public CSVParser(Reader input) throws IOException {
count = 0;
parsedValues = new ArrayList<>();
BufferedReader bufferedReader = null;
try {
String sCurrentLine;
bufferedReader = new BufferedReader(input);
bufferedReader.readLine(); // Discard title line
while ((sCurrentLine = bufferedReader.readLine()) != null) {
count++;
String[] split = sCurrentLine.split("\",\"");
if (split.length > 1) {
split[0] = StringUtils.strip(split[0], "\"");
split[split.length - 1] = StringUtils.strip(split[split.length - 1], "\"");
parsedValues.add(split);
}
}
} catch (Exception ex) {
System.out.println(ex.getMessage());
} finally {
assert bufferedReader != null;
bufferedReader.close();
}
}
/**
* *
* <li><b>Trim/Strip</b> - removes leading and trailing whitespace Strip-->Strips any of a set of
* characters from the start and end of a String
*/
@Test
public void testTrimStripStringUtils() {
System.out.println(strOne + ":" + strOne.length());
System.out.println(StringUtils.trim(" " + strOne + " ").length());
System.out.println(StringUtils.strip(" " + strOne + " ").length());
System.out.println(StringUtils.strip("zabcyx", "xyz"));
}
/**
* Creates a internal molgenis id from a vcf entity
*
* @param vcfEntity
* @return the id
*/
public static String createId(Entity vcfEntity) {
StringBuilder id = new StringBuilder();
id.append(StringUtils.strip(vcfEntity.get(CHROM).toString()));
id.append("_");
id.append(StringUtils.strip(vcfEntity.get(POS).toString()));
id.append("_");
id.append(StringUtils.strip(vcfEntity.get(REF).toString()));
id.append("_");
id.append(StringUtils.strip(vcfEntity.get(ALT).toString()));
return id.toString();
}
/**
* Returns the annotations to which should be displayed together with their namespace.
*
* <p>This will check the "show_ns" paramter for determining. the annotations to display. It also
* iterates over all nodes of the graph matching the type.
*
* @param input The input for the visualizer.
* @param types Which types of nodes to include
* @return
*/
public static Set<String> computeDisplayedNamespace(
VisualizerInput input, List<Class<? extends SNode>> types) {
if (input == null) {
return new HashSet<>();
}
String showNamespaceConfig =
input.getMappings().getProperty(GridComponent.MAPPING_SHOW_NAMESPACE);
if (showNamespaceConfig != null) {
SDocumentGraph graph = input.getDocument().getDocumentGraph();
Set<String> annoPool = new LinkedHashSet<>();
for (Class<? extends SNode> t : types) {
annoPool.addAll(
SToken.class.isAssignableFrom(t)
? getAnnotationLevelSet(graph, null, t)
: getAnnotationLevelSet(graph, input.getNamespace(), t));
}
if ("true".equalsIgnoreCase(showNamespaceConfig)) {
// all annotations should be displayed with a namespace
return annoPool;
} else if ("false".equalsIgnoreCase(showNamespaceConfig)) {
return new LinkedHashSet<>();
} else {
Set<String> annos = new LinkedHashSet<>();
List<String> defs =
Splitter.on(',').omitEmptyStrings().trimResults().splitToList(showNamespaceConfig);
for (String s : defs) {
// is regular expression?
if (s.startsWith("/") && s.endsWith("/")) {
// go over all remaining items in our pool of all annotations and
// check if they match
Pattern regex = Pattern.compile(StringUtils.strip(s, "/"));
LinkedList<String> matchingAnnos = new LinkedList<>();
for (String a : annoPool) {
if (regex.matcher(a).matches()) {
matchingAnnos.add(a);
}
}
annos.addAll(matchingAnnos);
annoPool.removeAll(matchingAnnos);
} else {
annos.add(s);
annoPool.remove(s);
}
}
return annos;
}
}
return new LinkedHashSet<>();
}
private static String validateName(String name) {
name = StringUtils.strip(name);
byte[] nameBytes = name.getBytes();
for (byte b : nameBytes) {
if ((b >= 0 && b <= 31) || (b == 127)) {
throw new IllegalArgumentException("name contains unprintable character(s)");
}
}
if (name.startsWith(".")) {
throw new IllegalArgumentException("name starts with a dot");
}
name = StringUtils.strip(name, ".");
if (StringUtils.contains(name, "\"*/:<>?\\|")) {
throw new IllegalArgumentException("name contains illegal character(s)");
}
return name;
}
private void addToQuote(String value) {
value = StringUtils.strip(value, QuoteRequest.garbageToStrip);
value = StringUtils.remove(value, "<br");
boolean hasSpecialChar = QuoteRequest.goodPattern.matcher(value).find();
if (!hasSpecialChar) {
if (value.length() > 0) {
this.quoteSet.add(value);
}
}
}
public static void main(String[] args) {
PasswordEncoder enc = new BCryptPasswordEncoder();
Arrays.asList("root", "admin", "usuario")
.stream()
.forEach(
pass -> {
System.out.println(
String.format(
"'%s', '%s'", pass, StringUtils.strip(enc.encode(pass).substring(10))));
});
}
private void extractDescription(
@NotNull Element element, String queryString, DictionaryObjectBuilder objectBuilder) {
Element descriptionNode = element.getElementsByClass("info").first();
if (descriptionNode != null) {
String description = descriptionNode.text();
description = StringUtils.removeStart(description, "(");
description = StringUtils.removeEnd(description, ")");
if (!StringUtils.equalsIgnoreCase(
description, queryString)) // Set description only if it is different from request string
objectBuilder.setDescription(StringUtils.strip(description));
}
}
public String getDockerHostIpAddress(Map<String, String> environment) {
String ipAddress = LOCALHOST; // Default of localhost
String dockerMachineName = getDockerMachineName(environment);
if (!dockerMachineName.isEmpty()) {
LOG.debug("Docker machine name = " + dockerMachineName);
CommandLine commandline = CommandLine.parse(DOCKER_MACHINE_IP);
commandline.addArgument(dockerMachineName);
LOG.debug("Running exec: " + commandline.toString());
try {
ipAddress = StringUtils.strip(runCommand(commandline));
} catch (IOException e) {
LOG.error("Unable to run exec command to find ip address.", e);
}
} else {
ipAddress = getDocker0AdapterIPAddress();
}
LOG.debug("Returned IP address: " + ipAddress);
return ipAddress;
}
@NotNull
private DictionaryObject processSingleNode(
@NotNull Element element, @NotNull Language language, String queryString) {
DictionaryObjectBuilder objectBuilder = ImmutableDictionaryObject.builder();
objectBuilder.setLanguage(language);
// Extract entry text:
String context =
StringUtils.substringBefore(element.text(), element.getElementsByTag("a").first().text());
String generalForm = context + element.getElementsByTag("a").first().text();
objectBuilder.setGeneralForm(StringUtils.strip(generalForm));
// Extract description:
extractDescription(element, queryString, objectBuilder);
// Extract gender:
extractGender(element, objectBuilder);
return objectBuilder.build();
}
/**
* Looks for a cat with a label under a given parent
*
* @param label
* @param parentId
* @return id or -1 if not found
*/
public static long find(String label, Long parentId) {
label = StringUtils.strip(label);
String selection;
String[] selectionArgs;
if (parentId == null) {
selection = KEY_PARENTID + " is null";
selectionArgs = new String[] {label};
} else {
selection = KEY_PARENTID + " = ?";
selectionArgs = new String[] {String.valueOf(parentId), label};
}
selection += " and " + KEY_LABEL + " = ?";
Cursor mCursor =
cr().query(CONTENT_URI, new String[] {KEY_ROWID}, selection, selectionArgs, null);
if (mCursor.getCount() == 0) {
mCursor.close();
return -1;
} else {
mCursor.moveToFirst();
long result = mCursor.getLong(0);
mCursor.close();
return result;
}
}
@Override
public boolean run(
CommandSender sender,
Player sender_p,
Command cmd,
String commandLabel,
String[] args,
boolean senderIsConsole) {
if (args.length == 1) {
if ("list".equalsIgnoreCase(args[0])) {
playerMsg("Tags for all online players:");
for (final Player player : server.getOnlinePlayers()) {
final TFM_PlayerData playerdata = TFM_PlayerData.getPlayerData(player);
if (playerdata.getTag() != null) {
playerMsg(player.getName() + ": " + playerdata.getTag());
}
}
return true;
} else if ("clearall".equalsIgnoreCase(args[0])) {
if (!TFM_AdminList.isSuperAdmin(sender)) {
playerMsg(TFM_Command.MSG_NO_PERMS);
return true;
}
TFM_Util.adminAction(sender.getName(), "Removing all tags", false);
int count = 0;
for (final Player player : server.getOnlinePlayers()) {
final TFM_PlayerData playerdata = TFM_PlayerData.getPlayerData(player);
if (playerdata.getTag() != null) {
count++;
playerdata.setTag(null);
}
}
playerMsg(count + " tag(s) removed.");
return true;
} else if ("off".equalsIgnoreCase(args[0])) {
if (senderIsConsole) {
playerMsg(
"\"/tag off\" can't be used from the console. Use \"/tag clear <player>\" or \"/tag clearall\" instead.");
} else {
TFM_PlayerData.getPlayerData(sender_p).setTag(null);
playerMsg("Your tag has been removed.");
}
return true;
} else {
return false;
}
} else if (args.length >= 2) {
if ("clear".equalsIgnoreCase(args[0])) {
if (!TFM_AdminList.isSuperAdmin(sender)) {
playerMsg(TFM_Command.MSG_NO_PERMS);
return true;
}
final Player player = getPlayer(args[1]);
if (player == null) {
playerMsg(TFM_Command.PLAYER_NOT_FOUND);
return true;
}
TFM_PlayerData.getPlayerData(player).setTag(null);
playerMsg("Removed " + player.getName() + "'s tag.");
return true;
} else if ("set".equalsIgnoreCase(args[0])) {
final String inputTag = StringUtils.join(args, " ", 1, args.length);
final String outputTag =
TFM_Util.colorize(
StringUtils.replaceEachRepeatedly(
StringUtils.strip(inputTag),
new String[] {"" + ChatColor.COLOR_CHAR, "&k"},
new String[] {"", ""}))
+ ChatColor.RESET;
if (!TFM_AdminList.isSuperAdmin(sender)) {
final String rawTag = ChatColor.stripColor(outputTag).toLowerCase();
if (rawTag.length() > 20) {
playerMsg("That tag is too long (Max is 20 characters).");
return true;
}
String vartag = outputTag.toLowerCase();
if (vartag.contains("admin")
&& vartag.contains("mod")
&& vartag.contains("owner")
&& vartag.contains("moderator")
&& vartag.contains("developer")
&& vartag.contains("console")
&& vartag.contains("super admin")
&& vartag.contains("telnet admin")
&& vartag.contains("senior admin")) {
Command_smite.smite(sender_p, "[AutoSmite] You are not an administrator");
return true;
}
}
TFM_PlayerData.getPlayerData(sender_p).setTag(outputTag);
playerMsg("Tag set to '" + outputTag + "'.");
return true;
} else {
return false;
}
} else {
return false;
}
}
/**
* Returns the annotations to display according to the mappings configuration.
*
* <p>This will check the "annos" and "annos_regex" paramters for determining. the annotations to
* display. It also iterates over all nodes of the graph matching the type.
*
* @param input The input for the visualizer.
* @param type Which type of nodes to include
* @return
*/
public static List<String> computeDisplayAnnotations(
VisualizerInput input, Class<? extends SNode> type) {
if (input == null) {
return new LinkedList<>();
}
SDocumentGraph graph = input.getDocument().getDocumentGraph();
Set<String> annoPool =
SToken.class.isAssignableFrom(type)
? getAnnotationLevelSet(graph, null, type)
: getAnnotationLevelSet(graph, input.getNamespace(), type);
List<String> annos = new LinkedList<>(annoPool);
String annosConfiguration = input.getMappings().getProperty(MAPPING_ANNOS_KEY);
if (annosConfiguration != null && annosConfiguration.trim().length() > 0) {
String[] split = annosConfiguration.split(",");
annos.clear();
for (String s : split) {
s = s.trim();
// is regular expression?
if (s.startsWith("/") && s.endsWith("/")) {
// go over all remaining items in our pool of all annotations and
// check if they match
Pattern regex = Pattern.compile(StringUtils.strip(s, "/"));
LinkedList<String> matchingAnnos = new LinkedList<>();
for (String a : annoPool) {
if (regex.matcher(a).matches()) {
matchingAnnos.add(a);
}
}
annos.addAll(matchingAnnos);
annoPool.removeAll(matchingAnnos);
} else {
annos.add(s);
annoPool.remove(s);
}
}
}
// filter already found annotation names by regular expression
// if this was given as mapping
String regexFilterRaw = input.getMappings().getProperty(MAPPING_ANNO_REGEX_KEY);
if (regexFilterRaw != null) {
try {
Pattern regexFilter = Pattern.compile(regexFilterRaw);
ListIterator<String> itAnnos = annos.listIterator();
while (itAnnos.hasNext()) {
String a = itAnnos.next();
// remove entry if not matching
if (!regexFilter.matcher(a).matches()) {
itAnnos.remove();
}
}
} catch (PatternSyntaxException ex) {
log.warn("invalid regular expression in mapping for grid visualizer", ex);
}
}
return annos;
}
/**
* we currently do not need a full representation of a category as an object when we create an
* instance with an id, we only want to alter its label and are not interested in its parentId
* when we create an instance with a parentId, it is a new instance
*
* @param id
* @param label
* @param parentId
*/
public Category(Long id, String label, Long parentId) {
this.setId(id);
this.label = StringUtils.strip(label);
this.parentId = parentId;
}
String extractTextFromPageArea(PDPage page, TopLeftRectangularBox area) throws TaskIOException {
String text = new PdfTextExtractorByArea().extractTextFromArea(page, area.asRectangle());
String result = defaultIfBlank(text, "");
result = StringUtils.strip(result);
return result;
}
