Add CVX Importer

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CVXImporter.java

@@ -0,0 +1,108 @@
+package org.hl7.fhir.convertors.misc;
+
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Date;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.fhir.ucum.Utilities;
+import org.hl7.fhir.convertors.misc.CVXImporter.CVXSorter;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+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.ConceptDefinitionComponent;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
+import org.hl7.fhir.utilities.xml.XMLUtil;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+/**
+ * To use this class, download the CVX definitions from 
+ * https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx
+ * using the XML-new format, and then execute this class with two parameters:
+ * - the name of the downloaded file
+ * - a local name for the file https://github.com/FHIR/packages/blob/master/packages/fhir.tx.support.r4/package/CodeSystem-cvx.json
+ * 
+ * //.Users/grahamegrieve/work/packages/packages/fhir.tx.support.r4/package/CodeSystem-cvx.json
+ */
+
+public class CVXImporter {
+
+  public class CVXSorter implements Comparator<ConceptDefinitionComponent> {
+
+    @Override
+    public int compare(ConceptDefinitionComponent o1, ConceptDefinitionComponent o2) {
+      int i1 = Integer.parseInt(o1.getCode());
+      int i2 = Integer.parseInt(o2.getCode());
+      return i1-i2;
+    }
+
+  }
+
+  public static void main(String[] args) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException, ParserConfigurationException, SAXException {
+    new CVXImporter().doUpdate(args[0], args[1]);
+
+  }
+
+  private void doUpdate(String source, String dest) throws FHIRFormatError, FileNotFoundException, IOException, ParserConfigurationException, SAXException {
+    CodeSystem cvx = (CodeSystem) new JsonParser().parse(new FileInputStream(dest));
+    
+    String ldate = null;
+    
+    Document xml = XMLUtil.parseFileToDom(source);
+    Element cvxCodes = xml.getDocumentElement();
+    for (Element cvsInfo : XMLUtil.getNamedChildren(cvxCodes, "CVXInfo")) {
+      String desc = XMLUtil.getNamedChildText(cvsInfo, "ShortDescription").trim();
+      String name = XMLUtil.getNamedChildText(cvsInfo, "FullVaccinename").trim();
+      String code = XMLUtil.getNamedChildText(cvsInfo, "CVXCode").trim();
+      String notes = XMLUtil.getNamedChildText(cvsInfo, "Notes");
+      String status = XMLUtil.getNamedChildText(cvsInfo, "Status").trim();
+      String date = XMLUtil.getNamedChildText(cvsInfo, "LastUpdated").trim();
+      ConceptDefinitionComponent def = findCVXCode(cvx, code);
+      if (def == null) {
+        def = cvx.addConcept();
+        def.setCode(code);
+      } else {
+        def.getDesignation().clear();
+      }
+      def.setDisplay(name);
+      def.addDesignation().setValue(desc).setLanguage("en").setUse(new Coding().setSystem("http://snomed.info/sct").setCode("900000000000013009").setDisplay("Synonym"));
+      if (!Utilities.noString(notes)) {
+        def.forceProperty("notes").setValue(new StringType(notes.trim()));
+      }
+      def.forceProperty("vaccine-status").setValue(new CodeType(status.trim()));
+      String[] d = date.split("\\/");
+      String vdate = d[2]+"-"+Utilities.padLeft(d[0], '0', 2)+"-"+Utilities.padLeft(d[1], '0', 2);
+      def.forceProperty("last-updated").setValue(new DateTimeType(vdate));
+      if (ldate == null || ldate.compareTo(vdate) < 0) {
+        ldate = vdate;
+      }
+    }
+    Collections.sort(cvx.getConcept(), new CVXSorter());
+    cvx.setDateElement(new DateTimeType(ldate));
+    cvx.setVersion(ldate.replace("-", ""));
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), cvx);
+  }
+
+  private ConceptDefinitionComponent findCVXCode(CodeSystem cvx, String code) {
+    for (ConceptDefinitionComponent t : cvx.getConcept()) {
+      if (code.equals(t.getCode())) {
+        return t;
+      }
+    }
+    return null;
+  }
+}