Xml encoded fhir resource created with decimal element that has leading plus sign value couldn't be retrieved or modified (#5670)
* XML encoded FHIR resource created with decimal element that has leading plus sign value couldn't be retrieved or modified - implementation
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volodymyr-korzh
GitHub
parent
8c16f57c05
commit
8e69170c89
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@ -1413,14 +1413,18 @@ class ParserState<T> {
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myErrorHandler.invalidValue(location, value, "Attribute value must not be empty (\"\")");
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} else {
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if ("decimal".equals(myTypeName)) {
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if (value != null) {
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// remove leading plus sign from decimal value
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if (value.startsWith("+")) {
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value = value.substring(1);
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}
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/*
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* It may be possible to clean this up somewhat once the following PR is hopefully merged:
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* https://github.com/FasterXML/jackson-core/pull/611
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*
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* See TolerantJsonParser
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*/
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if ("decimal".equals(myTypeName)) {
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if (value != null)
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if (value.startsWith(".") && NumberUtils.isDigits(value.substring(1))) {
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value = "0" + value;
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} else {
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@ -1429,6 +1433,7 @@ class ParserState<T> {
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}
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}
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}
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}
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try {
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myInstance.setValueAsString(value);
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@ -30,6 +30,7 @@ import com.fasterxml.jackson.core.JsonGenerator;
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import com.fasterxml.jackson.core.JsonParser;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.core.StreamReadConstraints;
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import com.fasterxml.jackson.core.json.JsonReadFeature;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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@ -406,7 +407,9 @@ public class JacksonStructure implements JsonLikeStructure {
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}
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private static ObjectMapper createObjectMapper() {
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ObjectMapper retVal = JsonMapper.builder().build();
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ObjectMapper retVal = JsonMapper.builder()
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.enable(JsonReadFeature.ALLOW_LEADING_PLUS_SIGN_FOR_NUMBERS)
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.build();
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retVal = retVal.setNodeFactory(new JsonNodeFactory(true));
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retVal = retVal.enable(DeserializationFeature.USE_BIG_DECIMAL_FOR_FLOATS);
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retVal = retVal.enable(DeserializationFeature.FAIL_ON_TRAILING_TOKENS);
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@ -0,0 +1,6 @@
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---
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type: fix
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issue: 5667
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title: "Previously, creating an XML encoded FHIR resource with a decimal element that has a leading plus sign value
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would result in `JsonParseException` during the read operation from the database. Thus, making it impossible to
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retrieve or modify such resources. This has been fixed."
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@ -13,6 +13,7 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
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import java.io.IOException;
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import java.net.URL;
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import ca.uhn.fhir.util.ClasspathUtil;
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import org.hl7.fhir.r4.model.Appointment;
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import org.hl7.fhir.r4.model.AuditEvent;
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import org.hl7.fhir.r4.model.Bundle;
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@ -185,6 +186,19 @@ public class XmlParserR4Test extends BaseTest {
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assertEquals("12345", getPatientIdValue(bundle, 1));
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}
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@Test
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public void testParseResource_withDecimalElementHasLeadingPlus_resourceParsedCorrectly() {
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// setup
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String text = ClasspathUtil.loadResource("observation-decimal-element-with-leading-plus.xml");
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// execute
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Observation observation = ourCtx.newXmlParser().parseResource(Observation.class, text);
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// verify
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assertEquals("-3.0", observation.getReferenceRange().get(0).getLow().getValueElement().getValueAsString());
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assertEquals("3.0", observation.getReferenceRange().get(0).getHigh().getValueElement().getValueAsString());
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}
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private String getPatientIdValue(Bundle input, int entry) {
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final DocumentReference documentReference = (DocumentReference)input.getEntry().get(entry).getResource();
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final Patient patient = (Patient) documentReference.getSubject().getResource();
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@ -11,6 +11,7 @@ import ca.uhn.fhir.parser.json.JsonLikeStructure;
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import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
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import ca.uhn.fhir.parser.view.ExtPatient;
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import ca.uhn.fhir.util.AttachmentUtil;
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import ca.uhn.fhir.util.ClasspathUtil;
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import ca.uhn.fhir.util.ParametersUtil;
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import ca.uhn.fhir.util.TestUtil;
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import org.apache.commons.io.IOUtils;
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@ -19,6 +20,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.ICompositeType;
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import org.hl7.fhir.r4.model.Extension;
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import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Reference;
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import org.junit.jupiter.api.AfterAll;
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@ -31,6 +33,7 @@ import java.io.StringReader;
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import java.io.Writer;
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import java.math.BigDecimal;
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import java.math.BigInteger;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Iterator;
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@ -84,6 +87,27 @@ public class JsonLikeParserTest {
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}
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/**
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* Test that json number values with a leading plus sign are parsed without exception.
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* Previously, it was possible to save resources with leading plus sign numbers, e.g., "value": +3.0.
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* To ensure that we could read such resources back, the ObjectMapper configuration was updated by enabling:
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* {@link com.fasterxml.jackson.core.json.JsonReadFeature#ALLOW_LEADING_PLUS_SIGN_FOR_NUMBERS}
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* Reproduces: https://github.com/hapifhir/hapi-fhir/issues/5667
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*/
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@Test
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public void testJsonLikeParser_resourceHasDecimalElementWithLeadingPlus_isParsedCorrectly() {
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// setup
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String text = ClasspathUtil.loadResource("observation-decimal-element-with-leading-plus.json");
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IJsonLikeParser jsonLikeParser = (IJsonLikeParser) ourCtx.newJsonParser();
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// execute
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IBaseResource resource = jsonLikeParser.parseResource(text);
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// validate
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Observation observation = (Observation) resource;
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assertEquals("3.0", observation.getReferenceRange().get(0).getHigh().getValueElement().getValueAsString());
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}
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/**
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* Test JSON-Like writer using custom stream writer
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*
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@ -0,0 +1,64 @@
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{
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"resourceType": "Observation",
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"id": "1355",
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"meta": {
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"versionId": "1",
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"lastUpdated": "2024-02-02T10:00:08.286-07:00",
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"source": "#rxekXV5y3UZKAwxF"
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},
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"identifier": [
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{
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"system": "http://TEST.nl/fhir/NamingSystem/laboratory_observations",
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"value": "H_2211280010-BEART"
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}
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],
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"status": "preliminary",
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"category": [
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{
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"coding": [
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{
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"system": "5-Step briefing | SNOMED International",
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"code": "49581000146104",
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"display": "Laboratory test finding (finding)"
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}
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]
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}
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],
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"code": {
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"coding": [
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{
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"system": "Home – LOINC",
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"code": "8889-8",
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"display": "Heart rate by Pulse oximeter"
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}
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]
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},
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"subject": {
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"reference": "Patient/1354",
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"display": "Jongetje. Jongensnaamnaam van"
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},
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"effectiveDateTime": "2022-11-28T16:09:00+01:00",
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"performer": [
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{
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"reference": "Practitioner/P8",
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"display": "TEST"
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}
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],
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"referenceRange": [
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{
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"low": {
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"value": -3.0,
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"unit": "mmol/l",
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"system": "Home",
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"code": "mmol/l"
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},
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"high": {
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"value": +3.0,
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"unit": "mmol/l",
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"system": "Home",
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"code": "mmol/l"
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},
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"text": "-3.0 mmol/l - +3.0 mmol/l"
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}
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]
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}
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@ -0,0 +1,26 @@
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<Observation xmlns="http://hl7.org/fhir">
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<id value="0d87f02c-da2c-4551-9ead-2956f0165a4f"></id>
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<code>
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<coding>
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<system value="http://loinc.org"></system>
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<code value="8867-4"></code>
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</coding>
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</code>
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<valueString value="observationValue"></valueString>
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<status value="final"></status>
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<referenceRange>
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<low>
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<value value="-3.0"/>
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<unit value="mmol/l"/>
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<system value="Home"/>
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<code value="mmol/l"/>
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</low>
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<high>
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<value value="+3.0"/>
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<unit value="mmol/l"/>
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<system value="Home"/>
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<code value="mmol/l"/>
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</high>
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<text value="-3.0 mmol/l - +3.0 mmol/l"/>
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</referenceRange>
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</Observation>
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