updates to PHINVads and VSAC value set importing
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3ff241bcf8
commit
da91f17011
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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.IOException;
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import java.io.InputStream;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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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.cache.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.cache.NpmPackage;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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import org.w3c.dom.Document;
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public class OIDBasedValueSetImporter {
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protected IWorkerContext context;
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protected void init() throws FileNotFoundException, FHIRException, IOException {
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FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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NpmPackage npm = pcm.loadPackage("hl7.fhir.r5.core", "current");
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SimpleWorkerContext ctxt = SimpleWorkerContext.fromPackage(npm);
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ctxt.setAllowLoadingDuplicates(true);
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ctxt.loadFromPackage(pcm.loadPackage("hl7.terminology"), null);
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context = ctxt;
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}
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protected String fixVersionforSystem(String url, String csver) {
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if ("http://snomed.info/sct".equals(url)) {
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return "http://snomed.info/sct/731000124108/version/"+csver;
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}
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if ("http://loinc.org".equals(url)) {
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return csver;
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}
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if ("http://www.nlm.nih.gov/research/umls/rxnorm".equals(url)) {
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if (csver.length() == 8) {
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return csver.substring(4,6)+csver.substring(6,8)+csver.substring(0,4);
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} else {
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return csver;
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}
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}
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return csver;
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}
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protected ConceptSetComponent getInclude(ValueSet vs, String url, String csver) {
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for (ConceptSetComponent t : vs.getCompose().getInclude()) {
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if (csver == null) {
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if (t.getSystem().equals(url) && !t.hasVersion()) {
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return t;
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}
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} else {
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if (t.getSystem().equals(url) && t.hasVersion() && t.getVersion().equals(csver)) {
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return t;
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}
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}
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}
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ConceptSetComponent c = vs.getCompose().addInclude();
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c.setSystem(url);
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c.setVersion(csver);
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return c;
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}
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protected Document loadXml(InputStream fn) throws Exception {
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DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
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factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
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factory.setFeature("http://xml.org/sax/features/external-general-entities", false);
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factory.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
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factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
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factory.setXIncludeAware(false);
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factory.setExpandEntityReferences(false);
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factory.setNamespaceAware(true);
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DocumentBuilder builder = factory.newDocumentBuilder();
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return builder.parse(fn);
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}
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}
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@ -23,28 +23,18 @@ import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.cache.NpmPackage;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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public class PhinVadsImporter {
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public class PhinVadsImporter extends OIDBasedValueSetImporter {
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public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException {
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// new PhinVadsImporter().importValueSet(TextFile.fileToBytes("C:\\work\\org.hl7.fhir\\packages\\us.cdc.phinvads-source\\source\\PHVS_BirthDefectsLateralityatDiagnosis_HL7_V1.txt"));
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PhinVadsImporter self = new PhinVadsImporter();
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self.init();
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self.process(args[0], args[1]);
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}
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private IWorkerContext context;
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public PhinVadsImporter() {
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public PhinVadsImporter() throws FileNotFoundException, FHIRException, IOException {
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super();
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}
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private void init() throws FileNotFoundException, FHIRException, IOException {
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FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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NpmPackage npm = pcm.loadPackage("hl7.fhir.r5.core", "current");
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SimpleWorkerContext ctxt = SimpleWorkerContext.fromPackage(npm);
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ctxt.setAllowLoadingDuplicates(true);
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ctxt.loadFromPackage(pcm.loadPackage("hl7.terminology"), null);
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context = ctxt;
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init();
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}
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private void process(String source, String dest) {
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@ -84,6 +74,8 @@ public class PhinVadsImporter {
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vs.setDescription(rdr.cell("Value Set Definition"));
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if ("Published".equals(rdr.cell("Value Set Status"))) {
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vs.setStatus(PublicationStatus.ACTIVE);
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} else {
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vs.setStatus(PublicationStatus.DRAFT);
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}
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if (rdr.has("VS Last Updated Date")) {
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vs.setDate(new SimpleDateFormat("mm/dd/yyyy").parse(rdr.cell("VS Last Updated Date")));
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@ -109,40 +101,5 @@ public class PhinVadsImporter {
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return vs;
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}
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private String fixVersionforSystem(String url, String csver) {
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if ("http://snomed.info/sct".equals(url)) {
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return "http://snomed.info/sct|http://snomed.info/sct/731000124108/"+csver;
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}
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if ("http://loinc.org".equals(url)) {
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return csver;
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}
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if ("http://www.nlm.nih.gov/research/umls/rxnorm".equals(url)) {
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if (csver.length() == 8) {
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return csver.substring(4,6)+csver.substring(6,8)+csver.substring(0,4);
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} else {
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return csver;
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}
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}
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return csver;
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}
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private ConceptSetComponent getInclude(ValueSet vs, String url, String csver) {
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for (ConceptSetComponent t : vs.getCompose().getInclude()) {
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if (csver == null) {
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if (t.getSystem().equals(url) && !t.hasVersion()) {
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return t;
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}
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} else {
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if (t.getSystem().equals(url) && t.hasVersion() && t.getVersion().equals(csver)) {
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return t;
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}
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}
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}
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ConceptSetComponent c = vs.getCompose().addInclude();
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c.setSystem(url);
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c.setVersion(csver);
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return c;
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}
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}
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@ -0,0 +1,109 @@
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package org.hl7.fhir.convertors.misc;
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import java.io.ByteArrayInputStream;
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import java.io.File;
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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.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.List;
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import javax.xml.bind.annotation.XmlElement;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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import org.hl7.fhir.r5.formats.JsonParser;
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import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
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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.CSVReader;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.cache.NpmPackage;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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import org.hl7.fhir.utilities.xml.XMLUtil;
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import org.w3c.dom.Element;
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public class VSACImporter extends OIDBasedValueSetImporter {
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public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException {
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// new PhinVadsImporter().importValueSet(TextFile.fileToBytes("C:\\work\\org.hl7.fhir\\packages\\us.cdc.phinvads-source\\source\\PHVS_BirthDefectsLateralityatDiagnosis_HL7_V1.txt"));
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VSACImporter self = new VSACImporter();
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self.process(args[0], args[1]);
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}
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public VSACImporter() throws FileNotFoundException, FHIRException, IOException {
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super();
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init();
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}
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private void process(String source, String dest) {
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for (File f : new File(source).listFiles()) {
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try {
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System.out.println("Process "+f.getName());
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List<ValueSet> vsl = importValueSet(TextFile.fileToBytes(f));
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for (ValueSet vs : vsl) {
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if (vs.getId() != null) {
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new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-"+vs.getId()+".json")), vs);
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}
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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}
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}
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private List<ValueSet> importValueSet(byte[] source) throws Exception {
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List<ValueSet> res = new ArrayList<ValueSet>();
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Element x = loadXml(new ByteArrayInputStream(source)).getDocumentElement();
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List<Element> vl = XMLUtil.getNamedChildren(x, "DescribedValueSet");
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for (Element v : vl) {
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ValueSet vs = new ValueSet();
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vs.setId(v.getAttribute("ID"));
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vs.setUrl("http://vsac.nlm.nih.gov/fhir/ValueSet/"+vs.getId());
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vs.getMeta().setSource("https://vsac.nlm.nih.gov/valueset/"+vs.getId()+"/expansion");
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vs.setVersion(v.getAttribute("version"));
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vs.setTitle(v.getAttribute("displayName"));
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vs.setName(Utilities.titleize(vs.getTitle()).replace(" ", ""));
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Element d = XMLUtil.getNamedChild(v, "Purpose");
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if (d != null) {
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vs.setDescription(d.getTextContent());
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}
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Element s = XMLUtil.getNamedChild(v, "Status");
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if (s != null && "Active".equals(s.getTextContent())) {
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vs.setStatus(PublicationStatus.ACTIVE);
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} else {
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vs.setStatus(PublicationStatus.DRAFT);
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}
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Element dt = XMLUtil.getNamedChild(v, "RevisionDate");
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if (dt != null) {
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vs.getDateElement().setValueAsString(dt.getTextContent());
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}
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Element cl = XMLUtil.getNamedChild(v, "ConceptList");
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Element cc = XMLUtil.getFirstChild(cl);
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while (cc != null) {
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String code = cc.getAttribute("code");
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String display = cc.getAttribute("displayName");
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String csoid = cc.getAttribute("codeSystem");
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String csver = cc.getAttribute("codeSystemVersion");
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String url = context.oid2Uri(csoid);
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if (url == null) {
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url = "urn:oid:"+csoid;
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}
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csver = fixVersionforSystem(url, csver);
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ConceptSetComponent inc = getInclude(vs, url, csver);
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inc.addConcept().setCode(code).setDisplay(display);
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cc = XMLUtil.getNextSibling(cc);
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}
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res.add(vs);
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}
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return res;
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}
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}
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