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FHIR converter is a Java based library that enables converting Hl7v2 messages to FHIR resources
/*
* (C) Copyright IBM Corp. 2020
*
* 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.List;
import java.util.Locale;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang3.BooleanUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
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.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.codesystems.ConditionCategory;
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.SystemUrlLookup;
import io.github.linuxforhealth.core.terminology.TerminologyLookup;
import io.github.linuxforhealth.hl7.data.date.DateUtil;
public class SimpleDataValueResolver {
private static final Logger LOGGER = LoggerFactory.getLogger(SimpleDataValueResolver.class);
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 DATE_TIME = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null) {
return DateUtil.formatToDateTime(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 INSTANT = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
if (val != null) {
return DateUtil.formatToZonedDateTime(val);
}
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, e);
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 AdministrativeGender.NULL.toCode();
} else {
return AdministrativeGender.UNKNOWN.toCode();
}
};
public static final ValueExtractor OBSERVATION_STATUS_CODE_FHIR =
(Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, ObservationStatus.class);
if (code != null) {
return code;
} else if (val == null) {
return ObservationStatus.NULL.toCode();
} else {
return ObservationStatus.UNKNOWN.toCode();
}
};
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 {
return null;
}
};
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 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 OBJECT = (Object value) -> {
return value;
};
public static final ValueExtractor CODING_SYSTEM_V2 = (Object value) -> {
String table = Hl7DataHandlerUtil.getTableNumber(value);
String val = Hl7DataHandlerUtil.getStringValue(value);
if (table != null && val != null) {
return TerminologyLookup.lookup(table, val);
} else if (val != null) {
return new SimpleCode(val, null, null);
} else {
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 AllergyIntoleranceCriticality.UNABLETOASSESS.toCode();
}
};
public static final ValueExtractor ALLERGY_INTOLERANCE_CATEGORY_CODE_FHIR =
(Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String code = getFHIRCode(val, AllergyIntoleranceCategory.class);
if (code != null) {
return code;
} else {
return null;
}
};
public static final ValueExtractor SYSTEM_URL = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
String systemUrl = SystemUrlLookup.getSystemUrl(val);
if (systemUrl != null) {
return systemUrl;
} else {
return val;
}
};
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 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, value: {}", value, e);
return null;
}
} else {
LOGGER.info("Value for UUID is null, value: {}", value);
return null;
}
}
private static boolean isValidUUID(String val) {
try {
UUID.fromString(val);
return true;
} catch (IllegalArgumentException e) {
LOGGER.warn("Not a valid UUID ", e);
return false;
}
}
private static String getFHIRCode(String hl7Value, Class fhirConceptClassName) {
if (hl7Value != null) {
Map mapping = Hl7v2Mapping.getMapping(fhirConceptClassName.getSimpleName());
if (mapping != null && !mapping.isEmpty()) {
return mapping.get(StringUtils.upperCase(hl7Value, Locale.ENGLISH));
}
}
return null;
}
}