/** 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;
}
}
}