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Add support for active only to VSAC importer

This commit is contained in:
Grahame Grieve 2024-09-22 06:38:04 -04:00
parent 859bac5367
commit 15278061f9
1 changed files with 30 additions and 6 deletions
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36
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
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@ -45,10 +45,10 @@ public class VSACImporter extends OIDBasedValueSetImporter {
public static void main(String[] args) throws FHIRException, IOException, ParseException, URISyntaxException {
VSACImporter self = new VSACImporter();
self.process(args[0], args[1], args[2], "true".equals(args[3]));
self.process(args[0], args[1], args[2], "true".equals(args[3]), "true".equals(args[4]));
}
private void process(String source, String dest, String apiKey, boolean onlyNew) throws FHIRException, IOException, URISyntaxException {
private void process(String source, String dest, String apiKey, boolean onlyNew, boolean onlyActive) throws FHIRException, IOException, URISyntaxException {
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(source));
csv.readHeaders();
Map<String, String> errs = new HashMap<>();
@ -75,13 +75,20 @@ public class VSACImporter extends OIDBasedValueSetImporter {
System.out.println("Loading");
List<String> oids = new ArrayList<>();
List<String> allOids = new ArrayList<>();
while (csv.line()) {
String oid = csv.cell("OID");
if (!onlyNew || !(ManagedFileAccess.file(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
oids.add(oid);
String status = csv.cell("Expansion Status");
if (!onlyActive || "Active".equals(status)) {
String oid = csv.cell("OID");
allOids.add(oid);
if (!onlyNew || !(ManagedFileAccess.file(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
oids.add(oid);
}
}
}
Collections.sort(oids);
System.out.println("Cleaning");
cleanValueSets(allOids, dest);
System.out.println("Go: "+oids.size()+" oids");
int i = 0;
int j = 0;
@ -108,6 +115,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
errs.put(oid, e.getMessage());
}
}
OperationOutcome oo = new OperationOutcome();
for (String oid : errs.keySet()) {
oo.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.EXCEPTION).setDiagnostics(errs.get(oid)).addLocation(oid);
@ -116,6 +124,22 @@ public class VSACImporter extends OIDBasedValueSetImporter {
System.out.println("Done. " + i + " ValueSets in "+Utilities.describeDuration(System.currentTimeMillis() - tt));
}
private void cleanValueSets(List<String> allOids, String dest) throws IOException {
cleanValueSets(allOids, new File(Utilities.path(dest)));
}
private void cleanValueSets(List<String> allOids, File file) {
for (File f : file.listFiles()) {
if (f.getName().startsWith("ValueSet-")) {
String oid = f.getName().substring(9).replace(".json", "");
if (!allOids.contains(oid)) {
f.delete();
}
}
}
}
private long estimate(int i, int size, long tt) {
long elapsed = System.currentTimeMillis() - tt;
long average = elapsed / i;
@ -201,7 +225,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
}
vs.setName(makeValidName(vs.getName()));
JurisdictionUtilities.setJurisdictionCountry(vs.getJurisdiction(), "US");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
return true;
}
}