/** Faz as validações solicitadas no manual de integração */
public String isValid() {
if (getTpAmb() == null || getTpAmb().length() != 1) {
return "Tipo de Ambiente inválido";
}
if (getcUF() == null || getcUF().length() != 2) {
return "Código da UF inválido";
}
if (getAno() == null || getAno().length() != 2) {
return "O Ano de inutilização é inválido";
}
if (getCNPJ() == null || getCNPJ().length() != 14) {
return "CNPJ inválido";
}
if (getMod() == null || getMod().length() != 2 || !TextUtil.isNumber(getMod())) {
return "Modelo da NF inválido";
}
if (getSerie() == null
|| getSerie().length() < 1
|| getSerie().length() > 3
|| !TextUtil.isNumber(getSerie())) {
return "Série da NF inválida";
}
if (getnNFIni() == null
|| getnNFIni().length() < 1
|| getnNFIni().length() > 9
|| !NumberUtils.isNumber(getnNFIni())) {
return "Número Inicial da NF para inutilização é inválido";
}
if (getnNFFin() == null
|| getnNFFin().length() < 1
|| getnNFFin().length() > 9
|| !NumberUtils.isNumber(getnNFFin())) {
return "Número Final da NF para inutilização é inválido";
}
if (getxJust() == null || getxJust().length() < 15) {
return "Justificativa deve ser maior que 15 caracteres";
}
if (Integer.parseInt(getnNFIni()) > Integer.parseInt(getnNFFin())) {
return "Número Final da NF não pode ser menor que Número Inicial da NF";
}
setID();
return null;
} // isValid
@RequestMapping(value = "/find.html")
public ModelAndView find(@RequestParam(value = "q", required = false) String q) {
ModelAndView mav = new ModelAndView();
mav.addObject("operation", "find");
if (StringUtils.isEmpty(q)) {
mav.setViewName("find");
return mav;
}
try {
if (NumberUtils.isNumber(q) && StringUtils.length(q) == 7) {
return show(Integer.valueOf(q));
} else {
long startTs = System.currentTimeMillis();
List<TConcept> concepts = nodeService.findConcepts(q);
mav.addObject("concepts", concepts);
long endTs = System.currentTimeMillis();
mav.addObject("q", q);
mav.addObject("elapsed", new Long(endTs - startTs));
}
} catch (Exception e) {
mav.addObject("error", e.getMessage());
}
mav.setViewName("find");
return mav;
}
@Override
public boolean validate() {
if (NumberUtils.isNumber(_textf.getText())) {
return true;
}
return false;
}
/**
* 对字符串进行混淆，字符串必须是有效整数数字
*
* @param id
* @return
*/
public static String chaos(String id) {
if (StringUtils.isEmpty(id)) {
return StringUtils.EMPTY;
} else if (!NumberUtils.isNumber(id)) {
return StringUtils.EMPTY;
}
return chaos(Long.valueOf(id));
}
/**
* Returns the value as a {@link Double} value. The returned value will be <code>0</code> or
* <code>1</code> if the {@link #value} is a boolean value. If {@link #value} can not be converted
* into a number, a {@link NumberFormatException} is thrown.
*
* @return {@link #value} as {@link Double}
*/
public double getValueAsDouble() {
if (NumberUtils.isNumber(value)) {
return NumberUtils.createDouble(value);
}
if (isBooleanValue(value)) {
return BooleanUtils.toBoolean(value) ? 1 : 0;
}
throw new NumberFormatException();
}
private static Object initializeStringValue(final String value) {
if (value == null) {
throw new IllegalArgumentException("The left hand side value cannot be null");
}
if (NumberUtils.isNumber(value)) {
return Integer.valueOf(value);
}
return value;
}
/**
* 新增或更新用户月度活跃时长统计，返回执行结果
*
* @param uidList 月度活跃uid分页清单
* @param millisList 对应用户在线时长list
* @param monthStr 统计月度，yyyyMM
* @return 执行结果
*/
public boolean batchAddOrUpdateMAUStats(
List<String> uidList, List<String> millisList, String monthStr) {
if (uidList == null || millisList == null || uidList.isEmpty() || millisList.isEmpty()) {
return false;
}
if (uidList.size() != millisList.size()) {
return false;
}
int listSize = uidList.size();
boolean result = false;
Connection conn = null;
PreparedStatement ps = null;
String sql =
"INSERT INTO `ssyh_main`.`mau_stats`"
+ "(`month_str`,`uid`,`stay_seconds`,`stay_minutes`,`stay_hours`) VALUES(?,?,?,?,?) "
+ "ON DUPLICATE KEY UPDATE `stay_seconds` = ?,`stay_minutes`=?,`stay_hours`=?;";
try {
conn = DBUtil.getConnection();
// 关闭事务自动提交
conn.setAutoCommit(false);
ps = conn.prepareStatement(sql);
for (int i = 0; i < listSize; i++) {
String uid = uidList.get(i);
String millisStr = millisList.get(i);
long stayMillis = NumberUtils.isNumber(millisStr) ? Long.parseLong(millisStr) : 0L;
MAUStatsBean bean = new MAUStatsBean(monthStr, uid, stayMillis);
// insert参数
ps.setString(1, bean.getMonthStr());
ps.setString(2, bean.getUid());
ps.setInt(3, bean.getStaySeconds());
ps.setInt(4, bean.getStayMinutes());
ps.setDouble(5, bean.getStayHours());
// update参数
ps.setInt(6, bean.getStaySeconds());
ps.setInt(7, bean.getStayMinutes());
ps.setDouble(8, bean.getStayHours());
ps.addBatch();
}
ps.executeBatch();
// 关闭事务自动提交
conn.setAutoCommit(true);
result = true;
} catch (SQLException e) {
result = false;
logger.error("addOrUpdateMAUStats exception:" + e.getMessage(), e);
} finally {
DBUtil.close(null, ps, conn);
}
return result;
}
/* (non-Javadoc)
* @see org.springframework.web.servlet.mvc.AbstractController#handleRequestInternal(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
*/
@Override
protected ModelAndView handleRequestInternal(
HttpServletRequest request, HttpServletResponse response) throws Exception {
String query = request.getParameter("query");
if (StringUtils.isBlank(query)) {
return new ModelAndView(getSearchView());
}
String p = request.getParameter("p");
int currentPage = 1;
if (NumberUtils.isNumber(p)) {
currentPage = Integer.parseInt(p);
}
if (currentPage < 1) {
currentPage = 1;
}
CompassSearchCommand searchCommand = new CompassSearchCommand();
searchCommand.setPage(new Integer(currentPage - 1));
searchCommand.setQuery(query);
ModelAndView mv = new ModelAndView();
mv.addObject("query", query);
mv.addObject("p", currentPage);
List<String> errors = new ArrayList<String>();
try {
CompassSearchResults searchResults = searchHelper.search(searchCommand);
List<CompassHitWapper> hits = new ArrayList<CompassHitWapper>();
for (int i = 0; i < searchResults.getHits().length; i++) {
CompassHitWapper hit = new CompassHitWapper(searchResults.getHits()[i]);
hits.add(hit);
}
CompassSearchResultsWrapper results = new CompassSearchResultsWrapper(searchResults);
results.setHits(hits);
mv.addObject(getSearchResultsName(), results);
} catch (SearchEngineQueryParseException ex) {
errors.add(TextUtil.escapeHTML(ex.getMessage()));
mv.addObject("errors", errors);
} catch (Exception ex) {
errors.add(TextUtil.escapeHTML(ex.getMessage()));
mv.addObject("errors", errors);
}
mv.setViewName(getSearchResultsView());
return mv;
}
// really an update
public boolean saveSetting(Account account, String key, String value) throws ControllerException {
// check if a search boost setting. hack: expecting that search boosts will only use numeric
// values TODO
if (NumberUtils.isNumber(value)) {
try {
SearchBoostField boostField = SearchBoostField.valueOf(key.toUpperCase());
if (boostField != null) {
key = "BOOST_" + boostField.name();
}
} catch (Exception e) {
Logger.debug(e.getMessage());
}
}
try {
return dao.saveOrUpdatePreference(account, key, value) != null;
} catch (DAOException e) {
throw new ControllerException(e);
}
}
/**
* 修复地区名称为地区代码 (comInterview)
*
* @param page
*/
public void fixComInterviewJobLocationToCode(Page<ComInterview> page) {
if (page == null || CollectionUtils.isEmpty(page.getItems())) {
return;
}
for (ComInterview comInterview : page.getItems()) {
if (StringUtils.isNotBlank(comInterview.getJobLocation())) {
List<Integer> jobLocationList = Lists.newArrayList();
String[] jobLocationArr = comInterview.getJobLocation().split(",");
for (String location : jobLocationArr) {
Integer code = OptionMap.getCityCodeByAddr(location);
if (code != null && code > 0 && !NumberUtils.isNumber(location)) {
jobLocationList.add(code);
}
}
if (CollectionUtils.isNotEmpty(jobLocationList)) {
comInterview.setJobLocation(StringUtils.join(jobLocationList, ","));
}
}
}
}
/** Ensures that all fields are set. */
private void dialogChanged() {
if (projectProviders == null) {
setEnabled(false);
updateStatus(Messages.error_new_project_metadata_not_found);
return;
}
providerDescription.setText(
projectProviders.get(providerName.getSelectionIndex()).getDescription());
if (isDemo()) {
if (!this.providerName.getText().equals(projectProviders.get(0).getDisplayName())) {
this.providerName.setText(projectProviders.get(0).getDisplayName()); // AS/400
setEnabled(false);
updateStatus(null);
}
return;
} else {
setEnabled(true);
}
if (hostName.getText().length() == 0) {
updateStatus(Messages.error_host_name_not_specified);
return;
}
if (hostPort.getText().length() == 0) {
updateStatus(Messages.errror_host_port_not_specified);
return;
}
if (!NumberUtils.isNumber(hostPort.getText())) {
updateStatus(Messages.error_port_not_numeric);
return;
}
if (codePage.getText().length() == 0) {
updateStatus(Messages.error_code_page_not_specified);
return;
}
this.updateStatus(null);
}
/**
* {@inheritDoc}
*
* @see
* org.kuali.kra.common.specialreview.service.SpecialReviewService#addProtocolFundingSourceForSpecialReview(java.lang.String,
* java.lang.String, java.lang.String, java.lang.String, java.lang.String)
*/
public void addProtocolFundingSourceForSpecialReview(
String protocolNumber,
String fundingSourceNumber,
String fundingSourceTypeCode,
String fundingSourceName,
String fundingSourceTitle) {
Protocol protocol = getProtocolFinderDao().findCurrentProtocolByNumber(protocolNumber);
if (protocol != null
&& StringUtils.isNotBlank(fundingSourceNumber)
&& NumberUtils.isNumber(fundingSourceTypeCode)) {
ProtocolFundingSource protocolFundingSource = new ProtocolFundingSource();
protocolFundingSource.setProtocolNumber(protocolNumber);
protocolFundingSource.setFundingSourceNumber(fundingSourceNumber);
protocolFundingSource.setFundingSourceTypeCode(fundingSourceTypeCode);
protocolFundingSource.setFundingSourceName(fundingSourceName);
protocolFundingSource.setFundingSourceTitle(fundingSourceTitle);
protocol.getProtocolFundingSources().add(protocolFundingSource);
getBusinessObjectService().save(protocol);
}
}
public static boolean isNumber(List<String> args, int index) {
return NumberUtils.isNumber(args.get(index));
}
/**
* Determines the CSV parser setup from the first few lines. Also parses the next few lines,
* tossing out comments and blank lines.
*
* <p>If the separator is GUESS_SEP, then it is guessed by looking at tokenization and column
* count of the first few lines.
*
* <p>If ncols is -1, then it is guessed similarly to the separator.
*
* <p>singleQuotes is honored in all cases (and not guessed).
*/
static ParseSetup guessSetup(
byte[] bits,
byte sep,
int ncols,
boolean singleQuotes,
int checkHeader,
String[] columnNames,
byte[] columnTypes,
String[][] naStrings) {
String[] lines = getFirstLines(bits);
if (lines.length == 0) throw new H2OParseSetupException("No data!");
// Guess the separator, columns, & header
String[] labels;
final String[][] data = new String[lines.length][];
if (lines.length == 1) { // Ummm??? Only 1 line?
if (sep == GUESS_SEP) {
if (lines[0].split(",").length > 2) sep = (byte) ',';
else if (lines[0].split(" ").length > 2) sep = ' ';
else { // one item, guess type
data[0] = new String[] {lines[0]};
byte[] ctypes = new byte[1];
String[][] domains = new String[1][];
if (NumberUtils.isNumber(data[0][0])) {
ctypes[0] = Vec.T_NUM;
} else { // non-numeric
ValueString str = new ValueString(data[0][0]);
if (ParseTime.isTime(str)) ctypes[0] = Vec.T_TIME;
else if (ParseUUID.isUUID(str)) ctypes[0] = Vec.T_UUID;
else { // give up and guess enum
ctypes[0] = Vec.T_ENUM;
domains[0] = new String[] {data[0][0]};
}
}
// FIXME should set warning message and let fall through
return new ParseSetup(
ParserType.CSV,
GUESS_SEP,
singleQuotes,
checkHeader,
1,
null,
ctypes,
domains,
naStrings,
data,
FileVec.DFLT_CHUNK_SIZE);
}
}
data[0] = determineTokens(lines[0], sep, singleQuotes);
ncols = (ncols > 0) ? ncols : data[0].length;
if (checkHeader == GUESS_HEADER) {
if (ParseSetup.allStrings(data[0])) {
labels = data[0];
checkHeader = HAS_HEADER;
} else {
labels = null;
checkHeader = NO_HEADER;
}
} else if (checkHeader == HAS_HEADER) labels = data[0];
else labels = null;
} else { // 2 or more lines
// First guess the field separator by counting occurrences in first few lines
if (sep == GUESS_SEP) { // first guess the separator
sep = guessSeparator(lines[0], lines[1], singleQuotes);
if (sep == GUESS_SEP && lines.length > 2) {
sep = guessSeparator(lines[1], lines[2], singleQuotes);
if (sep == GUESS_SEP) sep = guessSeparator(lines[0], lines[2], singleQuotes);
}
if (sep == GUESS_SEP) sep = (byte) ' '; // Bail out, go for space
}
// Tokenize the first few lines using the separator
for (int i = 0; i < lines.length; ++i) data[i] = determineTokens(lines[i], sep, singleQuotes);
// guess columns from tokenization
ncols = guessNcols(columnNames, data);
// Asked to check for a header, so see if 1st line looks header-ish
if (checkHeader == HAS_HEADER
|| (checkHeader == GUESS_HEADER && ParseSetup.hasHeader(data[0], data[1]))) {
checkHeader = HAS_HEADER;
labels = data[0];
} else {
checkHeader = NO_HEADER;
labels = columnNames;
}
// See if compatible headers
if (columnNames != null && labels != null) {
if (labels.length != columnNames.length)
throw new H2OParseSetupException(
"Already have "
+ columnNames.length
+ " column labels, but found "
+ labels.length
+ " in this file");
else {
for (int i = 0; i < labels.length; ++i)
if (!labels[i].equalsIgnoreCase(columnNames[i])) {
throw new H2OParseSetupException(
"Column "
+ (i + 1)
+ " label '"
+ labels[i]
+ "' does not match '"
+ columnNames[i]
+ "'");
}
labels = columnNames; // Keep prior case & count in any case
}
}
}
// Assemble the setup understood so far
ParseSetup resSetup =
new ParseSetup(
ParserType.CSV,
sep,
singleQuotes,
checkHeader,
ncols,
labels,
null,
null /*domains*/,
naStrings,
data);
// now guess the types
if (columnTypes == null || ncols != columnTypes.length) {
InputStream is = new ByteArrayInputStream(bits);
CsvParser p = new CsvParser(resSetup, null);
PreviewParseWriter dout = new PreviewParseWriter(resSetup._number_columns);
try {
p.streamParse(is, dout);
resSetup._column_previews = dout;
} catch (Throwable e) {
throw new RuntimeException(e);
}
} else {
// If user sets column type as unknown/bad, guess numeric.
for (int i = 0; i < columnTypes.length; i++)
if (columnTypes[i] == Vec.T_BAD) columnTypes[i] = Vec.T_NUM;
resSetup._column_types = columnTypes;
resSetup._na_strings = null;
}
// Return the final setup
return resSetup;
}
@Override
public boolean performOk() {
String txtResultType = comboRDBResultType.getText();
String txtSelectLimit = textSelectLimit.getText();
String txtResultPage = textResultPage.getText();
String txtQueryTimtout = textQueryTimeout.getText();
String txtOraclePlan = textOraclePlan.getText();
String txtRDBNumberColumnIsComman = comboRDBNumberComma.getText();
String txtFontInfo = lblUserFont.getText();
String txtCommitCount = textCommitCount.getText();
String txtShownInTheColumn = textShowInTheColumn.getText();
if (!NumberUtils.isNumber(txtSelectLimit)) {
MessageDialog.openError(
getShell(),
"Confirm",
Messages.get().DefaultPreferencePage_0
+ Messages.get().RDBPreferencePage_0); // $NON-NLS-1$
textSelectLimit.setFocus();
return false;
}
if (!NumberUtils.isNumber(txtResultPage)) {
MessageDialog.openError(
getShell(),
"Confirm",
Messages.get().DefaultPreferencePage_other_labelText_1
+ Messages.get().RDBPreferencePage_0); // $NON-NLS-1$
textResultPage.setFocus();
return false;
}
if (!NumberUtils.isNumber(txtQueryTimtout)) {
MessageDialog.openError(
getShell(), "Confirm", "Query timeout is " + Messages.get().RDBPreferencePage_0);
textQueryTimeout.setFocus();
return false;
}
if (!NumberUtils.isNumber(txtCommitCount)) {
MessageDialog.openError(
getShell(), "Confirm", "Commit count is " + Messages.get().RDBPreferencePage_0);
textCommitCount.setFocus();
return false;
}
if ("".equals(txtOraclePlan)) { // $NON-NLS-1$
MessageDialog.openError(
getShell(), "Confirm", Messages.get().RDBPreferencePage_3); // $NON-NLS-1$
return false;
}
if (!NumberUtils.isNumber(txtShownInTheColumn)) {
MessageDialog.openError(getShell(), "Confirm", Messages.get().RDBPreferencePage_0);
textShowInTheColumn.setFocus();
return false;
}
// 테이블에 저장
try {
TadpoleSystem_UserInfoData.updateRDBUserInfoData(
txtSelectLimit,
txtResultPage,
txtQueryTimtout,
txtOraclePlan,
txtRDBNumberColumnIsComman,
txtFontInfo,
txtCommitCount,
txtShownInTheColumn,
txtResultType);
// session 데이터를 수정한다.
SessionManager.setUserInfo(PreferenceDefine.RDB_RESULT_TYPE, txtResultType);
SessionManager.setUserInfo(PreferenceDefine.SELECT_LIMIT_COUNT, txtSelectLimit);
SessionManager.setUserInfo(PreferenceDefine.SELECT_RESULT_PAGE_PREFERENCE, txtResultPage);
SessionManager.setUserInfo(PreferenceDefine.SELECT_QUERY_TIMEOUT, txtQueryTimtout);
SessionManager.setUserInfo(PreferenceDefine.ORACLE_PLAN_TABLE, txtOraclePlan);
SessionManager.setUserInfo(
PreferenceDefine.RDB_RESULT_NUMBER_IS_COMMA, txtRDBNumberColumnIsComman);
SessionManager.setUserInfo(PreferenceDefine.RDB_RESULT_FONT, txtFontInfo);
SessionManager.setUserInfo(PreferenceDefine.RDB_COMMIT_COUNT, txtCommitCount);
SessionManager.setUserInfo(
PreferenceDefine.RDB_CHARACTER_SHOW_IN_THE_COLUMN, txtShownInTheColumn);
} catch (Exception e) {
logger.error("RDBPreference saveing", e);
MessageDialog.openError(
getShell(),
"Confirm",
Messages.get().RDBPreferencePage_5 + e.getMessage()); // $NON-NLS-1$
return false;
}
return super.performOk();
}
private void doMain() throws SAXParseException, IOException {
Normalizer normalizer = null;
if (useTokenizer) {
normalizer = Normalizer.getInstance();
}
PrintWriter reversedWordsWriter =
analysisPlacesOut != null
? new PrintWriter(new File(analysisPlacesOut, "reversedWords.txt"))
: new PrintWriter(System.out);
BufferedReader bufferedReader = new BufferedReader(new FileReader(placesIn));
int lineCount = 0;
while (bufferedReader.ready()) {
String nextLine = bufferedReader.readLine();
nextLine = nextLine.trim().toLowerCase();
if (nextLine.length() == 0) continue;
lineCount++;
if (lineCount % 5000 == 0) System.out.println("indexing line " + lineCount);
placesCountCC.add(nextLine);
totalPlacesCount++;
String[] placeList = nextLine.split(SPLIT_REGEX);
for (String place : placeList) {
place = place.trim();
if (place.length() == 0) continue;
if (NumberUtils.isNumber(place)) {
numbersCountCC.add(place);
totalNumbersCount++;
} else {
wordsCountCC.add(place);
totalWordsCount++;
}
}
int lastCommaIndx = nextLine.lastIndexOf(",");
String lastWord = nextLine.substring(lastCommaIndx + 1).trim();
if (lastWord.length() > 0) {
endingsOfPlacesCC.add(lastWord);
endingsOfPlacesTotalCount++;
}
if (lineCount % REVERSE_EVERY_N == 0) {
StringBuilder reversedWord = new StringBuilder(nextLine);
reversedWordsWriter.println(reversedWord.reverse());
}
if ((useTokenizer) && (lineCount % TOKENIZE_EVERY_N == 0)) {
List<List<String>> levels = normalizer.tokenize(nextLine);
for (List<String> levelWords : levels) {
tokenizerPlacesCountCC.addAll(levelWords);
totalTokenizerPlacesCount += levelWords.size();
}
}
}
System.out.println("total number of lines in files " + lineCount);
System.out.println("Indexed a total of " + totalPlacesCount + " places.");
System.out.println("Found a total of " + getPlacesCountCC().size() + " unique places.");
getPlacesCountCC()
.writeSorted(
false,
1,
analysisPlacesOut != null
? new PrintWriter(new File(analysisPlacesOut, "placesCount.txt"))
: new PrintWriter(System.out));
System.out.println("Indexed a total of " + totalWordsCount + " words.");
System.out.println("Found a total of " + getWordsCountCC().size() + " unique words.");
getWordsCountCC()
.writeSorted(
false,
1,
analysisPlacesOut != null
? new PrintWriter(new File(analysisPlacesOut, "wordsCount.txt"))
: new PrintWriter(System.out));
System.out.println("Indexed a total of " + totalNumbersCount + " numbers.");
System.out.println("Found a total of " + getNumbersCountCC().size() + " unique numbers.");
getNumbersCountCC()
.writeSorted(
false,
1,
analysisPlacesOut != null
? new PrintWriter(new File(analysisPlacesOut, "numbersCount.txt"))
: new PrintWriter(System.out));
System.out.println("Indexed a total of " + endingsOfPlacesTotalCount + " endings.");
System.out.println("Found a total of " + getEndingsOfPlacesCC().size() + " unique endings.");
getEndingsOfPlacesCC()
.writeSorted(
false,
1,
analysisPlacesOut != null
? new PrintWriter(new File(analysisPlacesOut, "endingsCount.txt"))
: new PrintWriter(System.out));
if (useTokenizer) {
System.out.println("Indexed a total of " + totalTokenizerPlacesCount + " normalized words.");
System.out.println(
"Found a total of " + getTokenizerPlacesCountCC().size() + " normalized words.");
getTokenizerPlacesCountCC()
.writeSorted(
false,
1,
analysisPlacesOut != null
? new PrintWriter(new File(analysisPlacesOut, "normalizedWordsCount.txt"))
: new PrintWriter(System.out));
}
}
@RequestMapping(value = "/map.html")
public ModelAndView map(
@RequestParam(value = "q1", required = false) String q1,
@RequestParam(value = "q2", required = false) String q2,
@RequestParam(value = "q3", required = false) String q3,
@RequestParam(value = "if", required = false, defaultValue = UimaUtils.MIMETYPE_STRING)
String inputFormat,
@RequestParam(value = "of", required = true, defaultValue = "html") String outputFormat,
@RequestParam(value = "ofs", required = false, defaultValue = "pretty")
String outputFormatStyle,
@RequestParam(value = "sgf", required = false) String[] styGroupFilter,
@RequestParam(value = "scf", required = false) String[] styCodeFilter) {
ModelAndView mav = new ModelAndView();
mav.addObject("operation", "map");
// validate parameters (at least one of o, q, u or t must
// be supplied, otherwise show the input form
mav.addObject("q1", StringUtils.isEmpty(q1) ? "" : q1);
mav.addObject("q2", StringUtils.isEmpty(q2) ? "" : q2);
mav.addObject("q3", StringUtils.isEmpty(q3) ? "" : q3);
String q =
StringUtils.isNotEmpty(q1)
? q1
: StringUtils.isNotEmpty(q2) ? q2 : StringUtils.isNotEmpty(q3) ? q3 : null;
if (StringUtils.isEmpty(q)) {
setViewName(mav, outputFormat, outputFormatStyle);
return mav;
}
try {
if (NumberUtils.isNumber(q) && StringUtils.length(q) == 7) {
return show(Integer.valueOf(q));
} else {
// show list of concepts
String text = q;
if ((q.startsWith("http://") && UimaUtils.MIMETYPE_HTML.equals(inputFormat))) {
URL u = new URL(q);
BufferedReader br = new BufferedReader(new InputStreamReader(u.openStream()));
StringBuilder tbuf = new StringBuilder();
String line = null;
while ((line = br.readLine()) != null) {
tbuf.append(line).append("\n");
}
br.close();
text = tbuf.toString();
}
List<ConceptAnnotation> annotations = new ArrayList<ConceptAnnotation>();
long startTs = System.currentTimeMillis();
JCas jcas = UimaUtils.runAE(conceptMappingAE, text, inputFormat, null);
FSIndex fsindex = jcas.getAnnotationIndex(ConceptAnnotation.type);
for (Iterator<ConceptAnnotation> it = fsindex.iterator(); it.hasNext(); ) {
ConceptAnnotation annotation = it.next();
annotations.add(annotation);
}
CollectionUtils.filter(annotations, new StyGroupPredicate(styGroupFilter));
CollectionUtils.filter(annotations, new StyCodePredicate(styCodeFilter));
annotations = filterSubsumedConcepts(q, annotations);
if (annotations.size() == 0) {
mav.addObject("error", "No concepts found");
} else {
mav.addObject("text", text);
mav.addObject("annotations", annotations);
long endTs = System.currentTimeMillis();
mav.addObject("elapsed", new Long(endTs - startTs));
}
setViewName(mav, outputFormat, outputFormatStyle);
}
} catch (Exception e) {
mav.addObject("error", e.getMessage());
setViewName(mav, outputFormat, outputFormatStyle);
}
return mav;
}
/**
* Checks if the value of this object is a boolean or numeric value.
*
* @return <code>true</code> if the value is a boolean or number, otherwise <code>false</code>
*/
public boolean isBooleanOrNumeric() {
return isBooleanValue(value) || NumberUtils.isNumber(value);
}
// For example, here is a line from the 5kb chr1 MAPQGE30 raw observed contact matrix
// (GM12878_combined/5kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_5kb.RAWobserved):
// 40000000 40100000 59.0
// To normalize this entry using the KR normalization vector, one would divide 59.0 by the 8001st
// line ((40000000/5000)+1=8001) and the 8021st line ((40100000/5000)+1=8021)
// of GM12878_combined/5kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_5kb.KRnorm. The 8001st
// line of the KR norm file is 1.2988778370674694;
// The 8021st line of the KR norm file is 1.6080499717941548. So the corresponding KR normalized
// entry for the entry above is 59.0/(1.2988778370674694*1.6080499717941548)
// or 28.24776973966101.
// If the KR normalization vector file is empty or all NaNs, then the KR algorithm didn’t converge
// on that particular matrix (likely due to sparsity of the matrix).
private static void processNormalizedInterContactInformation(
String fileToRead,
String baseName,
String normMethod,
String chrSmaller,
String chrLarger,
ArrayList<DesiredChrContact> contactsToCheck,
String resolution,
double minValue,
TextFile outWriter)
throws IOException {
// ReadIn normalization chr1
TextFile inputNormChr1 =
new TextFile(
baseName + "\\chr" + chrSmaller + "_" + resolution + "." + normMethod, TextFile.R);
ArrayList<String> normFactorSmallerChr = inputNormChr1.readAsArrayList();
inputNormChr1.close();
// System.out.println("Done reading norm factor 1");
// ReadIn normalization chr2
TextFile inputNormChr2 =
new TextFile(
baseName + "\\chr" + chrLarger + "_" + resolution + "." + normMethod, TextFile.R);
ArrayList<String> normFactorLargerChr = inputNormChr2.readAsArrayList();
inputNormChr2.close();
// System.out.println("Done reading norm factor 2");
if (!Gpio.exists(fileToRead + ".sorted")) {
umcg.genetica.io.chrContacts.SortInterChrContacts.readNonSortedWriteSorted(
fileToRead, fileToRead + ".sorted");
}
int numberToBeMatched = 0;
LineIterator it = FileUtils.lineIterator(new File(fileToRead + ".sorted"), "UTF-8");
try {
while (it.hasNext()) {
String[] parts = StringUtils.split(it.nextLine(), '\t');
int posChr1 = org.apache.commons.lang.math.NumberUtils.createInteger(parts[0]);
int posChr2 = org.apache.commons.lang.math.NumberUtils.createInteger(parts[1]);
while (numberToBeMatched < contactsToCheck.size()) {
if (posChr1 < contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
break;
} else if (posChr1 == contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
if (posChr2 < contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
break;
}
if (posChr2 == contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
if (((posChr1 / getNumericResolution(resolution)) + 1)
> normFactorSmallerChr.size()) {
System.out.println(baseName);
System.out.println("Smaller");
System.out.println((posChr1 / getNumericResolution(resolution) + 1));
System.out.println(normFactorSmallerChr.size());
System.exit(-1);
}
if (((posChr2 / getNumericResolution(resolution)) + 1) > normFactorLargerChr.size()) {
System.out.println(baseName);
System.out.println("Larger");
System.out.println((posChr2 / getNumericResolution(resolution)) + 1);
System.out.println(normFactorLargerChr.size());
System.exit(-1);
}
String factor1Base =
normFactorSmallerChr.get((posChr1 / getNumericResolution(resolution)) + 1);
String factor2Base =
normFactorLargerChr.get((posChr2 / getNumericResolution(resolution)) + 1);
double factor1 = 1.0;
double factor2 = 1.0;
if (NumberUtils.isNumber(factor1Base) && NumberUtils.isNumber(factor2Base)) {
factor1 = Double.parseDouble(factor1Base);
factor2 = Double.parseDouble(factor2Base);
} else if (NumberUtils.isNumber(factor1Base)) {
factor1 = Double.parseDouble(factor1Base);
System.out.println("Error in files.");
System.out.println("Base 2 is reset to 1");
} else if (NumberUtils.isNumber(factor2Base)) {
factor2 = Double.parseDouble(factor2Base);
System.out.println("Error in files.");
System.out.println("Base 1 is reset to 1");
}
double contact =
org.apache.commons.lang.math.NumberUtils.createDouble(parts[2])
/ (factor1 * factor2);
if (contact >= minValue) {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\tContact\t"
+ contact
+ "\t"
+ org.apache.commons.lang.math.NumberUtils.createDouble(parts[2]));
numberToBeMatched++;
} else {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\t-\t-\t-");
numberToBeMatched++;
}
} else if (posChr2 > contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\t-\t-\t-");
numberToBeMatched++;
}
} else if (posChr1 > contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\t-\t-\t-");
numberToBeMatched++;
}
}
}
} finally {
LineIterator.closeQuietly(it);
}
}
/**
* @param requestVO
* @return
*/
@Transactional(propagation = Propagation.REQUIRED)
public int saveFindings(FindingsRequestVO requestVO) {
Project project =
getEntityManager().find(Project.class, Long.parseLong(requestVO.getProjectId()));
// FINDINGS
List<Finding> findingsList = new ArrayList<Finding>();
for (FindingsVO findingsVO : CollectionUtil.safe(requestVO.getFindingsList())) {
Finding findings = null;
if (DataValidator.isNotEmpty(findingsVO.getFindingsCategoryId())
|| DataValidator.isNotEmpty(findingsVO.getFindingsText())) {
if (!DataValidator.isNewRecord(findingsVO.getFindingsId())) {
findings =
getEntityManager().find(Finding.class, Long.parseLong(findingsVO.getFindingsId()));
} else {
findings = new Finding();
if (findingsVO.getFindingsCategoryId() != null) {
if (NumberUtils.isNumber(findingsVO.getFindingsCategoryId())) {
findings.setFindingsCategory(
getEntityManager()
.find(
FindingsCategory.class,
Long.parseLong(findingsVO.getFindingsCategoryId())));
} else {
FindingsCategory findingsCategory = new FindingsCategory();
findingsCategory.setFindingsCategoryDesc(findingsVO.getFindingsCategoryId());
findingsCategory.setFindingsCategoryName(findingsVO.getFindingsCategoryId());
getEntityManager().persist(findingsCategory);
findings.setFindingsCategory(findingsCategory);
}
}
findings.setFindingsText(
(findingsVO.getFindingsText() == null)
? RoadmapConstants.EMPTY_STRING
: findingsVO.getFindingsText().replace("&", "&"));
findings.setProject(project);
getEntityManager().persist(findings);
}
findings.setFindingsText(
(findingsVO.getFindingsText() == null)
? RoadmapConstants.EMPTY_STRING
: findingsVO.getFindingsText().replace("&", "&"));
findings.setImportance(findingsVO.getImportance());
if (!DataValidator.isNewRecord(findingsVO.getFindingsCategoryId())
&& NumberUtils.isNumber(findingsVO.getFindingsCategoryId())) {
FindingsCategory findingsCategory =
getEntityManager()
.find(FindingsCategory.class, Long.parseLong(findingsVO.getFindingsCategoryId()));
findings.setFindingsCategory(findingsCategory);
}
findingsList.add(findings);
}
}
// OPPORTUNITY
List<Opportunity> opportunityList = new ArrayList<Opportunity>();
for (OpportunityVO opportunityVO : CollectionUtil.safe(requestVO.getOpportunityList())) {
Opportunity opportunity = null;
if (DataValidator.isNotEmpty(opportunityVO.getOpportunityCategoryId())
|| DataValidator.isNotEmpty(opportunityVO.getOpportunityText())) {
if (!DataValidator.isNewRecord(opportunityVO.getOpportunityId())) {
opportunity =
getEntityManager()
.find(Opportunity.class, Long.parseLong(opportunityVO.getOpportunityId()));
} else {
opportunity = new Opportunity();
if (opportunityVO.getOpportunityCategoryId() != null) {
if (NumberUtils.isNumber(opportunityVO.getOpportunityCategoryId())
&& isValidId(opportunityVO.getOpportunityCategoryId())) {
opportunity.setOpportunityCategory(
getEntityManager()
.find(
OpportunityCategory.class,
Long.parseLong(opportunityVO.getOpportunityCategoryId())));
} else {
OpportunityCategory opportunityCategory = new OpportunityCategory();
opportunityCategory.setOpportunityCategoryDesc(
opportunityVO.getOpportunityCategoryId());
opportunityCategory.setOpportunityCategoryName(
opportunityVO.getOpportunityCategoryId());
getEntityManager().persist(opportunityCategory);
getEntityManager().flush();
opportunity.setOpportunityCategory(opportunityCategory);
}
}
opportunity.setOpportunityText(opportunityVO.getOpportunityText());
opportunity.setProject(project);
getEntityManager().persist(opportunity);
}
opportunity.setOpportunityText(opportunityVO.getOpportunityText());
if (!DataValidator.isNewRecord(opportunityVO.getOpportunityCategoryId())
&& NumberUtils.isNumber(opportunityVO.getOpportunityCategoryId())
&& isValidId(opportunityVO.getOpportunityCategoryId())) {
OpportunityCategory opportunityCategory =
getEntityManager()
.find(
OpportunityCategory.class,
Long.parseLong(opportunityVO.getOpportunityCategoryId()));
opportunity.setOpportunityCategory(opportunityCategory);
}
opportunityList.add(opportunity);
}
}
List<Finding> projectFindingsListForRemoval =
(List<Finding>)
CollectionUtils.removeAll(CollectionUtil.safe(project.getFindings()), findingsList);
for (Finding findingForRemoval : projectFindingsListForRemoval) {
getEntityManager().remove(findingForRemoval);
getEntityManager().flush();
project.removeFinding(findingForRemoval);
}
List<Opportunity> projectOpportunityListForRemoval =
(List<Opportunity>)
CollectionUtils.removeAll(
CollectionUtil.safe(project.getOpportunities()), opportunityList);
for (Opportunity opportunityForRemoval : projectOpportunityListForRemoval) {
getEntityManager().remove(opportunityForRemoval);
getEntityManager().flush();
project.removeOpportunity(opportunityForRemoval);
}
return RoadmapConstants.SAVE_SUCCESS;
}
private static boolean validNumber(String numberStr) {
return numberStr != null && NumberUtils.isNumber(numberStr);
}
public CParser(String sql, String outputFileName, int speed, int delay) {
CSQL csql = new CSQL();
csql.parser(sql);
if (!csql.getTable().equals("arduino")) {
System.err.println("Unknown table: " + csql.getTable());
System.exit(0);
}
int digitalPins[] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
int analogPins[] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
String columns[] = {
"din1", "din2", "din3", "din4", "din5", "din6", "din7", "din8", "din9", "din10",
"din11", "din12", "din13", "din14", "din15", "din16", "din17", "din18", "din19", "din20",
"ain1", "ain2", "ain3", "ain4", "ain5", "ain6", "ain7", "ain8", "ain9", "ain10",
"ain11", "ain12", "ain13", "ain14", "ain15", "ain16", "ain17", "ain18", "ain19", "ain20"
};
for (String field : csql.getFields()) {
// カラム名が存在するか確認する
if (!Arrays.asList(columns).contains(field)) {
System.err.println("Unknown column: " + field);
System.exit(0);
}
int pinIndex = Integer.valueOf(field.substring(3));
if (field.startsWith("din")) {
digitalPins[pinIndex] = 1;
} else {
analogPins[pinIndex] = 1;
}
}
for (Expression expression : csql.getConditions()) {
// WHERE句のカラム名が存在するか確認する
String left = "";
String right = "";
if (expression instanceof EqualsTo) {
left = ((EqualsTo) expression).getLeftExpression().toString();
right = ((EqualsTo) expression).getRightExpression().toString();
} else if (expression instanceof GreaterThan) {
left = ((GreaterThan) expression).getLeftExpression().toString();
right = ((GreaterThan) expression).getRightExpression().toString();
} else if (expression instanceof GreaterThanEquals) {
left = ((GreaterThanEquals) expression).getLeftExpression().toString();
right = ((GreaterThanEquals) expression).getRightExpression().toString();
} else if (expression instanceof MinorThan) {
left = ((MinorThan) expression).getLeftExpression().toString();
right = ((MinorThan) expression).getRightExpression().toString();
} else if (expression instanceof MinorThanEquals) {
left = ((MinorThanEquals) expression).getLeftExpression().toString();
right = ((MinorThanEquals) expression).getRightExpression().toString();
} else if (expression instanceof NotEqualsTo) {
left = ((NotEqualsTo) expression).getLeftExpression().toString();
right = ((NotEqualsTo) expression).getRightExpression().toString();
}
if (!Arrays.asList(columns).contains(left)) {
System.err.println("Unknown column: " + left);
System.exit(0);
}
int pinIndex = Integer.valueOf(left.substring(3));
if (left.startsWith("din")) {
digitalPins[pinIndex] = 1;
} else {
analogPins[pinIndex] = 1;
}
if (!NumberUtils.isNumber(right)) {
System.err.println("missing value for " + right);
System.exit(0);
}
}
StringBuffer condition = new StringBuffer(" ");
for (String token : csql.getWhere().split(" ")) {
// WHERE句のSQL文法をC言語文法に書き換える
if (token.equals("=")) {
condition.append("== ");
} else if (token.equals("AND")) {
condition.append("&& ");
} else if (token.equals("OR")) {
condition.append("|| ");
} else {
condition.append(token + " ");
}
}
try {
File file = new File(outputFileName);
PrintWriter printWriter = new PrintWriter(new BufferedWriter(new FileWriter(file)));
// setup
printWriter.println("void setup() {");
printWriter.println(String.format(" Serial.begin(%d);", speed));
for (int i = 0; i < digitalPins.length; i++) {
if (digitalPins[i] == 1) printWriter.println(String.format(" pinMode(%d, INPUT);", i));
}
printWriter.println("}");
printWriter.println("");
// loop
printWriter.println("void loop() {");
for (int i = 0; i < digitalPins.length; i++) {
if (digitalPins[i] == 1)
printWriter.println(String.format(" int din%d = digitalRead(%d);", i, i));
}
for (int i = 0; i < analogPins.length; i++) {
if (analogPins[i] == 1)
printWriter.println(String.format(" int ain%d = analogRead(%d);", i, i));
}
// if
printWriter.println(String.format(" if(%s) {", condition.toString()));
printWriter.println(" Serial.print(\"[ \");");
for (String field : csql.getFields()) {
printWriter.println(String.format(" Serial.print(%s);", field));
printWriter.println(" Serial.print(\" \");");
}
printWriter.println(" Serial.print(\"]\");");
printWriter.println(" }");
printWriter.println(String.format(" delay(%d);", delay));
printWriter.println("}");
printWriter.close();
} catch (IOException e) {
e.printStackTrace();
}
}
