Add first take on IPS builder
This commit is contained in:
Grahame Grieve
parent
f2f10bf27b
commit
2f105d85ab
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@ -0,0 +1,430 @@
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package org.hl7.fhir.r4.ips;
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import java.util.Date;
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import java.util.List;
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import org.hl7.fhir.r4.ips.IPSBuilder.TypeAndId;
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import org.hl7.fhir.r4.model.Age;
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import org.hl7.fhir.r4.model.Annotation;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.r4.model.Bundle.BundleType;
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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.Patient;
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import org.hl7.fhir.r4.model.Period;
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import org.hl7.fhir.r4.model.Quantity;
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import org.hl7.fhir.r4.model.Range;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.Type;
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import org.hl7.fhir.r4.model.Composition.CompositionStatus;
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import org.hl7.fhir.r4.model.Composition.SectionComponent;
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import org.hl7.fhir.r4.model.Condition;
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import org.hl7.fhir.r4.model.Device;
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import org.hl7.fhir.r4.model.DomainResource;
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import org.hl7.fhir.r4.model.Dosage;
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import org.hl7.fhir.r4.model.Identifier;
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import org.hl7.fhir.r4.model.Medication;
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import org.hl7.fhir.r4.model.MedicationStatement;
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import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
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import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.VersionUtil;
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import org.hl7.fhir.utilities.xhtml.XhtmlNode;
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public class IPSBuilder {
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public static class TypeAndId {
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private String type;
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private String id;
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protected TypeAndId(String type, String id) {
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super();
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this.type = type;
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this.id = id;
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}
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public String getType() {
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return type;
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}
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public String getId() {
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return id;
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}
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}
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public static Bundle generateIPS(FHIRToolingClient server, String patientId) {
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Patient pat = server.fetchResource(Patient.class, patientId);
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Bundle bnd = initBundle();
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Composition cmp = initComposition(bnd, server.getAddress(), pat);
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pat = processPatient(bnd, server.getAddress(), pat);
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// addMedications(bnd, cmp, server, patientId);
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addConditions(bnd, cmp, server, patientId);
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return bnd;
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}
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private static Bundle initBundle() {
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Bundle bnd = new Bundle();
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bnd.getIdentifier().setSystem("urn:ietf:rfc:3986");
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bnd.getIdentifier().setValue(Utilities.makeUuidUrn());
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bnd.setType(BundleType.DOCUMENT);
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bnd.setTimestamp(new Date());
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return bnd;
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}
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private static Composition initComposition(Bundle bnd, String url, Patient pat) {
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Composition cmp = new Composition();
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cmp.setIdBase(Utilities.makeUuidLC());
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cmp.setStatus(CompositionStatus.FINAL);
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cmp.getType().addCoding().setSystem("http://loinc.org").setCode("60591-5");
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cmp.setDate(new Date());
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cmp.setTitle("International Patient Summary");
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cmp.getSubject().setReference("Patient/"+pat.getIdBase());
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cmp.addAuthor().setReference("Device/java");
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bnd.addEntry().setResource(cmp).setFullUrl(Utilities.pathURL(url, "Composition", cmp.getIdBase()));
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Device dev = new Device();
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dev.setId("java");
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dev.addDeviceName().setName("Java Core Library");
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dev.addVersion().setValue(VersionUtil.getVersion());
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return cmp;
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}
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private static Patient processPatient(Bundle bnd, String url, Patient pat) {
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bnd.addEntry().setResource(pat).setFullUrl(Utilities.pathURL(url, "Patient", pat.getIdBase()));
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return pat;
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}
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private static void addMedications(Bundle bnd, Composition cmp, FHIRToolingClient server, String patientId) {
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Bundle sb = server.search("MedicationStatement", "?patient="+patientId+"&_include=MedicationStatement:medication&_include=MedicationStatement:source");
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SectionComponent sct = cmp.addSection();
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sct.setTitle("Medications");
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sct.getCode().addCoding().setSystem("http://loinc.org").setCode("10160-0");
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sct.getText().setStatus(NarrativeStatus.GENERATED);
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var x = sct.getText().getDiv();
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var tbl = x.table("grid");
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var tr = tbl.tr();
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tr.th().tx("Medication");
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tr.th().tx("Category");
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tr.th().tx("Status");
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tr.th().tx("When");
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tr.th().tx("Dosage");
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tr.th().tx("Reason");
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tr.th().tx("Source");
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tr.th().tx("Notes");
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boolean ok = false;
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for (BundleEntryComponent be : sb.getEntry()) {
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if (be.hasResource() && be.getResource() instanceof MedicationStatement) {
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MedicationStatement mdstmt = (MedicationStatement) be.getResource();
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ok = true;
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bnd.addEntry().setResource(mdstmt).setFullUrl(Utilities.pathURL(server.getAddress(), "MedicationStatement", mdstmt.getIdBase()));
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sct.addEntry().setReference("MedicationStatement/"+mdstmt.getIdBase());
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tr = tbl.tr();
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if (mdstmt.hasMedicationReference()) {
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Medication med = findMedication(sb, server, mdstmt, mdstmt.getMedicationReference());
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if (med == null) {
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tr.td().b().tx("Unknown?");
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} else {
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tr.td().tx(summarise(med));
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bnd.addEntry().setResource(med).setFullUrl(Utilities.pathURL(server.getAddress(), "Medication", med.getIdBase()));
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}
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} else {
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tr.td().tx(genCC(mdstmt.getMedicationCodeableConcept()));
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}
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tr.td().tx(genCC(mdstmt.getCategory()));
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var td = tr.td();
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td.tx(mdstmt.getStatus().getDisplay());
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if (mdstmt.hasStatusReason()) {
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td.tx(" (");
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td.tx(genCC(mdstmt.getStatusReason()));
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td.tx(")");
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}
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tr.td().tx(genDT(mdstmt.getEffective()));
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genDosages(tr.td(), mdstmt.getDosage());
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tr.td().tx(genReference(mdstmt, mdstmt.getInformationSource(), bnd, sb, server));
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genNotes(tr.td(), mdstmt.getNote());
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}
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}
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if (!ok) {
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Condition cnd = new Condition();
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cnd.setId(Utilities.makeUuidLC());
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cnd.getText().setStatus(NarrativeStatus.GENERATED);
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var rx = cnd.getText().getDiv();
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rx.tx("No information is provided about the patient's medical problems");
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tr = tbl.tr();
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tr.td().colspan(7).tx("No information is provided about the patient's medical problems");
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cnd.getClinicalStatus().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical").setCode("active").setDisplay("Active");
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cnd.getCode().addCoding().setSystem("http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips").setCode("no-problem-info").setDisplay("No information about current problems");
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cnd.getSubject().setReference("Patient/"+patientId);
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}
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}
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private static void genDosages(XhtmlNode x, List<Dosage> dosages) {
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if (dosages == null || dosages.size() == 0) {
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} else if (dosages.size() == 1) {
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genDosage(x, dosages.get(0));
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} else {
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var ul = x.ul();
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for (Dosage d : dosages) {
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genDosage(ul.li(), d);
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}
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}
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}
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private static void genDosage(XhtmlNode x, Dosage dosage) {
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x.tx(dosage.getText());
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if (dosage.hasAsNeeded()) {
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x.nbsp();
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if (dosage.hasAsNeededBooleanType()) {
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if (dosage.getAsNeededBooleanType().booleanValue()) {
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x.tx(" (as needed)");
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}
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} else {
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x.tx(genDT(dosage.getAsNeeded()));
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}
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} else if (dosage.hasTiming()) {
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x.nbsp();
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x.tx(genDT(dosage.getTiming()));
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}
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if (dosage.hasSite()) {
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x.tx(". ");
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x.tx(genDT(dosage.getSite()));
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}
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if (dosage.hasRoute()) {
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x.tx(". ");
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x.tx(genDT(dosage.getRoute()));
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}
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}
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private static Medication findMedication(Bundle sb, FHIRToolingClient server, MedicationStatement mdstmt, Reference ref) {
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if (ref == null || !ref.hasReference()) {
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return null;
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}
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if (ref.getReference().startsWith("#")) {
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} else {
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}
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return null;
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}
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private static void addConditions(Bundle bnd, Composition cmp, FHIRToolingClient server, String patientId) {
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Bundle sb = server.search("Condition", "?patient="+patientId); //+"&_include=MedicationStatement:asserter");
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SectionComponent sct = cmp.addSection();
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sct.setTitle("Problems");
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sct.getCode().addCoding().setSystem("http://loinc.org").setCode("11450-4");
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sct.getText().setStatus(NarrativeStatus.GENERATED);
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var x = sct.getText().getDiv();
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var tbl = x.table("grid");
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var tr = tbl.tr();
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tr.th().tx("Code");
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tr.th().tx("Category");
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tr.th().tx("Severity");
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tr.th().tx("Status");
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tr.th().tx("Onset");
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tr.th().tx("Abatement");
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tr.th().tx("Source");
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tr.th().tx("Notes");
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boolean ok = false;
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for (BundleEntryComponent be : sb.getEntry()) {
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if (be.hasResource() && be.getResource() instanceof Condition) {
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Condition cnd = (Condition) be.getResource();
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ok = true;
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bnd.addEntry().setResource(cnd).setFullUrl(Utilities.pathURL(server.getAddress(), "Condition", cnd.getIdBase()));
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sct.addEntry().setReference("Condition/"+cnd.getIdBase());
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tr = tbl.tr();
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tr.td().tx(genCC(cnd.getCode()));
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tr.td().tx(genCC(cnd.getCategory()));
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tr.td().tx(genCC(cnd.getSeverity()));
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tr.td().tx(genStatus(cnd));
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tr.td().tx(genDT(cnd.getOnset()));
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tr.td().tx(genDT(cnd.getAbatement()));
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tr.td().tx(genSource(cnd, bnd, sb, server));
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genNotes(tr.td(), cnd.getNote());
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}
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}
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if (!ok) {
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Condition cnd = new Condition();
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cnd.setId(Utilities.makeUuidLC());
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cnd.getText().setStatus(NarrativeStatus.GENERATED);
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var rx = cnd.getText().getDiv();
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rx.tx("No information is provided about the patient's medical problems");
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tr = tbl.tr();
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tr.td().colspan(7).tx("No information is provided about the patient's medical problems");
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cnd.getClinicalStatus().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical").setCode("active").setDisplay("Active");
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cnd.getCode().addCoding().setSystem("http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips").setCode("no-problem-info").setDisplay("No information about current problems");
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cnd.getSubject().setReference("Patient/"+patientId);
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}
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}
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private static String genReference(DomainResource src, Reference ref, Bundle bnd, Bundle search, FHIRToolingClient server) {
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if (ref == null || ref.isEmpty()) {
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return null;
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}
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boolean contained = false;
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DomainResource tgt = null;
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if (ref.hasReference()) {
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if (ref.getReference().startsWith("#")) {
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tgt = (DomainResource) src.getContained(ref.getReference());
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contained = true;
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} else {
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TypeAndId tid = getTypeAndId(server.getAddress(), ref.getReference());
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if (tid != null) {
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tgt = findInBundle(bnd, Utilities.pathURL(server.getAddress(), tid.getType(), tid.getId()));
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if (tgt == null) {
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tgt = findInBundle(search, Utilities.pathURL(server.getAddress(), tid.getType(), tid.getId()));
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if (tgt == null) {
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tgt = (DomainResource) server.read(tid.getType(), tid.getId());
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}
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} else {
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contained = true;
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}
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}
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}
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}
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if (tgt != null) {
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if (!contained) {
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bnd.addEntry().setResource(tgt).setFullUrl(Utilities.pathURL(server.getAddress(), tgt.fhirType(), tgt.getIdBase()));
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}
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return summarise(tgt);
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} else if (ref.hasDisplay()) {
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return ref.getDisplay();
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} else if (ref.hasReference()) {
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return ref.getReference();
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} else if (ref.hasIdentifier()) {
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return genIdentifier(ref.getIdentifier());
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} else {
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return "unknown";
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}
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}
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private static TypeAndId getTypeAndId(String baseUrl, String url) {
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if (Utilities.noString(url)) {
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return null;
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}
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if (url.startsWith(baseUrl+"/")) {
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url = url.substring(baseUrl.length()+1);
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}
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String[] p = url.split("\\/");
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if (p.length > 1) {
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if ("_history".equals(p[p.length-2]) && p.length > 3) {
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return new TypeAndId(p[p.length-4], p[p.length-3]);
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} else {
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return new TypeAndId(p[p.length-2], p[p.length-1]);
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}
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}
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return null;
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}
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private static DomainResource findInBundle(Bundle bnd, String url) {
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for (BundleEntryComponent be : bnd.getEntry()) {
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if (url.equals(be.getFullUrl()) && be.hasResource() && be.getResource() instanceof DomainResource) {
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return (DomainResource) be.getResource();
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}
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}
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return null;
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}
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private static String summarise(DomainResource tgt) {
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// TODO Auto-generated method stub
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return null;
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}
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private static String genIdentifier(Identifier id) {
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return id.getValue();
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}
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private static void genNotes(XhtmlNode td, List<Annotation> notes) {
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if (notes.size() > 0) {
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if (notes.size() == 1) {
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genNote(td, notes.get(0));
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} else {
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var ul = td.ul();
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for (Annotation a : notes) {
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genNote(ul.li(), a);
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}
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}
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}
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}
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private static void genNote(XhtmlNode td, Annotation annotation) {
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td.tx(annotation.getText());
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}
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private static String genSource(Condition cnd, Bundle bnd, Bundle sb, FHIRToolingClient server) {
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if (cnd.hasAsserter()) {
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return genReference(cnd, cnd.getAsserter(), bnd, sb, server);
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} else if (cnd.hasRecorder()) {
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return genReference(cnd, cnd.getRecorder(), bnd, sb, server);
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} else {
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return null;
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}
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}
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private static String genDT(Type v) {
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if (v == null) {
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return null;
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}
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if (v.isPrimitive()) {
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return v.primitiveValue();
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}
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if (v instanceof Age) {
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return genQty((Age) v);
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}
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if (v instanceof Period) {
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Period p = (Period) v;
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return genDT(p.getStartElement())+" - "+genDT(p.getStartElement());
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}
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if (v instanceof Range) {
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Range p = (Range) v;
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return genDT(p.getLow())+" - "+genDT(p.getHigh());
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}
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return "not done: "+v.fhirType();
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}
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private static String genQty(Quantity v) {
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return v.getValue().toPlainString()+v.getUnit();
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}
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private static String genStatus(Condition cnd) {
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if (cnd.hasClinicalStatus() && cnd.hasVerificationStatus()) {
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return genCC(cnd.getClinicalStatus()) +"/"+genCC(cnd.getVerificationStatus());
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} else if (cnd.hasClinicalStatus()) {
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return genCC(cnd.getClinicalStatus());
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} else if (cnd.hasVerificationStatus()) {
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return genCC(cnd.getVerificationStatus());
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} else {
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return null;
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}
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}
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private static String genCC(List<CodeableConcept> list) {
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if (list != null && list.size() == 1) {
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return genCC(list.get(0));
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} else {
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return null;
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}
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}
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private static String genCC(CodeableConcept code) {
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if (code.hasText()) {
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return code.getText();
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} else if (code.hasCoding()) {
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Coding c = code.getCodingFirstRep();
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if (c.hasDisplay()) {
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return c.getDisplay();
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} else {
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return c.getCode();
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}
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} else {
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return null;
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}
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}
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}
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