)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:joinCommunityGroup")); int pos = url[0].indexOf("/configuration.social.json"); if (pos > 0) nameValuePairs.add(new BasicNameValuePair("path", url[0].substring(0, pos) + ".html")); else continue; // Invalid record } // Creates a new private message if (componentType.equals(MESSAGE)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createMessage")); nameValuePairs.add(new BasicNameValuePair("sendMail", "Sending...")); nameValuePairs.add(new BasicNameValuePair("content", record.get(4))); nameValuePairs.add(new BasicNameValuePair("subject", record.get(3))); nameValuePairs.add(new BasicNameValuePair("serviceSelector", "/bin/community")); nameValuePairs.add(new BasicNameValuePair("to", "/social/authors/" + record.get(2))); nameValuePairs.add(new BasicNameValuePair("userId", "/social/authors/" + record.get(2))); nameValuePairs.add(new BasicNameValuePair(":redirect", "//messaging.html")); nameValuePairs.add(new BasicNameValuePair(":formid", "generic_form")); nameValuePairs.add(new BasicNameValuePair(":formstart", "/content/sites/communities/messaging/compose/jcr:content/content/primary/start")); } // Creates a file or a folder if (componentType.equals(FILES)) { // Top level is always assumed to be a folder, second level files, and third and subsequent levels comments on files if (urlLevel == 0) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createFileLibraryFolder")); nameValuePairs.add(new BasicNameValuePair("name", record.get(2))); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } else if (urlLevel == 1) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createComment")); } } // Creates a question, a reply or mark a reply as the best answer if (componentType.equals(QNA)) { if (urlLevel == 0) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createQnaPost")); nameValuePairs.add(new BasicNameValuePair("subject", record.get(2))); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } else if (urlLevel == 1) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createQnaPost")); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } else if (urlLevel == 2) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:selectAnswer")); } } // Creates an article or a comment if (componentType.equals(JOURNAL) || componentType.equals(BLOG)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createJournalComment")); nameValuePairs.add(new BasicNameValuePair("subject", record.get(2))); StringBuffer message = new StringBuffer("<p>" + record.get(3) + "</p>"); //We might have more paragraphs to add to the blog or journal article for (int i = 6; i < record.size(); i++) { if (record.get(i).length() > 0) { message.append("<p>" + record.get(i) + "</p>"); } } //We might have some tags to add to the blog or journal article if (record.get(5).length() > 0) { nameValuePairs.add(new BasicNameValuePair("tags", record.get(5))); } nameValuePairs.add(new BasicNameValuePair("message", message.toString())); } // Creates a review or a comment if (componentType.equals(REVIEWS)) { nameValuePairs.add(new BasicNameValuePair("message", record.get(2))); // This might be a top level review, or a comment on a review or another comment if (urlLevel == 0) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createReview")); nameValuePairs.add(new BasicNameValuePair("ratings", record.get(3))); if (record.size() > 4 && record.get(4).length() > 0) { // If we are dealing with a non-existent resource, then the design drives the behavior nameValuePairs.add(new BasicNameValuePair("scf:resourceType", "social/reviews/components/hbs/reviews")); nameValuePairs.add(new BasicNameValuePair("scf:included", record.get(4))); } } else { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createComment")); } } // Creates a rating if (componentType.equals(RATINGS)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:postTallyResponse")); nameValuePairs.add(new BasicNameValuePair("tallyType", "Rating")); nameValuePairs.add(new BasicNameValuePair("response", record.get(2))); } // Creates a DAM asset if (componentType.equals(ASSET) && record.get(ASSET_INDEX_NAME).length() > 0) { nameValuePairs.add(new BasicNameValuePair("fileName", record.get(ASSET_INDEX_NAME))); } // Creates an enablement resource if (componentType.equals(RESOURCE)) { nameValuePairs.add(new BasicNameValuePair(":operation", "se:createResource")); List<NameValuePair> otherNameValuePairs = buildNVP(record, RESOURCE_INDEX_PROPERTIES); nameValuePairs.addAll(otherNameValuePairs); // Adding the site nameValuePairs.add(new BasicNameValuePair("site", "/content/sites/" + record.get(RESOURCE_INDEX_SITE) + "/resources/en")); // Building the cover image fragment if (record.get(RESOURCE_INDEX_THUMBNAIL).length() > 0) { nameValuePairs.add(new BasicNameValuePair("cover-image", doThumbnail(hostname, port, adminPassword, csvfile, record.get(RESOURCE_INDEX_THUMBNAIL)))); } else { nameValuePairs.add(new BasicNameValuePair("cover-image", "")); } // Building the asset fragment String coverPath = "/content/dam/" + record.get(RESOURCE_INDEX_SITE) + "/resource-assets/" + record.get(2) + "/jcr:content/renditions/cq5dam.thumbnail.319.319.png"; String coverSource = "dam"; String assets = "[{\"cover-img-path\":\"" + coverPath + "\",\"thumbnail-source\":\"" + coverSource + "\",\"asset-category\":\"enablementAsset:dam\",\"resource-asset-name\":null,\"state\":\"A\",\"asset-path\":\"/content/dam/" + record.get(RESOURCE_INDEX_SITE) + "/resource-assets/" + record.get(2) + "\"}]"; nameValuePairs.add(new BasicNameValuePair("assets", assets)); logger.debug("assets:" + assets); } // Creates a learning path if (componentType.equals(LEARNING)) { nameValuePairs.add(new BasicNameValuePair(":operation", "se:editLearningPath")); List<NameValuePair> otherNameValuePairs = buildNVP(record, RESOURCE_INDEX_PROPERTIES); nameValuePairs.addAll(otherNameValuePairs); // Adding the site nameValuePairs.add(new BasicNameValuePair("site", "/content/sites/" + record.get(RESOURCE_INDEX_SITE) + "/resources/en")); // Building the cover image fragment if (record.get(RESOURCE_INDEX_THUMBNAIL).length() > 0) { nameValuePairs.add(new BasicNameValuePair("card-image", doThumbnail(hostname, port, adminPassword, csvfile, record.get(RESOURCE_INDEX_THUMBNAIL)))); } // Building the learning path fragment StringBuffer assets = new StringBuffer("[\""); if (learningpaths.get(record.get(2)) != null) { ArrayList<String> paths = learningpaths.get(record.get(2)); int i = 0; for (String path : paths) { assets.append("{\\\"type\\\":\\\"linked-resource\\\",\\\"path\\\":\\\""); assets.append(path); assets.append("\\\"}"); if (i++ < paths.size() - 1) { assets.append("\",\""); } } } else { logger.debug("No asset for this learning path"); } assets.append("\"]"); nameValuePairs.add(new BasicNameValuePair("learningpath-items", assets.toString())); logger.debug("Learning path:" + assets.toString()); } // Creates a calendar event if (componentType.equals(CALENDAR)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createEvent")); try { JSONObject event = new JSONObject(); // Building the JSON fragment for a new calendar event event.accumulate("subject", record.get(2)); event.accumulate("message", record.get(3)); event.accumulate("location", record.get(4)); event.accumulate("tags", ""); event.accumulate("undefined", "update"); String startDate = record.get(5); startDate = startDate.replaceAll("YYYY", Integer.toString(Calendar.getInstance().get(Calendar.YEAR))); startDate = startDate.replaceAll("MM", Integer.toString(1 + Calendar.getInstance().get(Calendar.MONTH))); event.accumulate("start", startDate); String endDate = record.get(6); endDate = endDate.replaceAll("YYYY", Integer.toString(Calendar.getInstance().get(Calendar.YEAR))); endDate = endDate.replaceAll("MM", Integer.toString(1 + Calendar.getInstance().get(Calendar.MONTH))); event.accumulate("end", endDate); nameValuePairs.add(new BasicNameValuePair("event", event.toString())); } catch (Exception ex) { logger.error(ex.getMessage()); } } // Constructing a multi-part POST request MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.setMode(HttpMultipartMode.BROWSER_COMPATIBLE); for (NameValuePair nameValuePair : nameValuePairs) { builder.addTextBody(nameValuePair.getName(), nameValuePair.getValue(), ContentType.create("text/plain", MIME.UTF8_CHARSET)); } // See if we have attachments for this new post - or some other actions require a form nonetheless if ((componentType.equals(ASSET) || componentType.equals(AVATAR) || componentType.equals(FORUM) || (componentType.equals(JOURNAL)) || componentType.equals(BLOG)) && record.size() > 4 && record.get(ASSET_INDEX_NAME).length() > 0) { File attachment = new File(csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + record.get(ASSET_INDEX_NAME)); ContentType ct = ContentType.MULTIPART_FORM_DATA; if (record.get(ASSET_INDEX_NAME).indexOf(".mp4") > 0) { ct = ContentType.create("video/mp4", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".jpg") > 0 || record.get(ASSET_INDEX_NAME).indexOf(".jpeg") > 0) { ct = ContentType.create("image/jpeg", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".png") > 0) { ct = ContentType.create("image/png", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".pdf") > 0) { ct = ContentType.create("application/pdf", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".zip") > 0) { ct = ContentType.create("application/zip", MIME.UTF8_CHARSET); } builder.addBinaryBody("file", attachment, ct, attachment.getName()); logger.debug("Adding file to payload with name: " + attachment.getName() + " and type: " + ct.getMimeType()); } // If it's a resource or a learning path, we need the path to the resource for subsequent publishing String jsonElement = "location"; if (componentType.equals(RESOURCE)) { jsonElement = "changes/argument"; } if (componentType.equals(LEARNING)) { jsonElement = "path"; } if (componentType.equals(ASSET)) { jsonElement = null; } // This call generally returns the path to the content fragment that was just created location = Loader.doPost(hostname, port, url[urlLevel], userName, password, builder.build(), jsonElement); // If we are loading a DAM asset, we are waiting for all renditions to be generated before proceeding if (componentType.equals(ASSET)) { int pathIndex = url[urlLevel].lastIndexOf(".createasset.html"); if (pathIndex > 0) doWaitPath(hostname, port, adminPassword, url[urlLevel].substring(0, pathIndex) + "/" + record.get(ASSET_INDEX_NAME) + "/jcr:content/renditions", "nt:file"); } // Let's see if it needs to be added to a learning path if (componentType.equals(RESOURCE) && record.get(RESOURCE_INDEX_PATH).length() > 0 && location != null) { // Adding the location to a list of a resources for this particular Learning Path if (learningpaths.get(record.get(RESOURCE_INDEX_PATH)) == null) learningpaths.put(record.get(RESOURCE_INDEX_PATH), new ArrayList<String>()); logger.debug("Adding resource to Learning path: " + record.get(RESOURCE_INDEX_PATH)); ArrayList<String> locations = learningpaths.get(record.get(RESOURCE_INDEX_PATH)); locations.add(location); learningpaths.put(record.get(RESOURCE_INDEX_PATH), locations); } // If it's a Learning Path, we publish it when possible if (componentType.equals(LEARNING) && !port.equals(altport) && location != null) { // Publishing the learning path List<NameValuePair> publishNameValuePairs = new ArrayList<NameValuePair>(); publishNameValuePairs.add(new BasicNameValuePair(":operation", "se:publishEnablementContent")); publishNameValuePairs.add(new BasicNameValuePair("replication-action", "activate")); logger.debug("Publishing a learning path from: " + location); Loader.doPost(hostname, port, location, userName, password, new UrlEncodedFormEntity(publishNameValuePairs), null); // Waiting for the learning path to be published Loader.doWait(hostname, altport, "admin", adminPassword, location.substring(1 + location.lastIndexOf("/")) // Only search for groups with the learning path in it ); // Decorate the resources within the learning path with comments and ratings, randomly generated ArrayList<String> paths = learningpaths.get(record.get(2)); for (String path : paths) { doDecorate(hostname, altport, path, record, analytics); } } // If it's an Enablement Resource, a lot of things need to happen... // Step 1. If it's a SCORM resource, we wait for the SCORM metadata workflow to be complete before proceeding // Step 2. We publish the resource // Step 3. We set a new first published date on the resource (3 weeks earlier) so that reporting data is more meaningful // Step 4. We wait for the resource to be available on publish (checking that associated groups are available) // Step 5. We retrieve the json for the resource on publish to retrieve the Social endpoints // Step 6. We post ratings and comments for each of the enrollees on publish if (componentType.equals(RESOURCE) && !port.equals(altport) && location != null) { // Wait for the data to be fully copied doWaitPath(hostname, port, adminPassword, location + "/assets/asset", "nt:file"); // If we are dealing with a SCORM asset, we wait a little bit before publishing the resource to that the SCORM workflow is completed if (record.get(2).indexOf(".zip") > 0) { doSleep(10000, "SCORM Resource, waiting for workflow to complete"); } // Publishing the resource List<NameValuePair> publishNameValuePairs = new ArrayList<NameValuePair>(); publishNameValuePairs.add(new BasicNameValuePair(":operation", "se:publishEnablementContent")); publishNameValuePairs.add(new BasicNameValuePair("replication-action", "activate")); logger.debug("Publishing a resource from: " + location); Loader.doPost(hostname, port, location, userName, password, new UrlEncodedFormEntity(publishNameValuePairs), null); // Waiting for the resource to be published Loader.doWait(hostname, altport, "admin", adminPassword, location.substring(1 + location.lastIndexOf("/")) // Only search for groups with the resource path in it ); // Setting the first published timestamp so that reporting always comes with 3 weeks of data after building a new demo instance DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss"); Calendar cal = Calendar.getInstance(); cal.add(Calendar.DATE, REPORTINGDAYS); List<NameValuePair> publishDateNameValuePairs = new ArrayList<NameValuePair>(); publishDateNameValuePairs .add(new BasicNameValuePair("date-first-published", dateFormat.format(cal.getTime()))); logger.debug("Setting the publish date for a resource from: " + location); doPost(hostname, port, location, userName, password, new UrlEncodedFormEntity(publishDateNameValuePairs), null); // Adding comments and ratings for this resource doDecorate(hostname, altport, location, record, analytics); } } } catch (IOException e) { logger.error(e.getMessage()); } }
From source file:com.cyberway.issue.io.arc.ARCReader.java
/** * Command-line interface to ARCReader.//from w w w . j a va 2s . com * * Here is the command-line interface: * <pre> * usage: java com.cyberway.issue.io.arc.ARCReader [--offset=#] ARCFILE * -h,--help Prints this message and exits. * -o,--offset Outputs record at this offset into arc file.</pre> * * <p>See in <code>$HERITRIX_HOME/bin/arcreader</code> for a script that'll * take care of classpaths and the calling of ARCReader. * * <p>Outputs using a pseudo-CDX format as described here: * <a href="http://www.archive.org/web/researcher/cdx_legend.php">CDX * Legent</a> and here * <a href="http://www.archive.org/web/researcher/example_cdx.php">Example</a>. * Legend used in below is: 'CDX b e a m s c V (or v if uncompressed) n g'. * Hash is hard-coded straight SHA-1 hash of content. * * @param args Command-line arguments. * @throws ParseException Failed parse of the command line. * @throws IOException * @throws java.text.ParseException */ public static void main(String[] args) throws ParseException, IOException, java.text.ParseException { Options options = getOptions(); options.addOption(new Option("p", "parse", false, "Parse headers.")); PosixParser parser = new PosixParser(); CommandLine cmdline = parser.parse(options, args, false); List cmdlineArgs = cmdline.getArgList(); Option[] cmdlineOptions = cmdline.getOptions(); HelpFormatter formatter = new HelpFormatter(); // If no args, print help. if (cmdlineArgs.size() <= 0) { usage(formatter, options, 0); } // Now look at options passed. long offset = -1; boolean digest = false; boolean strict = false; boolean parse = false; String format = CDX; for (int i = 0; i < cmdlineOptions.length; i++) { switch (cmdlineOptions[i].getId()) { case 'h': usage(formatter, options, 0); break; case 'o': offset = Long.parseLong(cmdlineOptions[i].getValue()); break; case 's': strict = true; break; case 'p': parse = true; break; case 'd': digest = getTrueOrFalse(cmdlineOptions[i].getValue()); break; case 'f': format = cmdlineOptions[i].getValue().toLowerCase(); boolean match = false; // List of supported formats. final String[] supportedFormats = { CDX, DUMP, GZIP_DUMP, HEADER, NOHEAD, CDX_FILE }; for (int ii = 0; ii < supportedFormats.length; ii++) { if (supportedFormats[ii].equals(format)) { match = true; break; } } if (!match) { usage(formatter, options, 1); } break; default: throw new RuntimeException("Unexpected option: " + +cmdlineOptions[i].getId()); } } if (offset >= 0) { if (cmdlineArgs.size() != 1) { System.out.println("Error: Pass one arcfile only."); usage(formatter, options, 1); } ARCReader arc = ARCReaderFactory.get((String) cmdlineArgs.get(0), offset); arc.setStrict(strict); // We must parse headers if we need to skip them. if (format.equals(NOHEAD) || format.equals(HEADER)) { parse = true; } arc.setParseHttpHeaders(parse); outputRecord(arc, format); } else { for (Iterator i = cmdlineArgs.iterator(); i.hasNext();) { String urlOrPath = (String) i.next(); try { ARCReader r = ARCReaderFactory.get(urlOrPath); r.setStrict(strict); r.setParseHttpHeaders(parse); r.setDigest(digest); output(r, format); } catch (RuntimeException e) { // Write out name of file we failed on to help with // debugging. Then print stack trace and try to keep // going. We do this for case where we're being fed // a bunch of ARCs; just note the bad one and move // on to the next. System.err.println("Exception processing " + urlOrPath + ": " + e.getMessage()); e.printStackTrace(System.err); System.exit(1); } } } }
From source file:org.kuali.student.git.importer.ConvertBuildTagBranchesToGitTags.java
/** * @param args/*from www .j a va2 s . c o m*/ */ public static void main(String[] args) { if (args.length < 3 || args.length > 6) { System.err.println("USAGE: <git repository> <bare> <ref mode> [<ref prefix> <username> <password>]"); System.err.println("\t<bare> : 0 (false) or 1 (true)"); System.err.println("\t<ref mode> : local or name of remote"); System.err.println("\t<ref prefix> : refs/heads (default) or say refs/remotes/origin (test clone)"); System.exit(-1); } boolean bare = false; if (args[1].trim().equals("1")) { bare = true; } String remoteName = args[2].trim(); String refPrefix = Constants.R_HEADS; if (args.length == 4) refPrefix = args[3].trim(); String userName = null; String password = null; if (args.length == 5) userName = args[4].trim(); if (args.length == 6) password = args[5].trim(); try { Repository repo = GitRepositoryUtils.buildFileRepository(new File(args[0]).getAbsoluteFile(), false, bare); Git git = new Git(repo); ObjectInserter objectInserter = repo.newObjectInserter(); Collection<Ref> repositoryHeads = repo.getRefDatabase().getRefs(refPrefix).values(); RevWalk rw = new RevWalk(repo); Map<String, ObjectId> tagNameToTagId = new HashMap<>(); Map<String, Ref> tagNameToRef = new HashMap<>(); for (Ref ref : repositoryHeads) { String branchName = ref.getName().substring(refPrefix.length() + 1); if (branchName.contains("tag") && branchName.contains("builds")) { String branchParts[] = branchName.split("_"); int buildsIndex = ArrayUtils.indexOf(branchParts, "builds"); String moduleName = StringUtils.join(branchParts, "_", buildsIndex + 1, branchParts.length); RevCommit commit = rw.parseCommit(ref.getObjectId()); ObjectId tag = GitRefUtils.insertTag(moduleName, commit, objectInserter); tagNameToTagId.put(moduleName, tag); tagNameToRef.put(moduleName, ref); } } BatchRefUpdate batch = repo.getRefDatabase().newBatchUpdate(); List<RefSpec> branchesToDelete = new ArrayList<>(); for (Entry<String, ObjectId> entry : tagNameToTagId.entrySet()) { String tagName = entry.getKey(); // create the reference to the tag object batch.addCommand( new ReceiveCommand(null, entry.getValue(), Constants.R_TAGS + tagName, Type.CREATE)); // delete the original branch object Ref branch = tagNameToRef.get(entry.getKey()); if (remoteName.equals("local")) { batch.addCommand(new ReceiveCommand(branch.getObjectId(), null, branch.getName(), Type.DELETE)); } else { String adjustedBranchName = branch.getName().substring(refPrefix.length() + 1); branchesToDelete.add(new RefSpec(":" + Constants.R_HEADS + adjustedBranchName)); } } // create the tags batch.execute(rw, new TextProgressMonitor()); if (!remoteName.equals("local")) { // push the tag to the remote right now PushCommand pushCommand = git.push().setRemote(remoteName).setPushTags() .setProgressMonitor(new TextProgressMonitor()); if (userName != null) pushCommand.setCredentialsProvider(new UsernamePasswordCredentialsProvider(userName, password)); Iterable<PushResult> results = pushCommand.call(); for (PushResult pushResult : results) { if (!pushResult.equals(Result.NEW)) { log.warn("failed to push tag " + pushResult.getMessages()); } } // delete the branches from the remote results = git.push().setRemote(remoteName).setRefSpecs(branchesToDelete) .setProgressMonitor(new TextProgressMonitor()).call(); log.info(""); } // Result result = GitRefUtils.createTagReference(repo, moduleName, tag); // // if (!result.equals(Result.NEW)) { // log.warn("failed to create tag {} for branch {}", moduleName, branchName); // continue; // } // // if (deleteMode) { // result = GitRefUtils.deleteRef(repo, ref); // // if (!result.equals(Result.NEW)) { // log.warn("failed to delete branch {}", branchName); // continue; // } objectInserter.release(); rw.release(); } catch (Exception e) { log.error("unexpected Exception ", e); } }
From source file:com.cloud.test.stress.TestClientWithAPI.java
public static void main(String[] args) { String host = "http://localhost"; String port = "8092"; String devPort = "8080"; String apiUrl = "/client/api"; try {// w w w .j av a 2 s . c om // Parameters List<String> argsList = Arrays.asList(args); Iterator<String> iter = argsList.iterator(); while (iter.hasNext()) { String arg = iter.next(); // host if (arg.equals("-h")) { host = "http://" + iter.next(); } if (arg.equals("-p")) { port = iter.next(); } if (arg.equals("-dp")) { devPort = iter.next(); } if (arg.equals("-t")) { numThreads = Integer.parseInt(iter.next()); } if (arg.equals("-s")) { sleepTime = Long.parseLong(iter.next()); } if (arg.equals("-a")) { accountName = iter.next(); } if (arg.equals("-c")) { cleanUp = Boolean.parseBoolean(iter.next()); if (!cleanUp) sleepTime = 0L; // no need to wait if we don't ever // cleanup } if (arg.equals("-r")) { repeat = Boolean.parseBoolean(iter.next()); } if (arg.equals("-u")) { numOfUsers = Integer.parseInt(iter.next()); } if (arg.equals("-i")) { internet = Boolean.parseBoolean(iter.next()); } if (arg.equals("-w")) { wait = Integer.parseInt(iter.next()); } if (arg.equals("-z")) { zoneId = iter.next(); } if (arg.equals("-snapshot")) { snapshot_test = "yes"; } if (arg.equals("-so")) { serviceOfferingId = iter.next(); } if (arg.equals("-do")) { diskOfferingId = iter.next(); } if (arg.equals("-no")) { networkOfferingId = iter.next(); } if (arg.equals("-pass")) { vmPassword = iter.next(); } if (arg.equals("-url")) { downloadUrl = iter.next(); } } final String server = host + ":" + port + "/"; final String developerServer = host + ":" + devPort + apiUrl; s_logger.info("Starting test against server: " + server + " with " + numThreads + " thread(s)"); if (cleanUp) s_logger.info("Clean up is enabled, each test will wait " + sleepTime + " ms before cleaning up"); if (numOfUsers > 0) { s_logger.info("Pre-generating users for test of size : " + numOfUsers); users = new String[numOfUsers]; Random ran = new Random(); for (int i = 0; i < numOfUsers; i++) { users[i] = Math.abs(ran.nextInt()) + "-user"; } } for (int i = 0; i < numThreads; i++) { new Thread(new Runnable() { @Override public void run() { do { String username = null; try { long now = System.currentTimeMillis(); Random ran = new Random(); if (users != null) { username = users[Math.abs(ran.nextInt()) % numOfUsers]; } else { username = Math.abs(ran.nextInt()) + "-user"; } NDC.push(username); s_logger.info("Starting test for the user " + username); int response = executeDeployment(server, developerServer, username, snapshot_test); boolean success = false; String reason = null; if (response == 200) { success = true; if (internet) { s_logger.info("Deploy successful...waiting 5 minute before SSH tests"); Thread.sleep(300000L); // Wait 60 // seconds so // the windows VM // can boot up and do a sys prep. if (accountName == null) { s_logger.info("Begin Linux SSH test for account " + _account.get()); reason = sshTest(_linuxIP.get(), _linuxPassword.get(), snapshot_test); } if (reason == null) { s_logger.info( "Linux SSH test successful for account " + _account.get()); s_logger.info("Begin WindowsSSH test for account " + _account.get()); reason = sshTest(_linuxIP.get(), _linuxPassword.get(), snapshot_test); // reason = sshWinTest(_windowsIP.get()); } // release the linux IP now... _linuxIP.set(null); // release the Windows IP now _windowsIP.set(null); } // sleep for 3 min before getting the latest network stat // s_logger.info("Sleeping for 5 min before getting the lates network stat for the account"); // Thread.sleep(300000); // verify that network stat is correct for the user; if it's not - stop all the resources // for the user // if ((reason == null) && (getNetworkStat(server) == false) ) { // s_logger.error("Stopping all the resources for the account " + _account.get() + // " as network stat is incorrect"); // int stopResponseCode = executeStop( // server, developerServer, // username, false); // s_logger // .info("stop command finished with response code: " // + stopResponseCode); // success = false; // since the SSH test // // } else if (reason == null) { if (internet) { s_logger.info( "Windows SSH test successful for account " + _account.get()); } else { s_logger.info("deploy test successful....now cleaning up"); if (cleanUp) { s_logger.info( "Waiting " + sleepTime + " ms before cleaning up vms"); Thread.sleep(sleepTime); } else { success = true; } } if (usageIterator >= numThreads) { int eventsAndBillingResponseCode = executeEventsAndBilling(server, developerServer); s_logger.info( "events and usage records command finished with response code: " + eventsAndBillingResponseCode); usageIterator = 1; } else { s_logger.info( "Skipping events and usage records for this user: usageIterator " + usageIterator + " and number of Threads " + numThreads); usageIterator++; } if ((users == null) && (accountName == null)) { s_logger.info("Sending cleanup command"); int cleanupResponseCode = executeCleanup(server, developerServer, username); s_logger.info("cleanup command finished with response code: " + cleanupResponseCode); success = (cleanupResponseCode == 200); } else { s_logger.info("Sending stop DomR / destroy VM command"); int stopResponseCode = executeStop(server, developerServer, username, true); s_logger.info("stop(destroy) command finished with response code: " + stopResponseCode); success = (stopResponseCode == 200); } } else { // Just stop but don't destroy the // VMs/Routers s_logger.info("SSH test failed for account " + _account.get() + "with reason '" + reason + "', stopping VMs"); int stopResponseCode = executeStop(server, developerServer, username, false); s_logger.info( "stop command finished with response code: " + stopResponseCode); success = false; // since the SSH test // failed, mark the // whole test as // failure } } else { // Just stop but don't destroy the // VMs/Routers s_logger.info("Deploy test failed with reason '" + reason + "', stopping VMs"); int stopResponseCode = executeStop(server, developerServer, username, true); s_logger.info("stop command finished with response code: " + stopResponseCode); success = false; // since the deploy test // failed, mark the // whole test as failure } if (success) { s_logger.info("***** Completed test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds"); } else { s_logger.info("##### FAILED test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds with reason : " + reason); } s_logger.info("Sleeping for " + wait + " seconds before starting next iteration"); Thread.sleep(wait); } catch (Exception e) { s_logger.warn("Error in thread", e); try { int stopResponseCode = executeStop(server, developerServer, username, true); s_logger.info("stop response code: " + stopResponseCode); } catch (Exception e1) { } } finally { NDC.clear(); } } while (repeat); } }).start(); } } catch (Exception e) { s_logger.error(e); } }
From source file:de.mfo.jsurf.Main.java
/** * @param args//ww w. java 2s. co m */ public static void main(String[] args) { String jsurf_filename = ""; Options options = new Options(); options.addOption("s", "size", true, "width (and height) of a image (default: " + size + ")"); options.addOption("q", "quality", true, "quality of the rendering: 0 (low), 1 (medium, default), 2 (high), 3 (extreme)"); options.addOption("o", "output", true, "output PNG into this file (- means standard output. Use ./- to denote a file literally named -.)"); CommandLineParser parser = new PosixParser(); HelpFormatter formatter = new HelpFormatter(); String cmd_line_syntax = "jsurf [options] jsurf_file"; String help_header = "jsurf is a renderer for algebraic surfaces. If - is specified as a filename the jsurf file is read from standard input. " + "Use ./- to denote a file literally named -."; String help_footer = ""; try { CommandLine cmd = parser.parse(options, args); if (cmd.getArgs().length > 0) jsurf_filename = cmd.getArgs()[0]; else { formatter.printHelp(cmd_line_syntax, help_header, options, help_footer); return; } if (cmd.hasOption("output")) { } if (cmd.hasOption("size")) size = Integer.parseInt(cmd.getOptionValue("size")); int quality = 1; if (cmd.hasOption("quality")) quality = Integer.parseInt(cmd.getOptionValue("quality")); switch (quality) { case 0: aam = AntiAliasingMode.ADAPTIVE_SUPERSAMPLING; aap = AntiAliasingPattern.OG_1x1; break; case 2: aam = AntiAliasingMode.ADAPTIVE_SUPERSAMPLING; aap = AntiAliasingPattern.OG_4x4; break; case 3: aam = AntiAliasingMode.SUPERSAMPLING; aap = AntiAliasingPattern.OG_4x4; break; case 1: aam = AntiAliasingMode.ADAPTIVE_SUPERSAMPLING; aap = AntiAliasingPattern.QUINCUNX; } } catch (ParseException exp) { System.out.println("Unexpected exception:" + exp.getMessage()); System.exit(-1); } catch (NumberFormatException nfe) { formatter.printHelp(cmd_line_syntax, help_header, options, help_footer); System.exit(-1); } final Properties jsurf = new Properties(); try { if (jsurf_filename.equals("-")) jsurf.load(System.in); else jsurf.load(new FileReader(jsurf_filename)); FileFormat.load(jsurf, asr); } catch (Exception e) { System.err.println("Unable to read jsurf file " + jsurf_filename); e.printStackTrace(); System.exit(-2); } asr.setAntiAliasingMode(aam); asr.setAntiAliasingPattern(aap); // display the image in a window final String window_title = "jsurf: " + jsurf_filename; SwingUtilities.invokeLater(new Runnable() { public void run() { JFrame f = new JFrame(window_title); f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); JSurferRenderPanel p = null; try { p = new JSurferRenderPanel(jsurf); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } f.setContentPane(p); // f.getContentPane().add( new JLabel( new ImageIcon( window_image ) ) ); f.pack(); // f.setResizable( false ); f.setVisible(true); } }); }
From source file:com.willwinder.universalgcodesender.MainWindow.java
/** * @param args the command line arguments *//*from ww w . j av a 2 s . com*/ public static void main(String args[]) { /* Set the Nimbus look and feel */ //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) "> /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel. * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html */ try { for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) { if ("Nimbus".equals(info.getName())) { javax.swing.UIManager.setLookAndFeel(info.getClassName()); break; } } } catch (ClassNotFoundException ex) { java.util.logging.Logger.getLogger(MainWindow.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (InstantiationException ex) { java.util.logging.Logger.getLogger(MainWindow.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (IllegalAccessException ex) { java.util.logging.Logger.getLogger(MainWindow.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (javax.swing.UnsupportedLookAndFeelException ex) { java.util.logging.Logger.getLogger(MainWindow.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } //</editor-fold> // Fix look and feel to use CMD+C/X/V/A instead of CTRL if (SystemUtils.IS_OS_MAC) { Collection<InputMap> ims = new ArrayList<>(); ims.add((InputMap) UIManager.get("TextField.focusInputMap")); ims.add((InputMap) UIManager.get("TextArea.focusInputMap")); ims.add((InputMap) UIManager.get("EditorPane.focusInputMap")); ims.add((InputMap) UIManager.get("FormattedTextField.focusInputMap")); ims.add((InputMap) UIManager.get("PasswordField.focusInputMap")); ims.add((InputMap) UIManager.get("TextPane.focusInputMap")); int c = KeyEvent.VK_C; int v = KeyEvent.VK_V; int x = KeyEvent.VK_X; int a = KeyEvent.VK_A; int meta = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); for (InputMap im : ims) { im.put(KeyStroke.getKeyStroke(c, meta), DefaultEditorKit.copyAction); im.put(KeyStroke.getKeyStroke(v, meta), DefaultEditorKit.pasteAction); im.put(KeyStroke.getKeyStroke(x, meta), DefaultEditorKit.cutAction); im.put(KeyStroke.getKeyStroke(a, meta), DefaultEditorKit.selectAllAction); } } /* Create the form */ GUIBackend backend = new GUIBackend(); final MainWindow mw = new MainWindow(backend); /* Apply the settings to the MainWindow bofore showing it */ mw.arrowMovementEnabled.setSelected(mw.settings.isManualModeEnabled()); mw.stepSizeSpinner.setValue(mw.settings.getManualModeStepSize()); boolean unitsAreMM = mw.settings.getDefaultUnits().equals("mm"); mw.mmRadioButton.setSelected(unitsAreMM); mw.inchRadioButton.setSelected(!unitsAreMM); mw.fileChooser = new JFileChooser(mw.settings.getLastOpenedFilename()); mw.commPortComboBox.setSelectedItem(mw.settings.getPort()); mw.baudrateSelectionComboBox.setSelectedItem(mw.settings.getPortRate()); mw.scrollWindowCheckBox.setSelected(mw.settings.isScrollWindowEnabled()); mw.showVerboseOutputCheckBox.setSelected(mw.settings.isVerboseOutputEnabled()); mw.showCommandTableCheckBox.setSelected(mw.settings.isCommandTableEnabled()); mw.showCommandTableCheckBoxActionPerformed(null); mw.firmwareComboBox.setSelectedItem(mw.settings.getFirmwareVersion()); mw.setSize(mw.settings.getMainWindowSettings().width, mw.settings.getMainWindowSettings().height); mw.setLocation(mw.settings.getMainWindowSettings().xLocation, mw.settings.getMainWindowSettings().yLocation); mw.addComponentListener(new ComponentListener() { @Override public void componentResized(ComponentEvent ce) { mw.settings.getMainWindowSettings().height = ce.getComponent().getSize().height; mw.settings.getMainWindowSettings().width = ce.getComponent().getSize().width; } @Override public void componentMoved(ComponentEvent ce) { mw.settings.getMainWindowSettings().xLocation = ce.getComponent().getLocation().x; mw.settings.getMainWindowSettings().yLocation = ce.getComponent().getLocation().y; } @Override public void componentShown(ComponentEvent ce) { } @Override public void componentHidden(ComponentEvent ce) { } }); /* Display the form */ java.awt.EventQueue.invokeLater(new Runnable() { @Override public void run() { mw.setVisible(true); } }); mw.initFileChooser(); Runtime.getRuntime().addShutdownHook(new Thread() { @Override public void run() { if (mw.fileChooser.getSelectedFile() != null) { mw.settings.setLastOpenedFilename(mw.fileChooser.getSelectedFile().getAbsolutePath()); } mw.settings.setDefaultUnits(mw.inchRadioButton.isSelected() ? "inch" : "mm"); mw.settings.setManualModeStepSize(mw.getStepSize()); mw.settings.setManualModeEnabled(mw.arrowMovementEnabled.isSelected()); mw.settings.setPort(mw.commPortComboBox.getSelectedItem().toString()); mw.settings.setPortRate(mw.baudrateSelectionComboBox.getSelectedItem().toString()); mw.settings.setScrollWindowEnabled(mw.scrollWindowCheckBox.isSelected()); mw.settings.setVerboseOutputEnabled(mw.showVerboseOutputCheckBox.isSelected()); mw.settings.setCommandTableEnabled(mw.showCommandTableCheckBox.isSelected()); mw.settings.setFirmwareVersion(mw.firmwareComboBox.getSelectedItem().toString()); SettingsFactory.saveSettings(mw.settings); if (mw.pendantUI != null) { mw.pendantUI.stop(); } } }); // Check command line for a file to open. boolean open = false; for (String arg : args) { if (open) { try { backend.setGcodeFile(new File(arg)); } catch (Exception ex) { Logger.getLogger(MainWindow.class.getName()).log(Level.SEVERE, null, ex); System.exit(1); } } if (arg.equals("--open") || arg.equals("-o")) { open = true; } } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *//*from w w w . j av a 2 s. c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); } DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(DiaFile.Filename + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:FDREstimator.ExportWithEstimatedFDR.java
/** * @param args the command line arguments *//* w ww . ja v a2 s .co m*/ public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException, XmlPullParserException, InterruptedException, SQLException { System.out.println( "================================================================================================="); System.out.println("Umpire search result parser(version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length == 0) { System.out.println( "command : java -jar -Xmx1G Umpire-SearchResultParser.jar [Options] [Combined ProtXML file] [PepXML files...]"); System.out.println(""); System.out.println("ProtXML extension: *.prot.xml or *.ProtXML"); System.out.println("PepXML extension: *.pep.xml or *.PepXML"); System.out.println("\nOptions"); System.out.println("\t-MP\tMin protein parsing probability\tex: -MP0.1f (default: -1, no filtering)"); System.out.println("\t-Mp\tMin PSM parsing probability\tex: -Mp0.1f (default: -1, no filtering)"); System.out.println("\t-fP\tProtein FDR\tex: -fP0.01 (default: 0.01, no filtering: -1)"); System.out.println("\t-fp\tPeptide FDR\tex: -fp0.05 (default: 0.01, no filtering: -1)"); System.out.println("\t-d\tDecoy tag prefix\tex: -dDECOY (default: rev_)"); System.out.println( "\t-C\t(0 or 1) Correct mass diff derived from isotope error\tex:-C0 (default:0, no correction)"); System.out.println("\t-fa\tFasta file"); System.out.println("\t-N\tOutput filename"); System.out.println( "\t-pt\tInitial protein probability filtering threshold\tex: -pt0.5 (default: 0.5, no filtering : -1)"); System.out.println( "\t-rf\tR factor threshold, proteins with protein probablity less than the threshold will be used to estimate the R factor \n\t\tex: -rf0.2 (default: 0.2, do not use R factor: -1)"); return; } ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "parser_debug.log"); float protFDR = 0.01f; float pepFDR = 0.01f; float MinpepProb = -1f; float MinprotProb = -1f; boolean CorrectMassDiff = false; String DecoyTag = "rev_"; String Fasta = ""; String Outputname = ""; float protprob = 0.5f; float rfthreshold = 0.2f; String ProtXML = ""; ArrayList<String> PepXML = new ArrayList<>(); for (int i = 0; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].startsWith("-fP")) { protFDR = Float.parseFloat(args[i].substring(3)); Logger.getRootLogger().info("Protein FDR: " + protFDR); } if (args[i].startsWith("-fp")) { pepFDR = Float.parseFloat(args[i].substring(3)); Logger.getRootLogger().info("Peptide FDR: " + pepFDR); } if (args[i].startsWith("-MP")) { MinprotProb = Float.parseFloat(args[i].substring(3)); Logger.getRootLogger().info("Min protein parsing probability: " + MinprotProb); } if (args[i].startsWith("-Mp")) { MinpepProb = Float.parseFloat(args[i].substring(3)); Logger.getRootLogger().info("Min PSM parsing probability: " + MinpepProb); } if (args[i].startsWith("-d")) { DecoyTag = args[i].substring(2); Logger.getRootLogger().info("Decoy tag: " + DecoyTag); } if (args[i].startsWith("-fa")) { Fasta = args[i].substring(3); Logger.getRootLogger().info("Fasta file: " + Fasta); } if (args[i].startsWith("-N")) { Outputname = args[i].substring(2); Logger.getRootLogger().info("Output filename: " + Outputname); } if (args[i].startsWith("-C")) { if (args[i].substring(2).equals("1")) { CorrectMassDiff = true; } Logger.getRootLogger().info("Correct mass diff: " + CorrectMassDiff); } if (args[i].startsWith("-pt")) { protprob = Float.parseFloat(args[i].substring(3)); Logger.getRootLogger().info("Initial protein probablity filtering threshold: " + protprob); } if (args[i].startsWith("-rf")) { rfthreshold = Float.parseFloat(args[i].substring(3)); Logger.getRootLogger().info("R factor threshold: " + rfthreshold); } } if (args[i].endsWith(".pep.xml") || args[i].endsWith(".PepXML")) { PepXML.add(args[i]); } if (args[i].endsWith(".prot.xml") || args[i].endsWith(".ProtXML")) { ProtXML = args[i]; } } if (!Outputname.equals("")) { Outputname = Outputname + "_"; } Outputname = Outputname + MSUmpire.Utility.DateTimeTag.GetTag(); LCMSID lcmsid = new LCMSID(Outputname, DecoyTag, Fasta); for (String pepxml : PepXML) { LCMSID pepxmlid = new LCMSID(pepxml, DecoyTag, Fasta); PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, MinpepProb, CorrectMassDiff); if (pepFDR != -1f) { pepxmlid.FilterByPepDecoyFDR(DecoyTag, pepFDR); } Logger.getRootLogger().info("peptide No.:" + pepxmlid.GetPepIonList().size() + "; Peptide level threshold: " + pepxmlid.PepProbThreshold); for (PepIonID pepID : pepxmlid.GetPepIonList().values()) { lcmsid.AddPeptideID(pepID); } } if (!"".equals(ProtXML)) { ProtXMLParser protxmlparser = new ProtXMLParser(lcmsid, ProtXML, MinprotProb); lcmsid.DecoyTag = DecoyTag; if (protprob != -1f) { lcmsid.RemoveLowLocalPWProtein(protprob); } float rf = 1f; if (rfthreshold != -1f) { rf = lcmsid.GetRFactor(rfthreshold); } if (protFDR != -1f) { lcmsid.FilterByProteinDecoyFDRUsingMaxIniProb(lcmsid.DecoyTag, protFDR / rf); } if (!"".equals(Fasta)) { lcmsid.LoadSequence(); } lcmsid.ReMapProPep(); lcmsid.ExportProtID(); } lcmsid.CreateInstanceForAllPepIon(); lcmsid.ExportPepID(); Logger.getRootLogger().info("Protein No.:" + lcmsid.ProteinList.size() + "; All peptide ions.:" + lcmsid.GetPepIonList().size()); }
From source file:com.netscape.cms.servlet.test.DRMTest.java
public static void main(String args[]) throws InvalidKeyException, NoSuchAlgorithmException, InvalidKeySpecException, SignatureException, IOException { String host = null;/*from w w w . j a v a 2 s .c o m*/ String port = null; String token_pwd = null; String db_dir = "./"; String protocol = "http"; String clientCertNickname = "KRA Administrator of Instance pki-kra's SjcRedhat Domain ID"; // parse command line arguments Options options = new Options(); options.addOption("h", true, "Hostname of the DRM"); options.addOption("p", true, "Port of the DRM"); options.addOption("w", true, "Token password"); options.addOption("d", true, "Directory for tokendb"); options.addOption("s", true, "Attempt Optional Secure SSL connection"); options.addOption("c", true, "Optional SSL Client cert Nickname"); try { CommandLineParser parser = new PosixParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { host = cmd.getOptionValue("h"); } else { System.err.println("Error: no hostname provided."); usage(options); } if (cmd.hasOption("p")) { port = cmd.getOptionValue("p"); } else { System.err.println("Error: no port provided"); usage(options); } if (cmd.hasOption("w")) { token_pwd = cmd.getOptionValue("w"); } else { System.err.println("Error: no token password provided"); usage(options); } if (cmd.hasOption("d")) { db_dir = cmd.getOptionValue("d"); } if (cmd.hasOption("s")) { if (cmd.getOptionValue("s") != null && cmd.getOptionValue("s").equals("true")) { protocol = "https"; } } if (cmd.hasOption("c")) { String nick = cmd.getOptionValue("c"); if (nick != null && protocol.equals("https")) { clientCertNickname = nick; } } } catch (ParseException e) { System.err.println("Error in parsing command line options: " + e.getMessage()); usage(options); } // used for crypto operations byte iv[] = { 0x1, 0x1, 0x1, 0x1, 0x1, 0x1, 0x1, 0x1 }; try { iv = genIV(8); } catch (Exception e) { log("Can't generate initialization vector use default: " + e.toString()); } // used for wrapping to send data to DRM String transportCert = null; // Data to be archived SymmetricKey vek = null; String passphrase = null; // Session keys and passphrases for recovery SymmetricKey sessionKey = null; byte[] wrappedRecoveryKey = null; String recoveryPassphrase = null; byte[] wrappedRecoveryPassphrase = null; // retrieved data (should match archived data) byte[] encryptedData = null; String recoveredKey = null; // various ids used in recovery/archival operations KeyId keyId = null; String clientKeyId = null; RequestId recoveryRequestId = null; // Variables for data structures from calls KeyRequestResponse requestResponse = null; Key keyData = null; KeyInfo keyInfo = null; // Initialize token try { CryptoManager.initialize(db_dir); } catch (AlreadyInitializedException e) { // it is ok if it is already initialized } catch (Exception e) { log("INITIALIZATION ERROR: " + e.toString()); System.exit(1); } // Set base URI and get client KRAClient client; SystemCertClient systemCertClient; KeyClient keyClient; NSSCryptoProvider nssCrypto; try { ClientConfig config = new ClientConfig(); config.setServerURI(protocol + "://" + host + ":" + port + "/kra"); config.setCertNickname(clientCertNickname); config.setCertDatabase(db_dir); config.setCertPassword(token_pwd); nssCrypto = new NSSCryptoProvider(config); client = new KRAClient(new PKIClient(config, nssCrypto)); systemCertClient = (SystemCertClient) client.getClient("systemcert"); keyClient = (KeyClient) client.getClient("key"); } catch (Exception e) { e.printStackTrace(); return; } // Test 1: Get transport certificate from DRM transportCert = systemCertClient.getTransportCert().getEncoded(); transportCert = transportCert.substring(CertData.HEADER.length(), transportCert.indexOf(CertData.FOOTER)); keyClient.setTransportCert(transportCert); log("Transport Cert retrieved from DRM: " + transportCert); // Test 2: Get list of completed key archival requests log("\n\nList of completed archival requests"); KeyRequestInfoCollection list = keyClient.listRequests("complete", "securityDataEnrollment"); if (list.getTotal() == 0) { log("No requests found"); } else { Iterator<KeyRequestInfo> iter = list.getEntries().iterator(); while (iter.hasNext()) { KeyRequestInfo info = iter.next(); printRequestInfo(info); } } // Test 3: Get list of key recovery requests log("\n\nList of completed recovery requests"); KeyRequestInfoCollection list2 = keyClient.listRequests("complete", "securityDataRecovery"); if (list2.getTotal() == 0) { log("No requests found"); } else { Iterator<KeyRequestInfo> iter2 = list2.getEntries().iterator(); while (iter2.hasNext()) { KeyRequestInfo info = iter2.next(); printRequestInfo(info); } } // Test 4: Generate and archive a symmetric key log("Archiving symmetric key"); clientKeyId = "UUID: 123-45-6789 VEK " + Calendar.getInstance().getTime().toString(); try { vek = nssCrypto.generateSessionKey(); byte[] encoded = nssCrypto.createPKIArchiveOptions(transportCert, vek, null, KeyRequestResource.DES3_ALGORITHM, 0, iv); KeyRequestResponse info = keyClient.archivePKIOptions(clientKeyId, KeyRequestResource.SYMMETRIC_KEY_TYPE, KeyRequestResource.DES3_ALGORITHM, 0, encoded); log("Archival Results:"); printRequestInfo(info.getRequestInfo()); keyId = info.getKeyId(); } catch (Exception e) { log("Exception in archiving symmetric key:" + e.getMessage()); e.printStackTrace(); } //Test 5: Get keyId for active key with client ID log("Getting key ID for symmetric key"); keyInfo = keyClient.getActiveKeyInfo(clientKeyId); printKeyInfo(keyInfo); KeyId keyId2 = keyInfo.getKeyId(); if (keyId2 == null) { log("No archived key found"); } else { log("Archived Key found: " + keyId); } if (!keyId.equals(keyId2)) { log("Error: key ids from search and archival do not match"); } else { log("Success: keyids from search and archival match."); } // Test 6: Submit a recovery request for the symmetric key using a session key log("Submitting a recovery request for the symmetric key using session key"); try { sessionKey = nssCrypto.generateSessionKey(); wrappedRecoveryKey = CryptoUtil.wrapSymmetricKey(nssCrypto.getManager(), nssCrypto.getToken(), transportCert, sessionKey); keyData = keyClient.retrieveKey(keyId, wrappedRecoveryKey); } catch (Exception e) { log("Exception in recovering symmetric key using session key: " + e.getMessage()); } encryptedData = keyData.getEncryptedData(); try { recoveredKey = Utils.base64encode(nssCrypto.unwrapWithSessionKey(encryptedData, sessionKey, KeyRequestResource.DES3_ALGORITHM, keyData.getNonceData())); } catch (Exception e) { log("Exception in unwrapping key: " + e.toString()); e.printStackTrace(); } if (!recoveredKey.equals(Utils.base64encode(vek.getEncoded()))) { log("Error: recovered and archived keys do not match!"); } else { log("Success: recoverd and archived keys match!"); } // Test 7: Submit a recovery request for the symmetric key using a passphrase log("Submitting a recovery request for the symmetric key using a passphrase"); recoveryPassphrase = "Gimme me keys please"; try { sessionKey = nssCrypto.generateSessionKey(); wrappedRecoveryPassphrase = nssCrypto.wrapWithSessionKey(recoveryPassphrase, iv, sessionKey, KeyRequestResource.DES3_ALGORITHM); wrappedRecoveryKey = nssCrypto.wrapSessionKeyWithTransportCert(sessionKey, transportCert); keyData = keyClient.retrieveKeyUsingWrappedPassphrase(keyId, wrappedRecoveryKey, wrappedRecoveryPassphrase, iv); } catch (Exception e) { log("Exception in recovering symmetric key using passphrase" + e.toString()); e.printStackTrace(); } encryptedData = keyData.getEncryptedData(); try { recoveredKey = Utils.base64encode(nssCrypto.unwrapWithPassphrase(encryptedData, recoveryPassphrase)); } catch (Exception e) { log("Error: unable to unwrap key using passphrase"); e.printStackTrace(); } if (recoveredKey == null || !recoveredKey.equals(Utils.base64encode(vek.getEncoded()))) { log("Error: recovered and archived keys do not match!"); } else { log("Success: recovered and archived keys do match!"); } passphrase = "secret12345"; // Test 8: Generate and archive a passphrase clientKeyId = "UUID: 123-45-6789 RKEK " + Calendar.getInstance().getTime().toString(); try { requestResponse = keyClient.archivePassphrase(clientKeyId, passphrase); log("Archival Results:"); printRequestInfo(requestResponse.getRequestInfo()); keyId = requestResponse.getKeyId(); } catch (Exception e) { log("Exception in archiving symmetric key:" + e.toString()); e.printStackTrace(); } //Test 9: Get keyId for active passphrase with client ID log("Getting key ID for passphrase"); keyInfo = keyClient.getActiveKeyInfo(clientKeyId); printKeyInfo(keyInfo); keyId2 = keyInfo.getKeyId(); if (keyId2 == null) { log("No archived key found"); } else { log("Archived Key found: " + keyId); } if (!keyId.equals(keyId2)) { log("Error: key ids from search and archival do not match"); } else { log("Success: key ids from search and archival do match!"); } // Test 10: Submit a recovery request for the passphrase using a session key log("Submitting a recovery request for the passphrase using session key"); sessionKey = null; wrappedRecoveryKey = null; try { keyData = keyClient.retrieveKeyByPassphrase(keyId, recoveryPassphrase); } catch (Exception e) { log("Exception in recovering passphrase using session key: " + e.getMessage()); } encryptedData = keyData.getEncryptedData(); try { recoveredKey = new String(nssCrypto.unwrapWithPassphrase(encryptedData, recoveryPassphrase), "UTF-8"); } catch (Exception e) { log("Exception in unwrapping key: " + e.toString()); e.printStackTrace(); } if (recoveredKey == null || !recoveredKey.equals(passphrase)) { log("Error: recovered and archived passphrases do not match!"); } else { log("Success: recovered and archived passphrases do match!"); } // Test 11: Submit a recovery request for the passphrase using a passphrase try { sessionKey = nssCrypto.generateSessionKey(); wrappedRecoveryKey = nssCrypto.wrapSessionKeyWithTransportCert(sessionKey, transportCert); wrappedRecoveryPassphrase = nssCrypto.wrapWithSessionKey(recoveryPassphrase, iv, sessionKey, KeyRequestResource.DES3_ALGORITHM); keyData = keyClient.retrieveKeyUsingWrappedPassphrase(keyId, wrappedRecoveryKey, wrappedRecoveryPassphrase, iv); } catch (Exception e1) { e1.printStackTrace(); System.out.println("Test 17: " + e1.getMessage()); System.exit(-1); } encryptedData = keyData.getEncryptedData(); try { recoveredKey = new String(nssCrypto.unwrapWithPassphrase(encryptedData, recoveryPassphrase), "UTF-8"); } catch (Exception e) { log("Error: cannot unwrap key using passphrase"); e.printStackTrace(); } if (recoveredKey == null || !recoveredKey.equals(passphrase)) { log("Error: recovered and archived passphrases do not match!"); } else { log("Success: recovered and archived passphrases do match!"); } // Test 12: Get key log("Getting passphrase: " + keyId); try { keyData = keyClient.retrieveKeyByPassphrase(keyId, recoveryPassphrase); } catch (Exception e1) { e1.printStackTrace(); } encryptedData = keyData.getEncryptedData(); try { recoveredKey = new String(nssCrypto.unwrapWithPassphrase(encryptedData, recoveryPassphrase), "UTF-8"); } catch (Exception e) { log("Error: Can't unwrap recovered key using passphrase"); e.printStackTrace(); } if (recoveredKey == null || !recoveredKey.equals(passphrase)) { log("Error: recovered and archived passphrases do not match!"); } else { log("Success: recovered and archived passphrases do match!"); } // Test 13: Get non-existent request RequestId requestId = new RequestId("0xabcdef"); log("Getting non-existent request: " + requestId.toHexString()); try { keyClient.getRequestInfo(requestId); log("Error: getting non-existent request does not throw an exception"); } catch (RequestNotFoundException e) { log("Success: getting non-existent request throws an exception: " + e.getMessage() + " (" + e.getRequestId().toHexString() + ")"); } // Test 14: Request x509 key recovery // This test requires to retrieve keyId and matching certificate // from installed instances of CA and DRM String keyID = "1"; String b64Certificate = "MIIC+TCCAeGgAwIBAgIBDDANBgkqhkiG9w0BAQsFADBOMSswKQYDVQQKDCJ1c2Vy" + "c3lzLnJlZGhhdC5jb20gU2VjdXJpdHkgRG9tYWluMR8wHQYDVQQDDBZDQSBTaWdu" + "aW5nIENlcnRpZmljYXRlMB4XDTEzMTAyNTE5MzQwM1oXDTE0MDQyMzE5MzQwM1ow" + "EzERMA8GCgmSJomT8ixkAQEMAXgwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB" + "ALhLfGmKvxFsKXPh49q1QsluXU3WlyS1XnpDLgOAhgTNgO4sG6CpPdv6hZYIvQBb" + "ZQ5bhuML+NXK+Q+EIiNk1cUTxgL3a30sPzy6QaFWxwM8i4uXm4nCBYv7T+n4V6/O" + "xHIM2Ch/dviAb3vz+M9trErv9t+d2H8jNXT3sHuDb/kvAgMBAAGjgaAwgZ0wHwYD" + "VR0jBBgwFoAUh1cxWFRY+nMsx4odQQI1GqyFxP8wSwYIKwYBBQUHAQEEPzA9MDsG" + "CCsGAQUFBzABhi9odHRwOi8vZG9ndGFnMjAudXNlcnN5cy5yZWRoYXQuY29tOjgw" + "ODAvY2Evb2NzcDAOBgNVHQ8BAf8EBAMCBSAwHQYDVR0lBBYwFAYIKwYBBQUHAwIG" + "CCsGAQUFBwMEMA0GCSqGSIb3DQEBCwUAA4IBAQCvmbUzQOouE2LgQQcKfmgwwJMJ" + "9tMrPwDUtyFdaIFoPL4uZaujSscaN4IWK2r5vIMJ65jwYCI7sI9En2ZfO28J9dQj" + "lpqu6TaJ+xtaMk7OvXpVB7lJk73HAttMGjETlkoq/6EjxcugmJsDqVD0b2tO7Vd0" + "hroBe2uPDHM2ASewZF415lUcRh0URtmxSazTInbyxpmy1wgSJQ0C6fMCeT+hUFlA" + "0P4k1TIprapGVq7FpKcqlhK2gTBfTSnoO7gmXG/9MxJiYpb/Aph8ptXq6quHz1Mj" + "greWr3xTsy6gF2yphUEkGHh4v22XvK+FLx9Jb6zloMWA2GG9gpUpvMnl1fH4"; log("Requesting X509 key recovery."); recoveryRequestId = keyClient.recoverKey(new KeyId(keyID), null, null, null, b64Certificate) .getRequestInfo().getRequestId(); log("Requesting X509 key recovery request: " + recoveryRequestId); // Test 55: Approve x509 key recovery log("Approving X509 key recovery request: " + recoveryRequestId); keyClient.approveRequest(recoveryRequestId); // Test 16: Recover x509 key log("Recovering X509 key based on request: " + recoveryRequestId); try { // KeyData recoveredX509Key = client.recoverKey(recoveryRequestId, "netscape"); // log("Success: X509Key recovered: "+ recoveredX509Key.getP12Data()); } catch (RequestNotFoundException e) { log("Error: recovering X509Key"); } // Test 1: Get transport certificate from DRM transportCert = systemCertClient.getTransportCert().getEncoded(); transportCert = transportCert.substring(CertData.HEADER.length(), transportCert.indexOf(CertData.FOOTER)); log("Transport Cert retrieved from DRM: " + transportCert); // Test 17: Get list of completed key archival requests log("\n\nList of completed archival requests"); list = keyClient.listRequests("complete", IRequest.SYMKEY_GENERATION_REQUEST); if (list.getTotal() == 0) { log("No requests found"); } else { Iterator<KeyRequestInfo> iter = list.getEntries().iterator(); while (iter.hasNext()) { KeyRequestInfo info = iter.next(); printRequestInfo(info); } } // test 18: Generate symmetric key clientKeyId = "Symmetric Key #1234f " + Calendar.getInstance().getTime().toString(); List<String> usages = new ArrayList<String>(); usages.add(SymKeyGenerationRequest.DECRYPT_USAGE); usages.add(SymKeyGenerationRequest.ENCRYPT_USAGE); KeyRequestResponse genKeyResponse = keyClient.generateSymmetricKey(clientKeyId, KeyRequestResource.AES_ALGORITHM, 128, usages, null); printRequestInfo(genKeyResponse.getRequestInfo()); keyId = genKeyResponse.getKeyId(); // test 19: Get keyId for active key with client ID log("Getting key ID for symmetric key"); keyInfo = keyClient.getActiveKeyInfo(clientKeyId); printKeyInfo(keyInfo); keyId2 = keyInfo.getKeyId(); if (keyId2 == null) { log("No archived key found"); } else { log("Archived Key found: " + keyId); } if (!keyId.equals(keyId2)) { log("Error: key ids from search and archival do not match"); } else { log("Success: keyids from search and archival match."); } // Test 20: Submit a recovery request for the symmetric key using a session key log("Submitting a recovery request for the symmetric key using session key"); try { sessionKey = nssCrypto.generateSessionKey(); wrappedRecoveryKey = nssCrypto.wrapSessionKeyWithTransportCert(sessionKey, transportCert); keyData = keyClient.retrieveKey(keyId, wrappedRecoveryKey); } catch (Exception e) { log("Exception in recovering symmetric key using session key: " + e.getMessage()); } encryptedData = keyData.getEncryptedData(); try { recoveredKey = new String(nssCrypto.unwrapWithSessionKey(encryptedData, sessionKey, KeyRequestResource.DES3_ALGORITHM, keyData.getNonceData())); } catch (Exception e) { log("Exception in unwrapping key: " + e.toString()); e.printStackTrace(); } // test 21: Generate symmetric key - invalid algorithm try { genKeyResponse = keyClient.generateSymmetricKey("Symmetric Key #1235", "AFS", 128, usages, null); } catch (Exception e) { log("Exception: " + e); } // test 22: Generate symmetric key - invalid key size try { genKeyResponse = keyClient.generateSymmetricKey("Symmetric Key #1236", "AES", 0, usages, null); } catch (Exception e) { log("Exception: " + e); } // test 23: Generate symmetric key - usages not defined try { genKeyResponse = keyClient.generateSymmetricKey("Symmetric Key #1236", "DES", 56, null, null); } catch (Exception e) { log("Exception: " + e); } // Test 24: Generate and archive a symmetric key of type AES log("Archiving symmetric key"); clientKeyId = "UUID: 123-45-6789 VEK " + Calendar.getInstance().getTime().toString(); try { vek = nssCrypto.generateSymmetricKey(KeyRequestResource.AES_ALGORITHM, 128); byte[] encoded = CryptoUtil.createPKIArchiveOptions(nssCrypto.getManager(), nssCrypto.getToken(), transportCert, vek, null, KeyGenAlgorithm.DES3, 0, new IVParameterSpec(iv)); KeyRequestResponse response = keyClient.archivePKIOptions(clientKeyId, KeyRequestResource.SYMMETRIC_KEY_TYPE, KeyRequestResource.AES_ALGORITHM, 128, encoded); log("Archival Results:"); printRequestInfo(response.getRequestInfo()); keyId = response.getKeyId(); } catch (Exception e) { log("Exception in archiving symmetric key:" + e.getMessage()); e.printStackTrace(); } //Test 25: Get keyId for active key with client ID log("Getting key ID for symmetric key"); keyInfo = keyClient.getActiveKeyInfo(clientKeyId); printKeyInfo(keyInfo); keyId2 = keyInfo.getKeyId(); if (keyId2 == null) { log("No archived key found"); } else { log("Archived Key found: " + keyId); } if (!keyId.equals(keyId2)) { log("Error: key ids from search and archival do not match"); } else { log("Success: keyids from search and archival match."); } // Test 26: Submit a recovery request for the symmetric key log("Submitting a recovery request for the symmetric key without using session key"); try { keyData = keyClient.retrieveKey(keyId); } catch (Exception e) { log("Exception in recovering symmetric key using session key: " + e.getMessage()); } // Since no session key is provided externally, the retrieveKey method // generates a session key, wraps it with transport cert and completes the request. // The encrypted data is then unwrapped using the temporary session key and set to // the attribute privateData. recoveredKey = Utils.base64encode(keyData.getData()); if (!recoveredKey.equals(Utils.base64encode(vek.getEncoded()))) { log("Error: recovered and archived keys do not match!"); } else { log("Success: recoverd and archived keys match!"); } // Test 27: Get key info log("getting key info for existing key"); printKeyInfo(keyClient.getKeyInfo(keyId)); //Test 28: Modify status log("modify the key status"); keyClient.modifyKeyStatus(keyId, KeyResource.KEY_STATUS_INACTIVE); keyInfo = keyClient.getKeyInfo(keyId); printKeyInfo(keyInfo); //Test 29: Confirm no more active keys with this ID log("look for active keys with this id"); clientKeyId = keyInfo.getClientKeyID(); try { keyInfo = keyClient.getActiveKeyInfo(clientKeyId); printKeyInfo(keyInfo); } catch (ResourceNotFoundException e) { log("Success: ResourceNotFound exception thrown: " + e); } // Test asymmetric key generation. String[] algs = { "RSA", "DSA" }; for (int i = 0; i < algs.length; i++) { // Test 30: Generate Asymmetric keys - RSA key System.out.println("\nTesting asymmetric key generation for algorithm " + algs[i]); clientKeyId = "AsymKey #" + Calendar.getInstance().getTimeInMillis(); usages.clear(); usages.add(AsymKeyGenerationRequest.SIGN); usages.add(AsymKeyGenerationRequest.VERIFY); KeyRequestResponse response = keyClient.generateAsymmetricKey(clientKeyId, algs[i], 1024, usages, null); printRequestInfo(response.getRequestInfo()); System.out.println(); // Test 31: Get information of the newly generated asymmetric keys System.out.println("Fetch information of the newly generated asymmetric keys."); System.out.println(); KeyInfo info = keyClient.getKeyInfo(response.getKeyId()); printKeyInfo(info); System.out.println(); // Test 32: Retrieve private key data System.out.println("Retrieving and verifying the generated private key."); try { keyData = keyClient.retrieveKey(response.getKeyId()); } catch (Exception e) { log("Exception retrieving the private key data."); e.printStackTrace(); } // Test 33: Verify the generated key pair. if (isKeyPairValid(algs[i], keyData.getData(), info.getPublicKey())) { log("The key pair generated using " + algs[i] + " algorithm is valid."); } else { log("The key pair generated using " + algs[i] + " algorithm is invalid."); } System.out.println(); } // Test 34: }
From source file:de.morbz.osmpoispbf.Scanner.java
public static void main(String[] args) { System.out.println("OsmPoisPbf " + VERSION + " started"); // Get input file if (args.length < 1) { System.out.println("Error: Please provide an input file"); System.exit(-1);//w ww . java 2 s . co m } String inputFile = args[args.length - 1]; // Get output file String outputFile; int index = inputFile.indexOf('.'); if (index != -1) { outputFile = inputFile.substring(0, index); } else { outputFile = inputFile; } outputFile += ".csv"; // Setup CLI parameters options = new Options(); options.addOption("ff", "filterFile", true, "The file that is used to filter categories"); options.addOption("of", "outputFile", true, "The output CSV file to be written"); options.addOption("rt", "requiredTags", true, "Comma separated list of tags that are required [name]"); options.addOption("ut", "undesiredTags", true, "Comma separated list of tags=value combinations that should be filtered [key=value]"); options.addOption("ot", "outputTags", true, "Comma separated list of tags that are exported [name]"); options.addOption("ph", "printHeader", false, "If flag is set, the `outputTags` are printed as first line in the output file."); options.addOption("r", "relations", false, "Parse relations"); options.addOption("nw", "noWays", false, "Don't parse ways"); options.addOption("nn", "noNodes", false, "Don't parse nodes"); options.addOption("u", "allowUnclosedWays", false, "Allow ways that aren't closed"); options.addOption("d", "decimals", true, "Number of decimal places of coordinates [7]"); options.addOption("s", "separator", true, "Separator character for CSV [|]"); options.addOption("v", "verbose", false, "Print all found POIs"); options.addOption("h", "help", false, "Print this help"); // Parse parameters CommandLine line = null; try { line = (new DefaultParser()).parse(options, args); } catch (ParseException exp) { System.err.println(exp.getMessage()); printHelp(); System.exit(-1); } // Help if (line.hasOption("help")) { printHelp(); System.exit(0); } // Get filter file String filterFile = null; if (line.hasOption("filterFile")) { filterFile = line.getOptionValue("filterFile"); } // Get output file if (line.hasOption("outputFile")) { outputFile = line.getOptionValue("outputFile"); } // Check files if (inputFile.equals(outputFile)) { System.out.println("Error: Input and output files are the same"); System.exit(-1); } File file = new File(inputFile); if (!file.exists()) { System.out.println("Error: Input file doesn't exist"); System.exit(-1); } // Check OSM entity types boolean parseNodes = true; boolean parseWays = true; boolean parseRelations = false; if (line.hasOption("noNodes")) { parseNodes = false; } if (line.hasOption("noWays")) { parseWays = false; } if (line.hasOption("relations")) { parseRelations = true; } // Unclosed ways allowed? if (line.hasOption("allowUnclosedWays")) { onlyClosedWays = false; } // Get CSV separator char separator = '|'; if (line.hasOption("separator")) { String arg = line.getOptionValue("separator"); if (arg.length() != 1) { System.out.println("Error: The CSV separator has to be exactly 1 character"); System.exit(-1); } separator = arg.charAt(0); } Poi.setSeparator(separator); // Set decimals int decimals = 7; // OSM default if (line.hasOption("decimals")) { String arg = line.getOptionValue("decimals"); try { int dec = Integer.valueOf(arg); if (dec < 0) { System.out.println("Error: Decimals must not be less than 0"); System.exit(-1); } else { decimals = dec; } } catch (NumberFormatException ex) { System.out.println("Error: Decimals have to be a number"); System.exit(-1); } } Poi.setDecimals(decimals); // Verbose mode? if (line.hasOption("verbose")) { printPois = true; } // Required tags if (line.hasOption("requiredTags")) { String arg = line.getOptionValue("requiredTags"); requiredTags = arg.split(","); } // Undesired tags if (line.hasOption("undesiredTags")) { String arg = line.getOptionValue("undesiredTags"); undesiredTags = new HashMap<>(); for (String undesired : arg.split(",")) { String[] keyVal = undesired.split("="); if (keyVal.length != 2) { System.out.println("Error: Undesired Tags have to formated like tag=value"); System.exit(-1); } if (!undesiredTags.containsKey(keyVal[0])) { undesiredTags.put(keyVal[0], new HashSet<>(1)); } undesiredTags.get(keyVal[0]).add(keyVal[1]); } } // Output tags if (line.hasOption("outputTags")) { String arg = line.getOptionValue("outputTags"); outputTags = arg.split(","); } // Get filter rules FilterFileParser parser = new FilterFileParser(filterFile); filters = parser.parse(); if (filters == null) { System.exit(-1); } // Setup CSV output try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), "UTF8")); } catch (IOException e) { System.out.println("Error: Output file error"); System.exit(-1); } // Print Header if (line.hasOption("printHeader")) { String header = "category" + separator + "osm_id" + separator + "lat" + separator + "lon"; for (int i = 0; i < outputTags.length; i++) { header += separator + outputTags[i]; } try { writer.write(header + "\n"); } catch (IOException e) { System.out.println("Error: Output file write error"); System.exit(-1); } } // Setup OSMonaut EntityFilter filter = new EntityFilter(parseNodes, parseWays, parseRelations); Osmonaut naut = new Osmonaut(inputFile, filter, false); // Start watch StopWatch stopWatch = new StopWatch(); stopWatch.start(); // Start OSMonaut String finalSeparator = String.valueOf(separator); naut.scan(new IOsmonautReceiver() { boolean entityNeeded; @Override public boolean needsEntity(EntityType type, Tags tags) { // Are there any tags? if (tags.size() == 0) { return false; } // Check required tags for (String tag : requiredTags) { if (!tags.hasKey(tag)) { return false; } } entityNeeded = getCategory(tags, filters) != null; if (undesiredTags != null && entityNeeded) { for (String key : undesiredTags.keySet()) { if (tags.hasKey(key)) { for (String val : undesiredTags.get(key)) { if (tags.hasKeyValue(key, val)) { return false; } } } } } return entityNeeded; } @Override public void foundEntity(Entity entity) { // Check if way is closed if (onlyClosedWays && entity.getEntityType() == EntityType.WAY) { if (!((Way) entity).isClosed()) { return; } } // Get category Tags tags = entity.getTags(); String cat = getCategory(tags, filters); if (cat == null) { return; } // Get center LatLon center = entity.getCenter(); if (center == null) { return; } // Make OSM-ID String type = ""; switch (entity.getEntityType()) { case NODE: type = "node"; break; case WAY: type = "way"; break; case RELATION: type = "relation"; break; } String id = String.valueOf(entity.getId()); // Make output tags String[] values = new String[outputTags.length]; for (int i = 0; i < outputTags.length; i++) { String key = outputTags[i]; if (tags.hasKey(key)) { values[i] = tags.get(key).replaceAll(finalSeparator, "").replaceAll("\"", ""); } } // Make POI poisFound++; Poi poi = new Poi(values, cat, center, type, id); // Output if (printPois && System.currentTimeMillis() > lastMillis + 40) { printPoisFound(); lastMillis = System.currentTimeMillis(); } // Write to file try { writer.write(poi.toCsv() + "\n"); } catch (IOException e) { System.out.println("Error: Output file write error"); System.exit(-1); } } }); // Close writer try { writer.close(); } catch (IOException e) { System.out.println("Error: Output file close error"); System.exit(-1); } // Output results stopWatch.stop(); printPoisFound(); System.out.println(); System.out.println("Elapsed time in milliseconds: " + stopWatch.getElapsedTime()); // Quit System.exit(0); }