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fix bug in NpmPackage loader

This commit is contained in:
Grahame Grieve 2019-11-19 06:37:18 +11:00
parent 9b04cff812
commit 0dfc060665
3 changed files with 66 additions and 7 deletions
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20
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/CodeableConcept.java
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@ -58,6 +58,7 @@ import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
import ca.uhn.fhir.model.api.annotation.Description;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.dstu2.model.Coding;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
/**
@ -252,6 +253,25 @@ public class CodeableConcept extends Type implements ICompositeType {
;
}
// added from java-adornments.txt:
public boolean hasCoding(String system, String code) {
for (Coding c : getCoding()) {
if (system.equals(c.getSystem()) && code.equals(c.getCode()))
return true;
}
return false;
}
public CodeableConcept(Coding code) {
super();
addCoding(code);
}
// end addition
}

51
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/importers/Mimic14Importer.java
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@ -952,6 +952,7 @@ public class Mimic14Importer {
bnd.setType(BundleType.COLLECTION);
csv.readHeaders();
int t = 0;
Set<String> rell = new HashSet<>();
while (csv.line()) {
Encounter enc = new Encounter();
t++;
@ -970,16 +971,35 @@ public class Mimic14Importer {
}
// ignore insurance
if (csv.has("language")) {
pat.getCommunication().clear();
pat.addCommunication().getLanguage().setText(csv.cell("language"));
String lang = ini.getStringProperty("language", csv.cell("language"));
if (lang == null) {
System.out.println("Unknown language: "+csv.cell("language"));
} else {
pat.getCommunication().clear();
pat.addCommunication().getLanguage().addCoding(iniCodeToCoding(lang, "urn:ietf:bcp:47", "language", csv.cell("language")));
}
}
if (csv.has("religion")) {
ToolingExtensions.removeExtension(pat, "http://hl7.org/fhir/StructureDefinition/patient-religion");
pat.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/patient-religion").setValue(new CodeableConcept().setText(csv.cell("religion")));
String religion = ini.getStringProperty("religion", csv.cell("religion"));
if (religion == null) {
if (!rell.contains(csv.cell("religion"))) {
System.out.println("unknown religion "+csv.cell("religion"));
}
rell.add(csv.cell("religion"));
} else {
ToolingExtensions.removeExtension(pat, "http://hl7.org/fhir/StructureDefinition/patient-religion");
pat.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/patient-religion").setValue(new CodeableConcept(iniCodeToCoding(religion, null, "religion", csv.cell("religion"))));
}
}
if (csv.has("marital_status")) {
pat.getMaritalStatus().getCoding().clear();
pat.getMaritalStatus().addCoding().setSystem("http://mimic.physionet.org/fhir/MaritalStatus").setCode(csv.cell("marital_status"));
String ms = ini.getStringProperty("marital-status", csv.cell("marital_status"));
if (ms == null) {
System.out.println("Unknown marital-status: "+csv.cell("marital_status"));
} else {
pat.getMaritalStatus().getCoding().clear();
pat.getMaritalStatus().addCoding(iniCodeToCoding(ms, null, "marital-status", csv.cell("marital_status")));
}
}
if (csv.has("ethnicity")) {
ToolingExtensions.removeExtension(pat, "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
@ -999,6 +1019,25 @@ public class Mimic14Importer {
return bnd;
}
private Coding iniCodeToCoding(String code, String defSystem, String context, String value) {
Coding res = new Coding();
if (code.contains("#")) {
res.setSystem(code.substring(0, code.indexOf("#")).trim());
code = code.substring(code.indexOf("#")+1);
} else if (defSystem == null) {
throw new Error("Code for "+value+" in section ["+context+"] does not contain a system, and a system is required");
} else {
res.setSystem(defSystem);
}
if (code.contains(": ")) {
res.setCode(code.substring(0, code.indexOf(":")));
res.setDisplay(code.substring(code.indexOf(":")+1).trim());
} else {
res.setCode(code.trim());
}
return res;
}
private Bundle processPatients(String src) throws FileNotFoundException, IOException {
System.out.print("Processing Patients... ");
CSVReader csv = new CSVReader(new FileInputStream(src));

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
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@ -192,7 +192,7 @@ public class NpmPackage {
try {
res.readIndexFile((JsonObject) JsonTrackingParser.parseJson(new String(res.content.get("package/.index.json"))));
} catch (Exception e) {
TextFile.bytesToFile(res.content.get("package/.index.json"), "c:\\temp\\.index.json");
TextFile.bytesToFile(res.content.get("package/.index.json"), Utilities.path("[tmp]", ".index.json"));
throw new IOException("Error parsing package/.index.json: "+e.getMessage(), e);
}
return res;