Merge pull request #1452 from trifork/feat/support-bulk-import-format

Added feature for generating the parameters file
synthetichealth · May 16, 2024 · ecc34a8 · ecc34a8
2 parents 34bcc75 + c3584b4
commit ecc34a8
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diff --git a/src/main/java/org/mitre/synthea/export/Exporter.java b/src/main/java/org/mitre/synthea/export/Exporter.java
@@ -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;
@@ -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;

diff --git a/src/main/resources/synthea.properties b/src/main/resources/synthea.properties
@@ -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.