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update extension extractor

This commit is contained in:
Grahame Grieve 2023-02-02 16:40:09 +11:00
parent f7ad38cc34
commit d6cc2f46d0
1 changed files with 47 additions and 9 deletions
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56
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionExtractor.java
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@ -5,6 +5,8 @@ import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.CanonicalResourceManager;
@ -21,17 +23,21 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
public class ExtensionExtractor {
public static void main(String[] args) throws FHIRFormatError, FileNotFoundException, IOException {
new ExtensionExtractor().process(args[0]);
}
private void process(String dst) throws IOException {
Set<String> ids = new HashSet<>();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
NpmPackage r5 = pcm.loadPackage("hl7.fhir.r5.core", "current");
CanonicalResourceManager<CodeSystem> cslist = new CanonicalResourceManager<CodeSystem>(true);
@ -67,7 +73,7 @@ public class ExtensionExtractor {
sd.setSnapshot(null);
String fn;
if (sd.getContext().size() == 0) {
save(sd, dst,"none");
save(sd, dst,"none", ids);
} else if (sd.getContext().size() > 1) {
boolean dt = true;
for (StructureDefinitionContextComponent x : sd.getContext()) {
@ -75,16 +81,16 @@ public class ExtensionExtractor {
dt = dt && isDataType(s);
}
if (dt) {
save(sd, dst,"datatypes");
save(sd, dst,"datatypes", ids);
} else {
save(sd, dst,"multiple");
save(sd, dst,"multiple", ids);
}
} else {
String s = extractType(sd.getContextFirstRep().getExpression());
if (isDataType(s)) {
save(sd, dst,"datatypes");
save(sd, dst,"datatypes", ids);
} else {
save(sd, dst,s);
save(sd, dst,s, ids);
}
}
} else {
@ -118,21 +124,53 @@ public class ExtensionExtractor {
for (ValueSet vs : vslist.getList()) {
StructureDefinition sd = (StructureDefinition) vs.getUserData("ext");
String s = sd.getUserString("folder");
save(vs, dst, s);
save(vs, dst, s, ids);
}
for (CodeSystem cs : cslist.getList()) {
ValueSet vs = ((ArrayList<ValueSet>) cs.getUserData("vsl")).get(0);
String s = vs.getUserString("folder");
save(cs, dst,s);
save(cs, dst,s, ids);
}
deleteMatchingResources(ids, new File("/Users/grahamegrieve/work/r5/source"));
}
private void save(CanonicalResource cr, String dst, String folder) throws IOException {
private void deleteMatchingResources(Set<String> ids, File folder) {
for (File f : folder.listFiles()) {
if (f.isDirectory()) {
deleteMatchingResources(ids, f);
} else if (f.getName().endsWith(".json")) {
try {
JsonObject json = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(f);
if (json.has("resourceType") && json.has("id") && ids.contains(json.asString("id"))) {
System.out.println("Delete "+f.getAbsolutePath());
f.delete();
}
} catch (Exception e) {
// nothing
}
} else if (f.getName().endsWith(".xml")) {
try {
Element xml = XMLUtil.parseFileToDom(f.getAbsolutePath()).getDocumentElement();
if (XMLUtil.hasNamedChild(xml, "id") && ids.contains(XMLUtil.getNamedChildValue(xml, "id"))) {
System.out.println("Delete "+f.getAbsolutePath());
f.delete();
}
} catch (Exception e) {
// nothing
}
}
}
}
private void save(CanonicalResource cr, String dst, String folder, Set<String> ids) throws IOException {
// TODO Auto-generated method stub
cr.setText(null);
if (!cr.hasTitle()) {
cr.setTitle(Utilities.unCamelCase(cr.getName()));
}
ids.add(cr.getId());
String fn = Utilities.path(dst, folder, cr.fhirType()+"-"+cr.getId()+".xml");
cr.setUserData("folder", folder);
if (!new File(fn).exists()) {