update ICD11Generator
This commit is contained in:
Grahame Grieve
parent
af97232036
commit
9e87161ec5
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@ -9,6 +9,8 @@ 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 java.util.HashSet;
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import java.util.Set;
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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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@ -38,25 +40,109 @@ 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 class ICD11Generator {
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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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new ICD11Generator().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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CodeSystem cs = makeMMSCodeSystem();
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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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processMMSEntity(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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cs = makeEntityCodeSystem();
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root = fetchJson(Utilities.pathURL(base, "/icd/entity"));
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cs.setVersion(root.get("releaseId").getAsString());
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cs.setDateElement(new DateTimeType(root.get("releaseDate").getAsString()));
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cs.setTitle(readString(root, "title"));
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Set<String> ids = new HashSet<>();
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for (JsonElement child : root.getAsJsonArray("child")) {
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processEntity(cs, ids, base, tail(child.getAsString()), 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-foundation.xml")), cs);
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makeFullVs2(dest, cs);
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System.out.println("finished");
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}
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private void processEntity(CodeSystem cs, Set<String> ids, String base, String id, String dest) throws IOException {
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if (!ids.contains(id)) {
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System.out.print(".");
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ids.add(id);
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org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc = cs.addConcept().setCode(id);
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JsonObject entity = fetchJson(Utilities.pathURL(base, "icd", "entity", id));
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cc.setDisplay(readString(entity, "title"));
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String d = readString(entity, "definition");
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if (d != null) {
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cc.setDefinition(d);
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}
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if (entity.has("inclusion")) {
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for (JsonElement child : entity.getAsJsonArray("inclusion")) {
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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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if (co.has("foundationReference")) {
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cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/foundation").setCode(tail(co.get("foundationReference").getAsString())).setDisplay(v)).setCode("inclusion");
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}
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}
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}
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}
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if (entity.has("exclusion")) {
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for (JsonElement child : entity.getAsJsonArray("exclusion")) {
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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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if (co.has("foundationReference")) {
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cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/foundation").setCode(tail(co.get("foundationReference").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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if (entity.has("narrowerTerm")) {
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for (JsonElement child : entity.getAsJsonArray("narrowerTerm")) {
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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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if (co.has("narrowerTerm")) {
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cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/foundation").setCode(tail(co.get("foundationReference").getAsString())).setDisplay(v)).setCode("narrowerTerm");
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}
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}
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}
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}
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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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if (entity.has("synonym")) {
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for (JsonElement j : entity.getAsJsonArray("synonym")) {
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String v = readString((JsonObject) j, "label");
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if (v != null && !v.equals(cc.getDisplay())) {
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addDesignation(v, cc, "http://id.who.int/icd11/mms/designation", "synonym");
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}
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}
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}
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for (JsonElement j : entity.getAsJsonArray("parent")) {
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String v = j.getAsString();
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if (!"http://id.who.int/icd/entity".equals(v)) {
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cc.addProperty().setValue(new CodeType(tail(v))).setCode("narrowerTerm");
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}
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}
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if (entity.has("child")) {
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for (JsonElement j : entity.getAsJsonArray("child")) {
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String v = j.getAsString();
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cc.addProperty().setValue(new CodeType(tail(v))).setCode("child");
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processEntity(cs, ids, base, tail(v), dest);
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}
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}
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}
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}
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private void makeFullVs(String dest, CodeSystem cs) throws FileNotFoundException, IOException {
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@ -64,8 +150,8 @@ public class ICD11CodeSystemGenerator {
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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.setName("ICDMMSAll");
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vs.setTitle("Value Set for all ICD 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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@ -78,7 +164,26 @@ public class ICD11CodeSystemGenerator {
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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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private void makeFullVs2(String dest, CodeSystem cs) throws FileNotFoundException, IOException {
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String url = "http://id.who.int/icd11/ValueSet/all-foundation";
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ValueSet vs = new ValueSet();
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vs.setId("all-foundation");
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vs.setUrl(url);
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vs.setName("ICDFoundationAll");
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vs.setTitle("Value Set for all ICD Foundation Concepts");
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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-foundation.xml")), vs);
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}
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private void processMMSEntity(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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@ -128,7 +233,6 @@ public class ICD11CodeSystemGenerator {
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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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@ -158,7 +262,7 @@ public class ICD11CodeSystemGenerator {
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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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processMMSEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
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}
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}
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}
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@ -243,7 +347,7 @@ public class ICD11CodeSystemGenerator {
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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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private CodeSystem makeMMSCodeSystem() {
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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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@ -260,16 +364,41 @@ public class ICD11CodeSystemGenerator {
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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, "kind", "The kind of artifact this concept represents", PropertyType.CODE).setUri("http://id.who.int/icd11/properties#kind");
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CodeSystemUtilities.defineCodeSystemProperty(cs, "terms", "Other keywords for searching", PropertyType.STRING).setUri("http://id.who.int/icd11/properties#terms");
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CodeSystemUtilities.defineCodeSystemProperty(cs, "codingNote", "Coding advice for this concept", PropertyType.STRING).setUri("http://id.who.int/icd11/properties#codingNote");
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CodeSystemUtilities.defineCodeSystemProperty(cs, "exclusion", "References to diseases that are excluded from this concept", PropertyType.CODING).setUri("http://id.who.int/icd11/properties#exclusion");
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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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CodeSystemUtilities.defineCodeSystemProperty(cs, "postcoordinationScale", "", PropertyType.CODE).setUri("http://id.who.int/icd11/properties#postcoordinationScale");
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return cs;
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}
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private CodeSystem makeEntityCodeSystem() {
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CodeSystem cs = new CodeSystem();
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cs.setId("icd11-foundation");
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cs.setUrl("http://id.who.int/icd11/foundation");
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cs.setName("ICD11Entity");
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cs.setTitle("ICD-11 Entities (Foundation)");
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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.ISA); // though we aren't going to have a heirarchy
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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-foundation");
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cs.setContent(CodeSystemContentMode.COMPLETE);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "exclusion", "References to diseases that are excluded from this concept", PropertyType.CODING).setUri("http://id.who.int/icd11/properties#exclusion");
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CodeSystemUtilities.defineCodeSystemProperty(cs, "inclusion", "References to diseases that are included from this concept", PropertyType.CODING).setUri("http://id.who.int/icd11/properties#inclusion");
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CodeSystemUtilities.defineCodeSystemProperty(cs, "narrowerTerm", "Narrower terms for this entity", PropertyType.CODE).setUri("http://id.who.int/icd11/properties#narrowerTerm");
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CodeSystemUtilities.defineCodeSystemProperty(cs, "parent", "Parent for this concept", PropertyType.CODE);
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CodeSystemUtilities.defineCodeSystemProperty(cs, "child", "Child for this concept", 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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