DocumentCleanupForNoEntryAndNoSectionTest.java example

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package gov.samhsa.acs.documentsegmentation.tools.redact.impl.postredactionlevel;

import static org.junit.Assert.assertEquals;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
import static org.mockito.Matchers.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
import gov.samhsa.acs.brms.domain.FactModel;
import gov.samhsa.acs.brms.domain.RuleExecutionContainer;
import gov.samhsa.acs.common.tool.DocumentAccessor;
import gov.samhsa.acs.common.tool.DocumentAccessorImpl;
import gov.samhsa.acs.common.tool.DocumentXmlConverter;
import gov.samhsa.acs.common.tool.DocumentXmlConverterImpl;
import gov.samhsa.acs.common.tool.FileReader;
import gov.samhsa.acs.common.tool.FileReaderImpl;
import gov.samhsa.acs.common.tool.SimpleMarshaller;
import gov.samhsa.acs.common.tool.SimpleMarshallerImpl;
import gov.samhsa.acs.common.tool.exception.SimpleMarshallerException;
import gov.samhsa.acs.documentsegmentation.tools.EmbeddedClinicalDocumentExtractor;
import gov.samhsa.acs.documentsegmentation.tools.EmbeddedClinicalDocumentExtractorImpl;

import java.io.IOException;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;

import javax.xml.xpath.XPathExpressionException;

import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.runners.MockitoJUnitRunner;
import org.slf4j.Logger;
import org.springframework.test.util.ReflectionTestUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

@RunWith(MockitoJUnitRunner.class)
public class DocumentCleanupForNoEntryAndNoSectionTest {
	
	public static final String TEST_PATH = "sampleC32-redactionHandlers/";
	public static final String FACTMODEL_PATH = "factmodel/";
	public static final String RULEEXECUTIONCONTAINER_PATH = "ruleexecutioncontainer/";
	
	private FileReader fileReader;
	private SimpleMarshaller marshaller;
	private DocumentAccessor documentAccessor;
	private DocumentXmlConverter documentXmlConverter;
	private EmbeddedClinicalDocumentExtractor embeddedClinicalDocumentExtractor;
	
	private DocumentCleanupForNoEntryAndNoSection sut;

	@Before
	public void setUp() throws Exception {
		fileReader = new FileReaderImpl();
		marshaller = new SimpleMarshallerImpl();
		documentAccessor = new DocumentAccessorImpl();
		documentXmlConverter = new DocumentXmlConverterImpl();
		embeddedClinicalDocumentExtractor = new EmbeddedClinicalDocumentExtractorImpl(documentXmlConverter, documentAccessor);
		sut = new DocumentCleanupForNoEntryAndNoSection(documentAccessor);
	}

	@After
	public void tearDown() throws Exception {
	}

	@Test
	public void testExecute_CleanUpSectionComponentsWithNoEntries() throws IOException, SimpleMarshallerException, XPathExpressionException {
		// Arrange
		String c32FileName = "MIE_SampleC32-sectionWithNoEntries.xml";
		String factmodelXml = fileReader.readFile(TEST_PATH + FACTMODEL_PATH + c32FileName);
		String c32 = embeddedClinicalDocumentExtractor.extractClinicalDocumentFromFactModel(factmodelXml);
		String ruleExecutionContainerXml = fileReader.readFile(TEST_PATH + RULEEXECUTIONCONTAINER_PATH + c32FileName);
		RuleExecutionContainer ruleExecutionContainer = marshaller.unmarshalFromXml(RuleExecutionContainer.class, ruleExecutionContainerXml);
		Document c32Document = documentXmlConverter.loadDocument(c32);
		Document factModelDocument = documentXmlConverter.loadDocument(factmodelXml);
		FactModel factModel = marshaller.unmarshalFromXml(FactModel.class, factmodelXml);
		List<Node> listOfNodes = new LinkedList<Node>();
		Set<String> redactSectionCodesAndGeneratedEntryIds = new HashSet<String>();
		
		// Act
		sut.execute(c32Document, factModel.getXacmlResult(), factModel,
				factModelDocument, ruleExecutionContainer, listOfNodes,
				redactSectionCodesAndGeneratedEntryIds);
		
		// Assert		
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section").getLength());
		assertEquals(0, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='11450-4']]").getLength());
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='30954-2']]").getLength());
	}
	
	@Test
	public void testExecute_CleanUpSectionComponentsWithNoEntries_EmptySectionComponentsNull() throws IOException, SimpleMarshallerException, XPathExpressionException {
		// Arrange
		DocumentAccessor documentAccessorMock = mock(DocumentAccessor.class);
		sut = new DocumentCleanupForNoEntryAndNoSection(documentAccessorMock);
		String c32FileName = "MIE_SampleC32-sectionWithNoEntries.xml";
		String factmodelXml = fileReader.readFile(TEST_PATH + FACTMODEL_PATH + c32FileName);
		String c32 = embeddedClinicalDocumentExtractor.extractClinicalDocumentFromFactModel(factmodelXml);
		String ruleExecutionContainerXml = fileReader.readFile(TEST_PATH + RULEEXECUTIONCONTAINER_PATH + c32FileName);
		RuleExecutionContainer ruleExecutionContainer = marshaller.unmarshalFromXml(RuleExecutionContainer.class, ruleExecutionContainerXml);
		Document c32Document = documentXmlConverter.loadDocument(c32);
		Document factModelDocument = documentXmlConverter.loadDocument(factmodelXml);
		FactModel factModel = marshaller.unmarshalFromXml(FactModel.class, factmodelXml);
		List<Node> listOfNodes = new LinkedList<Node>();
		Set<String> redactSectionCodesAndGeneratedEntryIds = new HashSet<String>();
		when(documentAccessorMock.getNodeList(eq(c32Document), anyString())).thenReturn(null);
		
		// Act
		sut.execute(c32Document, factModel.getXacmlResult(), factModel,
				factModelDocument, ruleExecutionContainer, listOfNodes,
				redactSectionCodesAndGeneratedEntryIds);
		
		// Assert		
		assertEquals(2, documentAccessor.getNodeList(c32Document, "//hl7:section").getLength());
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='11450-4']]").getLength());
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='30954-2']]").getLength());
	}
	
	@Test
	public void testExecute_CleanUpSectionComponentsWithNoEntries_EmptySectionComponents_ParentNull() throws IOException, SimpleMarshallerException, XPathExpressionException {
		// Arrange
		Logger loggerMock = mock(Logger.class);
		DocumentAccessor documentAccessorMock = mock(DocumentAccessor.class);
		sut = new DocumentCleanupForNoEntryAndNoSection(documentAccessorMock);
		ReflectionTestUtils.setField(sut, "logger", loggerMock);
		String c32FileName = "MIE_SampleC32-sectionWithNoEntries.xml";
		String factmodelXml = fileReader.readFile(TEST_PATH + FACTMODEL_PATH + c32FileName);
		String c32 = embeddedClinicalDocumentExtractor.extractClinicalDocumentFromFactModel(factmodelXml);
		String ruleExecutionContainerXml = fileReader.readFile(TEST_PATH + RULEEXECUTIONCONTAINER_PATH + c32FileName);
		RuleExecutionContainer ruleExecutionContainer = marshaller.unmarshalFromXml(RuleExecutionContainer.class, ruleExecutionContainerXml);
		Document c32Document = documentXmlConverter.loadDocument(c32);
		Document factModelDocument = documentXmlConverter.loadDocument(factmodelXml);
		FactModel factModel = marshaller.unmarshalFromXml(FactModel.class, factmodelXml);
		List<Node> listOfNodes = new LinkedList<Node>();
		Set<String> redactSectionCodesAndGeneratedEntryIds = new HashSet<String>();
		NodeList nodeListMock = mock(NodeList.class);
		when(nodeListMock.getLength()).thenReturn(1);
		Node nodeMock = mock(Node.class);
		when(nodeListMock.item(0)).thenReturn(nodeMock);
		when(nodeMock.getParentNode()).thenReturn(null);
		when(documentAccessorMock.getNodeList(eq(c32Document), anyString())).thenReturn(nodeListMock);
		
		// Act
		sut.execute(c32Document, factModel.getXacmlResult(), factModel,
				factModelDocument, ruleExecutionContainer, listOfNodes,
				redactSectionCodesAndGeneratedEntryIds);
		
		// Assert		
		assertEquals(2, documentAccessor.getNodeList(c32Document, "//hl7:section").getLength());
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='11450-4']]").getLength());
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='30954-2']]").getLength());
		verify(loggerMock, times(1)).warn(anyString(), any(Throwable.class));
	}
	
	@Test
	public void testExecute_AddEmptySectionComponentIfNoneExists() throws IOException, SimpleMarshallerException, XPathExpressionException {
		// Arrange
		String c32FileName = "MIE_SampleC32-sectionWithNoEntriesAndNoOtherSections.xml";
		String factmodelXml = fileReader.readFile(TEST_PATH + FACTMODEL_PATH + c32FileName);
		String c32 = embeddedClinicalDocumentExtractor.extractClinicalDocumentFromFactModel(factmodelXml);
		String ruleExecutionContainerXml = fileReader.readFile(TEST_PATH + RULEEXECUTIONCONTAINER_PATH + c32FileName);
		RuleExecutionContainer ruleExecutionContainer = marshaller.unmarshalFromXml(RuleExecutionContainer.class, ruleExecutionContainerXml);
		Document c32Document = documentXmlConverter.loadDocument(c32);
		Document factModelDocument = documentXmlConverter.loadDocument(factmodelXml);
		FactModel factModel = marshaller.unmarshalFromXml(FactModel.class, factmodelXml);
		List<Node> listOfNodes = new LinkedList<Node>();
		Set<String> redactSectionCodesAndGeneratedEntryIds = new HashSet<String>();
		
		// Act
		sut.execute(c32Document, factModel.getXacmlResult(), factModel,
				factModelDocument, ruleExecutionContainer, listOfNodes,
				redactSectionCodesAndGeneratedEntryIds);
		
		// Assert		
		assertEquals(1, documentAccessor.getNodeList(c32Document, "//hl7:section").getLength());
		assertEquals(0, documentAccessor.getNodeList(c32Document, "//hl7:section").item(0).getChildNodes().getLength());
		assertEquals(0, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='11450-4']]").getLength());
		assertEquals(0, documentAccessor.getNodeList(c32Document, "//hl7:section[hl7:code[@code='30954-2']]").getLength());
	}
}