/** 根据视图同步定义的columnPair,获取需要反查的字段列表,不包括主键 */ private List<String> buildMaxColumnsFromColumnPairs( List<DataMediaPair> mediaPairs, List<EventColumn> pks) { Set<String> allColumns = new HashSet<String>(); Map<String, EventColumn> pkMap = new HashMap<String, EventColumn>(pks.size(), 1f); for (EventColumn pk : pks) { pkMap.put(StringUtils.lowerCase(pk.getColumnName()), pk); } for (DataMediaPair mediaPair : mediaPairs) { // 一个源库可以对应多个目标,多路复制 List<ColumnPair> columnPairs = mediaPair.getColumnPairs(); if (CollectionUtils.isEmpty(columnPairs) || mediaPair.getColumnPairMode().isExclude()) { // 1. 如果有一个没有视图定义,说明需要所有字段 // 2. 如果有一个表存在exclude模式,简单处理,直接反查所有字段,到后面进行过滤 return new ArrayList<String>(); // 返回空集合,代表没有view // filter,需要所有字段 } else { for (ColumnPair columnPair : columnPairs) { String columnName = columnPair.getSourceColumn().getName(); if (!pkMap.containsKey(StringUtils.lowerCase(columnName))) { allColumns.add(columnPair.getSourceColumn().getName()); // 加入的为非主键 } } } } return new ArrayList<String>(allColumns); }
/** * 设置排序方式向. * * @param order 可选值为desc或asc,多个排序字段时用','分隔. */ public void setOrder(final String order) { // 检查order字符串的合法值 String[] orders = StringUtils.split(StringUtils.lowerCase(order), ','); for (String orderStr : orders) { if (!StringUtils.equals(DESC, orderStr) && !StringUtils.equals(ASC, orderStr)) throw new IllegalArgumentException("排序方向 " + orderStr + "不是合法值 "); } this.order = StringUtils.lowerCase(order); }
public static UUID getIndexId( EntityRef connectingEntity, String connectionType, String connectedEntityType, ConnectedEntityRef... pairedConnections) { UUID uuid = null; try { if (connectionsNull(pairedConnections) && ((connectionType == null) && (connectedEntityType == null))) { return connectingEntity.getUuid(); } ByteArrayOutputStream byteStream = new ByteArrayOutputStream(16 + (32 * pairedConnections.length)); byteStream.write(uuidToBytesNullOk(connectingEntity.getUuid())); for (ConnectedEntityRef connection : pairedConnections) { String type = connection.getConnectionType(); UUID id = connection.getUuid(); byteStream.write(ascii(StringUtils.lowerCase(type))); byteStream.write(uuidToBytesNullOk(id)); } if (connectionType == null) { connectionType = NULL_ENTITY_TYPE; } if (connectedEntityType == null) { connectedEntityType = NULL_ENTITY_TYPE; } byteStream.write(ascii(StringUtils.lowerCase(connectionType))); byteStream.write(ascii(StringUtils.lowerCase(connectedEntityType))); byte[] raw_id = byteStream.toByteArray(); logger.info("raw connection index id: " + Hex.encodeHexString(raw_id)); uuid = UUID.nameUUIDFromBytes(raw_id); logger.info("connection index uuid: " + uuid); } catch (IOException e) { logger.error("Unable to create connection index UUID", e); } return uuid; }
/** * 转换成骆驼命名法返回 * * @param name * @return */ public static String getCamelName(String name) { if (StringUtils.isBlank(name)) { return null; } name = StringUtils.lowerCase(name); // 去掉前面的_ while (StringUtils.startsWith(name, "_")) { name = StringUtils.substring(name, 1); } // 去掉后面的_ while (StringUtils.endsWith(name, "_")) { name = StringUtils.substring(name, 0, name.length() - 1); } StringBuilder sb = new StringBuilder(); for (int i = 0; i < name.length(); i++) { char c = name.charAt(i); if (c == '_') { i++; sb.append(Character.toUpperCase(name.charAt(i))); continue; } sb.append(c); } return sb.toString(); }
private void addLink( Study study, Map<Integer, Term> stageForNode, Map<Integer, String> taxonForNode, LabeledCSVParser links, Location location) throws StudyImporterException, NodeFactoryException { Integer consumerNodeID = Integer.parseInt(links.getValueByLabel("ConsumerNodeID")); Integer resourceNodeID = Integer.parseInt(links.getValueByLabel("ResourceNodeID")); String linkType = links.getValueByLabel("LinkType"); InteractType interactType = interactionMapping.get(StringUtils.trim(StringUtils.lowerCase(linkType))); if (interactType == null) { throw new StudyImporterException( "failed to map interaction type [" + linkType + "] in line [" + links.lastLineNumber() + "]"); } Specimen consumer = nodeFactory.createSpecimen(study, taxonForNode.get(consumerNodeID)); consumer.setLifeStage(stageForNode.get(consumerNodeID)); consumer.setExternalId(getNamespace() + ":NodeID:" + consumerNodeID); consumer.caughtIn(location); String resourceName = taxonForNode.get(resourceNodeID); Specimen resource = nodeFactory.createSpecimen(study, resourceName); resource.setLifeStage(stageForNode.get(resourceNodeID)); resource.setExternalId(getNamespace() + ":NodeID:" + resourceNodeID); resource.caughtIn(location); consumer.interactsWith(resource, interactType); }
public void get(HttpServletRequest request, HttpServletResponse response) throws Exception { String redirectFrom = StringUtils.lowerCase( ServletRequestUtils.getRequiredStringParameter(request, "redirectFrom")); Redirection redirection = redirectionDao.getRedirection(redirectFrom); if (redirection == null) { response.sendError( HttpServletResponse.SC_BAD_REQUEST, "Web address " + redirectFrom + ".subsonic.org not registered."); return; } PrintWriter writer = response.getWriter(); String url = redirection.getRedirectTo(); if (!url.endsWith("/")) { url += "/"; } writer.println(url); url = redirection.getLocalRedirectTo(); if (!url.endsWith("/")) { url += "/"; } writer.println(url); }
/** * Log a step into test case result. * * @param tcName * @param result * @param msg */ public void logStep(String tcName, String result, String msg) { if ("".equals(tcName)) { tcName = oi.logRunningTC; if (!"".equals(result.trim())) { if ("false".equals(StringUtils.lowerCase(result.trim()))) { oi.logList.add( tcName + "," + result.trim() + ",At step " + init.currentStep + " of " + init.sumStep + "," + msg.trim()); } else { oi.logList.add(tcName + "," + result.trim() + "," + msg.trim()); } } } else { if (StringUtils.left(tcName, 4).equals("test")) { tcName = StringUtils.mid(tcName, 4, tcName.length()); } oi.logRunningTC = tcName; if ("".equals(result.trim())) { oi.logList.add(tcName + "," + init.logTcStart); } else { oi.logList.add(tcName + "," + result.trim()); } } }
protected String getView(final T component) { // build a jsp response based on the given view name otherwise use the component type return ControllerConstants.Views.Cms.ComponentPrefix + StringUtils.lowerCase( !StringUtils.isEmpty(component.getViewName()) ? component.getViewName() : getTypeCode(component)); }
@Test public void testRenderComponent() throws Exception { final ExtendedModelMap model = new ExtendedModelMap(); final String viewName = miniCartComponentController.handleComponent( request, response, model, miniCartComponentModel); Assert.assertEquals( ControllerConstants.Views.Cms.ComponentPrefix + StringUtils.lowerCase(miniCartComponentModel.getItemtype()), viewName); }
private Header createHeader( String binlogFile, LogHeader logHeader, String schemaName, String tableName) { // header会做信息冗余,方便以后做检索或者过滤 Header.Builder headerBuilder = Header.newBuilder(); headerBuilder.setVersion(version); headerBuilder.setLogfileName(binlogFile); headerBuilder.setLogfileOffset(logHeader.getLogPos() - logHeader.getEventLen()); headerBuilder.setServerId(logHeader.getServerId()); headerBuilder.setServerenCode(UTF_8); // 经过java输出后所有的编码为unicode headerBuilder.setExecuteTime(logHeader.getWhen() * 1000L); headerBuilder.setSourceType(Type.MYSQL); if (schemaName != null) { headerBuilder.setSchemaName(StringUtils.lowerCase(schemaName)); } if (tableName != null) { headerBuilder.setTableName(StringUtils.lowerCase(tableName)); } headerBuilder.setEventLength(logHeader.getEventLen()); return headerBuilder.build(); }
public static String cleanWWN(String wwn) { if (StringUtils.isBlank(wwn)) { return null; } wwn = StringUtils.lowerCase(StringUtils.trim(wwn)); if (!LOOSE_WWN_PATTERN.matcher(wwn).matches()) { return null; } wwn = StringUtils.replace(wwn, ":", ""); return wwn; }
@SuppressWarnings("unchecked") public <T> T getBean(Class<T> clazz) { if (appContext != null) { String className = clazz.getSimpleName(); String startName = className.substring(0, 1); String otherName = className.substring(1); String beanName = StringUtils.lowerCase(startName) + otherName; return (T) appContext.getBean(beanName); } return null; }
/** * 登陆验证码校验 * * @param captchaCode * @return */ public boolean checkCaptchaCode(String captchaCode) { if (StringUtils.isNotBlank(captchaCode)) { String captchaKey = Constants.REDIS_KEY_CAPTCHA_PREFIX + StringUtils.lowerCase(captchaCode); boolean checkFlag = redisEao.isKeyExist(captchaKey); System.out.println(checkFlag + "---------"); if (checkFlag) { redisEao.del(captchaKey); return true; } } return false; }
/** * DOC yyin Comment method "findCreatedTable". * * @param hiveConnectionItem * @param createTableName * @return */ private DBTableRepNode findCreatedTable( DatabaseConnectionItem hiveConnectionItem, String createTableName) { if (hiveConnectionItem == null) { return null; } // TDQ-10462 the table from the hive connection, only use lowercase. IRepositoryNode tableNode = TableUtils.findTableInConnection( hiveConnectionItem, StringUtils.lowerCase(createTableName)); if (tableNode != null && tableNode instanceof DBTableRepNode) { return (DBTableRepNode) tableNode; } return null; }
private void appendResourceNameCondition(StringBuilder sb) { if (StringUtils.isNotBlank(filter.getResourceName())) { sb.append( " AND s.project_id IN (SELECT rindex.resource_id FROM resource_index rindex WHERE rindex.kee LIKE '"); sb.append( escapePercentAndUnderscrore( StringEscapeUtils.escapeSql(StringUtils.lowerCase(filter.getResourceName())))); sb.append("%'"); appendEscapeForSomeDb(sb); if (!filter.getResourceQualifiers().isEmpty()) { sb.append(" AND rindex.qualifier IN "); appendInStatement(filter.getResourceQualifiers(), sb); } sb.append(") "); } }
private ForcedResolverValueLifetimeSettings getForcedDeviceClassSetting( ExtendedMap formItems, ForcedResolverValueLifetimeSettings defaultSetting) { String forcedDeviceClassParameter = formItems.getString(FORCE_VALUE_SETTING_KEY, defaultSetting.name()); ForcedResolverValueLifetimeSettings forcedDeviceClassSetting; try { forcedDeviceClassSetting = ForcedResolverValueLifetimeSettings.valueOf( StringUtils.lowerCase(forcedDeviceClassParameter)); } catch (IllegalArgumentException e) { throw new VerticalUserServicesException( "Force deviceclass setting is invalid: " + forcedDeviceClassParameter); } return forcedDeviceClassSetting; }
/** * @param resourceDTO * @param siteId * @param comment * @return * @throws IOException * @throws ValidationException */ @PreAuthorize( "@tiiltaAuthorization.hasPermission('TemplatingDjango', @userService.getConnected())") @RequestMapping( value = "/bender/{siteId:.+}/resource", method = RequestMethod.POST, headers = {"content-type=application/json"}) public ResponseEntity<BenderResource> createResource( @RequestBody @Valid BenderResource resourceDTO, @PathVariable("siteId") String siteId, @RequestParam(value = "comment", required = false) String comment) throws IOException, ValidationException { ResponseEntity<BenderResource> result = new ResponseEntity<>(null, new HttpHeaders(), HttpStatus.BAD_REQUEST); Site site = siteService.getSite(siteId); if (site == null) { throw new ValidationException("Le site est inconnu"); } User user = userService.getConnected(); resourceDTO.setSite(siteId); resourceDTO.setCreationDate(new Date()); resourceDTO.setUpdateDate(new Date()); // set Resource Path // format path with Path.get resourceDTO.setPath( Paths.get( resourceDTO.getPath() + File.separator + resourceDTO.getName() + "." + StringUtils.lowerCase(resourceDTO.getType())) .toString()); BenderResource createdResource = benderService.persist(resourceDTO); if (createdResource != null) result = new ResponseEntity<>( this.getResourceById(createdResource.getId(), null, siteId), new HttpHeaders(), HttpStatus.OK); return result; }
protected void doSubmitAction(Object cmd) throws Exception { NetworkSettingsCommand command = (NetworkSettingsCommand) cmd; settingsService.setPortForwardingEnabled(command.isPortForwardingEnabled()); settingsService.setUrlRedirectionEnabled(command.isUrlRedirectionEnabled()); settingsService.setUrlRedirectFrom(StringUtils.lowerCase(command.getUrlRedirectFrom())); if (!settingsService.isLicenseValid() && settingsService.getUrlRedirectTrialExpires() == null) { Date expiryDate = new Date(System.currentTimeMillis() + TRIAL_DAYS * 24L * 3600L * 1000L); settingsService.setUrlRedirectTrialExpires(expiryDate); } if (settingsService.getServerId() == null) { Random rand = new Random(System.currentTimeMillis()); settingsService.setServerId(String.valueOf(Math.abs(rand.nextLong()))); } settingsService.save(); networkService.initPortForwarding(); networkService.initUrlRedirection(true); }
@Override protected void handlerCustom( HttpServletRequest request, HttpServletResponse response, HttpSession session, ExtendedMap formItems, UserServicesService userServices, SiteKey siteKey, String operation) throws VerticalUserServicesException, VerticalEngineException, IOException, ClassNotFoundException, IllegalAccessException, InstantiationException, ParseException { PortalOperation portalOperation = null; try { portalOperation = PortalOperation.valueOf(StringUtils.lowerCase(operation)); } catch (IllegalArgumentException e) { throw new VerticalUserServicesException( "Operation: " + operation + " not supported in service " + " portal"); } ResolverContext resolverContext = new ResolverContext(request, getSite(siteKey)); switch (portalOperation) { case forcedeviceclass: handleForceDeviceClass(resolverContext, response, formItems); break; case resetdeviceclass: handleResetDeviceClass(resolverContext, response); break; case forcelocale: handleForceLocale(resolverContext, response, formItems); break; case resetlocale: handleResetLocale(resolverContext, response); break; } redirectToPage(request, response, formItems); }
/** * trucate the string. * * @param strMethod set the method string trucated. * @return string of method. */ private String trucateStringFromMethod(String strMethod) { final String strSet = "set"; final String strGet = "get"; final String strIs = "is"; if (!strMethod.startsWith(strSet) && !strMethod.startsWith(strGet) && !strMethod.startsWith(strIs)) { return null; } int posAfterSet = strSet.length(); if (strMethod.startsWith(strIs)) { posAfterSet = strIs.length(); } String strMethodField = strMethod.substring(posAfterSet); String strFieldFirstLetter = strMethodField.substring(0, 1); String strReplace = StringUtils.lowerCase(strFieldFirstLetter); strMethodField = strMethodField.replaceFirst(strFieldFirstLetter, strReplace); return strMethodField; }
@UnitTest public class MiniCartComponentControllerTest { private static final String COMPONENT_UID = "componentUid"; private static final String TEST_COMPONENT_UID = "MiniCart"; private static final String TEST_TYPE_CODE = "myTypeCode"; private static final String TEST_TYPE_VIEW = ControllerConstants.Views.Cms.ComponentPrefix + StringUtils.lowerCase(TEST_TYPE_CODE); private static final Integer TOTAL_UNIT_COUNT = Integer.valueOf(1); private static final BigDecimal SUB_TOTAL_VALUE = BigDecimal.valueOf(100); private static final BigDecimal TOTAL_VALUE = BigDecimal.valueOf(200); private static final BigDecimal DELIVERY_VALUE = BigDecimal.valueOf(20); private MiniCartComponentController miniCartComponentController; private MiniCartComponentModel miniCartComponentModel; @Mock private DefaultCMSComponentService cmsComponentService; @Mock private HttpServletRequest request; @Mock private HttpServletResponse response; @Mock private CartFacade cartFacade; @Before public void setUp() throws CMSItemNotFoundException { MockitoAnnotations.initMocks(this); miniCartComponentController = new MiniCartComponentController(); miniCartComponentController.setCmsComponentService(cmsComponentService); miniCartComponentModel = new MiniCartComponentModel(); final PriceData subTotal = new PriceData(); subTotal.setValue(SUB_TOTAL_VALUE); final PriceData totalPrice = new PriceData(); totalPrice.setValue(TOTAL_VALUE); final PriceData deliveryCost = new PriceData(); deliveryCost.setValue(DELIVERY_VALUE); final CartData cartData = new CartData(); cartData.setSubTotal(subTotal); cartData.setTotalPrice(totalPrice); cartData.setDeliveryCost(deliveryCost); cartData.setTotalUnitCount(TOTAL_UNIT_COUNT); given(cartFacade.getMiniCart()).willReturn(cartData); given(request.getAttribute(COMPONENT_UID)).willReturn(TEST_COMPONENT_UID); ReflectionTestUtils.setField( miniCartComponentController, "cartFacade", cartFacade, CartFacade.class); } @Test public void testSubtotal() throws Exception { final ExtendedModelMap model = new ExtendedModelMap(); miniCartComponentModel.setTotalDisplay(CartTotalDisplayType.SUBTOTAL); given(cmsComponentService.getSimpleCMSComponent(TEST_COMPONENT_UID)) .willReturn(miniCartComponentModel); miniCartComponentController.handleGet(request, response, model); final PriceData priceData = (PriceData) model.get(MiniCartComponentController.SUB_TOTAL); Assert.assertEquals(SUB_TOTAL_VALUE, priceData.getValue()); } @Test public void testTotal() throws Exception { final ExtendedModelMap model = new ExtendedModelMap(); miniCartComponentModel.setTotalDisplay(CartTotalDisplayType.TOTAL); given(cmsComponentService.getSimpleCMSComponent(TEST_COMPONENT_UID)) .willReturn(miniCartComponentModel); miniCartComponentController.handleGet(request, response, model); final PriceData priceData = (PriceData) model.get(MiniCartComponentController.TOTAL_PRICE); Assert.assertEquals(TOTAL_VALUE, priceData.getValue()); } @Test public void testTotalWithoutDelivery() throws Exception { final ExtendedModelMap model = new ExtendedModelMap(); miniCartComponentModel.setTotalDisplay(CartTotalDisplayType.TOTAL_WITHOUT_DELIVERY); given(cmsComponentService.getSimpleCMSComponent(TEST_COMPONENT_UID)) .willReturn(miniCartComponentModel); miniCartComponentController.handleGet(request, response, model); final PriceData priceData = (PriceData) model.get(MiniCartComponentController.TOTAL_NO_DELIVERY); Assert.assertEquals(TOTAL_VALUE.subtract(DELIVERY_VALUE), priceData.getValue()); } @Test public void testRenderComponent() throws Exception { final ExtendedModelMap model = new ExtendedModelMap(); final String viewName = miniCartComponentController.handleComponent( request, response, model, miniCartComponentModel); Assert.assertEquals(TEST_TYPE_VIEW, viewName); } }
protected String prepareUserUid(final String userUid) { return StringUtils.lowerCase(userUid); }
protected String getView(final T component) { // build a jsp response based on the component type return ControllerConstants.Views.Cms.ComponentPrefix + StringUtils.lowerCase(getTypeCode(component)); }
/** * Imports UploadBatch from tab/comma delimited File * * @param db database to import into * @param reader csv reader to load data from * @param defaults to set default values for each row * @param dbAction indicating wether to add,update,remove etc * @param missingValues indicating what value in the csv is treated as 'null' (e.g. "" or "NA") * @return number of elements imported */ public int importCsv( final Database db, CsvReader reader, final Tuple defaults, final DatabaseAction dbAction, final String missingValues) throws DatabaseException, IOException, Exception { // cache for entities of which xrefs couldn't be resolved (e.g. if there // is a self-refence) // these entities can be updated with their xrefs in a second round when // all entities are in the database // final List<UploadBatch> uploadBatchsMissingRefs = new // ArrayList<UploadBatch>(); final MutationService mutationService = new MutationService(); mutationService.setDatabase(db); final UploadService uploadService = new UploadService(); uploadService.setDatabase(db); final Submission submission = new Submission(); DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd"); submission.setDate(dateFormat.format(new Date())); submission.setReleasedate(dateFormat.format(new Date())); submission.setIdentifier("S" + new Date()); if (db instanceof JDBCDatabase) { List<Integer> submitters = new ArrayList<Integer>(); submitters.add(db.getLogin().getUserId()); submission.setSubmitters_Id(submitters); } else if (db instanceof JpaDatabase) { List<MolgenisUser> submitters = new ArrayList<MolgenisUser>(); submitters.add(db.findById(MolgenisUser.class, db.getLogin().getUserId())); // submission.setSubmitters(submitters); } db.add(submission); // cache for objects to be imported from file (in batch) // TODO: Danny: Use or loose /* final List<PatientSummaryVO> patientList = */ new ArrayList<PatientSummaryVO>(BATCH_SIZE); // wrapper to count final IntegerWrapper total = new IntegerWrapper(0); reader.setMissingValues(missingValues); Integer mutationIdentifier = uploadService.getMaxMutationIdentifier(); Integer patientIdentifier = uploadService.getMaxPatientIdentifier(); for (Tuple tuple : reader) { // parse object, setting defaults and values from file // if (lineNo > 5) return; PatientSummaryVO patientSummaryVO = new PatientSummaryVO(); patientSummaryVO.setSubmissionDate(submission.getDate()); patientSummaryVO.setPatientNumber(tuple.getString("Local patient number")); patientSummaryVO.setPatientGender( ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Gender")), "unknown")); patientSummaryVO.setPatientEthnicity(tuple.getString("Ethnicity")); patientSummaryVO.setPatientAge(ObjectUtils.toString(tuple.getString("Age"), "unknown")); patientSummaryVO.setPatientDeceased( ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Deceased")), "unknown")); patientSummaryVO.setPatientConsent( ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Signed consent")), "no")); patientSummaryVO.setVariantSummaryVOList(new ArrayList<MutationSummaryVO>()); if (StringUtils.isNotEmpty(tuple.getString("cDNA change_1"))) { MutationUploadVO mutationUploadVO = new MutationUploadVO(); mutationUploadVO.setGeneSymbol("COL7A1"); mutationUploadVO.setMutation(new Mutation()); mutationUploadVO.getMutation().setCdna_Notation("c." + tuple.getString("cDNA change_1")); mutationService.assignValuesFromNotation(mutationUploadVO); if (StringUtils.isNotEmpty(tuple.getString("Protein change_1"))) mutationUploadVO.getMutation().setAa_Notation("p." + tuple.getString("Protein change_1")); if (StringUtils.isNotEmpty(tuple.getString("Consequence_1"))) mutationUploadVO .getMutation() .setConsequence(ObjectUtils.toString(tuple.getString("Consequence_1"), "")); mutationUploadVO .getMutation() .setInheritance( ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Inheritance_1")), "")); mutationIdentifier = mutationIdentifier + 1; mutationUploadVO.getMutation().setIdentifier("M" + mutationIdentifier); mutationUploadVO.getMutation().setName("M" + mutationIdentifier); // Insert mutation if it does not exist already MutationSearchCriteriaVO criteria = new MutationSearchCriteriaVO(); criteria.setVariation(mutationUploadVO.getMutation().getCdna_Notation()); List<MutationSummaryVO> results = mutationService.findMutations(criteria); if (results.size() != 1) { uploadService.insert(mutationUploadVO); System.out.println(">>>Inserted mutation: " + mutationUploadVO.getMutation().toString()); } MutationSummaryVO mutationSummaryVO = new MutationSummaryVO(); mutationSummaryVO.setCdnaNotation(mutationUploadVO.getMutation().getCdna_Notation()); patientSummaryVO.getVariantSummaryVOList().add(mutationSummaryVO); } // Second mutation can be 'NA' or 'unknown': // Leave xref == null and add remark in mutation2remark if (StringUtils.isNotEmpty(tuple.getString("cDNA change_2"))) { if (tuple.getString("cDNA change_2").equalsIgnoreCase("na")) patientSummaryVO.setVariantComment(tuple.getString("cDNA change_2").toUpperCase()); else if (tuple.getString("cDNA change_2").equalsIgnoreCase("unknown")) patientSummaryVO.setVariantComment(tuple.getString("cDNA change_2").toUpperCase()); else { MutationUploadVO mutationUploadVO = new MutationUploadVO(); mutationUploadVO.setGeneSymbol("COL7A1"); mutationUploadVO.setMutation(new Mutation()); mutationUploadVO.getMutation().setCdna_Notation("c." + tuple.getString("cDNA change_2")); mutationService.assignValuesFromNotation(mutationUploadVO); if (StringUtils.isNotEmpty(tuple.getString("Protein change_2"))) mutationUploadVO .getMutation() .setAa_Notation("p." + tuple.getString("Protein change_2")); if (StringUtils.isNotEmpty(tuple.getString("Consequence_2"))) mutationUploadVO .getMutation() .setConsequence(ObjectUtils.toString(tuple.getString("Consequence_2"), "")); mutationUploadVO .getMutation() .setInheritance( ObjectUtils.toString( StringUtils.lowerCase(tuple.getString("Inheritance_2")), "")); mutationIdentifier = mutationIdentifier + 1; mutationUploadVO.getMutation().setIdentifier("M" + mutationIdentifier); mutationUploadVO.getMutation().setName("M" + mutationIdentifier); // Insert mutation if it does not exist already MutationSearchCriteriaVO criteria = new MutationSearchCriteriaVO(); criteria.setVariation(mutationUploadVO.getMutation().getCdna_Notation()); List<MutationSummaryVO> results = mutationService.findMutations(criteria); if (results.size() != 1) { uploadService.insert(mutationUploadVO); System.out.println( ">>>Inserted mutation: " + mutationUploadVO.getMutation().toString()); } MutationSummaryVO mutationSummaryVO = new MutationSummaryVO(); mutationSummaryVO.setCdnaNotation(mutationUploadVO.getMutation().getCdna_Notation()); patientSummaryVO.getVariantSummaryVOList().add(mutationSummaryVO); } } patientSummaryVO.setPhenotypeMajor( StringUtils.upperCase(tuple.getString("Phenotype major type"))); patientSummaryVO.setPhenotypeSub(StringUtils.lowerCase(tuple.getString("Phenotype Subtype"))); // PhenotypeDetailsVO phenotypeDetailsVO = new PhenotypeDetailsVO(); // patientSummaryVO.getPhenotypeDetails().setLocation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Location")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setBlistering(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Blistering")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setHands(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Hands")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setFeet(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Feet")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setArms(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Arms")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setLegs(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Legs")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setProximal_Body_Flexures(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Proximal body flexures")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setTrunk(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Trunk")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setMucous_Membranes(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Mucosa")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setSkin_Atrophy(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Skin atrophy")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setMilia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Milia")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setNail_Dystrophy(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Nail dystrophy")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setAlbopapuloid_Papules(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Albopapuloid papules")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setPruritic_Papules(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Pruritic papules")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setAlopecia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Alopecia")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setSquamous_Cell_Carcinomas(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Squamous cell carcinoma(s)")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setRevertant_Skin_Patch(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Revertant skin patch(es)")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setMechanism(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Mechanism")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setFlexion_Contractures(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Flexion contractures")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setPseudosyndactyly_Hands(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Pseudosyndactyly (hands)")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setMicrostomia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Microstomia")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setAnkyloglossia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Ankyloglossia")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setDysphagia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Swallowing difficulties/ dysphagia/ oesophagus strictures")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setGrowth_Retardation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Growth retardation")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setAnemia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Anaemia")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setRenal_Failure(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Renal failure")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setDilated_Cardiomyopathy(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Dilated cardiomyopathy")), // "unknown")); // // patientSummaryVO.getPhenotypeDetails().setColoboma(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Coloboma")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setCongenital_Heart_Defect(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Congenital heart defect")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setClp(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("C(L)P")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setChoanal_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Choanal anomaly")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setMental_Retardation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Mental retardation")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setGrowth_Retardation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Growth retardation")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setGenital_Hypoplasia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Genital hypoplasia")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setExternal_Ear_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("External ear anomaly")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setSemicircular_Canal_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Semicircular canal anomaly")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setHearing_Loss(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Hearing loss")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setTe_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("TE anomaly")), // "unknown")); // patientSummaryVO.getPhenotypeDetails().setCn_Dysfunction(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("CN dysfunction")), // "unknown")); // for (String field : // patientSummaryVO.getPhenotypeDetails().getFields(true)) // { // if ("".equals(patientSummaryVO.getPhenotypeDetails().get(field))) // patientSummaryVO.getPhenotypeDetails().set(field, "unknown"); // } // patientSummaryVO.getPhenotypeDetails().set(tuple.getString("")); if (tuple.getString("PubMed ID") != null && tuple.getString("Reference") != null) { List<PublicationVO> publicationVOs = new ArrayList<PublicationVO>(); String[] pubmeds = tuple.getString("PubMed ID").split(";"); String[] titles = tuple.getString("Reference").split(";"); for (int i = 0; i < pubmeds.length; i++) { PublicationVO publicationVO = new PublicationVO(); publicationVO.setPubmedId(pubmeds[i]); publicationVO.setName(titles[i]); publicationVO.setTitle(titles[i]); publicationVOs.add(publicationVO); } patientSummaryVO.setPublicationVOList(publicationVOs); patientSummaryVO.setPatientConsent("publication"); } patientIdentifier = patientIdentifier + 1; patientSummaryVO.setPatientIdentifier("P" + patientIdentifier); patientSummaryVO.setPatientName("P" + patientIdentifier); patientSummaryVO.setObservedValueVOList(new ArrayList<ObservedValueVO>()); ObservedValueVO observedValueVO; observedValueVO = new ObservedValueVO(); observedValueVO.setFeatureName("LH7:2 Amount of type VII collagen"); observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier()); observedValueVO.setValue(ObjectUtils.toString(tuple.getString("IF LH7:2"), "unknown")); patientSummaryVO.getObservedValueVOList().add(observedValueVO); observedValueVO = new ObservedValueVO(); observedValueVO.setFeatureName("IF Retention of type VII Collagen in basal cells"); observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier()); observedValueVO.setValue( ObjectUtils.toString(tuple.getString("IF Retention COLVII"), "unknown")); patientSummaryVO.getObservedValueVOList().add(observedValueVO); observedValueVO = new ObservedValueVO(); observedValueVO.setFeatureName("Anchoring fibrils Number"); observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier()); observedValueVO.setValue(ObjectUtils.toString(tuple.getString("EM AF_no"), "unknown")); patientSummaryVO.getObservedValueVOList().add(observedValueVO); observedValueVO = new ObservedValueVO(); observedValueVO.setFeatureName("Anchoring fibrils Ultrastructure"); observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier()); observedValueVO.setValue(ObjectUtils.toString(tuple.getString("EM AF_structure"), "unknown")); patientSummaryVO.getObservedValueVOList().add(observedValueVO); observedValueVO = new ObservedValueVO(); observedValueVO.setFeatureName("EM Retention of type VII Collagen in basal cells"); observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier()); observedValueVO.setValue( ObjectUtils.toString(tuple.getString("EM_Retention COLVII"), "unknown")); patientSummaryVO.getObservedValueVOList().add(observedValueVO); for (int i = 34; ; i++) { System.out.println(">>>i==" + i); String colName = tuple.getColName(i); System.out.println(">>>colName==" + colName); if (colName == null) break; observedValueVO = new ObservedValueVO(); observedValueVO.setFeatureName(colName); observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier()); observedValueVO.setValue(ObjectUtils.toString(tuple.getString(colName), "unknown")); patientSummaryVO.getObservedValueVOList().add(observedValueVO); } uploadService.insert(patientSummaryVO); total.set(total.get() + 1); // patientList.add(patientSummaryVO); // // //add to db when batch size is reached // if(patientList.size() == BATCH_SIZE) // { // //resolve foreign keys and copy those entities that could not be // resolved to the missingRefs list // uploadBatchsMissingRefs.addAll(resolveForeignKeys(db, // uploadBatchList)); // // //update objects in the database using xref_label defined // secondary key(s) 'id' defined in xref_label // db.update(uploadBatchList,dbAction, "id"); // // //clear for next batch // uploadBatchList.clear(); // // //keep count // total.set(total.get() + BATCH_SIZE); // } } // add remaining elements to the database // if(!uploadBatchList.isEmpty()) // { // //resolve foreign keys, again keeping track of those entities that // could not be solved // uploadBatchsMissingRefs.addAll(resolveForeignKeys(db, // uploadBatchList)); // //update objects in the database using xref_label defined secondary // key(s) 'id' defined in xref_label // db.update(uploadBatchList,dbAction, "id"); // } // // //second import round, try to resolve FK's for entities again as they // might have referred to entities in the imported list // List<UploadBatch> uploadBatchsStillMissingRefs = // resolveForeignKeys(db, uploadBatchsMissingRefs); // // //if there are still missing references, throw error and rollback // if(uploadBatchsStillMissingRefs.size() > 0){ // throw new // Exception("Import of 'UploadBatch' objects failed: attempting to resolve in-list references, // but there are still UploadBatchs referring to UploadBatchs that are neither in the database // nor in the list of to-be imported UploadBatchs. (the first one being: // "+uploadBatchsStillMissingRefs.get(0)+")"); // } // //else update the entities in the database with the found references // and return total // else // { // db.update(uploadBatchsMissingRefs,DatabaseAction.UPDATE, "id"); // // //output count // total.set(total.get() + uploadBatchList.size()); // logger.info("imported "+total.get()+" uploadBatch from CSV"); // // return total.get(); // } return total.get(); }
public String getMode() { return StringUtils.lowerCase(this.toString()); }
@Override public boolean matches(LogData logData) { return StringUtils.contains(StringUtils.lowerCase(logData.getMessage()), searchChar); }
@Override protected String getView(final PurchasedCategorySuggestionComponentModel component) { return ControllerConstants.Views.Cms.ComponentPrefix + StringUtils.lowerCase(SimpleSuggestionComponentModel._TYPECODE); }
private <T> T getBean(Class<T> aClass) { String name = aClass.getSimpleName(); name = StringUtils.lowerCase(name.substring(0, 1)) + name.substring(1); return (T) applicationContext.getBean(name); }
private String getLibraryName(HtmlLibrary library) { return StringUtils.replace( library.getName(true), "min", StringUtils.lowerCase(this.optimization.name())); }
private void doPreparedStatement( PreparedStatement ps, DbDialect dbDialect, LobCreator lobCreator, EventData data) throws SQLException { EventType type = data.getEventType(); // 注意insert/update语句对应的字段数序都是将主键排在后面 List<EventColumn> columns = new ArrayList<EventColumn>(); if (type.isInsert()) { columns.addAll(data.getColumns()); // insert为所有字段 columns.addAll(data.getKeys()); } else if (type.isDelete()) { columns.addAll(data.getKeys()); } else if (type.isUpdate()) { boolean existOldKeys = !CollectionUtils.isEmpty(data.getOldKeys()); columns.addAll(data.getUpdatedColumns()); // 只更新带有isUpdate=true的字段 columns.addAll(data.getKeys()); if (existOldKeys) { columns.addAll(data.getOldKeys()); } } for (int i = 0; i < columns.size(); i++) { int paramIndex = i + 1; EventColumn column = columns.get(i); int sqlType = column.getColumnType(); // 获取一下当前字段名的数据是否必填 Table table = dbDialect.findTable(data.getSchemaName(), data.getTableName()); Map<String, Boolean> isRequiredMap = new HashMap<String, Boolean>(); for (Column tableColumn : table.getColumns()) { isRequiredMap.put(StringUtils.lowerCase(tableColumn.getName()), tableColumn.isRequired()); } Boolean isRequired = isRequiredMap.get(StringUtils.lowerCase(column.getColumnName())); if (isRequired == null) { throw new ClaveException( String.format( "column name %s is not found in Table[%s]", column.getColumnName(), table.toString())); } Object param = SqlUtils.stringToSqlValue( column.getColumnValue(), sqlType, isRequired, dbDialect.isEmptyStringNulled()); try { switch (sqlType) { case Types.CLOB: lobCreator.setClobAsString(ps, paramIndex, (String) param); break; case Types.BLOB: lobCreator.setBlobAsBytes(ps, paramIndex, (byte[]) param); break; default: StatementCreatorUtils.setParameterValue(ps, paramIndex, sqlType, null, param); break; } } catch (SQLException ex) { logger.error( "## SetParam error , [table={}, sqltype={}, value={}]", new Object[] {data.getSchemaName() + "." + data.getTableName(), sqlType, param}); throw ex; } } }