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update PHINVads importer for URL and version issues

This commit is contained in:
Grahame Grieve 2020-08-24 17:13:56 +10:00
parent fe7efcf5a2
commit 86b9db4aec
1 changed files with 23 additions and 2 deletions
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25
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PhinVadsImporter.java
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@ -52,7 +52,9 @@ public class PhinVadsImporter {
try { try {
System.out.println("Process "+f.getName()); System.out.println("Process "+f.getName());
ValueSet vs = importValueSet(TextFile.fileToBytes(f)); ValueSet vs = importValueSet(TextFile.fileToBytes(f));
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-"+vs.getId()+".json")), vs); if (vs.getId() != null) {
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-"+vs.getId()+".json")), vs);
}
} catch (Exception e) { } catch (Exception e) {
e.printStackTrace(); e.printStackTrace();
} }
@ -74,7 +76,7 @@ public class PhinVadsImporter {
ValueSet vs = new ValueSet(); ValueSet vs = new ValueSet();
vs.setId(rdr.cell("Value Set OID")); vs.setId(rdr.cell("Value Set OID"));
vs.setUrl("https://phinvads.cdc.gov/fhir/ValueSet/"+vs.getId()); vs.setUrl("http://phinvads.cdc.gov/fhir/ValueSet/"+vs.getId());
vs.getMeta().setSource("https://phinvads.cdc.gov/vads/ViewValueSet.action?oid="+vs.getId()); vs.getMeta().setSource("https://phinvads.cdc.gov/vads/ViewValueSet.action?oid="+vs.getId());
vs.setVersion(rdr.cell("Value Set Version")); vs.setVersion(rdr.cell("Value Set Version"));
vs.setTitle(rdr.cell("Value Set Name")); vs.setTitle(rdr.cell("Value Set Name"));
@ -100,12 +102,31 @@ public class PhinVadsImporter {
if (url == null) { if (url == null) {
url = "urn:oid:"+csoid; url = "urn:oid:"+csoid;
} }
csver = fixVersionforSystem(url, csver);
ConceptSetComponent inc = getInclude(vs, url, csver); ConceptSetComponent inc = getInclude(vs, url, csver);
inc.addConcept().setCode(code).setDisplay(display); inc.addConcept().setCode(code).setDisplay(display);
} }
return vs; return vs;
} }
private String fixVersionforSystem(String url, String csver) {
if ("http://snomed.info/sct".equals(url)) {
return "http://snomed.info/sct|http://snomed.info/sct/731000124108/"+csver;
}
if ("http://loinc.org".equals(url)) {
return csver;
}
if ("http://www.nlm.nih.gov/research/umls/rxnorm".equals(url)) {
if (csver.length() == 8) {
return csver.substring(4,6)+csver.substring(6,8)+csver.substring(0,4);
} else {
return csver;
}
}
return csver;
}
private ConceptSetComponent getInclude(ValueSet vs, String url, String csver) { private ConceptSetComponent getInclude(ValueSet vs, String url, String csver) {
for (ConceptSetComponent t : vs.getCompose().getInclude()) { for (ConceptSetComponent t : vs.getCompose().getInclude()) {
if (csver == null) { if (csver == null) {