fix bugs around XML version + add ICD-11 generator
This commit is contained in:
Grahame Grieve
parent
991978c784
commit
c46d4dd779
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@ -0,0 +1,283 @@
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package org.hl7.fhir.convertors.misc;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.net.URL;
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import java.net.URLConnection;
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import java.text.DateFormat;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import org.hl7.fhir.r4.model.CodeType;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.formats.IParser.OutputStyle;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
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import org.hl7.fhir.r4.formats.XmlParser;
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import org.hl7.fhir.r4.formats.XmlParserBase.XmlVersion;
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import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
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import org.hl7.fhir.r4.model.CodeSystem.CodeSystemHierarchyMeaning;
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import org.hl7.fhir.r4.model.CodeSystem.ConceptPropertyComponent;
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import org.hl7.fhir.r4.model.CodeSystem.PropertyType;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
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import org.hl7.fhir.r4.utils.ToolingExtensions;
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import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
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import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.json.JSONUtil;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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public class ICD11CodeSystemGenerator {
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public static void main(String[] args) throws IOException {
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new ICD11CodeSystemGenerator().execute(args[0], args[1]);
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}
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private void execute(String base, String dest) throws IOException {
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CodeSystem cs = makeCodeSystem();
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JsonObject version = fetchJson(Utilities.pathURL(base, "/icd/release/11/mms"));
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String[] p = version.get("latestRelease").getAsString().split("\\/");
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cs.setVersion(p[6]);
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JsonObject root = fetchJson(url(base, version.get("latestRelease").getAsString()));
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cs.setDateElement(new DateTimeType(root.get("releaseDate").getAsString()));
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for (JsonElement child : root.getAsJsonArray("child")) {
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processEntity(cs, base, child.getAsString(), cs.addConcept(), dest);
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System.out.println();
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}
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new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
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makeFullVs(dest, cs);
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}
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private void makeFullVs(String dest, CodeSystem cs) throws FileNotFoundException, IOException {
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String url = "http://id.who.int/icd11/ValueSet/all-MMS";
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ValueSet vs = new ValueSet();
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vs.setId("all-MMS");
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vs.setUrl(url);
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vs.setName("VSMMSAll");
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vs.setTitle("Value Set for all MMS Codes");
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vs.setStatus(PublicationStatus.ACTIVE);
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vs.setExperimental(false);
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vs.setDate(cs.getDate());
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vs.setPublisher("WHO");
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vs.setCopyright("Consult WHO For terms of use");
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vs.setVersion(cs.getVersion());
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vs.setStatus(cs.getStatus());
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ConceptSetComponent inc = vs.getCompose().addInclude();
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inc.setSystem(cs.getUrl());
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new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
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}
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private void processEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
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System.out.print(".");
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JsonObject entity = fetchJson(url(base, ref));
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cc.setId(tail(ref));
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if (entity.has("code") && !Utilities.noString(entity.get("code").getAsString())) {
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cc.setCode(entity.get("code").getAsString());
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} else if (entity.has("blockId") && !Utilities.noString(entity.get("blockId").getAsString())) {
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cc.setCode(entity.get("blockId").getAsString());
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} else {
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cc.setCode(cc.getId());
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cc.addProperty().setCode("abstract").setValue(new BooleanType(true));
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}
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if (entity.has("classKind") && !Utilities.noString(entity.get("classKind").getAsString()) && !"category".equals(entity.get("classKind").getAsString())) {
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cc.addProperty().setCode("kind").setValue(new CodeType(entity.get("classKind").getAsString()));
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}
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cc.setDisplay(readString(entity, "title"));
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StringBuilder defn = new StringBuilder();
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String d = readString(entity, "definition");
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if (d != null) {
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defn.append(d);
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}
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if (d == null && (entity.has("inclusion") || entity.has("exclusion"))) {
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defn.append(cc.getDisplay());
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}
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if (entity.has("inclusion")) {
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defn.append(". Includes: ");
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boolean first = true;
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for (JsonElement child : entity.getAsJsonArray("inclusion")) {
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if (first) first = false; else defn.append(", ");
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defn.append(readString((JsonObject) child, "label"));
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}
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}
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if (entity.has("exclusion")) {
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defn.append(". Excludes: ");
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boolean first = true;
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for (JsonElement child : entity.getAsJsonArray("exclusion")) {
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if (first) first = false; else defn.append(", ");
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JsonObject co = (JsonObject) child;
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String v = readString(co, "label");
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if (v != null) {
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defn.append(v);
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if (co.has("linearizationReference")) {
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cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/mms").setCode(tail(co.get("linearizationReference").getAsString())).setDisplay(v)).setCode("exclusion");
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}
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}
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}
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}
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cc.setDefinition(defn.toString());
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addDesignation(readString(entity, "longDefinition"), cc, "http://id.who.int/icd11/mms/designation", "longDefinition");
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addDesignation(readString(entity, "fullySpecifiedName"), cc, "http://snomed.info/sct", "900000000000003001");
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addExtension(readString(entity, "fullySpecifiedName"), cc, "http://hl7.org/fhir/StructureDefinition/codesystem-concept-comments");
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addProperty(readString(entity, "codingNote"), cc, "codingNote");
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if (entity.has("indexTerm")) {
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// CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder("; ");
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// for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
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// processIndexTerm(cc, b, (JsonObject) child);
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// }
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// if (b.length() > 0) {
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// cc.addProperty().setCode("terms").setValue(new StringType(b.toString()));
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// }
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for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
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processIndexTerm(cc, (JsonObject) child);
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}
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}
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if (entity.has("postcoordinationScale")) {
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for (JsonElement child : entity.getAsJsonArray("postcoordinationScale")) {
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JsonObject o = (JsonObject) child;
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String name = tail(o.get("axisName").getAsString());
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ConceptPropertyComponent prop = cc.addProperty();
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prop.setCode("postcoordinationScale");
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prop.setValue(new CodeType(name));
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ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/required", o.get("requiredPostcoordination").getAsBoolean());
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ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/repeats", o.get("allowMultipleValues").getAsBoolean());
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if (o.has("scaleEntity")) {
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ToolingExtensions.addUriExtension(prop, "http://id.who.int/icd11/extensions/valueSet", buildValueSet(cs, cc.getCode(), name, o, dest));
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}
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}
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}
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if (entity.has("child")) {
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for (JsonElement child : entity.getAsJsonArray("child")) {
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processEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
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}
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}
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}
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private String buildValueSet(CodeSystem cs, String code, String name, JsonObject o, String dest) throws FileNotFoundException, IOException {
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String id = code+"-"+name;
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String url = "http://id.who.int/icd11/ValueSet/"+id;
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ValueSet vs = new ValueSet();
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vs.setId(id);
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vs.setUrl(url);
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vs.setName("VS"+name+"4"+code);
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vs.setTitle("Value Set for "+name+" on "+code);
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vs.setStatus(PublicationStatus.ACTIVE);
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vs.setExperimental(false);
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vs.setDate(cs.getDate());
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vs.setPublisher("WHO");
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vs.setCopyright("Consult WHO For terms of use");
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vs.setVersion(cs.getVersion());
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vs.setStatus(cs.getStatus());
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ConceptSetComponent inc = vs.getCompose().addInclude();
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inc.setSystem(cs.getUrl());
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for (JsonElement e : o.getAsJsonArray("scaleEntity")) {
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inc.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue(tail(e.getAsString()));
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}
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new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-"+id+".xml")), vs);
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return url;
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}
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private void processIndexTerm(org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, JsonObject child) {
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String s = readString(child, "label");
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if (s != null) {
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if (!s.equals(cc.getDisplay())) {
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cc.addDesignation().setValue(s).setUse(new Coding().setSystem("http://id.who.int/icd11/mms/designation").setCode("term"));
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}
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}
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}
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// private void processIndexTerm(org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, CommaSeparatedStringBuilder b, JsonObject child) {
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// String s = readString(child, "label");
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// if (s != null) {
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// if (!s.equals(cc.getDisplay())) {
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// b.append(s);
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// }
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// }
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//
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// }
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//
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private String tail(String ref) {
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return ref.substring(ref.lastIndexOf("/")+1);
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}
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private void addExtension(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String url) {
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if (v != null) {
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ToolingExtensions.setStringExtension(cc, url, v);
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}
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}
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private void addDesignation(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String system, String code) {
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if (v != null) {
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cc.addDesignation().setValue(v.replace("\r", "").replace("\n", "")).setUse(new Coding().setSystem(system).setCode(code));
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}
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}
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private void addProperty(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String code) {
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if (v != null) {
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cc.addProperty().setValue(new StringType(v.replace("\r", " ").replace("\n", ""))).setCode(code);
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}
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}
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private String readString(JsonObject obj, String name) {
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JsonObject p = obj.getAsJsonObject(name);
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if (p == null) {
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return null;
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}
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if (p.has("@value")) {
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return p.get("@value").getAsString();
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}
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return null;
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}
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private String url(String base, String u) {
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return u.replace("http://id.who.int", base);
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}
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private CodeSystem makeCodeSystem() {
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CodeSystem cs = new CodeSystem();
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cs.setId("icd11-mms");
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cs.setUrl("http://id.who.int/icd11/mms");
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cs.setName("ICD11MMS");
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cs.setTitle("ICD-11 MMS Linearization");
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cs.setStatus(PublicationStatus.ACTIVE);
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cs.setExperimental(false);
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cs.setDate(new Date());
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cs.setPublisher("WHO");
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cs.setCopyright("Consult WHO For terms of use");
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cs.setCaseSensitive(true);
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cs.setHierarchyMeaning(CodeSystemHierarchyMeaning.CLASSIFIEDWITH);
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cs.setCompositional(true);
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cs.setVersionNeeded(true);
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cs.setValueSet("http://id.who.int/icd11/ValueSet/all-MMS");
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cs.setContent(CodeSystemContentMode.COMPLETE);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "kind", "The kind of artifact this concept represents", PropertyType.CODE);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "terms", "Other keywords for searching", PropertyType.STRING);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "codingNote", "Coding advice for this concept", PropertyType.STRING);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "exclusion", "References to diseases that are excluded from this concept", PropertyType.CODING);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "abstract", "If concept is abstract", PropertyType.BOOLEAN);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "abstract", "If concept is abstract", PropertyType.BOOLEAN);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "postcoordinationScale", "", PropertyType.CODE);
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return cs;
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}
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private JsonObject fetchJson(String source) throws IOException {
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URL url = new URL(source);
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URLConnection c = url.openConnection();
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c.addRequestProperty("Accept", "application/json");
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c.addRequestProperty("API-Version", "v2");
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c.addRequestProperty("Accept-Language", "en");
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return (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(c.getInputStream()));
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}
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}
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@ -65,6 +65,11 @@ public class XmlParser extends XmlParserBase {
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super();
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}
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public XmlParser(XmlVersion ver) {
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super(ver);
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}
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public XmlParser(boolean allowUnknownContent) {
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super();
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setAllowUnknownContent(allowUnknownContent);
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@ -84,7 +84,21 @@ import org.xmlpull.v1.XmlPullParserFactory;
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* The two classes are separated to keep generated and manually maintained code apart.
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*/
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public abstract class XmlParserBase extends ParserBase implements IParser {
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public enum XmlVersion { V1_0, V1_1 }
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private XmlVersion version;
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public XmlParserBase(XmlVersion ver) {
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super();
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version = ver;
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}
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public XmlParserBase() {
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super();
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version = XmlVersion.V1_0;
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}
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@Override
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public ParserType getType() {
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return ParserType.XML;
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@ -152,7 +166,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
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*/
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@Override
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public void compose(OutputStream stream, Resource resource) throws IOException {
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XMLWriter writer = new XMLWriter(stream, "UTF-8");
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XMLWriter writer = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
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writer.setPretty(style == OutputStyle.PRETTY);
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writer.start();
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compose(writer, resource, writer.isPretty());
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@ -164,7 +178,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
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* @
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*/
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public void compose(OutputStream stream, Resource resource, boolean htmlPretty) throws IOException {
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XMLWriter writer = new XMLWriter(stream, "UTF-8");
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XMLWriter writer = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
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writer.setPretty(style == OutputStyle.PRETTY);
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writer.start();
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compose(writer, resource, htmlPretty);
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@ -177,7 +191,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
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* @
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*/
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public void compose(OutputStream stream, String rootName, Type type) throws IOException {
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xml = new XMLWriter(stream, "UTF-8");
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xml = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
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xml.setPretty(style == OutputStyle.PRETTY);
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xml.start();
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xml.setDefaultNamespace(FHIR_NS);
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@ -187,7 +201,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
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@Override
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public void compose(OutputStream stream, Type type, String rootName) throws IOException {
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xml = new XMLWriter(stream, "UTF-8");
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xml = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
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xml.setPretty(style == OutputStyle.PRETTY);
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xml.start();
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xml.setDefaultNamespace(FHIR_NS);
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@ -75,14 +75,22 @@ public class XMLWriter extends OutputStreamWriter implements IXMLWriter {
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private String[] specialAttributeNames = new String[] {"id", "name" };
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private boolean sortAttributes;
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private int attributeLineWrap;
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private boolean xml1_1;
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public final static int LINE_UNIX = 0;
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public final static int LINE_WINDOWS = 1;
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public XMLWriter(OutputStream stream, String charset, boolean xml1_1) throws UnsupportedEncodingException {
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super(stream, charset);
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this.stream = stream;
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this.charset = charset;
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this.xml1_1 = xml1_1;
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}
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public XMLWriter(OutputStream stream, String charset) throws UnsupportedEncodingException {
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super(stream, charset);
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this.stream = stream;
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this.charset = charset;
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this.xml1_1 = false;
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}
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protected boolean condition(boolean bTest, String message) throws IOException {
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@ -127,7 +135,7 @@ public class XMLWriter extends OutputStreamWriter implements IXMLWriter {
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attributes = null;
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try {
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if (xmlHeader) {
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write("<?xml version=\"1.0\" encoding=\""+getXMLCharsetName(charset)+"\"?>");
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write("<?xml version=\""+(xml1_1 ? "1.1" : "1.0")+"\" encoding=\""+getXMLCharsetName(charset)+"\"?>");
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if (prettyBase || prettyHeader)
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write(lineType == LINE_UNIX ? "\n" : "\r\n");
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}
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