r5 extension extractor
This commit is contained in:
Grahame Grieve
parent
1e6fd76ace
commit
f9b386d5b2
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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.util.ArrayList;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.r5.context.CanonicalResourceManager;
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import org.hl7.fhir.r5.formats.JsonParser;
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import org.hl7.fhir.r5.formats.XmlParser;
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import org.hl7.fhir.r5.model.CodeSystem;
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import org.hl7.fhir.r5.model.ElementDefinition;
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import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingAdditionalComponent;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionContextComponent;
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import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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import ca.uhn.fhir.model.api.IStreamingDatatype;
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public class ExtensionExtractor {
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public static void main(String[] args) throws FHIRFormatError, FileNotFoundException, IOException {
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new ExtensionExtractor().process(args[0]);
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}
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private void process(String dst) throws IOException {
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FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
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NpmPackage r5 = pcm.loadPackage("hl7.fhir.r5.core", "current");
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CanonicalResourceManager<CodeSystem> cslist = new CanonicalResourceManager<CodeSystem>(true);
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for (String r : r5.listResources("CodeSystem")) {
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CodeSystem cs = (CodeSystem) new JsonParser().parse(r5.load(r));
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cslist.see(cs, null);
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}
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CanonicalResourceManager<ValueSet> vslist = new CanonicalResourceManager<ValueSet>(true);
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for (String r : r5.listResources("ValueSet")) {
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ValueSet vs = (ValueSet) new JsonParser().parse(r5.load(r));
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vslist.see(vs, null);
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}
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for (ValueSet vs : vslist.getList()) {
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for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
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CodeSystem cs = cslist.get(inc.getSystem());
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if (cs != null) {
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if (!cs.hasUserData("vsl")) {
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cs.setUserData("vsl", new ArrayList<ValueSet>());
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}
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((ArrayList<ValueSet>) cs.getUserData("vsl")).add(vs);
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}
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}
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}
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for (String r : r5.listResources("StructureDefinition")) {
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StructureDefinition sd = (StructureDefinition) new JsonParser().parse(r5.load(r));
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if (sd.getType().equals("Extension") && sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
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String fn;
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if (sd.getContext().size() == 0) {
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fn = Utilities.path(dst, "null", sd.getId()+".json");
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} else if (sd.getContext().size() > 1) {
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boolean dt = true;
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for (StructureDefinitionContextComponent x : sd.getContext()) {
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String s = extractType(x.getExpression());
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dt = dt && isDataType(s);
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}
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if (dt) {
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fn = Utilities.path(dst, "datatypes", "multiple", sd.getId()+".xml");
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} else {
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fn = Utilities.path(dst, "multiple", sd.getId()+".xml");
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}
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} else {
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String s = extractType(sd.getContextFirstRep().getExpression());
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if (isDataType(s)) {
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fn = Utilities.path(dst, "datatypes", s, sd.getId()+".xml");
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} else {
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fn = Utilities.path(dst, s, sd.getId()+".xml");
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}
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Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
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new XmlParser().compose(new FileOutputStream(fn), sd);
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}
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for (ElementDefinition ed : sd.getSnapshot().getElement()) {
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seeBinding(ed.getBinding().getValueSet(), vslist, "ext", sd);
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for (ElementDefinitionBindingAdditionalComponent ab : ed.getBinding().getAdditional()) {
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seeBinding(ab.getValueSet(), vslist, "ext", sd);
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}
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}
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} else {
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for (ElementDefinition ed : sd.getSnapshot().getElement()) {
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seeBinding(ed.getBinding().getValueSet(), vslist, "core", sd);
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for (ElementDefinitionBindingAdditionalComponent ab : ed.getBinding().getAdditional()) {
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seeBinding(ab.getValueSet(), vslist, "core", sd);
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}
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}
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}
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}
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for (ValueSet vs : vslist.getList()) {
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if (vs.hasUserData("core") || !vs.hasUserData("ext")) {
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vslist.drop(vs.getId());
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}
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}
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for (CodeSystem cs : cslist.getList()) {
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boolean keep = false;
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if (cs.hasUserData("vsl" )) {
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keep = true;
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for (ValueSet vs : (ArrayList<ValueSet>) cs.getUserData("vsl")) {
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if (!vslist.has(vs.getUrl())) {
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keep = false;
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}
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}
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}
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if (!keep) {
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cslist.drop(cs.getId());
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}
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}
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for (ValueSet vs : vslist.getList()) {
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System.out.println(vs.getUrl());
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}
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for (CodeSystem cs : cslist.getList()) {
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System.out.println(cs.getUrl());
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}
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}
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private void seeBinding(String url, CanonicalResourceManager<ValueSet> vslist, String name, StructureDefinition sd) {
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ValueSet vs = vslist.get(url);
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if (vs != null) {
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vs.setUserData(name, sd);
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}
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}
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private boolean isDataType(String s) {
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return Utilities.existsInList(s,
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"PrimitiveType", "instant", "time", "date", "dateTime", "decimal", "boolean", "integer", "string",
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"uri", "base64Binary", "code", "id", "oid", "unsignedInt", "positiveInt", "markdown", "url", "canonical",
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"uuid", "integer64", "DataType", "BackboneType", "Identifier", "HumanName", "Address", "ContactPoint",
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"Timing", "Quantity", "SimpleQuantity", "Attachment", "Range", "Period", "Ratio", "RatioRange", "CodeableConcept",
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"Coding", "SampledData", "Age", "Distance", "Duration", "Count", "Money", "MoneyQuantity", "Annotation", "Signature", "DataType",
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"ContactDetail", "Contributor", "DataRequirement", "ParameterDefinition", "RelatedArtifact", "TriggerDefinition", "UsageContext",
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"Expression", "ExtendedContactDetail", "VirtualServiceDetail", "Availability", "MonetaryComponent", "DataType",
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"BackboneType", "Reference", "Narrative", "Extension", "Meta", "ElementDefinition", "Dosage", "xhtml", "CodeableReference");
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}
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private String extractType(String x) {
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String s = x;
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if (s.contains(".")) {
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s = s.substring(0, s.indexOf("."));
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}
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return s;
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}
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}
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