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Enhance vital signs narrative generation (#6590)
* add support for formatting observation.component entries in vital signs narrative generation * update
This commit is contained in:
David Raeside
GitHub
parent
ee194f2a44
commit
37ab80e250
@ -0,0 +1,5 @@
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---
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type: add
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issue: 6587
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title: "Enhanced the IPS vital signs narrative template to include code and value information for
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all entries in the `Observation.component` property."
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@ -247,3 +247,18 @@
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<th:block th:if="${!iter.last}" th:text="', '"/>
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</th:block>
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</th:block>
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<!-- /* Component list */ -->
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<th:block th:if="${list}" th:fragment="renderComponent (list)">
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<th:block th:each="item,iter : ${list}" th:if="${!list.empty}">
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<th:block th:if="${item.getCode().getCodingFirstRep().hasDisplay()}" th:text="${item.getCode().getCodingFirstRep().getDisplay()}">Display</th:block>
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<th:block th:if="${!item.getCode().getCodingFirstRep().hasDisplay()}" th:text="${item.getCode().getCodingFirstRep().getCode()}">Code</th:block>
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<th:block th:if="${item.hasValueQuantity()}" th:text="${item.getValueQuantity().getValue().toPlainString()}">Value</th:block>
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<th:block th:if="${item.hasValueIntegerType()}" th:text="${item.getValueIntegerType().getValueAsString()}">Value</th:block>
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<th:block th:if="${item.hasValueStringType()}" th:text="${item.getValueStringType().getValueAsString()}">Value</th:block>
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<th:block th:if="${item.hasValueCodeableConcept()}">
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<th:block th:insert=":: codeableConcept (cc=${item.getValueCodeableConcept()}, attr='display')"/>
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</th:block>
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<th:block th:if="${!iter.last}" th:text="', '"/>
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</th:block>
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</th:block>
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@ -4,6 +4,7 @@ Code: Observation.code.text || Observation.code.coding[x].display (separated by
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Result: Observation.valueQuantity || Observation.valueDateTime || Observation.valueCodeableConcept.text || Observation.valueCodeableConcept.coding[x].display (separated by <br />) || Observation.valueString
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Unit: Observation.valueQuantity.unit
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Interpretation: Observation.interpretation[0].text || Observation.interpretation[0].coding[x].display (separated by <br />)
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Component(s): Observation.component[x].display || Observation.component[x].code + Observation.component[x].value (items separated by comma)
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Comments: Observation.note[x].text (separated by <br />)
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Date: Observation.effectiveDateTime || Observation.effectivePeriod.start
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*/-->
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@ -16,6 +17,7 @@ Date: Observation.effectiveDateTime || Observation.effectivePeriod.start
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<th>Result</th>
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<th>Unit</th>
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<th>Interpretation</th>
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<th>Component(s)</th>
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<th>Comments</th>
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<th>Date</th>
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</tr>
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@ -23,12 +25,13 @@ Date: Observation.effectiveDateTime || Observation.effectivePeriod.start
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<tbody>
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<th:block th:each="entry : ${resource.entry}" th:object="${entry.getResource()}">
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<th:block th:unless='*{getResourceType().name() == "Composition"}'>
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<th:block th:with="extension=${entry.getResource().getExtensionByUrl('http://hl7.org/fhir/StructureDefinition/narrativeLink').getValue().getValue()}">
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<tr th:id="${#strings.arraySplit(extension, '#')[1]}">
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<th:block th:with="extension=${entry.getResource().getExtensionByUrl('http://hl7.org/fhir/StructureDefinition/narrativeLink')}">
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<tr th:id="${extension != null} ? ${#strings.arraySplit(extension.getValue().getValue(), '#')[1]} : ''">
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<td th:insert="~{IpsUtilityFragments :: codeableConcept (cc=*{getCode()},attr='display')}">Code</td>
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<td th:insert="~{IpsUtilityFragments :: renderValue (value=*{getValue()})}">Result</td>
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<td th:insert="~{IpsUtilityFragments :: renderValueUnit (value=*{getValue()})}">Unit</td>
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<td th:replace="~{IpsUtilityFragments :: firstFromCodeableConceptList (list=*{getInterpretation()})}">Interpretation</td>
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<td th:insert="~{IpsUtilityFragments :: firstFromCodeableConceptList (list=*{getInterpretation()})}">Interpretation</td>
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<td th:insert="~{IpsUtilityFragments :: renderComponent (list=*{getComponent()})}">Component(s)</td>
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<td th:insert="~{IpsUtilityFragments :: concat (list=*{getNote()},attr='text')}">Comments</td>
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<td th:insert="~{IpsUtilityFragments :: renderEffective (effective=*{getEffective()})}">Date</td>
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</tr>
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@ -25,6 +25,8 @@ import org.hl7.fhir.r4.model.AllergyIntolerance;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.CarePlan;
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import org.hl7.fhir.r4.model.ClinicalImpression;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.Composition;
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import org.hl7.fhir.r4.model.Condition;
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import org.hl7.fhir.r4.model.Consent;
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@ -45,6 +47,7 @@ import org.hl7.fhir.r4.model.Organization;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.PositiveIntType;
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import org.hl7.fhir.r4.model.Procedure;
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import org.hl7.fhir.r4.model.Quantity;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.Resource;
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import org.hl7.fhir.r4.model.StringType;
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@ -667,6 +670,59 @@ public class IpsGeneratorSvcImplTest {
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assertSame(strategy2, svc.selectGenerationStrategy("http://2"));
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}
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@Test
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public void testVitalSigns_withComponents() throws IOException {
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// Setup Patient
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initializeGenerationStrategy();
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registerPatientDaoWithRead();
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Observation observation1 = new Observation();
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observation1.setId("Observation/1");
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observation1.setStatus(Observation.ObservationStatus.FINAL);
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observation1.setCode(
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new CodeableConcept().addCoding(
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new Coding("http://loinc.org", "85354-9", "Blood pressure panel with all children optional")
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)
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);
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observation1.addComponent(
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new Observation.ObservationComponentComponent(
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new CodeableConcept(
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new Coding("http://loinc.org", "8480-6", "Systolic blood pressure")
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)
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).setValue(new Quantity().setValue(125).setUnit("mmHg").setSystem("http://unitsofmeasure.org").setCode("mm[Hg]"))
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);
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observation1.addComponent(
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new Observation.ObservationComponentComponent(
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new CodeableConcept(
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new Coding("http://loinc.org", "8462-4", "Diastolic blood pressure")
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)
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).setValue(new Quantity().setValue(75).setUnit("mmHg").setSystem("http://unitsofmeasure.org").setCode("mm[Hg]"))
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);
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ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(observation1, BundleEntrySearchModeEnum.MATCH);
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IFhirResourceDao<Observation> observationDao = registerResourceDaoWithNoData(Observation.class);
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when(observationDao.search(any(), any())).thenReturn(new SimpleBundleProvider(Lists.newArrayList(observation1)));
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registerRemainingResourceDaos();
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// Test
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID), null);
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// Verify
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Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
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Composition.SectionComponent section = findSection(compositions, DefaultJpaIpsGenerationStrategy.SECTION_CODE_VITAL_SIGNS);
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HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
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ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
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DomNodeList<DomElement> tables = narrativeHtml.getElementsByTagName("table");
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assertThat(tables).hasSize(1);
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HtmlTable table = (HtmlTable) tables.get(0);
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assertEquals("Code", table.getHeader().getRows().get(0).getCell(0).asNormalizedText());
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assertEquals("Blood pressure panel with all children optional", table.getBodies().get(0).getRows().get(0).getCell(0).asNormalizedText());
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assertEquals("Component(s)", table.getHeader().getRows().get(0).getCell(4).asNormalizedText());
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assertEquals("Systolic blood pressure 125 , Diastolic blood pressure 75", table.getBodies().get(0).getRows().get(0).getCell(4).asNormalizedText());
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}
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@Nonnull
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private Composition.SectionComponent findSection(Composition compositions, String theSectionCode) {
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return compositions
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