org.eclipse.ohf.ihe.xds.metadata.extract.cdar2
Class CDAR2Extractor

java.lang.Object
  org.eclipse.ohf.ihe.xds.metadata.extract.cdar2.CDAR2Extractor

All Implemented Interfaces:

DocumentEntryElementExtractor, DocumentEntryExtractor

public class CDAR2Extractor
extends java.lang.Object
implements DocumentEntryExtractor, DocumentEntryElementExtractor

Extracts XDS Document Entry Metadata from generic CDA R2 document

Author:

Sarah Knoop

Field Summary

static java.util.HashMap	ADMIN_GENDER_TABLE_001 Map between CDA R2 Administrative Gender codes and HL7v2.5 Table 001(Administrative Sex).
static java.lang.String	DESCRIPTOR Descriptor for Extractor

Constructor Summary

CDAR2Extractor(POCDMT000040ClinicalDocument cda)
Loads CDA Document

Method Summary

DocumentEntryType	extract() Entry point to invoke extraction process.
AuthorType[]	extractAuthors() Extracts the relevant authorInstitution, authorPerson, authorRole and authorSpeciality information from the CDA: ClinicalDocument/author/assignedAuthor.
AvailabilityStatusType	extractAvailabilityStatus() CDA R2 document header does not contain information corresponding to availablity status metadata.
CodedMetadataType	extractClassCode() Extracts the relevant classCode information from the CDA: ClinicalDocument/code.
InternationalStringType	extractComments() CDA R2 document header does not contain information corresponding to comments metadata.
CodedMetadataType	extractConfidentialityCode() Extracts the relevant confidentialityCode information from the CDA: ClinicalDocument/confidentialityCode.
java.lang.String	extractCreationTime() Extracts the relevant creationTime information from the CDA: ClinicalDocument/effectiveTime.
java.lang.String	extractEntryUUID() DocumentEntry.entryUUID is an XDS specific attribute and outside the scope of any CDA R2 document.
CodedMetadataType[]	extractEventCodes() This extraction routine, at this point, does not attempt to extract event code metadata from a generic CDA R2 document.
CodedMetadataType	extractFormatCode() DocumentEntry.formatCode is an XDS specific attribute and outside the scope of any CDA R2 document.
java.lang.String	extractHash() DocumentEntry.hash is a comptuted value and outside the scope of any CDA R2 document.
CodedMetadataType	extractHealthCareFacilityTypeCode() Extracts the relevant healthcareFacilityTypeCode information from the CDA: ClinicalDocument/componentOf/encompassingEncounter/location/code Note: healthcareFacilityTypeCode and practiceSettingCode data sources are the same in the CDA
java.lang.String	extractLanguageCode() Extracts the relevant languageCode information from the CDA: ClinicalDocument/languageCode
XCN	extractLegalAuthenticator() Extracts the relevant legalAuthenticator information from the CDA: ClinicalDocument/legalAuthenticator/assignedEntity/id and ClinicalDocument/legalAuthenticator/assignedEntity/assignedPerson/name NOTES: 1.
java.lang.String	extractMimeType() DocumentEntry.mimeType is an XDS specific attribute and outside the scope of any CDA R2 document.
java.lang.String	extractParentDocumentId() DocumentEntry.parentDocumentId expresses the id of a parent document to this CDA document in the XDS Regisry.
ParentDocumentRelationshipType	extractParentDocumentRelationship() DocumentEntry.parentDocumentRelationship expresses the relationship of this CDA to another document in the XDS Regisry.
CX	extractPatientId() DocumentEntry.patientId expresses the Affinity Domain level patient id used in the XDS Regisry.
CodedMetadataType	extractPracticeSettingCode() Extracts the relevant practiceSettingCode information from the CDA: ClinicalDocument/componentOf/encompassingEncounter/location/code Note: healthcareFacilityTypeCode and practiceSettingCode data sources are the same in the CDA
java.lang.String	extractServiceStartTime() Extracts the relevant serviceStartTime information from the CDA: ClinicalDocument/documentationOf/serviceEvent/effectiveTime This time is to be in UTC, but without the timezone offset or fractional seconds: [[[[[YYYY]MM]DD]HH]mm]ss].
java.lang.String	extractServiceStopTime() Extracts the relevant serviceStopTime information from the CDA: ClinicalDocument/documentationOf/serviceEvent/effectiveTime This time is to be in UTC, but without the timezone offset or fractional seconds: [[[[[YYYY]MM]DD]HH]mm]ss].
java.lang.String	extractSize() DocumentEntry.size is a comptuted value and outside the scope of any CDA R2 document.
CX	extractSourcePatientId() Extracts the relevant sourcePatientId information from the CDA: ClinicalDocument/recordTarget/patientRole/id NOTES: 1.
SourcePatientInfoType	extractSourcePatientInfo() Extracts the relevant sourcePatientInfo information from the CDA: ClinicalDocument/recordTarget/patientRole NOTES: 1.
InternationalStringType	extractTitle() Extracts the relevant title information from the CDA: ClinicalDocument/title
CodedMetadataType	extractTypeCode() Extracts the relevant typeCode information from the CDA: ClinicalDocument/code Note: typeCode and classCode data sources are the same in the CDA
java.lang.String	extractUniqueId() Extracts the relevant uniqueId information from the CDA: ClinicalDocument/id (format is id@root^id@extension)
java.lang.String	extractURI() DocumentEntry.URI is a comptuted value and outside the scope of any CDA R2 document.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DESCRIPTOR

public static final java.lang.String DESCRIPTOR

Descriptor for Extractor

See Also:

Constant Field Values

ADMIN_GENDER_TABLE_001

public static final java.util.HashMap ADMIN_GENDER_TABLE_001

Map between CDA R2 Administrative Gender codes and HL7v2.5 Table 001(Administrative Sex). Keys are CDAR2 AdministrativeGender object literal string representations and values are corresponding HL7v2.5 gender code values as strings.

Constructor Detail

CDAR2Extractor

public CDAR2Extractor(POCDMT000040ClinicalDocument cda)

Loads CDA Document

Parameters:

cda - the CDA R2 document to extract metadata from for the document entry metadata. Cannot be null.

Method Detail

extract

public DocumentEntryType extract()
                          throws MetadataExtractionException

Entry point to invoke extraction process.
NOTES:

1. Only the first ClinicalDocument/documentationOf instance will be considered for it's ServiceEvent time to fill values for serviceStartTime and serviceStopTime

2. Only the first ClinicalDocument/recordTarget instance will be considered for sourcePatientId (for which only the first patientRole/id on it's list will be taken) and sourcePatientInfo .

3. XDS metadata does not accept CX types that have more or fewer components than CX.1, CX.4.2,CX.4.3. Other corresponding componets will not be extracted.

4. XDS metadata validation for 2007 Connectathon will not accept DTM types beyond precision of YYYYMMDDHHMMSS. Precision has been truncated on values that include fractional seconds or time zone corrections

5. XDS metadata validation for 2007 Connectathon will not accept SourcePatientInfo beyond local patient ids, patient name, address, birthdate and gender. Other patient info in the CDA that corresponds to source patient info will not be extracted.

Specified by:

extract in interface DocumentEntryExtractor

Throws:

MetadataExtractionException

extractAuthors

public AuthorType[] extractAuthors()

Extracts the relevant authorInstitution, authorPerson, authorRole and authorSpeciality information from the CDA: ClinicalDocument/author/assignedAuthor. FIXME documentation CDA: ClinicalDocument/legalAuthenticator/assignedEntity/id and ClinicalDocument/legalAuthenticator/assignedEntity/assignedPerson/name
NOTES:

1. Only the first ClinicalDocument/legalAuthenticator/assignedEntity/id instance and first ClinicalDocument/legalAuthenticator/assignedEntity/assignedPerson/name instance will be considered for values for the legal authenticator XCN

Specified by:

extractAuthors in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractAuthors()

extractAvailabilityStatus

public AvailabilityStatusType extractAvailabilityStatus()

CDA R2 document header does not contain information corresponding to availablity status metadata.

Specified by:

extractAvailabilityStatus in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractAvailabilityStatus()

extractClassCode

public CodedMetadataType extractClassCode()

Extracts the relevant classCode information from the CDA: ClinicalDocument/code.
Note: typeCode and classCode data sources are the same in the CDA

Specified by:

extractClassCode in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractClassCode()

extractComments

public InternationalStringType extractComments()

CDA R2 document header does not contain information corresponding to comments metadata.

Specified by:

extractComments in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractComments()

extractConfidentialityCode

public CodedMetadataType extractConfidentialityCode()

Extracts the relevant confidentialityCode information from the CDA: ClinicalDocument/confidentialityCode.

Specified by:

extractConfidentialityCode in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractConfidentialityCode()

extractCreationTime

public java.lang.String extractCreationTime()

Extracts the relevant creationTime information from the CDA: ClinicalDocument/effectiveTime. This time is to be in UTC, but without the timezone offset or fractional seconds: [[[[[YYYY]MM]DD]HH]mm]ss]. Thus, this time is assumed to be in GMT. So, if the timestamp in the corresponding CDA element contains the timezone offset, this method will convert the timestamp to GMT. If the timezone offset is ommitted, then the timestamp is assumed to be in GMT.

Specified by:

extractCreationTime in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractCreationTime()

extractEntryUUID

public java.lang.String extractEntryUUID()

DocumentEntry.entryUUID is an XDS specific attribute and outside the scope of any CDA R2 document. Thus, it cannot be extracted.

Specified by:

extractEntryUUID in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractEntryUUID()

extractEventCodes

public CodedMetadataType[] extractEventCodes()

This extraction routine, at this point, does not attempt to extract event code metadata from a generic CDA R2 document.

Specified by:

extractEventCodes in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractEventCodes()

extractFormatCode

public CodedMetadataType extractFormatCode()

DocumentEntry.formatCode is an XDS specific attribute and outside the scope of any CDA R2 document. Thus, it cannot be extracted.

Specified by:

extractFormatCode in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractFormatCode()

extractHash

public java.lang.String extractHash()

DocumentEntry.hash is a comptuted value and outside the scope of any CDA R2 document. Thus, it cannot be extracted.

Specified by:

extractHash in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractHash()

extractHealthCareFacilityTypeCode

public CodedMetadataType extractHealthCareFacilityTypeCode()

Extracts the relevant healthcareFacilityTypeCode information from the CDA: ClinicalDocument/componentOf/encompassingEncounter/location/code
Note: healthcareFacilityTypeCode and practiceSettingCode data sources are the same in the CDA

Specified by:

extractHealthCareFacilityTypeCode in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractHealthCareFacilityTypeCode()

extractLanguageCode

public java.lang.String extractLanguageCode()

Extracts the relevant languageCode information from the CDA: ClinicalDocument/languageCode

Specified by:

extractLanguageCode in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractLanguageCode()

extractLegalAuthenticator

public XCN extractLegalAuthenticator()

Extracts the relevant legalAuthenticator information from the CDA: ClinicalDocument/legalAuthenticator/assignedEntity/id and ClinicalDocument/legalAuthenticator/assignedEntity/assignedPerson/name
NOTES:

1. Only the first ClinicalDocument/legalAuthenticator/assignedEntity/id instance and first ClinicalDocument/legalAuthenticator/assignedEntity/assignedPerson/name instance will be considered for values for the legal authenticator XCN

Specified by:

extractLegalAuthenticator in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractLanguageCode()

extractMimeType

public java.lang.String extractMimeType()

DocumentEntry.mimeType is an XDS specific attribute and outside the scope of any CDA R2 document. Thus, it cannot be extracted.

Specified by:

extractMimeType in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractMimeType()

extractParentDocumentId

public java.lang.String extractParentDocumentId()

DocumentEntry.parentDocumentId expresses the id of a parent document to this CDA document in the XDS Regisry. This is not necessairly the same parent document that is documented within the CDA. Thus, this information is not extracted.

Specified by:

extractParentDocumentId in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractParentDocumentId()

extractParentDocumentRelationship

public ParentDocumentRelationshipType extractParentDocumentRelationship()

DocumentEntry.parentDocumentRelationship expresses the relationship of this CDA to another document in the XDS Regisry. This is not necessairly the same relationship documented within the CDA. Thus, this infomation is not extracted.

Specified by:

extractParentDocumentRelationship in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractParentDocumentRelationship()

extractPatientId

public CX extractPatientId()

DocumentEntry.patientId expresses the Affinity Domain level patient id used in the XDS Regisry. In all cases, this is not necessairly the same patientId that is documented within the CDA. Thus, this information is not extracted.

Specified by:

extractPatientId in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractPatientId()

extractPracticeSettingCode

public CodedMetadataType extractPracticeSettingCode()

Extracts the relevant practiceSettingCode information from the CDA: ClinicalDocument/componentOf/encompassingEncounter/location/code
Note: healthcareFacilityTypeCode and practiceSettingCode data sources are the same in the CDA

Specified by:

extractPracticeSettingCode in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractPracticeSettingCode()

extractServiceStartTime

public java.lang.String extractServiceStartTime()

Extracts the relevant serviceStartTime information from the CDA: ClinicalDocument/documentationOf/serviceEvent/effectiveTime This time is to be in UTC, but without the timezone offset or fractional seconds: [[[[[YYYY]MM]DD]HH]mm]ss]. Thus, this time is assumed to be in GMT. So, if the timestamp in the corresponding CDA element contains the timezone offset, this method will convert the timestamp to GMT. If the timezone offset is ommitted, then the timestamp is assumed to be in GMT. NOTES:

1. Only the first ClinicalDocument/documentationOf instance will be considered for it's ServiceEvent time to fill values for serviceStartTime and serviceStopTime

2. XDS metadata validation for 2007 Connectathon will not accept DTM types beyond precision of YYYYMMDDHHMMSS. Precision has been truncated on values that include fractional seconds or time zone corrections

Specified by:

extractServiceStartTime in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractServiceStartTime()

extractServiceStopTime

public java.lang.String extractServiceStopTime()

Extracts the relevant serviceStopTime information from the CDA: ClinicalDocument/documentationOf/serviceEvent/effectiveTime This time is to be in UTC, but without the timezone offset or fractional seconds: [[[[[YYYY]MM]DD]HH]mm]ss]. Thus, this time is assumed to be in GMT. So, if the timestamp in the corresponding CDA element contains the timezone offset, this method will convert the timestamp to GMT. If the timezone offset is ommitted, then the timestamp is assumed to be in GMT.
NOTES:

1. Only the first ClinicalDocument/documentationOf instance will be considered for it's ServiceEvent time to fill values for serviceStartTime and serviceStopTime

2. XDS metadata validation for 2007 Connectathon will not accept DTM types beyond precision of YYYYMMDDHHMMSS. Precision has been truncated on values that include fractional seconds or time zone corrections

Specified by:

extractServiceStopTime in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractServiceStopTime()

extractSize

public java.lang.String extractSize()

DocumentEntry.size is a comptuted value and outside the scope of any CDA R2 document. Thus, it cannot be extracted.

Specified by:

extractSize in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractSize()

extractSourcePatientId

public CX extractSourcePatientId()

Extracts the relevant sourcePatientId information from the CDA: ClinicalDocument/recordTarget/patientRole/id
NOTES:

1. Only the first ClinicalDocument/recordTarget instance will be considered for sourcePatientId (for which only the first patientRole/id on it's list will be taken) and sourcePatientInfo .

2. XDS metadata does not accept CX types that have more or fewer components than CX.1, CX.4.2,CX.4.3. Other corresponding componets will not be extracted.

Specified by:

extractSourcePatientId in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractSourcePatientId()

extractSourcePatientInfo

public SourcePatientInfoType extractSourcePatientInfo()

Extracts the relevant sourcePatientInfo information from the CDA: ClinicalDocument/recordTarget/patientRole
NOTES:

1. Only the first ClinicalDocument/recordTarget instance will be considered for sourcePatientId (for which only the first patientRole/id on it's list will be taken) and sourcePatientInfo .

2. Extracts all id of the list of ids for PatientRole to PID-3 and the PatientRole/Patient/id

3. XDS metadata does not accept CX types that have more or fewer components than CX.1, CX.4.2,CX.4.3. Other corresponding componets will not be extracted.

4. XDS metadata validation for 2007 Connectathon will not accept SourcePatientInfo beyond local patient ids, patient name, address, birthdate and gender. Other patient info in the CDA that corresponds to source patient info will not be extracted.

5.Only the first address will be considered for extraction, only the first subelements of the AD type will be considered for extraction.

Specified by:

extractSourcePatientInfo in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractSourcePatientInfo()

extractTitle

public InternationalStringType extractTitle()

Extracts the relevant title information from the CDA: ClinicalDocument/title

Specified by:

extractTitle in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractTitle()

extractTypeCode

public CodedMetadataType extractTypeCode()

Extracts the relevant typeCode information from the CDA: ClinicalDocument/code
Note: typeCode and classCode data sources are the same in the CDA

Specified by:

extractTypeCode in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractTypeCode()

extractURI

public java.lang.String extractURI()

DocumentEntry.URI is a comptuted value and outside the scope of any CDA R2 document. Thus, it cannot be extracted.

Specified by:

extractURI in interface DocumentEntryElementExtractor

Returns:

null

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractURI()

extractUniqueId

public java.lang.String extractUniqueId()

Extracts the relevant uniqueId information from the CDA: ClinicalDocument/id (format is id@root^id@extension)

Specified by:

extractUniqueId in interface DocumentEntryElementExtractor

Returns:

Returns the populated attribute. Returns null if this attribute cannot be rendered from the source data.

See Also:

org.eclipse.ohf.ihe.xds.metadata.extract.DocumentEntryElementExtractor.extractUniqueId()