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Merge pull request hapifhir#1527 from hapifhir/2023-12-gg-big-tx-rework
2023 12 gg big tx rework
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org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CVXImporter.java
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| package org.hl7.fhir.convertors.misc; | ||
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| 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; | ||
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| import javax.xml.parsers.ParserConfigurationException; | ||
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| 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; | ||
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| /** | ||
| * 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 | ||
| */ | ||
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| public class CVXImporter { | ||
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| public class CVXSorter implements Comparator<ConceptDefinitionComponent> { | ||
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| @Override | ||
| public int compare(ConceptDefinitionComponent o1, ConceptDefinitionComponent o2) { | ||
| int i1 = Integer.parseInt(o1.getCode()); | ||
| int i2 = Integer.parseInt(o2.getCode()); | ||
| return i1-i2; | ||
| } | ||
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| } | ||
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| public static void main(String[] args) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException, ParserConfigurationException, SAXException { | ||
| new CVXImporter().doUpdate(args[0], args[1]); | ||
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| } | ||
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| private void doUpdate(String source, String dest) throws FHIRFormatError, FileNotFoundException, IOException, ParserConfigurationException, SAXException { | ||
| CodeSystem cvx = (CodeSystem) new JsonParser().parse(new FileInputStream(dest)); | ||
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| String ldate = null; | ||
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| 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); | ||
| } | ||
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| private ConceptDefinitionComponent findCVXCode(CodeSystem cvx, String code) { | ||
| for (ConceptDefinitionComponent t : cvx.getConcept()) { | ||
| if (code.equals(t.getCode())) { | ||
| return t; | ||
| } | ||
| } | ||
| return null; | ||
| } | ||
| } |
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