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Added feature for generating the parameters file #1452

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merged 3 commits into from
May 16, 2024
Merged

Added feature for generating the parameters file #1452

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ef2543e
Added feature for generating the parameters file
jkiddo Apr 28, 2024
52bff28
Reverting back to default
jkiddo Apr 28, 2024
c3584b4
Added config option and fixed checkstyle remarks
jkiddo Apr 30, 2024
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33 changes: 33 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 @@ -21,9 +21,12 @@
import java.util.concurrent.LinkedBlockingQueue;
import java.util.function.Predicate;

import com.google.common.base.Strings;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;

import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.mitre.synthea.engine.Generator;
import org.mitre.synthea.export.flexporter.Actions;
import org.mitre.synthea.export.flexporter.FhirPathUtils;
Expand Down Expand Up @@ -499,6 +502,36 @@ public static void runPostCompletionExports(Generator generator) {
*/
public static void runPostCompletionExports(Generator generator, ExporterRuntimeOptions options) {

if (Config.getAsBoolean("exporter.fhir.bulk_data")) {
IParser parser = FhirR4.getContext().newJsonParser();
parser.setPrettyPrint(false);
Parameters parameters = new Parameters()
.addParameter("inputFormat","application/fhir+ndjson");
File outDirectory = getOutputFolder("fhir", null);

File[] files = outDirectory.listFiles(pathname -> pathname.getName().endsWith("ndjson"));

String configHostname = Config.get("exporter.fhir.bulk_data.parameter_hostname");
String hostname = Strings.isNullOrEmpty(configHostname)
? "http://localhost:8080/" : configHostname;

for (File file : files) {
parameters.addParameter(
new Parameters.ParametersParameterComponent().setName("input")
.addPart(new Parameters.ParametersParameterComponent()
.setName("type")
.setValue(new StringType(file.getName().split("\\.")[0])))
.addPart(new Parameters.ParametersParameterComponent()
.setName("url")
.setValue(new StringType(hostname + file.getName()))));
}
overwriteFile(outDirectory.
toPath().
resolve("parameters.json"),
parser.encodeResourceToString(parameters));
}


if (options.deferExports) {
ExporterRuntimeOptions nonDeferredOptions = new ExporterRuntimeOptions(options);
nonDeferredOptions.deferExports = false;
Expand Down
2 changes: 2 additions & 0 deletions src/main/resources/synthea.properties
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Expand Up @@ -22,6 +22,8 @@ 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
# hostname embedded into the generated parameters file. Defaults to http://localhost:8000/
#exporter.fhir.bulk_data.parameter_hostname = http://example.org/
# 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 Down
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