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update ICF importer to handle grouping levels

This commit is contained in:
Grahame Grieve 2023-07-29 08:48:09 +10:00
parent 0165495626
commit 8a893ee793
1 changed files with 47 additions and 22 deletions
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69
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICFImporter.java
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@ -42,35 +42,60 @@ public class ICFImporter {
cs.setCopyright("© World Health Organization 2022\r\nSome rights reserved. This work is available under the Creative Commons Attribution-NoDerivatives 3.0 IGO license (CC BY-ND 3.0 IGO further specified at [[https://icd.who.int/en/docs/ICD11-license.pdf]]). \r\nUnder the terms of this license, you may copy and redistribute the work, provided the work is appropriately cited, as indicated below. In any use of this work, there should be no suggestion that WHO endorses any specific organization, products or services. The use of the WHO logo is not permitted. This license does not allow you to produce adaptations of the work (including translations) without permission from WHO.\r\nAny mediation relating to disputes arising under the license shall be conducted in accordance with the mediation rules of the World Intellectual Property Organization.\r\nThis FHIR version of ICD-11 was generated to support the FHIR Community. The definitive version of ICD-11 is available from [[https://icd.who.int/browse11/l-m/en]].\r\n");
cs.addProperty().setCode("icd11-uri").setDescription("Entity URI to map to ICD_11").setType(PropertyType.CODE);
cs.addProperty().setCode("kind").setDescription("Whether concept is chapter, block, or category").setType(PropertyType.CODE);
cs.addProperty().setCode("IsResidual").setDescription("True if the concept is not completely defined by ICD-11").setType(PropertyType.BOOLEAN);
Map<Integer, ConceptDefinitionComponent> codes = new HashMap<>();
Map<String, ConceptDefinitionComponent> codes = new HashMap<>();
int lastChapter = 0;
int lastBlock = 0;
while (csv.line()) {
String kind = csv.cell("ClassKind");
String code = csv.cell("Code");
if (!Utilities.noString(code)) {
ConceptDefinitionComponent c = new ConceptDefinitionComponent();
c.setCode(code);
c.setDisplay(fixDisplay(csv.cell("Title")));
c.addProperty().setCode("uri").setValue(new CodeType(csv.cell("Linearization (release) URI")));
String b = csv.cell("IsResidual").toLowerCase();
if (!"false".equals(b)) {
c.addProperty().setCode("IsResidual").setValue(new BooleanType(b));
if (Utilities.noString(code)) {
code = csv.cell("BlockId");
}
ConceptDefinitionComponent c = new ConceptDefinitionComponent();
c.setCode(code);
c.setDisplay(fixDisplay(csv.cell("Title")));
c.addProperty().setCode("uri").setValue(new CodeType(csv.cell("Linearization (release) URI")));
c.addProperty().setCode("kind").setValue(new CodeType(kind));
String b = csv.cell("IsResidual").toLowerCase();
if (!"false".equals(b)) {
c.addProperty().setCode("IsResidual").setValue(new BooleanType(b));
}
int level = Integer.parseInt(csv.cell("DepthInKind"));
String id = kind+"-"+level;
String parentId = null;
switch (kind) {
case "chapter":
parentId = null;
lastChapter = level;
break;
case "block":
parentId = "chapter-"+lastChapter;
lastBlock = level;
break;
case "category":
parentId = "block-"+lastBlock;
break;
}
Integer level = Integer.parseInt(csv.cell("DepthInKind"));
if (level == 1) {
cs.getConcept().add(c);
} else {
ConceptDefinitionComponent p = codes.get(level -1);
p.getConcept().add(c);
}
codes.put(level, c);
for (int i = level + 1; i < 100; i++) {
if (codes.containsKey(i)) {
codes.remove(i);
}
if (level > 1) {
parentId = kind+"-"+(level - 1);
}
System.out.println(code+" "+kind+" "+level+" "+id+" "+parentId+" ("+lastChapter+" "+lastBlock+")");
if (parentId == null) {
cs.getConcept().add(c);
} else {
ConceptDefinitionComponent p = codes.get(parentId);
p.getConcept().add(c);
}
codes.put(id, c);
for (int i = level + 1; i < 100; i++) {
if (codes.containsKey(i)) {
codes.remove(i);
}
}
}
csv.close();
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs);