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Add Dicom Package builder

This commit is contained in:
Grahame Grieve 2021-10-30 05:46:22 +11:00
parent 6ef5430834
commit fdb46024df
1 changed files with 182 additions and 0 deletions
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org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/DicomPackageBuilder.java Normal file
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package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.utils.NPMPackageGenerator;
import org.hl7.fhir.r4.utils.NPMPackageGenerator.Category;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
public class DicomPackageBuilder {
private String version;
private String dest;
private String source;
public static void main(String[] args) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
if (args.length == 0 || args[0].equals("-help")) {
System.out.println("Dicom Package Builder");
System.out.println("");
System.out.println("Before running, use FTP get the latest copy of ftp://medical.nema.org/MEDICAL/Dicom/Resources");
System.out.println("Then run with the following parameters (in order):");
System.out.println("1. the local folder that contains the copy of the FTP folder");
System.out.println("2. the local folder to put the package when it's created");
System.out.println("");
System.out.println("For help, see ");
return;
}
String source = args[0];
String dest = args[1];
DicomPackageBuilder self = new DicomPackageBuilder();
self.setSource(source);
self.setDest(dest);
self.execute();
}
private void execute() throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
CodeSystem cs = buildCodeSystem();
NPMPackageGenerator gen = new NPMPackageGenerator(Utilities.path(dest, "fhir.dicom#"+version+".tgz"), buildPackage());
int i = 2;
gen.addFile(Category.RESOURCE, "CodeSystem-"+cs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(cs));
ValueSet vs = buildAllValueSet();
gen.addFile(Category.RESOURCE, "ValueSet-"+vs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(vs));
Set<String> ids = new HashSet<>();
ids.add(vs.getId());
for (File f : new File(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
vs = (ValueSet) JsonParser.loadFile(new FileInputStream(f));
vs.setVersion(version);
if (vs.getId().length() > 64) {
vs.setId(vs.getId().substring(0, 64));
}
if (ids.contains(vs.getId())) {
throw new Error("Duplicate Id once Ids cut off at 64 char: "+vs.getId());
}
ids.add(vs.getId());
gen.addFile(Category.RESOURCE, "ValueSet-"+vs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(vs));
i++;
}
gen.finish();
System.out.println("Finished - "+i+" resources");
}
private ValueSet buildAllValueSet() {
ValueSet vs = new ValueSet();
vs.setId("all");
vs.setUrl("http://dicom.nema.org/resources/ValueSet/all");
vs.setVersion(version);
vs.setName("All DICOMTerminologyDefinitions");
vs.setTitle("All DICOM Controlled Terminology Definitions");
vs.setStatus(PublicationStatus.ACTIVE);
vs.setExperimental(false);
vs.setPublisher("FHIR Project on behalf of DICOM");
vs.setDate(new Date());
vs.setDescription("All DICOM Code Definitions (Coding Scheme Designator \"DCM\" Coding Scheme Version "+version);
vs.setPurpose("This value set is published as part of FHIR in order to make the codes available to FHIR terminology services and so implementers can easily leverage the codes");
vs.setCopyright("These codes are excerpted from Digital Imaging and Communications in Medicine (DICOM) Standard, Part 16: Content Mapping Resource, Copyright © 2011 by the National Electrical Manufacturers Association.");
vs.getCompose().getIncludeFirstRep().setSystem("http://dicom.nema.org/resources/ontology/DCM");
return vs;
}
private JsonObject buildPackage() {
JsonObject npm = new JsonObject();
npm.addProperty("tools-version", 3);
npm.addProperty("type", "fhir.ig");
npm.addProperty("license", "free");
npm.addProperty("author", "FHIR Project for DICOM");
npm.addProperty("name", "fhir.dicom");
npm.addProperty("url", "http://fhir.org/packages/fhir.dicom");
npm.addProperty("canonical", "http://fhir.org/packages/fhir.dicom");
npm.addProperty("version", version);
JsonArray fv = new JsonArray();
npm.add("fhirVersions", fv);
fv.add("4.0");
return npm;
}
private CodeSystem buildCodeSystem() throws ParserConfigurationException, FileNotFoundException, SAXException, IOException {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
Element rdf = doc.getDocumentElement();
Element d = XMLUtil.getFirstChild(rdf);
version = processVersion(XMLUtil.getNamedChildText(d, "versionInfo"));
CodeSystem cs = new CodeSystem();
cs.setId("DCM");
cs.setUrl("http://dicom.nema.org/resources/ontology/DCM");
cs.setVersion(version);
cs.setName("DICOMTerminologyDefinitions");
cs.setTitle("DICOM Controlled Terminology Definitions");
cs.getIdentifier().add(new Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:1.2.840.10008.2.16.4"));
cs.setStatus(PublicationStatus.ACTIVE);
cs.setExperimental(false);
cs.setPublisher("FHIR Project on behalf of DICOM");
cs.setDate(new Date());
cs.setDescription("DICOM Code Definitions (Coding Scheme Designator \"DCM\" Coding Scheme Version "+version);
cs.setPurpose("This code system is published as part of FHIR in order to make the codes available to FHIR terminology services and so implementers can easily leverage the codes");
cs.setCopyright("These codes are excerpted from Digital Imaging and Communications in Medicine (DICOM) Standard, Part 16: Content Mapping Resource, Copyright © 2011 by the National Electrical Manufacturers Association.");
cs.setCaseSensitive(true);
cs.setValueSet("http://dicom.nema.org/resources/ValueSet/all");
cs.setContent(CodeSystemContentMode.COMPLETE);
d = XMLUtil.getNextSibling(d);
while (d != null) {
String code = XMLUtil.getNamedChildText(d, "notation");
String display = XMLUtil.getNamedChildText(d, "prefLabel");
String definition = XMLUtil.getNamedChildText(d, "definition");
ConceptDefinitionComponent cc = new ConceptDefinitionComponent();
cs.getConcept().add(cc);
cc.setCode(code);
cc.setDisplay(display);
cc.setDefinition(definition);
d = XMLUtil.getNextSibling(d);
}
return cs;
}
private String processVersion(String s) {
String[] p = s.split("\\_");
return p[0].substring(0, 4)+"."+(1+(p[0].charAt(4) - 'a'))+"."+p[1];
}
private void setVersion(String version) {
this.version = version;
}
private void setDest(String dest) {
this.dest = dest;
}
private void setSource(String source) {
this.source = source;
}
}