/*******************************************************************************
* Open Behavioral Health Information Technology Architecture (OBHITA.org)
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
* * Neither the name of the <organization> nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
******************************************************************************/
package gov.samhsa.acs.documentsegmentation.tools;
import gov.samhsa.acs.brms.domain.ClinicalFact;
import gov.samhsa.acs.brms.domain.FactModel;
import gov.samhsa.acs.brms.domain.RuleExecutionContainer;
import gov.samhsa.acs.brms.domain.XacmlResult;
import gov.samhsa.acs.common.exception.DS4PException;
import gov.samhsa.acs.common.tool.DocumentAccessor;
import gov.samhsa.acs.common.tool.DocumentXmlConverter;
import gov.samhsa.acs.common.tool.SimpleMarshaller;
import gov.samhsa.acs.common.tool.exception.DocumentAccessorException;
import gov.samhsa.acs.documentsegmentation.tools.dto.RedactedDocument;
import gov.samhsa.acs.documentsegmentation.tools.redact.base.AbstractClinicalFactLevelRedactionHandler;
import gov.samhsa.acs.documentsegmentation.tools.redact.base.AbstractDocumentLevelRedactionHandler;
import gov.samhsa.acs.documentsegmentation.tools.redact.base.AbstractObligationLevelRedactionHandler;
import gov.samhsa.acs.documentsegmentation.tools.redact.base.AbstractPostRedactionLevelRedactionHandler;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import javax.xml.xpath.XPathExpressionException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
/**
* The Class DocumentRedactorImpl.
*/
public class DocumentRedactorImpl implements DocumentRedactor {
/** The logger. */
private final Logger logger = LoggerFactory.getLogger(this.getClass());
/** The marshaller. */
private final SimpleMarshaller marshaller;
/** The document xml converter. */
private final DocumentXmlConverter documentXmlConverter;
/** The document accessor. */
private final DocumentAccessor documentAccessor;
/** The document level redaction handlers. */
private final Set<AbstractDocumentLevelRedactionHandler> documentLevelRedactionHandlers;
/** The obligation level redaction handlers. */
private final Set<AbstractObligationLevelRedactionHandler> obligationLevelRedactionHandlers;
/** The clinical fact level redaction handlers. */
private final Set<AbstractClinicalFactLevelRedactionHandler> clinicalFactLevelRedactionHandlers;
/** The post redaction level redaction handlers. */
private final Set<AbstractPostRedactionLevelRedactionHandler> postRedactionLevelRedactionHandlers;
/**
* Instantiates a new document redactor impl.
*
* @param marshaller
* the marshaller
* @param documentXmlConverter
* the document xml converter
* @param documentAccessor
* the document accessor
* @param obligationLevelRedactionHandlers
* the obligation level redaction handlers
* @param clinicalFactLevelRedactionHandlers
* the clinical fact level redaction handlers
* @param postRedactionLevelRedactionHandlers
* the post redaction level redaction handlers
*/
public DocumentRedactorImpl(
SimpleMarshaller marshaller,
DocumentXmlConverter documentXmlConverter,
DocumentAccessor documentAccessor,
Set<AbstractDocumentLevelRedactionHandler> documentLevelRedactionHandlers,
Set<AbstractObligationLevelRedactionHandler> obligationLevelRedactionHandlers,
Set<AbstractClinicalFactLevelRedactionHandler> clinicalFactLevelRedactionHandlers,
Set<AbstractPostRedactionLevelRedactionHandler> postRedactionLevelRedactionHandlers) {
super();
this.marshaller = marshaller;
this.documentXmlConverter = documentXmlConverter;
this.documentAccessor = documentAccessor;
this.documentLevelRedactionHandlers = documentLevelRedactionHandlers;
this.obligationLevelRedactionHandlers = obligationLevelRedactionHandlers;
this.clinicalFactLevelRedactionHandlers = clinicalFactLevelRedactionHandlers;
this.postRedactionLevelRedactionHandlers = postRedactionLevelRedactionHandlers;
}
/*
* (non-Javadoc)
*
* @see gov.samhsa.acs.documentsegmentation.tools.DocumentRedactor#
* cleanUpEmbeddedClinicalDocumentFromFactModel(java.lang.String)
*/
@Override
public String cleanUpEmbeddedClinicalDocumentFromFactModel(
String factModelXml) {
try {
final Document factModel = documentXmlConverter
.loadDocument(factModelXml);
final Element embeddedClinicalDocument = documentAccessor
.getElement(factModel, "//hl7:EmbeddedClinicalDocument");
embeddedClinicalDocument.getParentNode().removeChild(
embeddedClinicalDocument);
return documentXmlConverter.convertXmlDocToString(factModel);
} catch (final DocumentAccessorException e) {
logger.error(e.getMessage(), e);
throw new DS4PException(e);
}
}
/*
* (non-Javadoc)
*
* @see gov.samhsa.acs.documentsegmentation.tools.DocumentRedactor#
* cleanUpGeneratedEntryIds(java.lang.String)
*/
@Override
public String cleanUpGeneratedEntryIds(String document) {
// Remove all generatedEntryId elements to clean up the clinical
// document
final String xPathExprGeneratedEntryId = "//hl7:generatedEntryId";
return cleanUpElements(document, xPathExprGeneratedEntryId);
}
/*
* (non-Javadoc)
*
* @see gov.samhsa.acs.documentsegmentation.tools.DocumentRedactor#
* cleanUpGeneratedServiceEventIds(java.lang.String)
*/
@Override
public String cleanUpGeneratedServiceEventIds(String document) {
// Remove all generatedServiceEventId elements to clean up the clinical
// document
final String xPathExprGeneratedEntryId = "//hl7:generatedServiceEventId";
return cleanUpElements(document, xPathExprGeneratedEntryId);
}
/*
* (non-Javadoc)
*
* @see
* gov.samhsa.acs.documentsegmentation.tools.DocumentRedactor#redactDocument
* (java.lang.String, gov.samhsa.acs.brms.domain.RuleExecutionContainer,
* gov.samhsa.acs.brms.domain.XacmlResult,
* gov.samhsa.acs.brms.domain.FactModel)
*/
@Override
public RedactedDocument redactDocument(String document,
RuleExecutionContainer ruleExecutionContainer, FactModel factModel) {
Document xmlDocument = null;
String tryPolicyDocument = null;
final List<Node> redactNodeList = new LinkedList<Node>();
final Set<String> redactSectionCodesAndGeneratedEntryIds = new HashSet<String>();
final Set<String> redactSectionSet = new HashSet<String>();
final Set<String> redactCategorySet = new HashSet<String>();
final XacmlResult xacmlResult = factModel.getXacmlResult();
try {
xmlDocument = documentXmlConverter.loadDocument(document);
final Document factModelDocument = documentXmlConverter
.loadDocument(marshaller.marshal(factModel));
// Document Level redaction handlers
for (final AbstractDocumentLevelRedactionHandler documentLevelRedactionHandler : documentLevelRedactionHandlers) {
documentLevelRedactionHandler.execute(xmlDocument,
redactSectionCodesAndGeneratedEntryIds, redactNodeList);
}
// OBLIGATION LEVEL REDACTION HANDLERS
for (final String obligation : xacmlResult.getPdpObligations()) {
for (final AbstractObligationLevelRedactionHandler obligationLevelRedactionHandler : obligationLevelRedactionHandlers) {
obligationLevelRedactionHandler.execute(xmlDocument,
xacmlResult, factModel, factModelDocument,
ruleExecutionContainer, redactNodeList,
redactSectionCodesAndGeneratedEntryIds,
redactSectionSet, obligation);
}
}
// CLINICAL FACT LEVEL REDACTION HANDLERS
for (final ClinicalFact fact : factModel.getClinicalFactList()) {
// For each clinical fact
for (final AbstractClinicalFactLevelRedactionHandler clinicalFactLevelRedactionHandler : clinicalFactLevelRedactionHandlers) {
clinicalFactLevelRedactionHandler.execute(xmlDocument,
xacmlResult, factModel, factModelDocument, fact,
ruleExecutionContainer, redactNodeList,
redactSectionCodesAndGeneratedEntryIds,
redactCategorySet);
}
}
// Create tryPolicyDocument before the actual redacting
tryPolicyDocument = documentXmlConverter
.convertXmlDocToString(xmlDocument);
// REDACTION
// Redact all nodes in redactNodeList
// (sections, entries, text nodes)
for (final Node nodeToBeReadacted : redactNodeList) {
redactNodeIfNotNull(nodeToBeReadacted);
}
// POST REDACTION LEVEL REDACTION HANDLERS
for (final AbstractPostRedactionLevelRedactionHandler postRedactionRedactionHandler : postRedactionLevelRedactionHandlers) {
postRedactionRedactionHandler.execute(xmlDocument, xacmlResult,
factModel, factModelDocument, ruleExecutionContainer,
redactNodeList, redactSectionCodesAndGeneratedEntryIds);
}
// Convert redacted document to xml string
document = documentXmlConverter.convertXmlDocToString(xmlDocument);
// Debug
// FileHelper.writeDocToFile(xmlDocument, "Redacted_C32.xml");
} catch (final Exception e) {
logger.error(e.getMessage(), e);
throw new DS4PException(e.toString(), e);
}
return new RedactedDocument(document, tryPolicyDocument,
redactSectionSet, redactCategorySet);
}
/**
* Clean up elements.
*
* @param document
* the document
* @param xPathExpr
* the x path expr
* @return the string
*/
private String cleanUpElements(String document, String xPathExpr) {
Document xmlDocument = null;
try {
xmlDocument = documentXmlConverter.loadDocument(document);
NodeList nodes = null;
nodes = documentAccessor.getNodeList(xmlDocument, xPathExpr);
if (nodes != null) {
for (int i = 0; i < nodes.getLength(); i++) {
final Node node = nodes.item(i);
final Element element = (Element) node;
element.getParentNode().removeChild(element);
}
}
document = documentXmlConverter.convertXmlDocToString(xmlDocument);
} catch (final XPathExpressionException e) {
logger.error(e.getMessage(), e);
throw new DS4PException(e.toString(), e);
} catch (final Exception e) {
logger.error(e.getMessage(), e);
throw new DS4PException(e.toString(), e);
}
return document;
}
/**
* Redact node if not null.
*
* @param nodeToBeRedacted
* the node to be redacted
*/
private void redactNodeIfNotNull(Node nodeToBeRedacted) {
if (nodeToBeRedacted != null) {
// If displayName contains the code, it will be found twice and can
// already be removed. Therefore, we need to check the parent
try {
nodeToBeRedacted.getParentNode().removeChild(nodeToBeRedacted);
} catch (final NullPointerException e) {
final StringBuilder builder = new StringBuilder();
builder.append("The node value '");
builder.append(nodeToBeRedacted.getNodeValue());
builder.append("' must have been removed already, it cannot be removed again. This might happen if one of the search text contains the other and multiple criterias match to mark the node to be redacted.");
logger.warn(builder.toString());
}
}
}
}