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update VSACImporter to get value sets from VSAC directly

This commit is contained in:
Grahame Grieve 2020-09-04 16:21:12 +10:00
parent 325c750814
commit fd6fe88528
1 changed files with 85 additions and 64 deletions
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149
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
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@ -1,26 +1,29 @@
package org.hl7.fhir.convertors.misc;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Element;
import java.io.*;
import java.net.URISyntaxException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.List;
public class VSACImporter extends OIDBasedValueSetImporter {
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException {
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException, URISyntaxException {
// new PhinVadsImporter().importValueSet(TextFile.fileToBytes("C:\\work\\org.hl7.fhir\\packages\\us.cdc.phinvads-source\\source\\PHVS_BirthDefectsLateralityatDiagnosis_HL7_V1.txt"));
VSACImporter self = new VSACImporter();
self.process(args[0], args[1]);
self.process(args[0], args[1], args[2], args[3]);
}
public VSACImporter() throws FileNotFoundException, FHIRException, IOException {
@ -28,69 +31,87 @@ public class VSACImporter extends OIDBasedValueSetImporter {
init();
}
private void process(String source, String dest) {
for (File f : new File(source).listFiles()) {
private void process(String source, String dest, String username, String password) throws FHIRException, FileNotFoundException, IOException, URISyntaxException {
CSVReader csv = new CSVReader(new FileInputStream(source));
csv.readHeaders();
FHIRToolingClient client = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir", username, password);
int i = 0;
while (csv.line()) {
String oid = csv.cell("OID");
try {
System.out.println("Process " + f.getName());
List<ValueSet> vsl = importValueSet(TextFile.fileToBytes(f));
for (ValueSet vs : vsl) {
if (vs.getId() != null) {
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
}
ValueSet vs = client.read(ValueSet.class, oid);
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-"+oid+".json")), vs);
i++;
if (i % 100 == 0) {
System.out.println(i);
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("Unable to fetch OID "+oid+": "+e.getMessage());
}
}
System.out.println("Done. "+i+" ValueSets");
// for (File f : new File(source).listFiles()) {
// try {
// System.out.println("Process " + f.getName());
// List<ValueSet> vsl = importValueSet(TextFile.fileToBytes(f));
// for (ValueSet vs : vsl) {
// if (vs.getId() != null) {
// new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
// }
// }
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
}
private List<ValueSet> importValueSet(byte[] source) throws Exception {
List<ValueSet> res = new ArrayList<ValueSet>();
Element x = loadXml(new ByteArrayInputStream(source)).getDocumentElement();
List<Element> vl = XMLUtil.getNamedChildren(x, "DescribedValueSet");
for (Element v : vl) {
ValueSet vs = new ValueSet();
vs.setId(v.getAttribute("ID"));
vs.setUrl("http://vsac.nlm.nih.gov/fhir/ValueSet/" + vs.getId());
vs.getMeta().setSource("https://vsac.nlm.nih.gov/valueset/" + vs.getId() + "/expansion");
vs.setVersion(v.getAttribute("version"));
vs.setTitle(v.getAttribute("displayName"));
vs.setName(Utilities.titleize(vs.getTitle()).replace(" ", ""));
Element d = XMLUtil.getNamedChild(v, "Purpose");
if (d != null) {
vs.setDescription(d.getTextContent());
}
Element s = XMLUtil.getNamedChild(v, "Status");
if (s != null && "Active".equals(s.getTextContent())) {
vs.setStatus(PublicationStatus.ACTIVE);
} else {
vs.setStatus(PublicationStatus.DRAFT);
}
Element dt = XMLUtil.getNamedChild(v, "RevisionDate");
if (dt != null) {
vs.getDateElement().setValueAsString(dt.getTextContent());
}
Element cl = XMLUtil.getNamedChild(v, "ConceptList");
Element cc = XMLUtil.getFirstChild(cl);
while (cc != null) {
String code = cc.getAttribute("code");
String display = cc.getAttribute("displayName");
String csoid = cc.getAttribute("codeSystem");
String csver = cc.getAttribute("codeSystemVersion");
String url = context.oid2Uri(csoid);
if (url == null) {
url = "urn:oid:" + csoid;
}
csver = fixVersionforSystem(url, csver);
ConceptSetComponent inc = getInclude(vs, url, csver);
inc.addConcept().setCode(code).setDisplay(display);
cc = XMLUtil.getNextSibling(cc);
}
res.add(vs);
}
return res;
}
// private List<ValueSet> importValueSet(byte[] source) throws Exception {
// List<ValueSet> res = new ArrayList<ValueSet>();
// Element x = loadXml(new ByteArrayInputStream(source)).getDocumentElement();
// List<Element> vl = XMLUtil.getNamedChildren(x, "DescribedValueSet");
// for (Element v : vl) {
// ValueSet vs = new ValueSet();
// vs.setId(v.getAttribute("ID"));
// vs.setUrl("http://cts.nlm.nih.gov/fhir/ValueSet/" + vs.getId());
// vs.getMeta().setSource("https://vsac.nlm.nih.gov/valueset/" + vs.getId() + "/expansion");
// vs.setVersion(v.getAttribute("version"));
// vs.setTitle(v.getAttribute("displayName"));
// vs.setName(Utilities.titleize(vs.getTitle()).replace(" ", ""));
// Element d = XMLUtil.getNamedChild(v, "Purpose");
// if (d != null) {
// vs.setDescription(d.getTextContent());
// }
// Element s = XMLUtil.getNamedChild(v, "Status");
// if (s != null && "Active".equals(s.getTextContent())) {
// vs.setStatus(PublicationStatus.ACTIVE);
// } else {
// vs.setStatus(PublicationStatus.DRAFT);
// }
// Element dt = XMLUtil.getNamedChild(v, "RevisionDate");
// if (dt != null) {
// vs.getDateElement().setValueAsString(dt.getTextContent());
// }
//
// Element cl = XMLUtil.getNamedChild(v, "ConceptList");
// Element cc = XMLUtil.getFirstChild(cl);
//
// while (cc != null) {
// String code = cc.getAttribute("code");
// String display = cc.getAttribute("displayName");
// String csoid = cc.getAttribute("codeSystem");
// String csver = cc.getAttribute("codeSystemVersion");
// String url = context.oid2Uri(csoid);
// if (url == null) {
// url = "urn:oid:" + csoid;
// }
// csver = fixVersionforSystem(url, csver);
// ConceptSetComponent inc = getInclude(vs, url, csver);
// inc.addConcept().setCode(code).setDisplay(display);
// cc = XMLUtil.getNextSibling(cc);
// }
//
// res.add(vs);
// }
// return res;
// }
}