Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* (C) Copyright IBM Corp. 2020, 2022
*
* SPDX-License-Identifier: Apache-2.0
*/
package io.github.linuxforhealth.hl7.data;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Base64;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.UUID;
import ca.uhn.hl7v2.model.v26.datatype.CE;
import ca.uhn.hl7v2.model.v26.datatype.CWE;
import ca.uhn.hl7v2.model.v26.datatype.DT;
import ca.uhn.hl7v2.model.v26.datatype.DTM;
import ca.uhn.hl7v2.model.v26.datatype.PPN;
import ca.uhn.hl7v2.model.v26.datatype.TS;
import ca.uhn.hl7v2.model.v26.datatype.XCN;
import ca.uhn.hl7v2.model.v26.group.VXU_V04_OBSERVATION;
import ca.uhn.hl7v2.model.v26.group.VXU_V04_ORDER;
import ca.uhn.hl7v2.model.v26.segment.OBX;
import ca.uhn.hl7v2.HL7Exception;
import ca.uhn.hl7v2.model.Varies;
import org.apache.commons.lang3.BooleanUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.hl7.fhir.dstu3.model.codesystems.MedicationRequestCategory;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCriticality;
import org.hl7.fhir.r4.model.DiagnosticReport.DiagnosticReportStatus;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.MedicationRequest;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.ServiceRequest.ServiceRequestStatus;
import org.hl7.fhir.r4.model.Specimen.SpecimenStatus;
import org.hl7.fhir.r4.model.codesystems.V3ActCode;
import org.hl7.fhir.r4.model.codesystems.V3MaritalStatus;
import org.hl7.fhir.r4.model.codesystems.ConditionCategory;
import org.hl7.fhir.r4.model.codesystems.MessageReasonEncounter;
import org.hl7.fhir.r4.model.codesystems.NameUse;
import org.hl7.fhir.r4.model.codesystems.SubscriberRelationship;
import org.hl7.fhir.r4.model.codesystems.V3ReligiousAffiliation;
import org.hl7.fhir.r4.model.codesystems.V3RoleCode;
import org.hl7.fhir.r4.model.codesystems.DiagnosisRole;
import org.hl7.fhir.r4.model.codesystems.ConditionClinical;
import org.hl7.fhir.r4.model.codesystems.ConditionVerStatus;
import org.hl7.fhir.r4.model.codesystems.CompositionStatus;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import io.github.linuxforhealth.api.ResourceValue;
import io.github.linuxforhealth.core.terminology.Hl7v2Mapping;
import io.github.linuxforhealth.core.terminology.SimpleCode;
import io.github.linuxforhealth.core.terminology.TerminologyLookup;
import io.github.linuxforhealth.core.terminology.UrlLookup;
import io.github.linuxforhealth.hl7.data.date.DateUtil;
public class SimpleDataValueResolver {
private static final Logger LOGGER = LoggerFactory.getLogger(SimpleDataValueResolver.class);
private static final String INVALID_CODE_MESSAGE_FULL = "Invalid input: code '%s' could not be mapped to values in system '%s' with original display '%s' and version '%s'.";
private static final String INVALID_CODE_MESSAGE_SHORT = "Invalid input: code '%s' could not be mapped to values in system '%s'.";
public static final ValueExtractor DATE = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null) {
return DateUtil.formatToDate(val);
}
return null;
};
public static final ValueExtractor STRING = (Object value) -> {
return Hl7DataHandlerUtil.getStringValue(value);
};
public static final ValueExtractor STRING_ALL = (Object value) -> {
return Hl7DataHandlerUtil.getStringValue(value, true);
};
public static final ValueExtractor VALID_ID = (Object value) -> {
String strValue = Hl7DataHandlerUtil.getStringValue(value);
if (strValue != null) {
strValue = strValue.toLowerCase();
return strValue.replaceAll("[^a-zA-Z0-9.]", "-");
}
return null;
};
// Clean up of SSN currently removes any dashes.
public static final ValueExtractor CLEAN_SSN = (Object value) -> {
String strValue = Hl7DataHandlerUtil.getStringValue(value);
if (strValue != null) {
return strValue.replaceAll("\\-", "");
}
return null;
};
public static final ValueExtractor URI_VAL = (Object value) -> {
try {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null && isValidUUID(val)) {
return new URI("urn", "uuid", val);
} else {
return null;
}
} catch (IllegalArgumentException | URISyntaxException e) {
LOGGER.warn("Value not valid URI, value: {}", value);
return null;
}
};
// Creates a display name; currently only handles XCN and PPN as input
public static final ValueExtractor PERSON_DISPLAY_NAME = (Object value) -> {
StringBuilder sb = new StringBuilder();
String valprefix = null;
String valfirst = null;
String valmiddle = null;
String valfamily = null;
String valsuffix = null;
if (value instanceof XCN) {
XCN xcn = (XCN) value;
valprefix = Hl7DataHandlerUtil.getStringValue(xcn.getPrefixEgDR());
valfirst = Hl7DataHandlerUtil.getStringValue(xcn.getGivenName());
valmiddle = Hl7DataHandlerUtil.getStringValue(xcn.getSecondAndFurtherGivenNamesOrInitialsThereof());
valfamily = Hl7DataHandlerUtil.getStringValue(xcn.getFamilyName());
valsuffix = Hl7DataHandlerUtil.getStringValue(xcn.getSuffixEgJRorIII());
} else if (value instanceof PPN) {
PPN ppn = (PPN) value;
valprefix = Hl7DataHandlerUtil.getStringValue(ppn.getPrefixEgDR());
valfirst = Hl7DataHandlerUtil.getStringValue(ppn.getGivenName());
valmiddle = Hl7DataHandlerUtil.getStringValue(ppn.getSecondAndFurtherGivenNamesOrInitialsThereof());
valfamily = Hl7DataHandlerUtil.getStringValue(ppn.getFamilyName());
valsuffix = Hl7DataHandlerUtil.getStringValue(ppn.getSuffixEgJRorIII());
}
if (valprefix != null) {
sb.append(valprefix).append(" ");
}
if (valfirst != null) {
sb.append(valfirst).append(" ");
}
if (valmiddle != null) {
sb.append(valmiddle).append(" ");
}
if (valfamily != null) {
sb.append(valfamily).append(" ");
}
if (valsuffix != null) {
sb.append(valsuffix).append(" ");
}
String name = sb.toString();
if (StringUtils.isNotBlank(name)) {
return name.trim();
} else
return null;
};
public static final ValueExtractor ADMINISTRATIVE_GENDER_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, AdministrativeGender.class);
if (code != null) {
return code;
} else if (val == null) {
return null;
} else {
return AdministrativeGender.UNKNOWN.toCode();
}
};
public static final ValueExtractor MEDREQ_STATUS_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, MedicationRequest.MedicationRequestStatus.class);
if (code != null) {
return code;
}
return "unknown"; // when the HL7 status codes get mapped in v2toFhirMapping, we will return code. "unknown" is being returned because the hl7 message is not mapped to fhir yet.
};
public static final ValueExtractor MEDREQ_CATEGORY_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, MedicationRequestCategory.class);
if (code != null) {
MedicationRequestCategory category = MedicationRequestCategory.fromCode(code);
return new SimpleCode(code, "http://terminology.hl7.org/CodeSystem/medicationrequest-category",
category.getDisplay()); // category.getSystem() returns http://hl7.org/fhir/medication-request-category which is invalid so we hardcode the system with the proper url
} else
return null;
};
public static final ValueExtractor OBSERVATION_STATUS_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, ObservationStatus.class);
};
// Handlers for searching Immunization.education siblings.
public static final ValueExtractor FIND_EDUCATION_REFERENCE_TEXT = (Object value) -> {
return getSelectedSiblingObservationTEXTfromObxGroup(value, "30956-7");
};
public static final ValueExtractor FIND_EDUCATION_DOCUMENT_TYPE_TEXT = (Object value) -> {
return getSelectedSiblingObservationTEXTfromObxGroup(value, "69764-9");
};
public static final ValueExtractor FIND_EDUCATION_PUBLICATION_DATE = (Object value) -> {
return getSelectedSiblingObservationDATEfromObxGroup(value, "29768-9");
};
public static final ValueExtractor FIND_EDUCATION_PRESENTATION_DATE = (Object value) -> {
return getSelectedSiblingObservationDATEfromObxGroup(value, "29769-7");
};
// Typed handler for CE & CWE return values from Immunization.education siblings
private static final String getSelectedSiblingObservationTEXTfromObxGroup(Object valueObx, String siblingCode) {
Object obj = getSelectedSiblingObservationVALUEfromObxGroup(valueObx, siblingCode);
// If we got an object, tease out the text value
if (obj != null) {
String returnVal = null;
if (obj instanceof CE) {
returnVal = Hl7DataHandlerUtil.getStringValue(((CE) obj).getText());
}
if (obj instanceof CWE) {
returnVal = Hl7DataHandlerUtil.getStringValue(((CWE) obj).getText());
}
// If there was no text value in the object, or the object was not an expected type default to "unspecified"
return returnVal != null ? returnVal : "unspecified";
}
// If no object was found, return null
return null;
}
// Typed handler for DT & TS return values from Immunization.education siblings
private static final String getSelectedSiblingObservationDATEfromObxGroup(Object valueObx, String siblingCode) {
Object obj = getSelectedSiblingObservationVALUEfromObxGroup(valueObx, siblingCode);
if (obj instanceof DT) {
return DateUtil.formatToDate(((DT)obj).getValue());
}
if (obj instanceof TS) {
return DateUtil.formatToDate(((TS)obj).getTime().toString());
}
if (obj instanceof DTM) {
String dateString = ((DTM)obj).getValue();
// DTMs potentially have more information than we need. Truncate after day, or return null.
return dateString.length() > 7 ? DateUtil.formatToDate(dateString.substring(0,8)) : null;
}
return null;
}
// Common handler for searching Immunization.education siblings. Used for immunization records where the
// immunization, the publication, and presentation are in different sibling OBX's grouped together by OBX.4.
// This special purpose routine finds the grandparent object, so we can search the correct sibling objects,
// which prevents search overreach and datableed.
// The return value is an unformatted object. It is up to the caller to check type and extract content to string.
private static final Object getSelectedSiblingObservationVALUEfromObxGroup(Object valueObx, String siblingCode) {
if (valueObx instanceof OBX) {
try {
OBX obx = (OBX) valueObx;
// Get the group number from OBX.4
String obx4GroupNum = obx.getObx4_ObservationSubID().getValueOrEmpty();
// OBX is contained in an OBSERVATION. Get the OBSERVATION by requesting the parent.
VXU_V04_OBSERVATION containingObservation = (VXU_V04_OBSERVATION) obx.getParent();
// The parent of the OBSERVATION is a VXU_V04_ORDER
VXU_V04_ORDER containingOrder = (VXU_V04_ORDER) containingObservation.getParent();
// Get the repeating 'sibling' OBSERVATION objects
List observations = containingOrder.getOBSERVATIONAll();
for (VXU_V04_OBSERVATION obsIter : observations) {
// For each OBSERVATION, get the OBX
OBX obsIterObx = obsIter.getOBX();
// If OBX.4 is the same group AND OBX.3.1 matches the siblingCode we want
if (obx4GroupNum.equals(obsIterObx.getObx4_ObservationSubID().getValueOrEmpty()) &&
obsIterObx.getObx3_ObservationIdentifier().getCwe1_Identifier().getValueOrEmpty()
.equals(siblingCode)) {
if (obsIterObx.getObservationValueReps() > 0) {
return obsIterObx.getObservationValue(0).getData();
}
return null;
}
}
} catch (HL7Exception e) {
return null; // If something fails
}
}
return null;
}
public static final ValueExtractor OBSERVATION_STATUS_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, ObservationStatus.class);
if (code != null) {
ObservationStatus status = ObservationStatus.fromCode(code);
return new SimpleCode(code, status.getSystem(), status.getDisplay());
} else {
// If code is null, it means the code wasn't known in our table, and can't be looked up.
// Make a message in the display.
String theSystem = ObservationStatus.REGISTERED.getSystem();
return new SimpleCode(null, theSystem, String.format(INVALID_CODE_MESSAGE_SHORT, val, theSystem));
}
};
public static final ValueExtractor SERVICE_REQUEST_STATUS = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, ServiceRequestStatus.class);
};
public static final ValueExtractor CONDITION_CATEGORY_CODES = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null) {
ConditionCategory status = ConditionCategory.fromCode(val);
return new SimpleCode(val, status.getSystem(), status.getDisplay());
} else {
return null;
}
};
public static final ValueExtractor RELIGIOUS_AFFILIATION_FHIR_CC = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, V3ReligiousAffiliation.class);
String text = Hl7DataHandlerUtil.getOriginalDisplayText(value);
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
V3ReligiousAffiliation status = V3ReligiousAffiliation.fromCode(code);
return new SimpleCode(code, status.getSystem(), status.getDisplay());
} else {
// // If code is null, it means the code wasn't known in our table, and can't be looked up.
// // Make a message in the display.
String religionSystem = V3ReligiousAffiliation._1028.getSystem();
return new SimpleCode(null, religionSystem,
String.format(INVALID_CODE_MESSAGE_FULL, val, religionSystem, text, version));
}
};
// Diagnosis Use needs special handling because the three input codes, A, F, and W
// need different systems because FHIR has a system for A, but not F and W.
// We check the value and based on the value, do the lookup in the right system.
// Note: values that come in know the table based on the field position.
public static final ValueExtractor DIAGNOSIS_USE = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null && (val.equals("F") || val.equals("W"))) {
// Process as table v2-0052
String table = Hl7DataHandlerUtil.getTableNumber(value);
if (table != null && val != null) {
// Found table and a code. Try looking it up.
SimpleCode coding = TerminologyLookup.lookup(table, val);
// A non-null, non-empty value in display means a good code from lookup.
if (coding != null && coding.getDisplay() != null && !coding.getDisplay().isEmpty()) {
return coding;
}
// Without a good table lookup, falls through to simple code handling below
}
}
// Otherwise process as a DiagnosisRole mapping (handles unknown codes)
String code = getFHIRCode(val, DiagnosisRole.class);
if (code != null) {
DiagnosisRole use = DiagnosisRole.fromCode(code);
return new SimpleCode(code, use.getSystem(), use.getDisplay());
} else {
return new SimpleCode(val, null, null);
}
};
public static final ValueExtractor CONDITION_CLINICAL_STATUS_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
//Test to see if val is a valid code.
ConditionClinical use = null;
try {
use = ConditionClinical.fromCode(val);
LOGGER.info("Found ConditionClinical code for '{}'.", val);
} catch (FHIRException e) {
LOGGER.warn("Could not find ConditionClinical code for '{}'.", val);
}
if (use != null) { // if it is then setup the simple code
return new SimpleCode(val, use.getSystem(), use.getDisplay());
} else { // otherwise we don't want the code at all
return null;
}
};
public static final ValueExtractor CONDITION_VERIFICATION_STATUS_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
//Test to see if val is a valid code.
ConditionVerStatus use = null;
try {
use = ConditionVerStatus.fromCode(val);
LOGGER.info("Found ConditionVerStatus code for '{}'.", val);
} catch (FHIRException e) {
LOGGER.warn("Could not find ConditionVerStatus code for '{}'.", val);
}
if (use != null) { // if it is then setup the simple code
return new SimpleCode(val, use.getSystem(), use.getDisplay());
} else { // otherwise we don't want the code at all
return null;
}
};
public static final ValueExtractor ACT_ENCOUNTER_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, V3ActCode.class);
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
V3ActCode act = V3ActCode.fromCode(code);
return new SimpleCode(code, act.getSystem(), act.getDisplay(), version);
} else if (val != null) { // if code does not map but is present, use the "val" as the code
return new SimpleCode(val, null, null);
} else
return null;
};
public static final ValueExtractor SPECIMEN_STATUS_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, SpecimenStatus.class);
};
public static final ValueExtractor DOC_REF_DOC_STATUS_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, CompositionStatus.class);
};
public static final ValueExtractor NAME_USE_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, NameUse.class);
};
public static final ValueExtractor ENCOUNTER_MODE_ARRIVAL_DISPLAY = (Object value) -> {
return getFHIRCode(Hl7DataHandlerUtil.getStringValue(value), "EncounterModeOfArrivalDisplay");
};
// Relationships are coded, mapped, and recoded in two different DIRECTIONS.
// See detailed notes in v2ToFhirMapping maps of V3RoleCode and SubscriberRelationship
// Maps from IN1.17 to http://terminology.hl7.org/CodeSystem/v3-RoleCode
// Used for Coverage.relationship
public static final ValueExtractor POLICYHOLDER_RELATIONSHIP_IN117 = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, "PolicyholderRelationshipIN117");
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
V3RoleCode relationship = V3RoleCode.fromCode(code);
return new SimpleCode(code, relationship.getSystem(), relationship.getDisplay(), version);
} else {
// If code is not found in our mapping, return the code itself with no system or display.
return new SimpleCode(val, null, null, null);
}
};
// Maps from IN2.72 to http://terminology.hl7.org/CodeSystem/v3-RoleCode
// Used for Coverage.relationship
public static final ValueExtractor POLICYHOLDER_RELATIONSHIP_IN272 = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, "PolicyholderRelationshipIN272");
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
V3RoleCode relationship = V3RoleCode.fromCode(code);
return new SimpleCode(code, relationship.getSystem(), relationship.getDisplay(), version);
} else {
// If code is not found in our mapping, return the code itself with no system or display.
return new SimpleCode(val, null, null, null);
}
};
// Maps from IN1.17 to http://terminology.hl7.org/CodeSystem/subscriber-relationship
// Used for RelatedPerson.relationship.
public static final ValueExtractor SUBSCRIBER_RELATIONSHIP_IN117 = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, "SubscriberRelationshipIN117");
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
SubscriberRelationship relationship = SubscriberRelationship.fromCode(code);
return new SimpleCode(code, relationship.getSystem(), relationship.getDisplay(), version);
} else {
// If code is not found in our mapping, return the code itself with no system or display.
return new SimpleCode(val, null, null, null);
}
};
// Maps from IN2.72 to http://terminology.hl7.org/CodeSystem/subscriber-relationship
// Used for RelatedPerson.relationship.
public static final ValueExtractor SUBSCRIBER_RELATIONSHIP_IN272 = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, "SubscriberRelationshipIN272");
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
SubscriberRelationship relationship = SubscriberRelationship.fromCode(code);
return new SimpleCode(code, relationship.getSystem(), relationship.getDisplay(), version);
} else {
// If code is not found in our mapping, return the code itself with no system or display.
return new SimpleCode(val, null, null, null);
}
};
// Maps from IN1.17 or IN2.72 to a boolean string TRUE if RelatedPerson should be created
public static final ValueExtractor RELATED_PERSON_NEEDED_IN117 = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, "RelatedPersonNeededIN117");
};
// Maps from IN1.17 or IN2.72 to a boolean string TRUE if RelatedPerson should be created
public static final ValueExtractor RELATED_PERSON_NEEDED_IN272 = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, "RelatedPersonNeededIN272");
};
public static final ValueExtractor MARITAL_STATUS = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String text = Hl7DataHandlerUtil.getOriginalDisplayText(value);
String code = getFHIRCode(val, V3MaritalStatus.class);
String version = Hl7DataHandlerUtil.getVersion(value);
if (code != null) {
V3MaritalStatus mar = V3MaritalStatus.fromCode(code);
return new SimpleCode(code, mar.getSystem(), mar.getDisplay(), version);
} else {
// If code is null, it means the code wasn't known in our table, and can't be looked up.
// Make a message in the display.
String theSystem = V3MaritalStatus.M.getSystem();
return new SimpleCode(null, theSystem,
String.format(INVALID_CODE_MESSAGE_FULL, val, theSystem, text, version));
}
};
public static final ValueExtractor BOOLEAN = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (null == val) {
return false;
}
return BooleanUtils.toBoolean(val);
};
public static final ValueExtractor INTEGER = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (null == val) {
return null;
}
if (NumberUtils.isCreatable(val)) {
return NumberUtils.createInteger(val);
} else {
LOGGER.warn("Value {} for INTEGER is not a valid number so returning null.", value);
return null;
}
};
public static final ValueExtractor FLOAT = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (null == val) {
return null;
}
if (NumberUtils.isCreatable(val)) {
return NumberUtils.createFloat(val);
} else {
LOGGER.warn("Value {} for DECIMAL is not a valid number so returning null.", value);
return null;
}
};
public static final ValueExtractor UUID_VAL = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getUUID(val);
};
public static final ValueExtractor BASE64_BINARY = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return Base64.getEncoder().encodeToString(val.getBytes());
};
public static final ValueExtractor OBJECT = (Object value) -> {
return value;
};
// Special case of a SYSTEM V2. Identifiers allow unknown codes.
// When an unknown code is detected, return a null so that the text is displayed instead.
// Only a known code returns a coding.
public static final ValueExtractor CODING_SYSTEM_V2_IDENTIFIER = (Object value) -> {
value = checkForAndUnwrapVariesObject(value);
String table = Hl7DataHandlerUtil.getTableNumber(value);
String code = Hl7DataHandlerUtil.getStringValue(value);
if (table != null && code != null) {
// Found table and a code. Try looking it up.
SimpleCode coding = TerminologyLookup.lookup(table, code);
// A non-null, non-empty value in display means a good code from lookup.
if (coding != null && coding.getDisplay() != null && !coding.getDisplay().isEmpty()) {
return coding;
}
}
// All other situations return null.
return null;
};
// Special case of a SYSTEM V2. User-defined tables IS allow unknown codes.
// When an unknown code is detected, return a coding with the code but no system,
// so the code is retained. Only a known code returns a system.
// Compare function CODING_SYSTEM_V2_IDENTIFIER for slightly different behavior
public static final ValueExtractor CODING_SYSTEM_V2_IS_USER_DEFINED_TABLE = (Object value) -> {
value = checkForAndUnwrapVariesObject(value);
String table = Hl7DataHandlerUtil.getTableNumber(value);
String code = Hl7DataHandlerUtil.getStringValue(value);
if (table != null && code != null) {
// Found table and a code. Try looking it up.
SimpleCode coding = TerminologyLookup.lookup(table, code);
// A non-null, non-empty value in display means a good code from lookup.
if (coding != null && coding.getDisplay() != null && !coding.getDisplay().isEmpty()) {
return coding;
} else {
// Otherwise, must be a user-defined code, so return the code without a system
return new SimpleCode(code, null, null, null);
}
} else if (table == null && code != null) {
// Handle a code with unknown table
return new SimpleCode(code, null, null, null);
}
// All other situations return null.
return null;
};
public static final ValueExtractor CODING_SYSTEM_V2_ALTERNATE = (Object value) -> {
value = checkForAndUnwrapVariesObject(value);
// ensure we have a CWE
if (value instanceof CWE) {
CWE cwe = (CWE) value;
String table = Hl7DataHandlerUtil.getStringValue(cwe.getCwe6_NameOfAlternateCodingSystem());
String code = Hl7DataHandlerUtil.getStringValue(cwe.getCwe4_AlternateIdentifier());
String text = Hl7DataHandlerUtil.getStringValue(cwe.getCwe5_AlternateText());
String version = Hl7DataHandlerUtil.getStringValue(cwe.getCwe8_AlternateCodingSystemVersionID());
return commonCodingSystemV2(table, code, text, version);
}
return null;
};
public static final ValueExtractor CODING_SYSTEM_V2 = (Object value) -> {
value = checkForAndUnwrapVariesObject(value);
String table = Hl7DataHandlerUtil.getTableNumber(value);
String code = Hl7DataHandlerUtil.getStringValue(value);
String text = Hl7DataHandlerUtil.getOriginalDisplayText(value);
String version = Hl7DataHandlerUtil.getVersion(value);
return commonCodingSystemV2(table, code, text, version);
};
public static final ValueExtractor UNIT_SYSTEM = (Object value) -> {
value = checkForAndUnwrapVariesObject(value);
String table = Hl7DataHandlerUtil.getTableNumber(value);
String code = Hl7DataHandlerUtil.getStringValue(value);
String text = Hl7DataHandlerUtil.getOriginalDisplayText(value);
String version = Hl7DataHandlerUtil.getVersion(value);
SimpleCode codingSystem = commonCodingSystemV2(table, code, text, version);
if (codingSystem.getSystem() != null) {
return codingSystem.getSystem();
}
return "http://unitsofmeasure.org";
};
// For OBX.5 and other dynamic encoded fields, the real class is wrapped in the Varies class, and must be extracted from data
private static final Object checkForAndUnwrapVariesObject(Object value) {
if (value instanceof Varies) {
Varies v = (Varies) value;
value = v.getData();
}
return value;
}
private static final SimpleCode commonCodingSystemV2(String table, String code, String text, String version) {
if (table != null && code != null) {
// Found table and a code. Try looking it up.
SimpleCode coding = TerminologyLookup.lookup(table, code);
if (coding != null) {
String display = coding.getDisplay();
// Successful display confirms a valid code and system
if (display != null) {
if (display.isEmpty()) {
// We have a table, code, but unknown display, so we can't tell if it's good, use the original display text
coding = new SimpleCode(coding.getCode(), coding.getSystem(), text, version);
}
coding.setVersion(version);
// We have a table, code, and display, so code was valid
return coding;
} else {
// Display was not found; create an error message in the display text
return new SimpleCode(null, coding.getSystem(),
String.format(INVALID_CODE_MESSAGE_FULL, code, coding.getSystem(), text, version));
}
} else {
// No success looking up the code, build our own fall-back system using table name
return new SimpleCode(code, "urn:id:" + table, text, version);
}
} else if (code != null) {
// A code but no system: build a simple systemless code
return new SimpleCode(code, null, text);
} else {
return null;
}
}
public static final ValueExtractor BUILD_IDENTIFIER_FROM_CWE = (Object value) -> {
if (value instanceof Varies) {
Varies variesValue = ((Varies) value);
if (variesValue.getData() instanceof CWE) {
value = (CWE) variesValue.getData();
}
}
if (value instanceof CWE) {
CWE newValue = ((CWE) value);
String identifier = newValue.getCwe1_Identifier().toString();
String text = newValue.getCwe2_Text().toString();
String codingSystem = newValue.getCwe3_NameOfCodingSystem().toString();
if (identifier != null) {
if (codingSystem != null) {
String join = identifier + "-" + codingSystem;
return join;
} else {
return identifier;
}
} else
return text;
}
return null;
};
public static final ValueExtractor ALLERGY_INTOLERANCE_CRITICALITY_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, AllergyIntoleranceCriticality.class);
if (code != null) {
return code;
} else {
return null;
}
};
public static final ValueExtractor ALLERGY_INTOLERANCE_CATEGORY_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, AllergyIntoleranceCategory.class);
};
public static final ValueExtractor DOSE_VALUE = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val.startsWith("999")) {
// 999 is used when the vaccination is refused. In this case we should return null.
return null;
} else
return val;
};
public static final ValueExtractor DOSE_SYSTEM = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String url = UrlLookup.getAssociatedUrl(val);
if (url != null) {
return url;
} else {
if (val != null && val.length() > 0) {
return "urn:id:" + val.replace(" ", "_");
}
}
return null;
};
public static final ValueExtractor SYSTEM_URL = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return UrlLookup.getAssociatedUrl(val);
};
// Convert an authority string to a valid system value
// Prepend "urn:id:"; convert any spaces to underscores
public static final ValueExtractor SYSTEM_ID = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null && val.length() > 0) {
return "urn:id:" + val.replace(" ", "_");
} else {
return null;
}
};
public static final ValueExtractor> ARRAY = (Object value) -> {
if (value != null) {
List list = new ArrayList<>();
list.add(value);
return list;
}
return null;
};
public static final ValueExtractor RELATIVE_REFERENCE = (Object value) -> {
Map mapValue = null;
if (value instanceof Map) {
mapValue = (Map) value;
} else if (value instanceof ResourceValue) {
ResourceValue rv = (ResourceValue) value;
mapValue = rv.getResource();
}
if (mapValue != null) {
String type = Hl7DataHandlerUtil.getStringValue(mapValue.get("resourceType"));
String refId = Hl7DataHandlerUtil.getStringValue(mapValue.get("id"));
if (StringUtils.isNotBlank(type) && StringUtils.isNotBlank(refId)) {
return type + "/" + refId;
}
}
return null;
};
public static final ValueExtractor DIAGNOSTIC_REPORT_STATUS_CODES = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, DiagnosticReportStatus.class);
if (code != null) {
return code;
} else {
return DiagnosticReportStatus.UNKNOWN.toCode();
}
};
public static final ValueExtractor NAMED_UUID = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (StringUtils.isNotBlank(val)) {
return UUID.nameUUIDFromBytes(val.getBytes());
}
return null;
};
public static final ValueExtractor MESSAGE_REASON_ENCOUNTER = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, MessageReasonEncounter.class);
if (code != null) {
MessageReasonEncounter en = MessageReasonEncounter.fromCode(code);
return new SimpleCode(code, en.getSystem(), en.getDisplay());
} else {
// If code is null, it means the code wasn't known in our table, and can't be looked up.
// Make a message in the display.
String theSystem = MessageReasonEncounter.ADMIT.getSystem();
return new SimpleCode(null, theSystem, String.format(INVALID_CODE_MESSAGE_SHORT, val, theSystem));
}
};
public static final ValueExtractor PATIENT_INSTRUCTION = (Object value) -> {
if (value instanceof CWE) {
CWE cwe = (CWE) value;
String cwe1 = cwe.getCwe1_Identifier().toString();
String cwe2 = cwe.getCwe2_Text().toString();
if (cwe1 != null) {
if (cwe2 != null) {
return cwe1 + ":" + cwe2;
}
} else if (cwe1 == null) {
return cwe2;
}
}
return null;
};
private SimpleDataValueResolver() {
}
private static UUID getUUID(String value) {
if (value != null) {
try {
return UUID.fromString(value);
} catch (IllegalArgumentException e) {
LOGGER.warn("Value not valid UUID");
return null;
}
} else {
LOGGER.info("Value for UUID is null");
return null;
}
}
private static boolean isValidUUID(String val) {
try {
UUID.fromString(val);
return true;
} catch (IllegalArgumentException e) {
LOGGER.warn("Could not extract valid UUID - not a valid UUID");
return false;
}
}
public static String getFHIRCode(String hl7Value, Class fhirConceptClassName) {
return getFHIRCode(hl7Value, fhirConceptClassName.getSimpleName());
}
public static String getFHIRCode(String hl7Value, String fhirMappingConceptName) {
if (hl7Value != null) {
Map mapping = Hl7v2Mapping.getMapping(fhirMappingConceptName);
if (mapping != null && !mapping.isEmpty()) {
return mapping.get(StringUtils.upperCase(hl7Value, Locale.ENGLISH));
} else {
return null;
}
} else {
return null;
}
}
}
