2023 10 gg cda parsing fix 2 (#1451)
* fix xml output to deal with namespaces properly * Improve rendering or xml_no_order * add command line demo app * fix CDA parsing error for sdtc:raceCode * Fix error message * Bump test case version --------- Co-authored-by: Grahame Grieve <grahameg@gmail.ccom> Co-authored-by: dotasek <dotasek.dev@gmail.com>
This commit is contained in:
Grahame Grieve
GitHub
parent
ff29b09083
commit
752ab7a3d1
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@ -0,0 +1,335 @@
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package org.hl7.fhir.r4.utils;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.net.URISyntaxException;
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import java.util.List;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r4.context.SimpleWorkerContext;
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import org.hl7.fhir.r4.formats.IParser.OutputStyle;
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import org.hl7.fhir.r4.formats.JsonParser;
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import org.hl7.fhir.r4.model.Base;
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import org.hl7.fhir.r4.model.BooleanType;
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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.CapabilityStatement;
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import org.hl7.fhir.r4.model.CodeType;
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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.Condition;
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import org.hl7.fhir.r4.model.HumanName;
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import org.hl7.fhir.r4.model.Immunization;
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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.Procedure;
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import org.hl7.fhir.r4.model.Property;
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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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import org.hl7.fhir.r4.model.Type;
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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.npm.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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public class CmdLineApp {
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private FHIRToolingClient client;
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private String currentId;
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private Resource currentResource;
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private SimpleWorkerContext context;
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private FHIRPathEngine fpe;
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public static void main(String[] args) throws IOException, Exception {
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new CmdLineApp().execute();
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}
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private void execute() throws IOException {
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System.out.print("Loading...");
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NpmPackage npm = new FilesystemPackageCacheManager(true).loadPackage("hl7.fhir.r4.core");
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context = SimpleWorkerContext.fromPackage(npm);
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fpe = new FHIRPathEngine(context);
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System.out.println(" Done");
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BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
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genMenu();
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boolean finished = false;
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do {
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System.out.print("> ");
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String cmd = reader.readLine();
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String[] p = cmd.split("\\s+");
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try {
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if (p.length == 1 && p[0].equals("x")) {
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finished = true;
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} else if (p.length == 1 && p[0].equals("?")) {
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genMenu();
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} else if (p.length >= 1 && p[0].equals("c")) {
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if (p.length == 1) {
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connectToServer("http://hapi.fhir.org/baseR4");
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} else {
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connectToServer(p[1]);
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}
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} else if (p.length >= 1 && p[0].equals("imm")) {
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if (p.length == 1) {
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if (currentResource == null || !(currentResource instanceof Patient)) {
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throw new FHIRException("Current resource must be a patient for this command");
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}
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getImmunizations();
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} else {
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select("Immunization", p[1]);
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}
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} else if (p.length >= 1 && p[0].equals("cnd")) {
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if (p.length == 1) {
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if (currentResource == null || !(currentResource instanceof Patient)) {
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throw new FHIRException("Current resource must be a patient for this command");
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}
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getConditions();
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} else {
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select("Condition", p[1]);
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}
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} else if (p.length >= 1 && p[0].equals("prc")) {
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if (p.length == 1) {
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if (currentResource == null || !(currentResource instanceof Patient)) {
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throw new FHIRException("Current resource must be a patient for this command");
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}
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getProcedures();
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} else {
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select("Procedure", p[1]);
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}
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} else if (p.length >= 1 && p[0].equals("v")) {
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if (p.length == 1) {
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viewResource();
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} else {
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viewResource(p[1]);
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}
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} else if (p.length >= 2 && p[0].equals("s")) {
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search(p);
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} else if (p.length >= 2 && p[0].equals("p")) {
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select("Patient", p[1]);
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} else if (p.length == 3 && p[0].equals("e")) {
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edit(p[1], p[2]);
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} else {
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System.out.println("Command unknown or not understood: "+cmd);
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}
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} catch (Exception e) {
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System.out.println("Error executing command "+p[0]+": "+e.getMessage());
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}
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} while (!finished);
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System.out.println("Finished!");
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}
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private void getImmunizations() {
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Bundle bnd = client.search("Immunization", "?patient="+currentId);
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System.out.println(""+bnd.getTotal()+" Immunizations found. Printing "+bnd.getEntry().size());
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for (BundleEntryComponent be : bnd.getEntry()) {
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Resource imm = be.getResource();
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System.out.println(summary(imm));
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}
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}
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private void getProcedures() {
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Bundle bnd = client.search("Procedure", "?patient="+currentId);
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System.out.println(""+bnd.getTotal()+" Procedures found. Printing "+bnd.getEntry().size());
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for (BundleEntryComponent be : bnd.getEntry()) {
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Resource imm = be.getResource();
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System.out.println(summary(imm));
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}
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}
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private void getConditions() {
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Bundle bnd = client.search("Condition", "?patient="+currentId);
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System.out.println(""+bnd.getTotal()+" Conditions found. Printing "+bnd.getEntry().size());
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for (BundleEntryComponent be : bnd.getEntry()) {
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Resource imm = be.getResource();
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System.out.println(summary(imm));
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}
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}
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private void edit(String path, String value) {
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if (path.contains(".")) {
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List<Base> list = fpe.evaluate(currentResource, fpe.parse(path.substring(0, path.lastIndexOf("."))));
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if (list.size() == 1) {
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path = path.substring(path.lastIndexOf(".")+1);
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Property p = list.get(0).getNamedProperty(path);
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Base b = makeValue(p, value);
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list.get(0).setProperty(path, b);
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} else {
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throw new FHIRException("Unable to set value at "+path+": "+list.size()+" matches");
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}
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} else {
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Property p = currentResource.getNamedProperty(path);
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Base b = makeValue(p, value);
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currentResource.setProperty(path, b);
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}
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currentResource = client.update(currentResource);
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}
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private Base makeValue(Property p, String value) {
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switch (p.getTypeCode()) {
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case "boolean" : return new BooleanType(value);
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case "code" : return new CodeType(value);
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case "string" : return new StringType(value);
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}
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throw new FHIRException("Unhandled type "+p.getTypeCode());
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}
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private void viewResource(String path) {
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System.out.println("Current Resource, query = "+path);
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List<Base> list = fpe.evaluate(currentResource, fpe.parse(path));
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for (Base b : list) {
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System.out.println(b.toString());
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}
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}
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private void viewResource() throws IOException {
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System.out.println("Current Resource:");
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System.out.println(new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(currentResource));
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}
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private void select(String type, String id) {
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if (type.equals("Patient")) {
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currentResource = client.fetchResource(Patient.class, id);
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} else if (type.equals("Immunization")) {
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currentResource = client.fetchResource(Immunization.class, id);
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} else if (type.equals("Condition")) {
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currentResource = client.fetchResource(Condition.class, id);
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} else if (type.equals("Procedure")) {
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currentResource = client.fetchResource(Procedure.class, id);
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} else {
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throw new FHIRException("Unhandled type "+type);
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}
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currentId = type+"/"+id;
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System.out.println("Resource = "+currentId+" "+summary(currentResource));
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}
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private String summary(Resource r) {
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if (r instanceof Patient) {
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Patient pat = (Patient) r;
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return pat.getIdBase()+" "+pat.getGender()+" "+pat.getBirthDateElement().asStringValue()+" "+name(pat);
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}
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if (r instanceof Immunization) {
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Immunization imm = (Immunization) r;
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return imm.getIdBase()+" "+imm.getOccurrenceDateTimeType().asStringValue()+" "+code(imm.getVaccineCode())+" "+imm.getLotNumber()+" ("+imm.getStatus()+")";
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}
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if (r instanceof Condition) {
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Condition cnd = (Condition) r;
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return cnd.getIdBase()+" "+code(cnd.getClinicalStatus())+" "+code(cnd.getVerificationStatus())+" "+code(cnd.getCode())+" "+cnd.getRecordedDateElement().asStringValue();
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}
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if (r instanceof Procedure) {
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Procedure prc = (Procedure) r;
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return prc.getIdBase()+" "+prc.getStatusElement().asStringValue()+" "+code(prc.getCode())+" "+code(prc.getCode())+" "+dt(prc.getPerformed());
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}
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return "??";
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}
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private String dt(Type type) {
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if (type == null) {
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return "";
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}
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if (type.isPrimitive()) {
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return type.primitiveValue();
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}
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if (type instanceof Period) {
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Period pd = (Period) type;
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return pd.getStartElement().asStringValue()+" -> "+pd.getEndElement().asStringValue();
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}
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return "??";
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}
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private String code(CodeableConcept cc) {
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for (Coding c : cc.getCoding()) {
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if (c.hasSystem()) {
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String d = c.hasDisplay() ? " ("+c.getDisplay()+")" : "";
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if (c.hasCode()) {
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switch (c.getSystem()) {
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case "http://hl7.org/fhir/sid/cvx": return "CVX "+c.getCode()+d;
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case "http://snomed.info/sct": return "SCT "+c.getCode()+d;
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default:
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if (Utilities.startsWithInList(c.getSystem(), "http://terminology.hl7.org")) {
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return c.getCode();
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} else {
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throw new FHIRException("Unknown system "+c.getSystem());
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}
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}
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}
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}
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}
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for (Coding c : cc.getCoding()) {
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if (c.hasCode()) {
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return c.getCode();
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}
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}
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if (cc.hasText()) {
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return cc.getText();
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}
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return "";
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}
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private void search(String[] p) {
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if (client == null) {
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throw new FHIRException("Not connected to to a server");
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}
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String search = "?name="+p[1];
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if (p.length > 2) {
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search = search +"&gender="+p[2];
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if (p.length > 3) {
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search = search +"&dob="+p[3];
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}
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}
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Bundle bnd = client.search("Patient", search);
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System.out.println(""+bnd.getTotal()+" Patients found. Printing "+bnd.getEntry().size());
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for (BundleEntryComponent be : bnd.getEntry()) {
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Patient pat = (Patient) be.getResource();
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System.out.println(summary(pat));
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}
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}
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private String name(Patient pat) {
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if (pat.getName().size() > 0) {
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return name(pat.getName().get(0));
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}
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return null;
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}
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private String name(HumanName n) {
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if (n.hasText()) {
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return n.getText();
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}
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if (n.hasFamily()) {
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if (n.hasGiven()) {
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return n.getGiven().get(0)+" "+n.getFamily().toUpperCase();
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} else {
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return n.getFamily().toUpperCase();
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}
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}
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return "??";
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}
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private void connectToServer(String url) throws URISyntaxException {
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client = new FHIRToolingClient(url, "FHIR-Command-Line-App");
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CapabilityStatement cs = client.getCapabilitiesStatementQuick();
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System.out.println("Connected to "+url+": "+cs.getSoftware().getName()+".");
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}
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private void genMenu() {
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System.out.println("Simple Client. Commands you can run:");
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System.out.println(" c {url} - connect to a server");
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System.out.println(" s {name} [{gender}] {{dob]} - find a patient record");
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System.out.println(" p {id} - choose a patient record");
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System.out.println(" v [{field}] - see a set of field(s) in the current resource, or the whole resource");
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System.out.println(" e {field} {value} - edit a field in the current resource");
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System.out.println(" imm [{id}] - get a list of the patient's immunizations, or use the resource for the id (then use e to edit it)");
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System.out.println(" cnd [{id}] - get a list of the patient's conditions, or use the resource for the id (then use e to edit it)");
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System.out.println(" prc [{id}] - get a list of the patient's procedures, or use the resource for the id (then use e to edit it)");
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System.out.println(" ? - print this again");
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System.out.println(" x - exit");
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}
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}
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@ -595,4 +595,23 @@ public class FHIRToolingClient {
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public void setLanguage(String lang) {
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this.acceptLang = lang;
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}
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public Bundle search(String type, String criteria) {
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return fetchFeed(Utilities.pathURL(base, type+criteria));
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}
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public <T extends Resource> T fetchResource(Class<T> resourceClass, String id) {
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org.hl7.fhir.r4.utils.client.network.ResourceRequest<Resource> result = null;
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try {
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result = client.issueGetResourceRequest(resourceAddress.resolveGetResource(resourceClass, id),
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getPreferredResourceFormat(), generateHeaders(), resourceClass.getName()+"/"+id, TIMEOUT_NORMAL);
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} catch (IOException e) {
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throw new FHIRException(e);
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}
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if (result.isUnsuccessfulRequest()) {
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throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
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(OperationOutcome) result.getPayload());
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}
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return (T) result.getPayload();
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}
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}
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@ -91,6 +91,10 @@ public class ResourceAddress {
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return baseServiceUri.resolve(nameForClassWithSlash(resourceClass) + "/" + opName);
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}
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public <T extends Resource> URI resolveGetResource(Class<T> resourceClass, String id) {
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return baseServiceUri.resolve(nameForClassWithSlash(resourceClass) + "/" + id);
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}
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public <T extends Resource> URI resolveOperationUri(Class<T> resourceClass, String opName,
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Map<String, String> parameters) {
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return appendHttpParameters(baseServiceUri.resolve(nameForClassWithSlash(resourceClass) + "$" + opName),
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@ -61,6 +61,7 @@ import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r5.formats.FormatUtilities;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.model.DateTimeType;
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import org.hl7.fhir.r5.model.ElementDefinition;
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import org.hl7.fhir.r5.model.ElementDefinition.PropertyRepresentation;
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import org.hl7.fhir.r5.model.Enumeration;
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import org.hl7.fhir.r5.model.StructureDefinition;
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@ -421,7 +422,11 @@ public class XmlParser extends ParserBase {
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element.getChildren().add(n);
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} else {
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String npath = path+"/"+pathPrefix(child.getNamespaceURI())+child.getLocalName();
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Element n = new Element(child.getLocalName(), property).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML);
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String name = child.getLocalName();
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if (!property.isChoice() && !name.equals(property.getName())) {
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name = property.getName();
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}
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Element n = new Element(name, property).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML);
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if (property.isList()) {
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n.setPath(element.getPath()+"."+property.getName()+"["+repeatCount+"]");
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} else {
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@ -769,7 +774,11 @@ public class XmlParser extends ParserBase {
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}
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if (linkResolver != null)
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xml.link(linkResolver.resolveProperty(element.getProperty()));
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xml.enter(element.getProperty().getXmlNamespace(),elementName);
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if (!xml.namespaceDefined(element.getProperty().getXmlNamespace())) {
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String abbrev = makeNamespaceAbbrev(element.getProperty(), xml);
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xml.namespace(element.getProperty().getXmlNamespace(), abbrev);
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}
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xml.enter(element.getProperty().getXmlNamespace(), elementName);
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if (!root && element.getSpecial() != null) {
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if (linkResolver != null)
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xml.link(linkResolver.resolveProperty(element.getProperty()));
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@ -791,6 +800,37 @@ public class XmlParser extends ParserBase {
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}
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}
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private String makeNamespaceAbbrev(Property property, IXMLWriter xml) {
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// it's a cosmetic thing, but we're going to try to come up with a nice namespace
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ElementDefinition ed = property.getDefinition();
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String ns = property.getXmlNamespace();
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String n = property.getXmlName();
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String diff = property.getName().toLowerCase().replace(n.toLowerCase(), "");
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if (!Utilities.noString(diff) && diff.length() <= 5 && Utilities.isToken(diff) && !xml.abbreviationDefined(diff)) {
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||||
return diff;
|
||||
}
|
||||
|
||||
int i = ns.length()-1;
|
||||
while (i > 0) {
|
||||
if (Character.isAlphabetic(ns.charAt(i)) || Character.isDigit(ns.charAt(i))) {
|
||||
i--;
|
||||
} else {
|
||||
break;
|
||||
}
|
||||
}
|
||||
String tail = ns.substring(i+1);
|
||||
if (!Utilities.noString(tail) && tail.length() <= 5 && Utilities.isToken(tail) && !xml.abbreviationDefined(tail)) {
|
||||
return tail;
|
||||
}
|
||||
|
||||
i = 0;
|
||||
while (xml.abbreviationDefined("ns"+i)) {
|
||||
i++;
|
||||
}
|
||||
return "ns"+i;
|
||||
}
|
||||
private String checkHeader(List<ValidationMessage> errors, InputStream stream) throws IOException {
|
||||
try {
|
||||
// the stream will either start with the UTF-8 BOF or with <xml
|
||||
|
|
|
|||
|
|
@ -1482,6 +1482,11 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
|
|||
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Namespace")+": ", null).addStyle("font-weight:bold"));
|
||||
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAMESPACE), null));
|
||||
}
|
||||
if (root && ToolingExtensions.readBoolExtension(profile, ToolingExtensions.EXT_XML_NO_ORDER)) {
|
||||
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
|
||||
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Order")+": ", null).addStyle("font-weight:bold"));
|
||||
c.getPieces().add(gen.new Piece(null, "The properties of this type can appear in any order in the XML", null));
|
||||
}
|
||||
if (definition.hasExtension(ToolingExtensions.EXT_JSON_EMPTY)) {
|
||||
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
|
||||
String code = ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_JSON_EMPTY);
|
||||
|
|
@ -3755,7 +3760,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
|
|||
}
|
||||
boolean no = root && ToolingExtensions.readBoolExtension(profile, ToolingExtensions.EXT_XML_NO_ORDER);
|
||||
if (no) {
|
||||
ret.tx("The children of this property can appear in any order in the XML.");
|
||||
ret.tx("The children of this type can appear in any order in the XML.");
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -249,7 +249,7 @@ Validation_VAL_Profile_MultipleMatches_other = Found multiple matching profiles
|
|||
Validation_VAL_Profile_NoDefinition = No definition found for resource type ''{0}''
|
||||
Validation_VAL_Profile_NoMatch = Unable to find a match for the specified profile among choices: {0}
|
||||
Validation_VAL_Profile_NoSnapshot = StructureDefinition {0} has no snapshot - validation is against the snapshot, so it must be provided
|
||||
Validation_VAL_Profile_NoType = The type of element {0} is not known, which is invalid. Valid types at this point are {1}
|
||||
Validation_VAL_Profile_NoType = The type of element {0} is not known - it could not be determined from the information available. Valid types at this point are {1}
|
||||
Validation_VAL_Profile_NotAllowed = This element is not allowed by the profile {0}
|
||||
Validation_VAL_Profile_NotSlice = This element does not match any known slice {0} and slicing is CLOSED: {1}
|
||||
Validation_VAL_Profile_OutOfOrder = As specified by profile {0}, Element ''{1}'' is out of order (found after {2})
|
||||
|
|
|
|||
|
|
@ -6215,12 +6215,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
if (ed.getRepresentation().isEmpty()) { // ignore xml attributes
|
||||
int count = 0;
|
||||
List<ElementDefinition> slices = null;
|
||||
if (ed.hasSlicing())
|
||||
if (ed.hasSlicing()) {
|
||||
slices = profileUtilities.getSliceList(profile, ed);
|
||||
for (ElementInfo ei : children)
|
||||
if (ei.definition == ed)
|
||||
}
|
||||
for (ElementInfo ei : children) {
|
||||
if (ei.definition == ed) {
|
||||
count++;
|
||||
else if (slices != null) {
|
||||
} else if (slices != null) {
|
||||
for (ElementDefinition sed : slices) {
|
||||
if (ei.definition == sed) {
|
||||
count++;
|
||||
|
|
@ -6228,6 +6229,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
if (ed.getMin() > 0) {
|
||||
if (problematicPaths.contains(ed.getPath()))
|
||||
hintPlural(errors, NO_RULE_DATE, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), count, I18nConstants.VALIDATION_VAL_PROFILE_NOCHECKMIN, profile.getVersionedUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), Integer.toString(ed.getMin()));
|
||||
|
|
@ -6238,9 +6240,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
}
|
||||
}
|
||||
if (ed.hasMax() && !ed.getMax().equals("*")) {
|
||||
if (problematicPaths.contains(ed.getPath()))
|
||||
if (problematicPaths.contains(ed.getPath())) {
|
||||
hintPlural(errors, NO_RULE_DATE, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), count, I18nConstants.VALIDATION_VAL_PROFILE_NOCHECKMAX, profile.getVersionedUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), ed.getMax());
|
||||
else if (count > Integer.parseInt(ed.getMax())) {
|
||||
} else if (count > Integer.parseInt(ed.getMax())) {
|
||||
ok = rulePlural(errors, NO_RULE_DATE, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), false, count, I18nConstants.VALIDATION_VAL_PROFILE_MAXIMUM, profile.getVersionedUrl(), ed.getPath(), ed.getId(), ed.getSliceName(),ed.getLabel(), stack.getLiteralPath(), ed.getMax(), Integer.toString(count)) && ok;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -20,7 +20,7 @@
|
|||
<properties>
|
||||
<guava_version>32.0.1-jre</guava_version>
|
||||
<hapi_fhir_version>6.4.1</hapi_fhir_version>
|
||||
<validator_test_case_version>1.4.7</validator_test_case_version>
|
||||
<validator_test_case_version>1.4.8</validator_test_case_version>
|
||||
<jackson_version>2.15.2</jackson_version>
|
||||
<junit_jupiter_version>5.9.2</junit_jupiter_version>
|
||||
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue