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NDJSON Exporter #1338

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NDJSON Exporter #1338

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d1f9890
exporter.ndjson.export; exporter.fhir.personal_data
awatson1978 Jul 23, 2023
6783c01
exporter.ndjson.export = false
awatson1978 Aug 15, 2023
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28 changes: 28 additions & 0 deletions src/main/java/org/mitre/synthea/export/Exporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -225,6 +225,8 @@ private static boolean exportRecord(Person person, String fileTag, long stopTime
writeNewFile(outFilePath, bundleJson);
}
}


if (Config.getAsBoolean("exporter.fhir.export")) {
File outDirectory = getOutputFolder("fhir", person);
if (Config.getAsBoolean("exporter.fhir.bulk_data")) {
Expand All @@ -236,13 +238,28 @@ private static boolean exportRecord(Person person, String fileTag, long stopTime
String entryJson = parser.encodeResourceToString(entry.getResource());
appendToFile(outFilePath, entryJson);
}
// } else if (Config.getAsBoolean("exporter.fhir.longitudinal_data")) {
} else if (Config.getAsBoolean("exporter.fhir.personal_data")) {
org.hl7.fhir.r4.model.Bundle bundle = FhirR4.convertToFHIR(person, stopTime);
//IParser parser = FhirR4.getContext().newNdJsonParser().setPrettyPrint(false);
IParser parser = FhirR4.getContext().newJsonParser().setPrettyPrint(false);
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
String filename = entry.getResource().getResourceType().toString() + ".ndjson";
Path outFilePath = outDirectory.toPath().resolve(filename);
String entryJson = parser.encodeResourceToString(entry.getResource());
appendToFile(outFilePath, entryJson);
}
} else {
String bundleJson = FhirR4.convertToFHIRJson(person, stopTime);
Path outFilePath = outDirectory.toPath().resolve(filename(person, fileTag, "json"));
writeNewFile(outFilePath, bundleJson);
}
FhirGroupExporterR4.addPatient((String) person.attributes.get(Person.ID));
}




if (Config.getAsBoolean("exporter.ccda.export")) {
String ccdaXml = CCDAExporter.export(person, stopTime);
File outDirectory = getOutputFolder("ccda", person);
Expand All @@ -255,6 +272,17 @@ private static boolean exportRecord(Person person, String fileTag, long stopTime
Path outFilePath = outDirectory.toPath().resolve(filename(person, fileTag, "json"));
writeNewFile(outFilePath, json);
}

if (Config.getAsBoolean("exporter.ndjson.export")) {
// NDJSON Export
// String ndJson = NdJsonExporter.export(person);
String json = JSONExporter.export(person);
File outDirectory = getOutputFolder("ndjson", person);
Path outFilePath = outDirectory.toPath().resolve(filename(person, fileTag, "ndjson"));
writeNewFile(outFilePath, json);
}


if (Config.getAsBoolean("exporter.csv.export")) {
try {
CSVExporter.getInstance().export(person, stopTime);
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3 changes: 3 additions & 0 deletions src/main/resources/synthea.properties
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Expand Up @@ -22,6 +22,7 @@ exporter.fhir.us_core_version = 5.0.1
exporter.fhir.transaction_bundle = true
# using bulk_data=true will ignore exporter.pretty_print
exporter.fhir.bulk_data = false
exporter.fhir.personal_data = true
# included_ and excluded_resources list out the resource types to include/exclude in the csv exporters.
# only one of these may be set at a time, if both are set then both will be ignored.
# if neither is set, then all resource types will be included.
Expand All @@ -38,7 +39,9 @@ exporter.practitioner.fhir_dstu2.export = false
exporter.encoding = UTF-8
exporter.json.export = false
exporter.json.include_module_history = false
exporter.ndjson.export = false
exporter.csv.export = false

# if exporter.csv.append_mode = true, then each run will add new data to any existing CSVs. if false, each run will clear out the files and start fresh
exporter.csv.append_mode = false
# if exporter.csv.folder_per_run = true, then each run will have CSVs placed into a unique subfolder. if false, each run will only use the top-level csv folder
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