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fix bugs around XML version + add ICD-11 generator

This commit is contained in:
Grahame Grieve 2020-03-17 11:10:50 +11:00
parent 991978c784
commit c46d4dd779
4 changed files with 315 additions and 5 deletions
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283
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICD11CodeSystemGenerator.java Normal file
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@ -0,0 +1,283 @@
package org.hl7.fhir.convertors.misc;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.URL;
import java.net.URLConnection;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.formats.XmlParserBase.XmlVersion;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemHierarchyMeaning;
import org.hl7.fhir.r4.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r4.model.CodeSystem.PropertyType;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r4.utils.ToolingExtensions;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
public class ICD11CodeSystemGenerator {
public static void main(String[] args) throws IOException {
new ICD11CodeSystemGenerator().execute(args[0], args[1]);
}
private void execute(String base, String dest) throws IOException {
CodeSystem cs = makeCodeSystem();
JsonObject version = fetchJson(Utilities.pathURL(base, "/icd/release/11/mms"));
String[] p = version.get("latestRelease").getAsString().split("\\/");
cs.setVersion(p[6]);
JsonObject root = fetchJson(url(base, version.get("latestRelease").getAsString()));
cs.setDateElement(new DateTimeType(root.get("releaseDate").getAsString()));
for (JsonElement child : root.getAsJsonArray("child")) {
processEntity(cs, base, child.getAsString(), cs.addConcept(), dest);
System.out.println();
}
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
makeFullVs(dest, cs);
}
private void makeFullVs(String dest, CodeSystem cs) throws FileNotFoundException, IOException {
String url = "http://id.who.int/icd11/ValueSet/all-MMS";
ValueSet vs = new ValueSet();
vs.setId("all-MMS");
vs.setUrl(url);
vs.setName("VSMMSAll");
vs.setTitle("Value Set for all MMS Codes");
vs.setStatus(PublicationStatus.ACTIVE);
vs.setExperimental(false);
vs.setDate(cs.getDate());
vs.setPublisher("WHO");
vs.setCopyright("Consult WHO For terms of use");
vs.setVersion(cs.getVersion());
vs.setStatus(cs.getStatus());
ConceptSetComponent inc = vs.getCompose().addInclude();
inc.setSystem(cs.getUrl());
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
}
private void processEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
System.out.print(".");
JsonObject entity = fetchJson(url(base, ref));
cc.setId(tail(ref));
if (entity.has("code") && !Utilities.noString(entity.get("code").getAsString())) {
cc.setCode(entity.get("code").getAsString());
} else if (entity.has("blockId") && !Utilities.noString(entity.get("blockId").getAsString())) {
cc.setCode(entity.get("blockId").getAsString());
} else {
cc.setCode(cc.getId());
cc.addProperty().setCode("abstract").setValue(new BooleanType(true));
}
if (entity.has("classKind") && !Utilities.noString(entity.get("classKind").getAsString()) && !"category".equals(entity.get("classKind").getAsString())) {
cc.addProperty().setCode("kind").setValue(new CodeType(entity.get("classKind").getAsString()));
}
cc.setDisplay(readString(entity, "title"));
StringBuilder defn = new StringBuilder();
String d = readString(entity, "definition");
if (d != null) {
defn.append(d);
}
if (d == null && (entity.has("inclusion") || entity.has("exclusion"))) {
defn.append(cc.getDisplay());
}
if (entity.has("inclusion")) {
defn.append(". Includes: ");
boolean first = true;
for (JsonElement child : entity.getAsJsonArray("inclusion")) {
if (first) first = false; else defn.append(", ");
defn.append(readString((JsonObject) child, "label"));
}
}
if (entity.has("exclusion")) {
defn.append(". Excludes: ");
boolean first = true;
for (JsonElement child : entity.getAsJsonArray("exclusion")) {
if (first) first = false; else defn.append(", ");
JsonObject co = (JsonObject) child;
String v = readString(co, "label");
if (v != null) {
defn.append(v);
if (co.has("linearizationReference")) {
cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/mms").setCode(tail(co.get("linearizationReference").getAsString())).setDisplay(v)).setCode("exclusion");
}
}
}
}
cc.setDefinition(defn.toString());
addDesignation(readString(entity, "longDefinition"), cc, "http://id.who.int/icd11/mms/designation", "longDefinition");
addDesignation(readString(entity, "fullySpecifiedName"), cc, "http://snomed.info/sct", "900000000000003001");
addExtension(readString(entity, "fullySpecifiedName"), cc, "http://hl7.org/fhir/StructureDefinition/codesystem-concept-comments");
addProperty(readString(entity, "codingNote"), cc, "codingNote");
if (entity.has("indexTerm")) {
// CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder("; ");
// for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
// processIndexTerm(cc, b, (JsonObject) child);
// }
// if (b.length() > 0) {
// cc.addProperty().setCode("terms").setValue(new StringType(b.toString()));
// }
for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
processIndexTerm(cc, (JsonObject) child);
}
}
if (entity.has("postcoordinationScale")) {
for (JsonElement child : entity.getAsJsonArray("postcoordinationScale")) {
JsonObject o = (JsonObject) child;
String name = tail(o.get("axisName").getAsString());
ConceptPropertyComponent prop = cc.addProperty();
prop.setCode("postcoordinationScale");
prop.setValue(new CodeType(name));
ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/required", o.get("requiredPostcoordination").getAsBoolean());
ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/repeats", o.get("allowMultipleValues").getAsBoolean());
if (o.has("scaleEntity")) {
ToolingExtensions.addUriExtension(prop, "http://id.who.int/icd11/extensions/valueSet", buildValueSet(cs, cc.getCode(), name, o, dest));
}
}
}
if (entity.has("child")) {
for (JsonElement child : entity.getAsJsonArray("child")) {
processEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
}
}
}
private String buildValueSet(CodeSystem cs, String code, String name, JsonObject o, String dest) throws FileNotFoundException, IOException {
String id = code+"-"+name;
String url = "http://id.who.int/icd11/ValueSet/"+id;
ValueSet vs = new ValueSet();
vs.setId(id);
vs.setUrl(url);
vs.setName("VS"+name+"4"+code);
vs.setTitle("Value Set for "+name+" on "+code);
vs.setStatus(PublicationStatus.ACTIVE);
vs.setExperimental(false);
vs.setDate(cs.getDate());
vs.setPublisher("WHO");
vs.setCopyright("Consult WHO For terms of use");
vs.setVersion(cs.getVersion());
vs.setStatus(cs.getStatus());
ConceptSetComponent inc = vs.getCompose().addInclude();
inc.setSystem(cs.getUrl());
for (JsonElement e : o.getAsJsonArray("scaleEntity")) {
inc.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue(tail(e.getAsString()));
}
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-"+id+".xml")), vs);
return url;
}
private void processIndexTerm(org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, JsonObject child) {
String s = readString(child, "label");
if (s != null) {
if (!s.equals(cc.getDisplay())) {
cc.addDesignation().setValue(s).setUse(new Coding().setSystem("http://id.who.int/icd11/mms/designation").setCode("term"));
}
}
}
// private void processIndexTerm(org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, CommaSeparatedStringBuilder b, JsonObject child) {
// String s = readString(child, "label");
// if (s != null) {
// if (!s.equals(cc.getDisplay())) {
// b.append(s);
// }
// }
//
// }
//
private String tail(String ref) {
return ref.substring(ref.lastIndexOf("/")+1);
}
private void addExtension(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String url) {
if (v != null) {
ToolingExtensions.setStringExtension(cc, url, v);
}
}
private void addDesignation(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String system, String code) {
if (v != null) {
cc.addDesignation().setValue(v.replace("\r", "").replace("\n", "")).setUse(new Coding().setSystem(system).setCode(code));
}
}
private void addProperty(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String code) {
if (v != null) {
cc.addProperty().setValue(new StringType(v.replace("\r", " ").replace("\n", ""))).setCode(code);
}
}
private String readString(JsonObject obj, String name) {
JsonObject p = obj.getAsJsonObject(name);
if (p == null) {
return null;
}
if (p.has("@value")) {
return p.get("@value").getAsString();
}
return null;
}
private String url(String base, String u) {
return u.replace("http://id.who.int", base);
}
private CodeSystem makeCodeSystem() {
CodeSystem cs = new CodeSystem();
cs.setId("icd11-mms");
cs.setUrl("http://id.who.int/icd11/mms");
cs.setName("ICD11MMS");
cs.setTitle("ICD-11 MMS Linearization");
cs.setStatus(PublicationStatus.ACTIVE);
cs.setExperimental(false);
cs.setDate(new Date());
cs.setPublisher("WHO");
cs.setCopyright("Consult WHO For terms of use");
cs.setCaseSensitive(true);
cs.setHierarchyMeaning(CodeSystemHierarchyMeaning.CLASSIFIEDWITH);
cs.setCompositional(true);
cs.setVersionNeeded(true);
cs.setValueSet("http://id.who.int/icd11/ValueSet/all-MMS");
cs.setContent(CodeSystemContentMode.COMPLETE);
CodeSystemUtilities.defineCodeSystemProperty(cs, "kind", "The kind of artifact this concept represents", PropertyType.CODE);
CodeSystemUtilities.defineCodeSystemProperty(cs, "terms", "Other keywords for searching", PropertyType.STRING);
CodeSystemUtilities.defineCodeSystemProperty(cs, "codingNote", "Coding advice for this concept", PropertyType.STRING);
CodeSystemUtilities.defineCodeSystemProperty(cs, "exclusion", "References to diseases that are excluded from this concept", PropertyType.CODING);
CodeSystemUtilities.defineCodeSystemProperty(cs, "abstract", "If concept is abstract", PropertyType.BOOLEAN);
CodeSystemUtilities.defineCodeSystemProperty(cs, "abstract", "If concept is abstract", PropertyType.BOOLEAN);
CodeSystemUtilities.defineCodeSystemProperty(cs, "postcoordinationScale", "", PropertyType.CODE);
return cs;
}
private JsonObject fetchJson(String source) throws IOException {
URL url = new URL(source);
URLConnection c = url.openConnection();
c.addRequestProperty("Accept", "application/json");
c.addRequestProperty("API-Version", "v2");
c.addRequestProperty("Accept-Language", "en");
return (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(c.getInputStream()));
}
}

5
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/formats/XmlParser.java
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@ -65,6 +65,11 @@ public class XmlParser extends XmlParserBase {
super(); super();
} }
public XmlParser(XmlVersion ver) {
super(ver);
}
public XmlParser(boolean allowUnknownContent) { public XmlParser(boolean allowUnknownContent) {
super(); super();
setAllowUnknownContent(allowUnknownContent); setAllowUnknownContent(allowUnknownContent);

22
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/formats/XmlParserBase.java
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@ -85,6 +85,20 @@ import org.xmlpull.v1.XmlPullParserFactory;
*/ */
public abstract class XmlParserBase extends ParserBase implements IParser { public abstract class XmlParserBase extends ParserBase implements IParser {
public enum XmlVersion { V1_0, V1_1 }
private XmlVersion version;
public XmlParserBase(XmlVersion ver) {
super();
version = ver;
}
public XmlParserBase() {
super();
version = XmlVersion.V1_0;
}
@Override @Override
public ParserType getType() { public ParserType getType() {
return ParserType.XML; return ParserType.XML;
@ -152,7 +166,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
*/ */
@Override @Override
public void compose(OutputStream stream, Resource resource) throws IOException { public void compose(OutputStream stream, Resource resource) throws IOException {
XMLWriter writer = new XMLWriter(stream, "UTF-8"); XMLWriter writer = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
writer.setPretty(style == OutputStyle.PRETTY); writer.setPretty(style == OutputStyle.PRETTY);
writer.start(); writer.start();
compose(writer, resource, writer.isPretty()); compose(writer, resource, writer.isPretty());
@ -164,7 +178,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
* @ * @
*/ */
public void compose(OutputStream stream, Resource resource, boolean htmlPretty) throws IOException { public void compose(OutputStream stream, Resource resource, boolean htmlPretty) throws IOException {
XMLWriter writer = new XMLWriter(stream, "UTF-8"); XMLWriter writer = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
writer.setPretty(style == OutputStyle.PRETTY); writer.setPretty(style == OutputStyle.PRETTY);
writer.start(); writer.start();
compose(writer, resource, htmlPretty); compose(writer, resource, htmlPretty);
@ -177,7 +191,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
* @ * @
*/ */
public void compose(OutputStream stream, String rootName, Type type) throws IOException { public void compose(OutputStream stream, String rootName, Type type) throws IOException {
xml = new XMLWriter(stream, "UTF-8"); xml = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
xml.setPretty(style == OutputStyle.PRETTY); xml.setPretty(style == OutputStyle.PRETTY);
xml.start(); xml.start();
xml.setDefaultNamespace(FHIR_NS); xml.setDefaultNamespace(FHIR_NS);
@ -187,7 +201,7 @@ public abstract class XmlParserBase extends ParserBase implements IParser {
@Override @Override
public void compose(OutputStream stream, Type type, String rootName) throws IOException { public void compose(OutputStream stream, Type type, String rootName) throws IOException {
xml = new XMLWriter(stream, "UTF-8"); xml = new XMLWriter(stream, "UTF-8", version == XmlVersion.V1_1);
xml.setPretty(style == OutputStyle.PRETTY); xml.setPretty(style == OutputStyle.PRETTY);
xml.start(); xml.start();
xml.setDefaultNamespace(FHIR_NS); xml.setDefaultNamespace(FHIR_NS);

10
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XMLWriter.java
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@ -75,14 +75,22 @@ public class XMLWriter extends OutputStreamWriter implements IXMLWriter {
private String[] specialAttributeNames = new String[] {"id", "name" }; private String[] specialAttributeNames = new String[] {"id", "name" };
private boolean sortAttributes; private boolean sortAttributes;
private int attributeLineWrap; private int attributeLineWrap;
private boolean xml1_1;
public final static int LINE_UNIX = 0; public final static int LINE_UNIX = 0;
public final static int LINE_WINDOWS = 1; public final static int LINE_WINDOWS = 1;
public XMLWriter(OutputStream stream, String charset, boolean xml1_1) throws UnsupportedEncodingException {
super(stream, charset);
this.stream = stream;
this.charset = charset;
this.xml1_1 = xml1_1;
}
public XMLWriter(OutputStream stream, String charset) throws UnsupportedEncodingException { public XMLWriter(OutputStream stream, String charset) throws UnsupportedEncodingException {
super(stream, charset); super(stream, charset);
this.stream = stream; this.stream = stream;
this.charset = charset; this.charset = charset;
this.xml1_1 = false;
} }
protected boolean condition(boolean bTest, String message) throws IOException { protected boolean condition(boolean bTest, String message) throws IOException {
@ -127,7 +135,7 @@ public class XMLWriter extends OutputStreamWriter implements IXMLWriter {
attributes = null; attributes = null;
try { try {
if (xmlHeader) { if (xmlHeader) {
write("<?xml version=\"1.0\" encoding=\""+getXMLCharsetName(charset)+"\"?>"); write("<?xml version=\""+(xml1_1 ? "1.1" : "1.0")+"\" encoding=\""+getXMLCharsetName(charset)+"\"?>");
if (prettyBase || prettyHeader) if (prettyBase || prettyHeader)
write(lineType == LINE_UNIX ? "\n" : "\r\n"); write(lineType == LINE_UNIX ? "\n" : "\r\n");
} }