Example usage for org.apache.commons.lang StringUtils containsOnly

List of usage examples for org.apache.commons.lang StringUtils containsOnly

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Introduction

In this page you can find the example usage for org.apache.commons.lang StringUtils containsOnly.

Prototype

public static boolean containsOnly(String str, String validChars)

Source Link

Document

Checks if the String contains only certain characters.

Usage

From source file:org.apache.ranger.plugin.resourcematcher.RangerAbstractResourceMatcher.java

@Override
public boolean isCompleteMatch(String resource, Map<String, Object> evalContext) {
    if (LOG.isDebugEnabled()) {
        LOG.debug("==> RangerAbstractResourceMatcher.isCompleteMatch(" + resource + ", " + evalContext + ")");
    }//from  ww w .  j  a  v  a 2 s .  c  om

    boolean ret = false;

    if (CollectionUtils.isEmpty(policyValues)) {
        ret = StringUtils.isEmpty(resource);
    } else if (policyValues.size() == 1) {
        String policyValue = policyValues.get(0);

        if (isMatchAny) {
            ret = StringUtils.containsOnly(resource, WILDCARD_ASTERISK);
        } else {
            ret = optIgnoreCase ? StringUtils.equalsIgnoreCase(resource, policyValue)
                    : StringUtils.equals(resource, policyValue);
        }

        if (policyIsExcludes) {
            ret = !ret;
        }
    }

    if (LOG.isDebugEnabled()) {
        LOG.debug("<== RangerAbstractResourceMatcher.isCompleteMatch(" + resource + ", " + evalContext + "): "
                + ret);
    }

    return ret;
}

From source file:org.intermine.bio.dataconversion.EnsemblSnpDbConverter.java

/**
 * Given an allele string read from the database determine the type of variation, e.g. snp,
 * in-del, etc.  This is a re-implementation of code from the Ensembl perl API, see:
 * http://www.ensembl.org/info/docs/Doxygen/variation-api/
 *    classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1Sequence.html
 * @param alleleStr the alleles to determine the type for
 * @return a variation class or null if none can be determined
 *//*from w  ww.  ja va 2 s .co  m*/
protected String determineType(String alleleStr) {
    String type = null;

    final String validBases = "ATUGCYRSWKMBDHVN";

    alleleStr = alleleStr.toUpperCase();
    if (!StringUtils.isBlank(alleleStr)) {
        // snp if e.g. A/C or A|C
        if (alleleStr.matches("^[" + validBases + "]([\\/\\|\\\\][" + validBases + "])+$")) {
            type = "snp";
        } else if ("CNV".equals(alleleStr)) {
            type = alleleStr.toLowerCase();
        } else if ("CNV_PROBE".equals(alleleStr)) {
            type = "cnv probe";
        } else if ("HGMD_MUTATION".equals(alleleStr)) {
            type = alleleStr.toLowerCase();
        } else {
            String[] alleles = alleleStr.split("[\\|\\/\\\\]");

            if (alleles.length == 1) {
                type = "het";
            } else if (alleles.length == 2) {
                if ((StringUtils.containsOnly(alleles[0], validBases) && "-".equals(alleles[1]))
                        || (StringUtils.containsOnly(alleles[1], validBases) && "-".equals(alleles[0]))) {
                    type = "in-del";
                } else if (containsOneOf(alleles[0], "LARGE", "INS", "DEL")
                        || containsOneOf(alleles[1], "LARGE", "INS", "DEL")) {
                    type = "named";
                } else if ((StringUtils.containsOnly(alleles[0], validBases) && alleles[0].length() > 1)
                        || (StringUtils.containsOnly(alleles[1], validBases) && alleles[1].length() > 1)) {
                    // AA/GC 2 alleles
                    type = "substitution";
                }
            } else if (alleles.length > 2) {
                if (containsDigit(alleles[0])) {
                    type = "microsat";
                } else if (anyContainChar(alleles, "-")) {
                    type = "mixed";
                }
            }
            if (type == null) {
                LOG.warn("Failed to work out allele type for: " + alleleStr);
            }
        }
    }

    return type;
}

From source file:org.intermine.bio.dataconversion.ModEncodeFeatureProcessor.java

private void processExpressionLevels(Connection connection) throws SQLException, ObjectStoreException {
    ResultSet res = getExpressionLevels(connection);
    Integer previousId = -1;/*w  w w. j ava 2 s.  c  om*/
    Item level = null;
    while (res.next()) {
        Integer id = res.getInt("expression_id");
        Integer featureId = res.getInt("feature_id");
        String name = res.getString("uniquename");
        String value = res.getString("value");
        String property = res.getString("property");
        String propValue = res.getString("propvalue");
        LOG.debug("EL: " + id + "|" + previousId + "->" + featureId + ":" + property + "|" + propValue);
        if (!id.equals(previousId)) {
            // if not first store prev level
            if (previousId > 0) {
                getChadoDBConverter().store(level);
            }
            level = createExpressionLevel(featureId, name, value);
        }
        // check if dcpm is a decimal number
        if ("dcpm".equalsIgnoreCase(property) && !StringUtils.containsOnly(propValue, ".0123456789")) {
            // in some cases (waterston) the value for dcpm is
            // 'nan' or 'na' or '.na' instead of a decimal number
            previousId = id;
            continue;
        }
        if (!EL_KNOWN_ATTRIBUTES.contains(property)) {
            LOG.debug("ExpressionLevel for feature_id = " + featureId + " has unknown attribute " + property);
            previousId = id;
            continue;
        }
        level.setAttribute(getPropName(property), propValue);
        previousId = id;
    }
    if (res.isAfterLast()) {
        getChadoDBConverter().store(level);
    }
    res.close();
}

From source file:org.kuali.kfs.coa.document.IndirectCostRecoveryRateMaintainableImpl.java

/**
 * Hook for quantity and setting asset numbers.
 * @see org.kuali.rice.kns.maintenance.KualiMaintainableImpl#addNewLineToCollection(java.lang.String)
 *//*from   w  ww .ja  va  2  s . c  o m*/
@Override
public void addNewLineToCollection(String collectionName) {

    // create handle for the addline section of the doc
    IndirectCostRecoveryRateDetail addLine = (IndirectCostRecoveryRateDetail) newCollectionLines
            .get(collectionName);
    List<IndirectCostRecoveryRateDetail> maintCollection = (List<IndirectCostRecoveryRateDetail>) ObjectUtils
            .getPropertyValue(getBusinessObject(), collectionName);

    if (StringUtils.isBlank(addLine.getSubAccountNumber())
            || StringUtils.containsOnly(addLine.getSubAccountNumber(), "-")) {
        addLine.setSubAccountNumber(KFSConstants.getDashSubAccountNumber());
    }
    if (StringUtils.isBlank(addLine.getFinancialSubObjectCode())
            || StringUtils.containsOnly(addLine.getFinancialSubObjectCode(), "-")) {
        addLine.setFinancialSubObjectCode(KFSConstants.getDashFinancialSubObjectCode());
    }

    Integer icrEntryNumberMax = 0;
    for (IndirectCostRecoveryRateDetail item : maintCollection) {
        if (icrEntryNumberMax < item.getAwardIndrCostRcvyEntryNbr()) {
            icrEntryNumberMax = item.getAwardIndrCostRcvyEntryNbr();
        }
    }

    // addLine.setActive(true); // TODO remove after active indicator fixes
    addLine.setNewCollectionRecord(true);
    addLine.setAwardIndrCostRcvyEntryNbr(icrEntryNumberMax + 1);
    maintCollection.add(addLine);
    initNewCollectionLine(collectionName);
}

From source file:org.kuali.kfs.coa.document.validation.impl.IndirectCostRecoveryRateRule.java

protected boolean processSubAccount(IndirectCostRecoveryRateDetail item) {
    boolean success = true;
    Map pkMap = new HashMap();
    String chart = item.getChartOfAccountsCode();
    String acct = item.getAccountNumber();
    String subAcct = item.getSubAccountNumber();
    if (StringUtils.isNotBlank(subAcct) && !StringUtils.containsOnly(subAcct, "-")) { // if doesn't contain only dashes
        if (!propertyIsWildcard(chart)) {
            pkMap.put(KFSPropertyConstants.CHART_OF_ACCOUNTS_CODE, chart);
        }//from  w  ww  .  ja v a  2s .com
        if (!propertyIsWildcard(acct)) {
            pkMap.put(KFSPropertyConstants.ACCOUNT_NUMBER, acct);
        }
        if (!propertyIsWildcard(subAcct) && StringUtils.isNotBlank(subAcct)
                && !StringUtils.containsOnly(subAcct, "-")) {
            pkMap.put(KFSPropertyConstants.SUB_ACCOUNT_NUMBER, subAcct);
            if (!checkExistenceFromTable(SubAccount.class, pkMap)) {
                logErrorUtility(KFSPropertyConstants.SUB_ACCOUNT_NUMBER, RiceKeyConstants.ERROR_EXISTENCE);
                success = false;
            }
        }
    }
    return success;
}

From source file:org.kuali.kfs.coa.document.validation.impl.IndirectCostRecoveryRateRule.java

protected boolean processSubObjectCode(IndirectCostRecoveryRateDetail item) { // chart being a wildcard implies account number being a wildcard, redundant checking?
    boolean success = true;
    Map pkMap = new HashMap();
    Integer year = indirectCostRecoveryRate.getUniversityFiscalYear();
    String chart = item.getChartOfAccountsCode();
    String acct = item.getAccountNumber();
    String objCd = item.getFinancialObjectCode();
    String subObjCd = item.getFinancialSubObjectCode();
    if (StringUtils.isNotBlank(subObjCd) && !propertyIsWildcard(subObjCd)
            && !StringUtils.containsOnly(subObjCd, "-")) {
        pkMap.put(KFSPropertyConstants.UNIVERSITY_FISCAL_YEAR, year);
        if (!propertyIsWildcard(chart)) {
            pkMap.put(KFSPropertyConstants.CHART_OF_ACCOUNTS_CODE, chart);
        }//  w  w  w.ja v a 2  s  .  c o m
        if (!propertyIsWildcard(acct)) {
            pkMap.put(KFSPropertyConstants.ACCOUNT_NUMBER, acct);
        }
        if (!propertyIsWildcard(objCd)) {
            pkMap.put(KFSPropertyConstants.FINANCIAL_OBJECT_CODE, objCd);
        }
        pkMap.put(KFSPropertyConstants.FINANCIAL_SUB_OBJECT_CODE, subObjCd);
        if (!GeneralLedgerConstants.PosterService.SYMBOL_USE_EXPENDITURE_ENTRY.equals(subObjCd)
                && !checkExistenceFromTable(SubObjectCode.class, pkMap)) {
            logErrorUtility(KFSPropertyConstants.FINANCIAL_SUB_OBJECT_CODE, RiceKeyConstants.ERROR_EXISTENCE);
            success = false;
        }
    }
    return success;
}

From source file:org.kuali.kfs.coa.document.validation.impl.IndirectCostRecoveryRateRule.java

protected boolean checkAccountNumberWildcardRules(IndirectCostRecoveryRateDetail item) {
    String accountNumber = item.getAccountNumber();
    boolean success = true;
    if (!accountNumber.equals(item.getChartOfAccountsCode())) {
        GlobalVariables.getMessageMap().putError(KFSPropertyConstants.CHART_OF_ACCOUNTS_CODE,
                KFSKeyConstants.IndirectCostRecovery.ERROR_DOCUMENT_ICR_WILDCARDS_MUST_MATCH,
                SpringContext.getBean(DataDictionaryService.class).getAttributeLabel(
                        IndirectCostRecoveryRateDetail.class, KFSPropertyConstants.ACCOUNT_NUMBER),
                SpringContext.getBean(DataDictionaryService.class).getAttributeLabel(
                        IndirectCostRecoveryRateDetail.class, KFSPropertyConstants.CHART_OF_ACCOUNTS_CODE));
        success = false;// ww  w .j  av a 2  s.  c om
    }

    String subAccountNumber = item.getSubAccountNumber();

    // If # is entered on account, then # "must" be entered for chart and sub account "must" be dashes.
    if (GeneralLedgerConstants.PosterService.SYMBOL_USE_ICR_FROM_ACCOUNT.equals(accountNumber)) {
        if (!GeneralLedgerConstants.PosterService.SYMBOL_USE_ICR_FROM_ACCOUNT
                .equals(item.getChartOfAccountsCode())
                && !StringUtils.containsOnly(subAccountNumber, KFSConstants.DASH)) {
            GlobalVariables.getMessageMap().putError(KFSPropertyConstants.SUB_ACCOUNT_NUMBER,
                    KFSKeyConstants.IndirectCostRecovery.ERROR_DOCUMENT_ICR_FIELD_MUST_BE_DASHES,
                    SpringContext.getBean(DataDictionaryService.class).getAttributeLabel(
                            IndirectCostRecoveryRateDetail.class, KFSPropertyConstants.ACCOUNT_NUMBER),
                    GeneralLedgerConstants.PosterService.SYMBOL_USE_ICR_FROM_ACCOUNT,
                    SpringContext.getBean(DataDictionaryService.class).getAttributeLabel(
                            IndirectCostRecoveryRateDetail.class, KFSPropertyConstants.SUB_ACCOUNT_NUMBER));
            success = false;
        }
    }

    if (GeneralLedgerConstants.PosterService.SYMBOL_USE_EXPENDITURE_ENTRY.equals(accountNumber)) {
        if (!(StringUtils.equals(GeneralLedgerConstants.PosterService.SYMBOL_USE_EXPENDITURE_ENTRY,
                subAccountNumber) || !StringUtils.containsOnly(subAccountNumber, KFSConstants.DASH))) {
            GlobalVariables.getMessageMap().putError(KFSPropertyConstants.SUB_ACCOUNT_NUMBER,
                    KFSKeyConstants.IndirectCostRecovery.ERROR_DOCUMENT_ICR_ACCOUNT_USE_EXPENDITURE_ENTRY_WILDCARD_RESTRICTION_ON_SUB_ACCOUNT);
            success = false;
        }
    }
    return success;
}

From source file:org.kuali.kfs.sys.businessobject.inquiry.KfsInquirableImpl.java

/**
 * Helper method to build an inquiry url for a result field. Special implementation to not build an inquiry link if the value is
 * all dashes.//w  ww  .j a  v a  2  s .co m
 * 
 * @param bo the business object instance to build the urls for
 * @param propertyName the property which links to an inquirable
 * @return String url to inquiry
 */
public HtmlData getInquiryUrl(BusinessObject businessObject, String attributeName, boolean forceInquiry) {
    try {
        if (PropertyUtils.isReadable(businessObject, attributeName)) {
            Object objFieldValue = ObjectUtils.getPropertyValue(businessObject, attributeName);
            String fieldValue = objFieldValue == null ? KFSConstants.EMPTY_STRING : objFieldValue.toString();

            if (StringUtils.containsOnly(fieldValue, KFSConstants.DASH)) {
                return new AnchorHtmlData();
            }
        }

        return super.getInquiryUrl(businessObject, attributeName, forceInquiry);
    } catch (Exception ex) {
        LOG.error("Unable to determine inquiry link for BO Class: " + businessObject.getClass()
                + " and property " + attributeName);
        LOG.debug("Unable to determine inquiry link for BO Class: " + businessObject.getClass()
                + " and property " + attributeName, ex);
        return new AnchorHtmlData();
    }
}

From source file:org.kuali.ole.coa.document.IndirectCostRecoveryRateMaintainableImpl.java

/**
 * Hook for quantity and setting asset numbers.
 * @see org.kuali.rice.kns.maintenance.KualiMaintainableImpl#addNewLineToCollection(java.lang.String)
 *//*from w w w  . j ava2  s .  co m*/
@Override
public void addNewLineToCollection(String collectionName) {

    // create handle for the addline section of the doc
    IndirectCostRecoveryRateDetail addLine = (IndirectCostRecoveryRateDetail) newCollectionLines
            .get(collectionName);
    List<IndirectCostRecoveryRateDetail> maintCollection = (List<IndirectCostRecoveryRateDetail>) ObjectUtils
            .getPropertyValue(getBusinessObject(), collectionName);

    if (StringUtils.isBlank(addLine.getSubAccountNumber())
            || StringUtils.containsOnly(addLine.getSubAccountNumber(), "-")) {
        addLine.setSubAccountNumber(OLEConstants.getDashSubAccountNumber());
    }
    if (StringUtils.isBlank(addLine.getFinancialSubObjectCode())
            || StringUtils.containsOnly(addLine.getFinancialSubObjectCode(), "-")) {
        addLine.setFinancialSubObjectCode(OLEConstants.getDashFinancialSubObjectCode());
    }

    Integer icrEntryNumberMax = 0;
    for (IndirectCostRecoveryRateDetail item : maintCollection) {
        if (icrEntryNumberMax < item.getAwardIndrCostRcvyEntryNbr()) {
            icrEntryNumberMax = item.getAwardIndrCostRcvyEntryNbr();
        }
    }

    // addLine.setActive(true); // TODO remove after active indicator fixes
    addLine.setNewCollectionRecord(true);
    addLine.setAwardIndrCostRcvyEntryNbr(icrEntryNumberMax + 1);
    maintCollection.add(addLine);
    initNewCollectionLine(collectionName);
}

From source file:org.kuali.ole.coa.document.validation.impl.IndirectCostRecoveryRateRule.java

protected boolean processSubAccount(IndirectCostRecoveryRateDetail item) {
    boolean success = true;
    Map pkMap = new HashMap();
    String chart = item.getChartOfAccountsCode();
    String acct = item.getAccountNumber();
    String subAcct = item.getSubAccountNumber();
    if (StringUtils.isNotBlank(subAcct) && !StringUtils.containsOnly(subAcct, "-")) { // if doesn't contain only dashes
        if (!propertyIsWildcard(chart)) {
            pkMap.put(OLEPropertyConstants.CHART_OF_ACCOUNTS_CODE, chart);
        }/*from  w  w  w .j a v  a2  s.co m*/
        if (!propertyIsWildcard(acct)) {
            pkMap.put(OLEPropertyConstants.ACCOUNT_NUMBER, acct);
        }
        if (!propertyIsWildcard(subAcct) && StringUtils.isNotBlank(subAcct)
                && !StringUtils.containsOnly(subAcct, "-")) {
            pkMap.put(OLEPropertyConstants.SUB_ACCOUNT_NUMBER, subAcct);
            if (!checkExistenceFromTable(SubAccount.class, pkMap)) {
                logErrorUtility(OLEPropertyConstants.SUB_ACCOUNT_NUMBER, RiceKeyConstants.ERROR_EXISTENCE);
                success = false;
            }
        }
    }
    return success;
}