org.bch.fhir.i2b2.service

Class FHIRToPDO

java.lang.Object

org.bch.fhir.i2b2.service.FHIRToPDO

Direct Known Subclasses:

ObservationToI2B2, PatientToI2B2, QResponseToI2B2

public abstract class FHIRToPDO
extends java.lang.Object

Abstract class that provides common methods for mapping fhir into i2b2

Author:

CHIP-IHL

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_EVENT_SOURCE
static java.lang.String	DEFAULT_PATIENT_SOURCE
protected java.lang.String	eventIde
protected java.lang.String	eventIdeSource
static java.lang.String	FHIR_TAG_VALUE_BOOLEAN
static java.lang.String	FHIR_TAG_VALUE_CODING
static java.lang.String	FHIR_TAG_VALUE_DECIMAL
static java.lang.String	FHIR_TAG_VALUE_INTEGER
static java.lang.String	FHIR_TAG_VALUE_QUANTITY
static java.lang.String	FHIR_TAG_VALUE_STRING
static java.lang.String	METADATA_CONCEPT_CD
protected java.lang.String	patientIde
protected java.lang.String	patientIdeSource

Constructor Summary

Constructors

Constructor and Description
FHIRToPDO()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addMetadataInObservationSet(java.lang.String info, java.lang.String conceptCdMetadada, ElementSet observationSet) Adds a metadata element associated to the current fhir resource.
protected ca.uhn.fhir.model.api.IResource	findResourceById(java.util.List<ca.uhn.fhir.model.api.IResource> resources, java.lang.String id)
protected java.lang.String	finishRow(java.lang.StringBuffer in, java.lang.String tag, java.lang.String value)
protected ElementSet	generateEIDSet()
protected ElementSet	generateEventSet(ca.uhn.fhir.model.dstu2.resource.Encounter enc)
protected ElementSet	generatePatientSet()
protected ElementSet	generatePIDSet()
protected java.lang.String	generateRow(java.lang.String tag, java.lang.String value)
protected java.lang.String	generateRow(java.lang.String tag, java.lang.String value, java.lang.String param)
protected java.lang.String	generateRow(java.lang.String tag, java.lang.String value, java.lang.String param1, java.lang.String param2)
protected java.lang.String	generateRow(java.lang.String tag, java.lang.String value, java.lang.String param1, java.lang.String param2, java.lang.String param3)
protected java.lang.String	genParamNum(java.lang.String paramName, java.lang.String valueNum)
protected java.lang.String	genParamStr(java.lang.String paramName, java.lang.String valueStr)
protected java.lang.String	getEventId(ca.uhn.fhir.model.dstu2.resource.Encounter enc)
abstract java.lang.String	getPDOXML(ca.uhn.fhir.model.dstu2.resource.BaseResource resource) Method to the implemented that returns the pdo xml equivalent of the fhir resource
protected boolean	isNumericType(java.lang.String type)
protected boolean	isRawConceptCD(java.lang.String type)

Methods inherited from class java.lang.Object

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

Field Detail

METADATA_CONCEPT_CD

public static final java.lang.String METADATA_CONCEPT_CD

See Also:

Constant Field Values

FHIR_TAG_VALUE_QUANTITY

public static final java.lang.String FHIR_TAG_VALUE_QUANTITY

See Also:

Constant Field Values

FHIR_TAG_VALUE_STRING

public static final java.lang.String FHIR_TAG_VALUE_STRING

See Also:

Constant Field Values

FHIR_TAG_VALUE_INTEGER

public static final java.lang.String FHIR_TAG_VALUE_INTEGER

See Also:

Constant Field Values

FHIR_TAG_VALUE_DECIMAL

public static final java.lang.String FHIR_TAG_VALUE_DECIMAL

See Also:

Constant Field Values

FHIR_TAG_VALUE_CODING

public static final java.lang.String FHIR_TAG_VALUE_CODING

See Also:

Constant Field Values

FHIR_TAG_VALUE_BOOLEAN

public static final java.lang.String FHIR_TAG_VALUE_BOOLEAN

See Also:

Constant Field Values

DEFAULT_PATIENT_SOURCE

public static final java.lang.String DEFAULT_PATIENT_SOURCE

See Also:

Constant Field Values

DEFAULT_EVENT_SOURCE

public static final java.lang.String DEFAULT_EVENT_SOURCE

See Also:

Constant Field Values

patientIdeSource

protected java.lang.String patientIdeSource

patientIde

protected java.lang.String patientIde

eventIdeSource

protected java.lang.String eventIdeSource

eventIde

protected java.lang.String eventIde

Constructor Detail

FHIRToPDO

public FHIRToPDO()

Method Detail

getPDOXML

public abstract java.lang.String getPDOXML(ca.uhn.fhir.model.dstu2.resource.BaseResource resource)
                                    throws FHIRI2B2Exception

Method to the implemented that returns the pdo xml equivalent of the fhir resource

Parameters:

resource - The fhir resource

Returns:

The pdo xml as String

Throws:

FHIRI2B2Exception - In case some error occurs

getEventId

protected java.lang.String getEventId(ca.uhn.fhir.model.dstu2.resource.Encounter enc)
                               throws FHIRI2B2Exception

Throws:

FHIRI2B2Exception

generateEventSet

protected ElementSet generateEventSet(ca.uhn.fhir.model.dstu2.resource.Encounter enc)
                               throws FHIRI2B2Exception

Throws:

FHIRI2B2Exception

generateEIDSet

protected ElementSet generateEIDSet()
                             throws FHIRI2B2Exception

Throws:

FHIRI2B2Exception

generatePIDSet

protected ElementSet generatePIDSet()
                             throws FHIRI2B2Exception

Throws:

FHIRI2B2Exception

generatePatientSet

protected ElementSet generatePatientSet()
                                 throws FHIRI2B2Exception

Throws:

FHIRI2B2Exception

finishRow

protected java.lang.String finishRow(java.lang.StringBuffer in,
                         java.lang.String tag,
                         java.lang.String value)

generateRow

protected java.lang.String generateRow(java.lang.String tag,
                           java.lang.String value)

generateRow

protected java.lang.String generateRow(java.lang.String tag,
                           java.lang.String value,
                           java.lang.String param)

generateRow

protected java.lang.String generateRow(java.lang.String tag,
                           java.lang.String value,
                           java.lang.String param1,
                           java.lang.String param2)

generateRow

protected java.lang.String generateRow(java.lang.String tag,
                           java.lang.String value,
                           java.lang.String param1,
                           java.lang.String param2,
                           java.lang.String param3)

genParamStr

protected java.lang.String genParamStr(java.lang.String paramName,
                           java.lang.String valueStr)

genParamNum

protected java.lang.String genParamNum(java.lang.String paramName,
                           java.lang.String valueNum)

isRawConceptCD

protected boolean isRawConceptCD(java.lang.String type)

isNumericType

protected boolean isNumericType(java.lang.String type)

findResourceById

protected ca.uhn.fhir.model.api.IResource findResourceById(java.util.List<ca.uhn.fhir.model.api.IResource> resources,
                                               java.lang.String id)

addMetadataInObservationSet

protected void addMetadataInObservationSet(java.lang.String info,
                               java.lang.String conceptCdMetadada,
                               ElementSet observationSet)
                                    throws FHIRI2B2Exception

Adds a metadata element associated to the current fhir resource. It does it by adding a new observation in an ElementSet of type ObservationSet

Parameters:

info - The metadata that will be stored in TVAL_CHAR

conceptCdMetadada - The desired ConceptCd

observationSet - The observation set

Throws:

FHIRI2B2Exception