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Library for common XD* operations and objects
/*
* Copyright (c) 2010, NHIN Direct Project
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* 2. 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.
* 3. Neither the name of the the NHIN Direct Project (nhindirect.org)
* 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 THE COPYRIGHT HOLDER OR CONTRIBUTORS 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 org.nhindirect.xd.common;
import static org.nhindirect.xd.common.DirectDocumentUtils.addSlot;
import static org.nhindirect.xd.common.DirectDocumentUtils.makeInternationalStringType;
import static org.nhindirect.xd.common.DirectDocumentUtils.makeSlot;
import static org.nhindirect.xd.common.DirectDocumentUtils.slotNotEmpty;
import java.io.File;
import java.io.IOException;
import java.math.BigInteger;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import javax.activation.MimetypesFileTypeMap;
import javax.xml.namespace.QName;
import oasis.names.tc.ebxml_regrep.xsd.rim._3.ClassificationType;
import oasis.names.tc.ebxml_regrep.xsd.rim._3.ExternalIdentifierType;
import oasis.names.tc.ebxml_regrep.xsd.rim._3.ExtrinsicObjectType;
import oasis.names.tc.ebxml_regrep.xsd.rim._3.SlotType1;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.time.DateUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.nhindirect.xd.common.exception.MetadataException;
import org.nhindirect.xd.common.type.ClassificationTypeEnum;
import org.nhindirect.xd.common.type.ExternalIdentifierTypeEnum;
import org.nhindirect.xd.common.type.ExtrinsicObjectTypeEnum;
import org.nhindirect.xd.common.type.FormatCodeEnum;
import org.nhindirect.xd.common.type.SlotType1Enum;
import org.nhindirect.xd.common.type.SubmitObjectsRequestEnum;
import org.nhindirect.xd.transform.pojo.SimplePerson;
import org.nhindirect.xd.transform.util.XmlUtils;
/**
* Abstract representation of a document with supporting metadata.
*
* TODO: This replace DirectDocument with this class.. wanted to wait to avoid
* any merge conflicts for ongoing XD* work.
*
* @author beau
*/
public class DirectDocument2
{
private byte[] data;
private Metadata metadata;
private static final Log LOGGER = LogFactory.getFactory().getInstance(DirectDocument2.class);
/**
* Default document constructor.
*/
public DirectDocument2()
{
this.metadata = new Metadata();
}
/**
* @param file
* @throws IOException
*/
public DirectDocument2(File file) throws IOException
{
this.data = FileUtils.readFileToByteArray(file);
this.metadata = new Metadata(file);
}
/**
* Get the value of metadata.
*
* @return the metadata.
*/
public Metadata getMetadata()
{
return metadata;
}
/**
* Set the value of metadata.
*
* @param metadata
* The metadata to set.
*/
public void setMetadata(Metadata metadata)
{
this.metadata = metadata;
}
/**
* Get the value of data.
*
* @return the data The value of data.
*/
public byte[] getData()
{
return data;
}
/**
* Set the value of data.
*
* @param data
* The data to set;
*/
public void setData(byte[] data)
{
this.data = data;
this.metadata.setHash(getSha1Hash(data));
this.metadata.setSize(new Long(data.length));
}
/**
* Abstract representation of document metadata.
*
* @author beau
*/
static public class Metadata
{
private String mimeType;
private String id;
private String description;
private Date creationTime;
private String languageCode;
private Date serviceStartTime;
private Date serviceStopTime;
private SimplePerson sourcePatient = new SimplePerson();
private String authorPerson;
private List authorInstitution = new ArrayList();
private String authorRole;
private String authorSpecialty;
private String classCode;
private String classCode_localized;
private String confidentialityCode;
private String confidentialityCode_localized;
private String formatCode;
private String formatCode_localized;
private String healthcareFacilityTypeCode;
private String healthcareFacilityTypeCode_localized;
private String practiceSettingCode;
private String practiceSettingCode_localized;
private String loinc;
private String loinc_localized;
private String patientId;
private String uniqueId;
private String hash;
private Long size;
private String submissionSetStatus;
private String uri;
/**
* Default constructor.
*/
public Metadata()
{
this.id = UUID.randomUUID().toString();
this.submissionSetStatus = "Original";
}
/**
* Construct a new DirectDocument2.Metadata with default values given a
* File object.
*
* @param file
* A File object from which to extract metadata.
*/
public Metadata(File file) throws IOException
{
super();
MimetypesFileTypeMap mimetypesFileTypeMap = new MimetypesFileTypeMap();
mimetypesFileTypeMap.addMimeTypes("application/msword doc dot wiz rtf");
mimetypesFileTypeMap.addMimeTypes("application/pdf pdf");
mimetypesFileTypeMap.addMimeTypes("application/postscript ai eps ps");
mimetypesFileTypeMap.addMimeTypes("application/vnd.ms-excel xls xlw xla xlc xlm xlt");
mimetypesFileTypeMap.addMimeTypes("application/vnd.ms-powerpoint ppt pps pot");
mimetypesFileTypeMap.addMimeTypes("application/x-javascript js");
mimetypesFileTypeMap.addMimeTypes("application/x-asap asp");
mimetypesFileTypeMap.addMimeTypes("application/x-latex latex");
mimetypesFileTypeMap.addMimeTypes("application/x-tar tar");
mimetypesFileTypeMap.addMimeTypes("application/x-texinfo texinfo texi");
mimetypesFileTypeMap.addMimeTypes("application/zip zip");
mimetypesFileTypeMap.addMimeTypes("text/css css");
mimetypesFileTypeMap.addMimeTypes("text/html htm html");
mimetypesFileTypeMap.addMimeTypes("text/plain txt");
mimetypesFileTypeMap.addMimeTypes("text/richtext rtx");
mimetypesFileTypeMap.addMimeTypes("text/xml xml");
// Best guess at MIME type from list above
this.mimeType = mimetypesFileTypeMap.getContentType(file);
// File size and hash
this.size = file.length();
this.hash = getSha1Hash(FileUtils.readFileToString(file));
}
/**
* @return
*/
protected ExtrinsicObjectType generateExtrinsicObjectType()
{
ExtrinsicObjectType eot = new ExtrinsicObjectType();
eot.setId(id);
eot.setMimeType(mimeType);
eot.setObjectType(ExtrinsicObjectTypeEnum.DOC.getObjectType());
List slots = eot.getSlot();
addSlot(slots, makeSlot(SlotType1Enum.CREATION_TIME, creationTime != null ? (new SimpleDateFormat("yyyyMMdd")).format(creationTime) : null));
addSlot(slots, makeSlot(SlotType1Enum.LANGUAGE_CODE, languageCode));
addSlot(slots, makeSlot(SlotType1Enum.SERVICE_START_TIME, serviceStartTime != null ? (new SimpleDateFormat("yyyyMMddHHmm")).format(serviceStartTime) : null));
addSlot(slots, makeSlot(SlotType1Enum.SERVICE_STOP_TIME, serviceStopTime != null ? (new SimpleDateFormat("yyyyMMddHHmm")).format(serviceStopTime) : null));
addSlot(slots, makeSlot(SlotType1Enum.SOURCE_PATIENT_ID, sourcePatient.getLocalId() + "^^^&" + sourcePatient.getLocalOrg() + "&ISO"));
addSlot(slots, makeSlot(SlotType1Enum.SOURCE_PATIENT_INFO, sourcePatient));
addSlot(slots, makeSlot(SlotType1Enum.HASH, hash));
addSlot(slots, makeSlot(SlotType1Enum.SIZE, size == null ? null : String.valueOf(size)));
addSlot(slots, makeSlot(SlotType1Enum.URI, uri == null ? null : uri));
eot.setName(makeInternationalStringType(classCode_localized));
eot.setDescription(makeInternationalStringType(description));
// author
ClassificationType authorClassification = new ClassificationType();
authorClassification.setClassifiedObject(id);
authorClassification.setNodeRepresentation(""); // required empty string
authorClassification.setId(ClassificationTypeEnum.DOC_AUTHOR.getClassificationId());
authorClassification.setClassificationScheme(ClassificationTypeEnum.DOC_AUTHOR.getClassificationScheme());
List authorClassificationSlots = authorClassification.getSlot();
addSlot(authorClassificationSlots, makeSlot(SlotType1Enum.AUTHOR_PERSON, authorPerson));
addSlot(authorClassificationSlots, makeSlot(SlotType1Enum.AUTHOR_INSTITUTION, authorInstitution));
addSlot(authorClassificationSlots, makeSlot(SlotType1Enum.AUTHOR_ROLE, authorRole));
addSlot(authorClassificationSlots, makeSlot(SlotType1Enum.AUTHOR_SPECIALTY, authorSpecialty));
eot.getClassification().add(authorClassification);
// classCode
if (classCode != null)
{
ClassificationType classCodeClassification = new ClassificationType();
classCodeClassification.setClassifiedObject(id);
classCodeClassification.setNodeRepresentation(classCode);
classCodeClassification.setName(makeInternationalStringType(classCode_localized));
classCodeClassification.setId(ClassificationTypeEnum.DOC_CLASS_CODE.getClassificationId());
classCodeClassification.setClassificationScheme(ClassificationTypeEnum.DOC_CLASS_CODE.getClassificationScheme());
List classCodeClassificationSlots = classCodeClassification.getSlot();
addSlot(classCodeClassificationSlots, makeSlot(SlotType1Enum.CODING_SCHEME, ClassificationTypeEnum.DOC_CLASS_CODE.getCodingScheme()));
eot.getClassification().add(classCodeClassification);
}
// confidentialityCode
if (confidentialityCode != null)
{
ClassificationType confidentialityCodeClassification = new ClassificationType();
confidentialityCodeClassification.setClassifiedObject(id);
confidentialityCodeClassification.setNodeRepresentation(confidentialityCode);
confidentialityCodeClassification.setName(makeInternationalStringType(confidentialityCode_localized));
confidentialityCodeClassification.setId(ClassificationTypeEnum.DOC_CONFIDENTIALITY_CODE.getClassificationId());
confidentialityCodeClassification.setClassificationScheme(ClassificationTypeEnum.DOC_CONFIDENTIALITY_CODE.getClassificationScheme());
List confidentialityCodeClassificationSlots = confidentialityCodeClassification.getSlot();
addSlot(confidentialityCodeClassificationSlots, makeSlot(SlotType1Enum.CODING_SCHEME, ClassificationTypeEnum.DOC_CONFIDENTIALITY_CODE.getCodingScheme()));
eot.getClassification().add(confidentialityCodeClassification);
}
// formatCode
if (formatCode != null)
{
ClassificationType formatCodeClassification = new ClassificationType();
formatCodeClassification.setClassifiedObject(id);
formatCodeClassification.setNodeRepresentation(formatCode);
formatCodeClassification.setName(makeInternationalStringType(formatCode_localized));
formatCodeClassification.setId(ClassificationTypeEnum.DOC_FORMAT_CODE.getClassificationId());
formatCodeClassification.setClassificationScheme(ClassificationTypeEnum.DOC_FORMAT_CODE.getClassificationScheme());
List formatCodeClassificationSlots = formatCodeClassification.getSlot();
addSlot(formatCodeClassificationSlots, makeSlot(SlotType1Enum.CODING_SCHEME, ClassificationTypeEnum.DOC_FORMAT_CODE.getCodingScheme()));
eot.getClassification().add(formatCodeClassification);
}
// healthcareFacilityTypeCode
if (healthcareFacilityTypeCode != null)
{
ClassificationType healthcareFacilityTypeCodeClassification = new ClassificationType();
healthcareFacilityTypeCodeClassification.setClassifiedObject(id);
healthcareFacilityTypeCodeClassification.setNodeRepresentation(healthcareFacilityTypeCode);
healthcareFacilityTypeCodeClassification.setName(makeInternationalStringType(healthcareFacilityTypeCode_localized));
healthcareFacilityTypeCodeClassification.setId(ClassificationTypeEnum.DOC_HEALTHCARE_FACILITY_TYPE_CODE.getClassificationId());
healthcareFacilityTypeCodeClassification.setClassificationScheme(ClassificationTypeEnum.DOC_HEALTHCARE_FACILITY_TYPE_CODE.getClassificationScheme());
List healthcareFacilityTypeCodeClassificationSlots = healthcareFacilityTypeCodeClassification.getSlot();
addSlot(healthcareFacilityTypeCodeClassificationSlots, makeSlot(SlotType1Enum.CODING_SCHEME, ClassificationTypeEnum.DOC_HEALTHCARE_FACILITY_TYPE_CODE.getCodingScheme()));
eot.getClassification().add(healthcareFacilityTypeCodeClassification);
}
// practiceSettingCode
if (practiceSettingCode != null)
{
ClassificationType practiceSettingCodeClassification = new ClassificationType();
practiceSettingCodeClassification.setClassifiedObject(id);
practiceSettingCodeClassification.setNodeRepresentation(practiceSettingCode);
practiceSettingCodeClassification.setName(makeInternationalStringType(practiceSettingCode_localized));
practiceSettingCodeClassification.setId(ClassificationTypeEnum.DOC_PRACTICE_SETTING_CODE.getClassificationId());
practiceSettingCodeClassification.setClassificationScheme(ClassificationTypeEnum.DOC_PRACTICE_SETTING_CODE.getClassificationScheme());
List practiceSettingCodeClassificationSlots = practiceSettingCodeClassification.getSlot();
addSlot(practiceSettingCodeClassificationSlots, makeSlot(SlotType1Enum.CODING_SCHEME, ClassificationTypeEnum.DOC_PRACTICE_SETTING_CODE.getCodingScheme()));
eot.getClassification().add(practiceSettingCodeClassification);
}
// loinc
if (loinc != null)
{
ClassificationType loincClassification = new ClassificationType();
loincClassification.setClassifiedObject(id);
loincClassification.setNodeRepresentation(loinc);
loincClassification.setName(makeInternationalStringType(loinc_localized));
loincClassification.setId(ClassificationTypeEnum.DOC_LOINC.getClassificationId());
loincClassification.setClassificationScheme(ClassificationTypeEnum.DOC_LOINC.getClassificationScheme());
List loincClassificationSlots = loincClassification.getSlot();
addSlot(loincClassificationSlots, makeSlot(SlotType1Enum.CODING_SCHEME, ClassificationTypeEnum.DOC_LOINC.getCodingScheme()));
eot.getClassification().add(loincClassification);
}
// patientId
ExternalIdentifierType xdsDocumentEntry_patientId = new ExternalIdentifierType();
xdsDocumentEntry_patientId.setValue(patientId);
xdsDocumentEntry_patientId.setRegistryObject(id);
xdsDocumentEntry_patientId.setId(ExternalIdentifierTypeEnum.DOC_PATIENT_ID.getIdentificationId());
xdsDocumentEntry_patientId.setIdentificationScheme(ExternalIdentifierTypeEnum.DOC_PATIENT_ID.getIdentificationScheme());
xdsDocumentEntry_patientId.setName(makeInternationalStringType(ExternalIdentifierTypeEnum.DOC_PATIENT_ID.getLocalizedString()));
eot.getExternalIdentifier().add(xdsDocumentEntry_patientId);
// uniqueId
ExternalIdentifierType xdsDocumentEntry_uniqueId = new ExternalIdentifierType();
xdsDocumentEntry_uniqueId.setValue(uniqueId);
xdsDocumentEntry_uniqueId.setRegistryObject(id);
xdsDocumentEntry_uniqueId.setId(ExternalIdentifierTypeEnum.DOC_UNIQUE_ID.getIdentificationId());
xdsDocumentEntry_uniqueId.setIdentificationScheme(ExternalIdentifierTypeEnum.DOC_UNIQUE_ID.getIdentificationScheme());
xdsDocumentEntry_uniqueId.setName(makeInternationalStringType(ExternalIdentifierTypeEnum.DOC_UNIQUE_ID.getLocalizedString()));
eot.getExternalIdentifier().add(xdsDocumentEntry_uniqueId);
return eot;
}
public void setValues(ExtrinsicObjectType eot) throws MetadataException
{
mimeType = eot.getMimeType();
id = eot.getId();
if (eot.getDescription() != null && eot.getDescription().getLocalizedString() != null && !eot.getDescription().getLocalizedString().isEmpty())
description = eot.getDescription().getLocalizedString().get(0).getValue();
for (SlotType1 slot : eot.getSlot())
{
if (SlotType1Enum.CREATION_TIME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
try
{
creationTime = DateUtils.parseDate(slot.getValueList().getValue().get(0),
new String[]
{ "yyyyMMddHHmmss", "yyyyMMddHHmm", "yyyyMMdd" });
}
catch (ParseException e)
{
LOGGER.error("Unable to parse creationTime", e);
throw new MetadataException("Unable to parse creationTime", e);
}
}
}
else if (SlotType1Enum.LANGUAGE_CODE.matches(slot.getName()))
{
if (slotNotEmpty(slot))
languageCode = slot.getValueList().getValue().get(0);
}
else if (SlotType1Enum.SERVICE_START_TIME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
try
{
serviceStartTime = DateUtils.parseDate(slot.getValueList().getValue().get(0),
new String[]
{ "yyyyMMddHHmmss", "yyyyMMddHHmm", "yyyyMMdd" });
}
catch (ParseException e)
{
LOGGER.error("Unable to parse serviceStartTime", e);
throw new MetadataException("Unable to parse serviceStartTime", e);
}
}
}
else if (SlotType1Enum.SERVICE_STOP_TIME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
try
{
serviceStopTime = DateUtils.parseDate(slot.getValueList().getValue().get(0),
new String[]
{ "yyyyMMddHHmmss", "yyyyMMddHHmm", "yyyyMMdd" });
}
catch (ParseException e)
{
LOGGER.error("Unable to parse serviceStopTime", e);
throw new MetadataException("Unable to parse serviceStopTime", e);
}
}
}
else if (SlotType1Enum.SOURCE_PATIENT_ID.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
String[] tokens = StringUtils.splitPreserveAllTokens(slot.getValueList().getValue().get(0), "^");
if (tokens != null && tokens.length >= 1)
sourcePatient.setLocalId(tokens[0]);
else
sourcePatient.setLocalId(slot.getValueList().getValue().get(0));
if (tokens != null && tokens.length >= 4)
{
tokens = StringUtils.splitPreserveAllTokens(slot.getValueList().getValue().get(0), "&");
if (tokens.length >= 2)
sourcePatient.setLocalOrg(tokens[1]);
}
}
}
else if (SlotType1Enum.SOURCE_PATIENT_INFO.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
for (String value : slot.getValueList().getValue())
{
if (StringUtils.startsWith(value, "PID-3|"))
{
// Already have this from sourcePatientId
}
else if (StringUtils.startsWith(value, "PID-5|"))
{
String[] split = StringUtils.splitPreserveAllTokens(value, "|");
String[] tokens = StringUtils.splitPreserveAllTokens(split[1], "^");
if (tokens != null && tokens.length >= 1)
sourcePatient.setLastName(tokens[0]);
if (tokens != null && tokens.length >= 2)
sourcePatient.setFirstName(tokens[1]);
if (tokens != null && tokens.length >= 3)
sourcePatient.setMiddleName(tokens[2]);
}
else if (StringUtils.startsWith(value, "PID-7|"))
{
String[] split = StringUtils.splitPreserveAllTokens(value, "|");
if (split.length >= 2)
sourcePatient.setBirthDateTime(split[1]);
}
else if (StringUtils.startsWith(value, "PID-8|"))
{
String[] split = StringUtils.splitPreserveAllTokens(value, "|");
if (split.length >= 2)
sourcePatient.setGenderCode(split[1]);
}
else if (StringUtils.startsWith(value, "PID-11|"))
{
String[] split = StringUtils.splitPreserveAllTokens(value, "|");
String[] tokens = StringUtils.splitPreserveAllTokens(split[1], "^");
if (tokens != null && tokens.length >= 1)
sourcePatient.setStreetAddress1(tokens[0]);
if (tokens != null && tokens.length >= 3)
sourcePatient.setCity(tokens[2]);
if (tokens != null && tokens.length >= 4)
sourcePatient.setState(tokens[3]);
if (tokens != null && tokens.length >= 5)
sourcePatient.setZipCode(tokens[4]);
if (tokens != null && tokens.length >= 6)
sourcePatient.setCountry(tokens[5]);
}
}
}
}
else if (SlotType1Enum.HASH.matches(slot.getName()))
{
if (slotNotEmpty(slot))
hash = slot.getValueList().getValue().get(0);
}
else if (SlotType1Enum.URI.matches(slot.getName()))
{
if (slotNotEmpty(slot))
uri = slot.getValueList().getValue().get(0);
}
else if (SlotType1Enum.SIZE.matches(slot.getName()))
{
if (slotNotEmpty(slot))
size = Long.valueOf(slot.getValueList().getValue().get(0));
}
}
for (ClassificationType ct : eot.getClassification())
{
if (ClassificationTypeEnum.DOC_AUTHOR.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.AUTHOR_PERSON.matches(slot.getName()))
{
if (slotNotEmpty(slot))
authorPerson = slot.getValueList().getValue().get(0);
}
else if (SlotType1Enum.AUTHOR_INSTITUTION.matches(slot.getName()))
{
if (slotNotEmpty(slot))
for (String value : slot.getValueList().getValue())
authorInstitution.add(value);
}
else if (SlotType1Enum.AUTHOR_ROLE.matches(slot.getName()))
{
if (slotNotEmpty(slot))
authorRole = slot.getValueList().getValue().get(0);
}
else if (SlotType1Enum.AUTHOR_SPECIALTY.matches(slot.getName()))
{
if (slotNotEmpty(slot))
authorSpecialty = slot.getValueList().getValue().get(0);
}
}
}
else if (ClassificationTypeEnum.DOC_CLASS_CODE.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.CODING_SCHEME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
@SuppressWarnings("unused") String codingScheme = slot.getValueList().getValue().get(0);
}
}
}
classCode = ct.getNodeRepresentation();
if (ct.getName() != null && ct.getName().getLocalizedString() != null && !ct.getName().getLocalizedString().isEmpty())
classCode_localized = ct.getName().getLocalizedString().get(0).getValue();
}
else if (ClassificationTypeEnum.DOC_CONFIDENTIALITY_CODE.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.CODING_SCHEME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
@SuppressWarnings("unused") String codingScheme = slot.getValueList().getValue().get(0);
}
}
}
confidentialityCode = ct.getNodeRepresentation();
if (ct.getName() != null && ct.getName().getLocalizedString() != null && !ct.getName().getLocalizedString().isEmpty())
confidentialityCode_localized = ct.getName().getLocalizedString().get(0).getValue();
}
else if (ClassificationTypeEnum.DOC_FORMAT_CODE.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.CODING_SCHEME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
@SuppressWarnings("unused") String codingScheme = slot.getValueList().getValue().get(0);
}
}
}
formatCode = ct.getNodeRepresentation();
if (ct.getName() != null && ct.getName().getLocalizedString() != null && !ct.getName().getLocalizedString().isEmpty())
formatCode_localized = ct.getName().getLocalizedString().get(0).getValue();
}
else if (ClassificationTypeEnum.DOC_HEALTHCARE_FACILITY_TYPE_CODE.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.CODING_SCHEME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
@SuppressWarnings("unused") String codingScheme = slot.getValueList().getValue().get(0);
}
}
}
healthcareFacilityTypeCode = ct.getNodeRepresentation();
if (ct.getName() != null && ct.getName().getLocalizedString() != null && !ct.getName().getLocalizedString().isEmpty())
healthcareFacilityTypeCode_localized = ct.getName().getLocalizedString().get(0).getValue();
}
else if (ClassificationTypeEnum.DOC_PRACTICE_SETTING_CODE.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.CODING_SCHEME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
@SuppressWarnings("unused") String codingScheme = slot.getValueList().getValue().get(0);
}
}
}
practiceSettingCode = ct.getNodeRepresentation();
if (ct.getName() != null && ct.getName().getLocalizedString() != null && !ct.getName().getLocalizedString().isEmpty())
practiceSettingCode_localized = ct.getName().getLocalizedString().get(0).getValue();
}
else if (ClassificationTypeEnum.DOC_LOINC.matchesScheme(ct.getClassificationScheme()))
{
for (SlotType1 slot : ct.getSlot())
{
if (SlotType1Enum.CODING_SCHEME.matches(slot.getName()))
{
if (slotNotEmpty(slot))
{
@SuppressWarnings("unused") String codingScheme = slot.getValueList().getValue().get(0);
}
}
}
loinc = ct.getNodeRepresentation();
if (ct.getName() != null && ct.getName().getLocalizedString() != null && !ct.getName().getLocalizedString().isEmpty())
loinc_localized = ct.getName().getLocalizedString().get(0).getValue();
}
}
for (ExternalIdentifierType eit : eot.getExternalIdentifier())
{
if (ExternalIdentifierTypeEnum.DOC_PATIENT_ID.matchesScheme(eit.getIdentificationScheme()))
{
patientId = eit.getValue();
}
else if (ExternalIdentifierTypeEnum.DOC_UNIQUE_ID.matchesScheme(eit.getIdentificationScheme()))
{
uniqueId = eit.getValue();
}
}
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#toString()
*/
@Override
public String toString()
{
QName qname = new QName(SubmitObjectsRequestEnum.EXTRINSIC_OBJECT.getNamespaceUri(), SubmitObjectsRequestEnum.EXTRINSIC_OBJECT.getName());
return XmlUtils.marshal(qname, generateExtrinsicObjectType(), ihe.iti.xds_b._2007.ObjectFactory.class);
}
/**
* @return the mimeType
*/
public String getMimeType()
{
return mimeType;
}
/**
* @param mimeType
* the mimeType to set
*/
public void setMimeType(String mimeType)
{
this.mimeType = mimeType;
}
/**
* @return the id
*/
public String getId()
{
return id;
}
/**
* @param id
* The id to set.
*/
public void setId(String id)
{
this.id = id;
}
/**
* @return the description
*/
public String getDescription()
{
return description;
}
/**
* @param description
* the description to set
*/
public void setDescription(String description)
{
this.description = description;
}
/**
* @return the creationTime
*/
public Date getCreationTime()
{
return creationTime;
}
/**
* @param creationTime
* the creationTime to set
*/
public void setCreationTime(Date creationTime)
{
this.creationTime = creationTime;
}
/**
* @return the languageCode
*/
public String getLanguageCode()
{
return languageCode;
}
/**
* @param languageCode
* the languageCode to set
*/
public void setLanguageCode(String languageCode)
{
this.languageCode = languageCode;
}
/**
* @return the serviceStartTime
*/
public Date getServiceStartTime()
{
return serviceStartTime;
}
/**
* @param serviceStartTime
* the serviceStartTime to set
*/
public void setServiceStartTime(Date serviceStartTime)
{
this.serviceStartTime = serviceStartTime;
}
/**
* @return the serviceStopTime
*/
public Date getServiceStopTime()
{
return serviceStopTime;
}
/**
* @param serviceStopTime
* the serviceStopTime to set
*/
public void setServiceStopTime(Date serviceStopTime)
{
this.serviceStopTime = serviceStopTime;
}
/**
* @return the sourcePatient
*/
public SimplePerson getSourcePatient()
{
return sourcePatient;
}
/**
* @param sourcePatient
* the sourcePatient to set
*/
public void setSourcePatient(SimplePerson sourcePatient)
{
this.sourcePatient = sourcePatient;
}
/**
* @return the authorPerson
*/
public String getAuthorPerson()
{
return authorPerson;
}
/**
* @param authorPerson
* the authorPerson to set
*/
public void setAuthorPerson(String authorPerson)
{
this.authorPerson = authorPerson;
}
/**
* @return the authorInstitution
*/
public List getAuthorInstitution()
{
return authorInstitution;
}
/**
* @param authorInstitution
* the authorInstitution to set
*/
public void setAuthorInstitution(List authorInstitution)
{
this.authorInstitution = authorInstitution;
}
/**
* @return the authorRole
*/
public String getAuthorRole()
{
return authorRole;
}
/**
* @param authorRole
* the authorRole to set
*/
public void setAuthorRole(String authorRole)
{
this.authorRole = authorRole;
}
/**
* @return the authorSpecialty
*/
public String getAuthorSpecialty()
{
return authorSpecialty;
}
/**
* @param authorSpecialty
* the authorSpecialty to set
*/
public void setAuthorSpecialty(String authorSpecialty)
{
this.authorSpecialty = authorSpecialty;
}
/**
* @return the classCode
*/
public String getClassCode()
{
return classCode;
}
/**
* @param classCode
* the classCode to set
*/
public void setClassCode(String classCode)
{
setClassCode(classCode, false);
}
/**
* @param classCode
* the classCode to set
* @param setLocalized
* whether or not to set the localized field with the same
* value
*/
public void setClassCode(String classCode, boolean setLocalized)
{
this.classCode = classCode;
if (setLocalized)
this.classCode_localized = classCode;
}
/**
* @return the classCode_localized
*/
public String getClassCode_localized()
{
return classCode_localized;
}
/**
* @param classCodeLocalized
* the classCode_localized to set
*/
public void setClassCode_localized(String classCodeLocalized)
{
classCode_localized = classCodeLocalized;
}
/**
* @return the confidentialityCode
*/
public String getConfidentialityCode()
{
return confidentialityCode;
}
/**
* @param confidentialityCode
* the confidentialityCode to set
*/
public void setConfidentialityCode(String confidentialityCode)
{
setConfidentialityCode(confidentialityCode, false);
}
/**
* @param confidentialityCode
* the confidentialityCode to set
* @param setLocalized
* whether or not to set the localized field with the same
* value
*/
public void setConfidentialityCode(String confidentialityCode, boolean setLocalized)
{
this.confidentialityCode = confidentialityCode;
if (setLocalized)
this.confidentialityCode_localized = confidentialityCode;
}
/**
* @return the confidentialityCode_localized
*/
public String getConfidentialityCode_localized()
{
return confidentialityCode_localized;
}
/**
* @param confidentialityCodeLocalized
* the confidentialityCode_localized to set
*/
public void setConfidentialityCode_localized(String confidentialityCodeLocalized)
{
confidentialityCode_localized = confidentialityCodeLocalized;
}
/**
* @return the formatCode
*/
public String getFormatCode()
{
return formatCode;
}
/**
* @param formatCode
* the formatCode to set
*/
public void setFormatCode(String formatCode)
{
setFormatCode(formatCode, false);
}
/**
* @param formatCode
* the formatCode to set
* @param setLocalized
* whether or not to set the localized field with the same
* value
*/
public void setFormatCode(String formatCode, boolean setLocalized)
{
this.formatCode = formatCode;
if (setLocalized)
formatCode_localized = formatCode;
}
/**
* @param formatCode
* the formatCode to set
*/
public void setFormatCode(FormatCodeEnum formatCode)
{
if (formatCode != null) {
setFormatCode(formatCode.getConceptCode());
setFormatCode_localized(formatCode.getConceptName());
}
}
/**
* @return the formatCode_localized
*/
public String getFormatCode_localized()
{
return formatCode_localized;
}
/**
* @param formatCodeLocalized
* the formatCode_localized to set
*/
public void setFormatCode_localized(String formatCodeLocalized)
{
formatCode_localized = formatCodeLocalized;
}
/**
* @return the healthcareFacilityTypeCode
*/
public String getHealthcareFacilityTypeCode()
{
return healthcareFacilityTypeCode;
}
/**
* @param healthcareFacilityTypeCode
* the healthcareFacilityTypeCode to set
*/
public void setHealthcareFacilityTypeCode(String healthcareFacilityTypeCode)
{
setHealthcareFacilityTypeCode(healthcareFacilityTypeCode, false);
}
/**
* @param healthcareFacilityTypeCode
* the healthcareFacilityTypeCode to set
* @param setLocalized
* whether or not to set the localized field with the same
* value
*/
public void setHealthcareFacilityTypeCode(String healthcareFacilityTypeCode, boolean setLocalized)
{
this.healthcareFacilityTypeCode = healthcareFacilityTypeCode;
if (setLocalized)
this.healthcareFacilityTypeCode_localized = healthcareFacilityTypeCode;
}
/**
* @return the healthcareFacilityTypeCode_localized
*/
public String getHealthcareFacilityTypeCode_localized()
{
return healthcareFacilityTypeCode_localized;
}
/**
* @param healthcareFacilityTypeCodeLocalized
* the healthcareFacilityTypeCode_localized to set
*/
public void setHealthcareFacilityTypeCode_localized(String healthcareFacilityTypeCodeLocalized)
{
healthcareFacilityTypeCode_localized = healthcareFacilityTypeCodeLocalized;
}
/**
* @return the practiceSettingCode
*/
public String getPracticeSettingCode()
{
return practiceSettingCode;
}
/**
* @param practiceSettingCode
* the practiceSettingCode to set
*/
public void setPracticeSettingCode(String practiceSettingCode)
{
setPracticeSettingCode(practiceSettingCode, false);
}
/**
* @param practiceSettingCode
* the practiceSettingCode to set
* @param setLocalized
* whether or not to set the localized field with the same
* value
*/
public void setPracticeSettingCode(String practiceSettingCode, boolean setLocalized)
{
this.practiceSettingCode = practiceSettingCode;
if (setLocalized)
this.practiceSettingCode_localized = practiceSettingCode;
}
/**
* @return the practiceSettingCode_localized
*/
public String getPracticeSettingCode_localized()
{
return practiceSettingCode_localized;
}
/**
* @param practiceSettingCodeLocalized
* the practiceSettingCode_localized to set
*/
public void setPracticeSettingCode_localized(String practiceSettingCodeLocalized)
{
practiceSettingCode_localized = practiceSettingCodeLocalized;
}
/**
* @return the loinc
*/
public String getLoinc()
{
return loinc;
}
/**
* @param loinc
* the loinc to set
*/
public void setLoinc(String loinc)
{
setLoinc(loinc, false);
}
/**
* @param loinc
* the loinc to set
* @param setLocalized
* whether or not to set the localized field with the same
* value
*/
public void setLoinc(String loinc, boolean setLocalized)
{
this.loinc = loinc;
if (setLocalized)
this.loinc_localized = loinc;
}
/**
* @return the loinc_localized
*/
public String getLoinc_localized()
{
return loinc_localized;
}
/**
* @param loincLocalized
* the loinc_localized to set
*/
public void setLoinc_localized(String loincLocalized)
{
loinc_localized = loincLocalized;
}
/**
* @return the patientId
*/
public String getPatientId()
{
return patientId;
}
/**
* @param patientId
* the patientId to set
*/
public void setPatientId(String patientId)
{
this.patientId = patientId;
}
/**
* @return the uniqueId
*/
public String getUniqueId()
{
return uniqueId;
}
/**
* @param uniqueId
* the uniqueId to set
*/
public void setUniqueId(String uniqueId)
{
this.uniqueId = uniqueId;
}
/**
* @return the submissionSetStatus
*/
public String getSubmissionSetStatus()
{
return submissionSetStatus;
}
/**
* @param submissionSetStatus
* the submissionSetStatus to set
*/
public void setSubmissionSetStatus(String submissionSetStatus)
{
this.submissionSetStatus = submissionSetStatus;
}
/**
* @return the hash
*/
public String getHash()
{
return hash;
}
/**
* @param hash
* the hash to set
*/
public void setHash(String hash)
{
if (StringUtils.isNotEmpty(this.hash) && !StringUtils.equalsIgnoreCase(this.hash, hash))
LOGGER.warn("Replacing existing value with new value");
this.hash = hash;
}
/**
* @return the size
*/
public Long getSize()
{
return size;
}
/**
* @param size
* the size to set
*/
public void setSize(Long size)
{
if (this.size != null && !this.size.equals(size))
LOGGER.warn("Replacing existing size with new value");
this.size = size;
}
/**
* @return the hash
*/
public String getURI()
{
return uri;
}
/**
* @param hash
* the hash to set
*/
public void setURI(String uri)
{
if (StringUtils.isNotEmpty(this.uri) && !StringUtils.equalsIgnoreCase(this.uri, uri))
LOGGER.warn("Replacing existing value with new value");
this.uri = uri;
}
}
/**
* Calculate the SHA-1 hash for the provided array of bytes.
*
* @param bytes
* Bytes from which to calculate the SHA-1 hash.
* @return the SHA-1 hash or null if unable to calculate.
*/
public static String getSha1Hash(byte[] bytes)
{
return getSha1Hash(new String(bytes));
}
/**
* Calculate the SHA-1 hash for the provided string.
*
* @param string
* The string from which to calculate the SHA-1 hash.
* @return the SHA-1 hash or null if unable to calculate.
*/
public static String getSha1Hash(String string)
{
MessageDigest messageDigest = null;
try
{
messageDigest = MessageDigest.getInstance("SHA-1");
}
catch (NoSuchAlgorithmException e)
{
LOGGER.error("Unable to calculate hash, returning null.", e);
return null;
}
messageDigest.update(string.getBytes(), 0, string.length());
byte[] sha1hash = messageDigest.digest();
char[]hex = Hex.encodeHex(sha1hash);
String newret = new String(hex);
//BigInteger bigInt = new BigInteger(sha1hash);
//return bigInt.toString(16);
return newret;
}
}
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