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OID Assigner utility

This commit is contained in:
Grahame Grieve 2024-03-14 16:45:32 +11:00
parent da3bb9e353
commit 6cc4da9d02
1 changed files with 308 additions and 0 deletions
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org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/OIDAssigner.java Normal file
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package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.VersionUtilities;
public class OIDAssigner {
public static void main(String[] args) throws Exception {
new OIDAssigner().execute(args[0], args[1], args[2]);
}
private void execute(String oidSource, String folder, String version) {
IniFile oids = new IniFile(oidSource);
File f = new File(folder);
process(oids, f, version);
}
private void process(IniFile oids, File folder, String version) {
for (File f : folder.listFiles()) {
if (f.isDirectory()) {
process(oids, f, version);
} else if (f.getName().endsWith(".xml")) {
processFile(oids, f, version, FhirFormat.XML);
} else if (f.getName().endsWith(".json")) {
processFile(oids, f, version, FhirFormat.JSON);
}
}
}
private void processFile(IniFile oids, File f, String version, FhirFormat fmt) {
switch (VersionUtilities.getMajMin(version)) {
case "1.0" : processFileR2(oids, f, fmt);
case "3.0" : processFileR3(oids, f, fmt);
case "4.0" : processFileR4(oids, f, fmt);
case "4.3" : processFileR4B(oids, f, fmt);
case "5.0" : processFileR5(oids, f, fmt);
}
}
private void processFileR2(IniFile oids, File f, FhirFormat fmt) {
org.hl7.fhir.dstu2.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.dstu2.formats.JsonParser() : new org.hl7.fhir.dstu2.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.dstu2.model.Resource r = parser.parse(new FileInputStream(f));
if (r instanceof org.hl7.fhir.dstu2.model.ValueSet) {
org.hl7.fhir.dstu2.model.ValueSet vs = (org.hl7.fhir.dstu2.model.ValueSet) r;
boolean hasOid = isOid(vs.getIdentifier());
if (!hasOid) {
String oid = getOid(oids, "ValueSet", vs.getUrl());
vs.setIdentifier(new org.hl7.fhir.dstu2.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.dstu2.model.ConceptMap) {
org.hl7.fhir.dstu2.model.ConceptMap cm = (org.hl7.fhir.dstu2.model.ConceptMap) r;
boolean hasOid = isOid(cm.getIdentifier());
if (!hasOid) {
String oid = getOid(oids, "ConceptMap", cm.getUrl());
cm.setIdentifier(new org.hl7.fhir.dstu2.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.dstu2.model.StructureDefinition) {
org.hl7.fhir.dstu2.model.StructureDefinition sd = (org.hl7.fhir.dstu2.model.StructureDefinition) r;
boolean hasOid = false;
for (org.hl7.fhir.dstu2.model.Identifier id : sd.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, "StructureDefinition", sd.getUrl());
sd.getIdentifier().add(new org.hl7.fhir.dstu2.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
}
}
private void processFileR3(IniFile oids, File f, FhirFormat fmt) {
org.hl7.fhir.dstu3.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.dstu3.formats.JsonParser() : new org.hl7.fhir.dstu3.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.dstu3.model.Resource r = parser.parse(new FileInputStream(f));
if (r instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
org.hl7.fhir.dstu3.model.CodeSystem cs = (org.hl7.fhir.dstu3.model.CodeSystem) r;
boolean hasOid = isOid(cs.getIdentifier());
if (!hasOid) {
String oid = getOid(oids, "CodeSystem", cs.getUrl());
cs.setIdentifier(new org.hl7.fhir.dstu3.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.dstu3.model.ValueSet) {
org.hl7.fhir.dstu3.model.ValueSet vs = (org.hl7.fhir.dstu3.model.ValueSet) r;
boolean hasOid = false;
for (org.hl7.fhir.dstu3.model.Identifier id : vs.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, "ValueSet", vs.getUrl());
vs.getIdentifier().add(new org.hl7.fhir.dstu3.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.dstu3.model.ConceptMap) {
org.hl7.fhir.dstu3.model.ConceptMap cm = (org.hl7.fhir.dstu3.model.ConceptMap) r;
boolean hasOid = isOid(cm.getIdentifier());
if (!hasOid) {
String oid = getOid(oids, "ConceptMap", cm.getUrl());
cm.setIdentifier(new org.hl7.fhir.dstu3.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.dstu3.model.StructureDefinition) {
org.hl7.fhir.dstu3.model.StructureDefinition sd = (org.hl7.fhir.dstu3.model.StructureDefinition) r;
boolean hasOid = false;
for (org.hl7.fhir.dstu3.model.Identifier id : sd.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, "StructureDefinition", sd.getUrl());
sd.getIdentifier().add(new org.hl7.fhir.dstu3.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
}
}
private void processFileR4(IniFile oids, File f, FhirFormat fmt) {
org.hl7.fhir.r4.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.r4.formats.JsonParser() : new org.hl7.fhir.r4.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.r4.model.Resource r = parser.parse(new FileInputStream(f));
if (r instanceof org.hl7.fhir.r4.model.CodeSystem) {
org.hl7.fhir.r4.model.CodeSystem cs = (org.hl7.fhir.r4.model.CodeSystem) r;
boolean hasOid = false;
for (org.hl7.fhir.r4.model.Identifier id : cs.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, "CodeSystem", cs.getUrl());
cs.getIdentifier().add(new org.hl7.fhir.r4.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.r4.model.ValueSet) {
org.hl7.fhir.r4.model.ValueSet vs = (org.hl7.fhir.r4.model.ValueSet) r;
boolean hasOid = false;
for (org.hl7.fhir.r4.model.Identifier id : vs.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, "ValueSet", vs.getUrl());
vs.getIdentifier().add(new org.hl7.fhir.r4.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.r4.model.ConceptMap) {
org.hl7.fhir.r4.model.ConceptMap cm = (org.hl7.fhir.r4.model.ConceptMap) r;
boolean hasOid = isOid(cm.getIdentifier());
if (!hasOid) {
String oid = getOid(oids, "ConceptMap", cm.getUrl());
cm.setIdentifier(new org.hl7.fhir.r4.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (r instanceof org.hl7.fhir.r4.model.StructureDefinition) {
org.hl7.fhir.r4.model.StructureDefinition sd = (org.hl7.fhir.r4.model.StructureDefinition) r;
boolean hasOid = false;
for (org.hl7.fhir.r4.model.Identifier id : sd.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, "StructureDefinition", sd.getUrl());
sd.getIdentifier().add(new org.hl7.fhir.r4.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
}
}
private void processFileR4B(IniFile oids, File f, FhirFormat fmt) {
org.hl7.fhir.r4b.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.r4b.formats.JsonParser() : new org.hl7.fhir.r4b.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.r4b.model.Resource r = parser.parse(new FileInputStream(f));
if (r instanceof org.hl7.fhir.r4b.model.CanonicalResource) {
org.hl7.fhir.r4b.model.CanonicalResource cs = (org.hl7.fhir.r4b.model.CanonicalResource) r;
boolean hasOid = false;
for (org.hl7.fhir.r4b.model.Identifier id : cs.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, r.fhirType(), cs.getUrl());
cs.getIdentifier().add(new org.hl7.fhir.r4b.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.r4b.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
}
}
private void processFileR5(IniFile oids, File f, FhirFormat fmt) {
org.hl7.fhir.r5.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.r5.formats.JsonParser() : new org.hl7.fhir.r5.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.r5.model.Resource r = parser.parse(new FileInputStream(f));
if (r instanceof org.hl7.fhir.r5.model.CanonicalResource) {
org.hl7.fhir.r5.model.CanonicalResource cs = (org.hl7.fhir.r5.model.CanonicalResource) r;
boolean hasOid = false;
for (org.hl7.fhir.r5.model.Identifier id : cs.getIdentifier()) {
if (isOid(id)) {
hasOid = true;
}
}
if (!hasOid) {
String oid = getOid(oids, r.fhirType(), cs.getUrl());
cs.getIdentifier().add(new org.hl7.fhir.r5.model.Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
save = true;
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
}
}
private boolean isOid(org.hl7.fhir.dstu2.model.Identifier id) {
return "urn:ietf:rfc:3986".equals(id.getSystem()) && id.hasValue() && id.getValue().startsWith("urn:oid:");
}
private boolean isOid(org.hl7.fhir.dstu3.model.Identifier id) {
return "urn:ietf:rfc:3986".equals(id.getSystem()) && id.hasValue() && id.getValue().startsWith("urn:oid:");
}
private boolean isOid(org.hl7.fhir.r4.model.Identifier id) {
return "urn:ietf:rfc:3986".equals(id.getSystem()) && id.hasValue() && id.getValue().startsWith("urn:oid:");
}
private boolean isOid(org.hl7.fhir.r4b.model.Identifier id) {
return "urn:ietf:rfc:3986".equals(id.getSystem()) && id.hasValue() && id.getValue().startsWith("urn:oid:");
}
private boolean isOid(org.hl7.fhir.r5.model.Identifier id) {
return "urn:ietf:rfc:3986".equals(id.getSystem()) && id.hasValue() && id.getValue().startsWith("urn:oid:");
}
private String getOid(IniFile oids, String rt, String url) {
String root = oids.getStringProperty("Roots", rt);
if (root == null) {
throw new Error("no OID.ini entry for "+rt);
}
String oid = oids.getStringProperty(rt, url);
if (oid != null) {
return oid;
}
int key = oids.getIntegerProperty("Key", rt);
key++;
oid = root+"."+key;
oids.setIntegerProperty("Key", rt, key, null);
oids.setStringProperty(rt, url, oid, null);
oids.save();
return oid;
}
}