Java Code Examples for org.apache.commons.lang.StringUtils#replaceEachRepeatedly()

private String signinWithSAML2POST(SAMLToken samlToken) throws TechnicalConnectorException {
   FileWriter fw = null;

   try {
      String template = ConnectorIOUtils.getResourceAsString("/sso/SSORequestSTSSAML2POST.xml");
      template = StringUtils.replaceEach(template, new String[]{"${reqId}", "${endpoint.idp.saml2.post}"}, new String[]{this.idGenerator.generateId(), this.getSAML2Post()});
      NodeList assertions = this.invokeSecureTokenService(ConnectorXmlUtils.flatten(template), samlToken).getElementsByTagNameNS("urn:oasis:names:tc:SAML:2.0:assertion", "Assertion");
      Validate.notNull(assertions);
      Validate.isTrue(assertions.getLength() == 1);
      Element assertion = (Element)assertions.item(0);
      String samlResponse = ConnectorIOUtils.getResourceAsString("/sso/bindingTemplate-SAMLResponse.xml");
      samlResponse = StringUtils.replaceEachRepeatedly(samlResponse, new String[]{"${SAMLResponseID}", "${SAMLResponseIssueInstant}", "${SAMLAssertion}"}, new String[]{IdGeneratorFactory.getIdGenerator("xsid").generateId(), (new DateTime()).toString(), this.toXMLString(assertion)});
      return new String(Base64.encode(ConnectorIOUtils.toBytes(ConnectorXmlUtils.flatten(samlResponse), Charset.UTF_8)));
   } finally {
      ConnectorIOUtils.closeQuietly(fw);
   }

}
 

/**
 * Split the given string into a string array using ':' as the separator. If
 * the separator is escaped like '\:', the separator is ignored.
 * 
 * @param configString
 * @return configString split into array.
 */
protected String[] splitConfigurationString(String configString) {

    if (StringUtils.isEmpty(configString)) {
        return new String[0];
    }

    String[] result = StringUtils
            .replaceEachRepeatedly(configString, new String[] { "\\:" }, new String[] { TEMP_COLON_REPLACEMENT })
            .split(":");
    for (int i = 0; i < result.length; i++) {
        result[i] = StringUtils.replaceEachRepeatedly(result[i], new String[] { TEMP_COLON_REPLACEMENT },
                new String[] { ":" });
    }
    return result;
}
 

/**
 * Transforms a given {@code value} to the equivalent MAF-valid value based on the given {@code key}.
 * @param key The {@code key} off of which to base the transformation.  This key is the final (transformed) key for output (i.e. the column name in the MAF file).
 * @param value The {@code value} to transform into a MAF-valid value.
 * @param referenceVersion The version of the reference used to create these annotations.
 * @return The MAF-valid equivalent of the given {@code value}.
 */
public static String mafTransform(final String key, final String value, final String referenceVersion) {

    switch (key) {
        case MafOutputRendererConstants.FieldName_Variant_Classification:
            if ( MafOutputRendererConstants.VariantClassificationMap.containsKey(value)) {
                return MafOutputRendererConstants.VariantClassificationMap.get(value);
            }
            break;
            
        case MafOutputRendererConstants.FieldName_Chromosome:
            if ( value.equals(MafOutputRendererConstants.FieldValue_Gencode_Chromosome_Mito) ) {
                return MafOutputRendererConstants.FieldValue_Chromosome_Mito;
            }
            else if ( value.toLowerCase().startsWith("chr") && (referenceVersion.toLowerCase().equals("hg19") || referenceVersion.toLowerCase().equals("b37"))) {
                final String trimVal = value.substring(3);
                if ( HG_19_CHR_SET.contains(trimVal)) {
                    return trimVal;
                }
            }
            break;
        case MafOutputRendererConstants.FieldName_Other_Transcripts:
            // Use apache commons string utils because it's much, much faster to do this replacement:
            return StringUtils.replaceEachRepeatedly(value, ORDERED_GENCODE_VARIANT_CLASSIFICATIONS.toArray(new String[]{}), ORDERED_MAF_VARIANT_CLASSIFICATIONS.toArray(new String[]{}));
    }

    return value;
 }
 

/**
 * Transforms a given {@code value} from a MAF-valid value to a general-purpose value based on the given {@code key}.
 * @param key The {@code key} off of which to base the transformation.  This key is the transformed key for output (i.e. the column name in the MAF file).
 * @param value The {@code value} to transform from a MAF-valid value into a general-purpose value.
 * @param referenceVersion The version of the reference used to create these annotations.
 * @return The general-purpose equivalent of the given MAF-valid {@code value}.
 */
public static String mafTransformInvert(final String key, final String value, final String referenceVersion ) {
    switch (key) {
        case MafOutputRendererConstants.FieldName_Variant_Classification:
            if ( MafOutputRendererConstants.VariantClassificationMapInverse.containsKey(value)) {
                return MafOutputRendererConstants.VariantClassificationMapInverse.get(value);
            }
            break;

        case MafOutputRendererConstants.FieldName_Chromosome:
            if ( value.equals(MafOutputRendererConstants.FieldValue_Chromosome_Mito) ) {
                return MafOutputRendererConstants.FieldValue_Gencode_Chromosome_Mito;
            }
            else if (referenceVersion.toLowerCase().equals("hg19") || referenceVersion.toLowerCase().equals("b37")) {
                if ( value.length() <= 2 ) {
                    if ( HG_19_CHR_SET.contains(value) ) {
                        return "chr" + value;
                    }
                }
            }
            break;
        case MafOutputRendererConstants.FieldName_Other_Transcripts:

            // Use apache commons string utils because it's much, much faster to do this replacement:
            // But we have to do the LINCRNA -> RNA conversion separately, so exclude those indices:
            String replacement = StringUtils.replaceEachRepeatedly(
                    value,
                    ORDERED_MAF_VARIANT_CLASSIFICATIONS.subList(0, ORDERED_MAF_VARIANT_CLASSIFICATIONS.size()-1).toArray(new String[]{}),
                    ORDERED_GENCODE_VARIANT_CLASSIFICATIONS.subList(0, ORDERED_MAF_VARIANT_CLASSIFICATIONS.size()-1).toArray(new String[]{})
            );

            // Handle the RNA/LINCRNA case specially:
            final String needle = MafOutputRendererConstants.VariantClassificationMap.get(GencodeFuncotation.VariantClassification.LINCRNA.toString());
            int indx = replacement.indexOf(needle);
            while ( indx != -1 ) {
                // make sure the previous letters are not LINC:
                if ( (indx <= 3 ) || ((indx > 3) && (!replacement.substring(indx - 4, indx).equals("LINC")))) {
                    replacement = replacement.substring(0, indx) + GencodeFuncotation.VariantClassification.LINCRNA.toString() + replacement.substring(indx + needle.length());
                    indx += needle.length();
                }
                else {
                    ++indx;
                }

                indx = replacement.indexOf(needle, indx);
            }

            return replacement;
    }

    return value;
}