fix bug in csv processor for BOM + search interversion generator
This commit is contained in:
Grahame Grieve
parent
3a5d7146a7
commit
881fdc9284
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@ -0,0 +1,297 @@
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package org.hl7.fhir.convertors.misc;
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import java.io.FileInputStream;
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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.io.UnsupportedEncodingException;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Date;
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import java.util.List;
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import org.hl7.fhir.convertors.misc.SearchParameterProcessor.SPRelationship;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.formats.JsonParser;
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import org.hl7.fhir.r5.model.ConceptMap;
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import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent;
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import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
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import org.hl7.fhir.r5.model.Enumerations.ConceptMapEquivalence;
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import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
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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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public class SearchParameterProcessor {
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public class SPRelationship {
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private String r4;
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private String r3;
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private String r2b;
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private String r2;
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public SPRelationship(String r4, String r3, String r2b, String r2) {
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super();
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this.r4 = r4;
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this.r3 = r3;
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this.r2b = r2b;
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this.r2 = r2;
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}
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public String getR4() {
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return r4;
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}
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public String getR3() {
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return r3;
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}
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public String getR2b() {
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return r2b;
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}
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public String getR2() {
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return r2;
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}
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public String getByCode(String code) {
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if ("R4".equals(code))
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return r4;
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if ("R3".equals(code))
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return r3;
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if ("R2b".equals(code))
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return r2b;
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if ("R2".equals(code))
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return r2;
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return null;
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}
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}
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private static final String ROOT = "C:\\work\\org.hl7.fhir\\org.fhir.interversion\\package";
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private List<SPRelationship> list = new ArrayList<>();
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private List<String> list4 = new ArrayList<>();
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private List<String> list3 = new ArrayList<>();
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private List<String> list2 = new ArrayList<>();
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private List<String> list2b = new ArrayList<>();
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private void load() throws FileNotFoundException, IOException, FHIRException {
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load4();
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load3();
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load2b();
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load2();
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loadCsv();
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check4();
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check3();
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check2b();
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check2();
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generate("R3", "R4", "STU3", "R4");
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generate("R4", "R3", "R4", "STU3");
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generate("R2", "R4", "DSTU2", "R4");
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generate("R4", "R2", "R4", "DSTU2");
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generate("R2", "R3", "DSTU2", "STU3");
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generate("R3", "R2", "STU3", "DSTU2");
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}
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private void generate(String src, String dst, String srcURL, String tgtURL) throws FileNotFoundException, IOException {
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ConceptMap map = new ConceptMap();
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map.setId("search-parameters-"+src+"-to-"+dst);
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map.setUrl("http://hl7.org/fhir/interversion/ConceptMap/"+map.getId());
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map.setName("SearchParameterMap"+src+dst);
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map.setTitle("Search Parameter Map - "+src+" to "+dst);
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map.setStatus(PublicationStatus.DRAFT);
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map.setDate(new Date());
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map.setExperimental(false);
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map.setPublisher("HL7");
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ConceptMapGroupComponent group = map.addGroup();
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group.setSource("http://hl7.org/fhir/"+srcURL);
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group.setTarget("http://hl7.org/fhir/"+tgtURL);
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for (SPRelationship sp : list) {
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String s = sp.getByCode(src);
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String d = sp.getByCode(dst);
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if (!Utilities.noString(s) && !Utilities.noString(d)) {
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SourceElementComponent e = makeElement(s, group);
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e.addTarget().setCode(d).setEquivalence(ConceptMapEquivalence.RELATEDTO);
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}
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}
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(ROOT, "ConceptMap-"+map.getId()+".json")), map);
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}
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private SourceElementComponent makeElement(String code, ConceptMapGroupComponent group) {
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for (SourceElementComponent e : group.getElement()) {
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if (e.getCode().equals(code))
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return e;
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}
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return group.addElement().setCode(code);
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}
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private void check4() {
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for (String s : list4) {
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boolean ok = false;
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for (SPRelationship t : list) {
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if (s.equals(t.r4))
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ok = true;
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}
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if (!ok)
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System.out.println("R4 missing : "+s);
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}
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for (SPRelationship sp : list) {
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if (!Utilities.noString(sp.r4)) {
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boolean ok = list4.contains(sp.r4);
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if (!ok)
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System.out.println("R4 extra : "+sp.r4);
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}
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}
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}
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private void check3() {
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for (String s : list3) {
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boolean ok = false;
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for (SPRelationship t : list) {
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if (s.equals(t.r3))
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ok = true;
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}
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if (!ok)
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System.out.println("R3 : "+s);
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}
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for (SPRelationship sp : list) {
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if (!Utilities.noString(sp.r3)) {
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boolean ok = list3.contains(sp.r3);
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if (!ok)
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System.out.println("R3 extra : "+sp.r3);
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}
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}
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}
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private void check2b() {
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for (String s : list2b) {
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boolean ok = false;
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for (SPRelationship t : list) {
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if (s.equals(t.r2b))
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ok = true;
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}
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if (!ok)
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System.out.println("R2b : "+s);
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}
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for (SPRelationship sp : list) {
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if (!Utilities.noString(sp.r2b)) {
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boolean ok = list2b.contains(sp.r2b);
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if (!ok)
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System.out.println("R2b extra : "+sp.r2b);
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}
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}
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}
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private void check2() {
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for (String s : list2) {
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boolean ok = false;
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for (SPRelationship t : list) {
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if (s.equals(t.r2))
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ok = true;
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}
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if (!ok)
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System.out.println("R2 : "+s);
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}
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for (SPRelationship sp : list) {
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if (!Utilities.noString(sp.r2)) {
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boolean ok = list2.contains(sp.r2);
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if (!ok)
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System.out.println("R2 extra : "+sp.r2);
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}
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}
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}
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private void load4() throws FHIRFormatError, FileNotFoundException, IOException {
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org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp4.json"));
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for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
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org.hl7.fhir.r4.model.SearchParameter sp = (org.hl7.fhir.r4.model.SearchParameter) be.getResource();
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for (org.hl7.fhir.r4.model.CodeType br : sp.getBase()) {
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if (!Utilities.existsInList(br.asStringValue(), "DomainResource", "Resource"))
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list4.add(br.asStringValue()+"."+sp.getCode());//+", "+sp.getType().toCode());
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}
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}
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Collections.sort(list4);
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System.out.println("R4 loaded - "+list4.size()+" parameters");
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}
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private void load3() throws FHIRFormatError, FileNotFoundException, IOException {
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org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp3.json"));
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for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
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org.hl7.fhir.dstu3.model.SearchParameter sp = (org.hl7.fhir.dstu3.model.SearchParameter) be.getResource();
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for (org.hl7.fhir.dstu3.model.CodeType br : sp.getBase()) {
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if (!Utilities.existsInList(br.asStringValue(), "DomainResource", "Resource"))
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list3.add(br.asStringValue()+"."+sp.getCode());//+", "+sp.getType().toCode());
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}
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}
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Collections.sort(list3);
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System.out.println("R3 loaded - "+list3.size()+" parameters");
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}
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private void load2() throws FHIRFormatError, FileNotFoundException, IOException {
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org.hl7.fhir.dstu2.model.Bundle bundle = (org.hl7.fhir.dstu2.model.Bundle) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp2.json"));
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for (org.hl7.fhir.dstu2.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
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org.hl7.fhir.dstu2.model.SearchParameter sp = (org.hl7.fhir.dstu2.model.SearchParameter) be.getResource();
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String br = sp.getBase();
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if (!Utilities.existsInList(br, "DomainResource", "Resource"))
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list2.add(br+"."+sp.getCode());//+", "+sp.getType().toCode());
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}
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Collections.sort(list2);
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System.out.println("R2 loaded - "+list2.size()+" parameters");
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}
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private void load2b() throws FHIRFormatError, FileNotFoundException, IOException {
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org.hl7.fhir.dstu2016may.model.Bundle bundle = (org.hl7.fhir.dstu2016may.model.Bundle) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp2b.json"));
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for (org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
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org.hl7.fhir.dstu2016may.model.SearchParameter sp = (org.hl7.fhir.dstu2016may.model.SearchParameter) be.getResource();
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String br = sp.getBase();
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if (!Utilities.existsInList(br, "DomainResource", "Resource"))
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list2b.add(br+"."+sp.getCode());//+", "+sp.getType().toCode());
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}
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Collections.sort(list2b);
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System.out.println("R2b loaded - "+list2b.size()+" parameters");
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}
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private void loadCsv() throws IOException, FHIRException {
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CSVReader csv = new CSVReader(new FileInputStream("C:\\work\\org.hl7.fhir\\org.fhir.interversion\\work\\search-params.csv"));
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csv.readHeaders();
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while (csv.line()) {
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String r4 = csv.cell("R4");
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String r3 = csv.cell("R3");
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String r2b = csv.cell("R2b");
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String r2 = csv.cell("R2");
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if (!Utilities.noString(r4) || !Utilities.noString(r3) || !Utilities.noString(r2b) || !Utilities.noString(r2)) {
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boolean ok = (!Utilities.noString(r4) && r4.contains(".")) ||
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(!Utilities.noString(r3) && r3.contains(".")) ||
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(!Utilities.noString(r2b) && r2b.contains(".")) ||
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(!Utilities.noString(r2) && r2.contains("."));
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if (ok) {
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list.add(new SPRelationship(r4, r3, r2b, r2));
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}
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}
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}
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System.out.println("Map loaded - "+list.size()+" entries");
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}
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// private void generate(String name) throws IOException {
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// StringBuilder b = new StringBuilder();
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//
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// String rn = "";
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// Collections.sort(list);
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// for (String s : list) {
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// String rnn = s.substring(0, s.indexOf("."));
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// if (!rnn.equals(rn)) {
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// rn = rnn;
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// b.append(rn+"\r\n");
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// }
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// b.append(s+"\r\n");
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// }
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// TextFile.stringToFile(b.toString(), name);
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// }
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//
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public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
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new SearchParameterProcessor().load();
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}
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}
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@ -70,7 +70,7 @@ public class CSVProcessor {
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public class DataReader extends CSVReader {
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public DataReader(InputStream data) throws UnsupportedEncodingException {
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public DataReader(InputStream data) throws FHIRException, IOException {
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super(data);
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}
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@ -125,7 +125,7 @@ public class CSVProcessor {
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this.source = source;
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}
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public void setData(InputStream data) {
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public void setData(InputStream data) throws FHIRException, IOException {
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try {
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this.data = new DataReader(data);
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} catch (UnsupportedEncodingException e) {
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@ -65,11 +65,18 @@ import org.hl7.fhir.exceptions.FHIRException;
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*/
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public class CSVReader extends InputStreamReader {
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public CSVReader(InputStream in) throws UnsupportedEncodingException {
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public CSVReader(InputStream in) throws FHIRException, IOException {
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super(in, "UTF-8");
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checkBOM();
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}
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private String[] cols;
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private void checkBOM() throws FHIRException, IOException {
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if (peek() == '\uFEFF')
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next();
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}
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private String[] cols;
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private String[] cells;
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public void readHeaders() throws IOException, FHIRException {
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@ -92,7 +99,7 @@ public class CSVReader extends InputStreamReader {
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public String cell(String name) {
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int index = -1;
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for (int i = 0; i < cols.length; i++) {
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if (name.equals(cols[i]))
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if (name.equals(cols[i].trim()))
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index = i;
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}
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if (index == -1)
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