Bugfix - Gradle Build Errors

build.gradle

@@ -13,19 +13,36 @@ buildscript {
     classpath "gradle.plugin.com.github.johnrengelman:shadow:7.1.2"
   }
 }
-apply plugin: "com.github.johnrengelman.shadow"
-
-// Apply the java plugin to add support for Java
-apply plugin: 'java'
+buildscript {
+  repositories {
+    mavenCentral()
+    maven {
+      url "https://oss.sonatype.org/content/repositories/snapshots"
+    }
+  }
+  dependencies {
+    // commons-io used in getting the version id below
+    classpath group: 'commons-io', name: 'commons-io', version: '2.5'
+    // note that commons-io is already a dependency
+    // of commons-csv in the primary dependencies above
+  }
+}
 
-sourceCompatibility = '11'
+plugins {
+  id 'java'
+  id 'application'
+  id 'eclipse'
+  id 'checkstyle'
+  id 'jacoco'
+  id 'maven-publish'
+  id 'signing'
+  id 'com.github.johnrengelman.shadow' version '7.1.2'
+}
 
-apply plugin: 'application'
-apply plugin: 'eclipse'
-apply plugin: 'checkstyle'
-apply plugin: 'jacoco'
-apply plugin: 'maven-publish'
-apply plugin: 'signing'
+java {
+    withJavadocJar()
+    withSourcesJar()
+}
 
 // In this section you declare where to find the dependencies of your project
 repositories {
@@ -147,20 +164,7 @@ test {
   }
 }
 
-buildscript {
-  repositories {
-    mavenCentral()
-    maven {
-      url "https://oss.sonatype.org/content/repositories/snapshots"
-    }
-  }
-  dependencies {
-    // commons-io used in getting the version id below
-    classpath group: 'commons-io', name: 'commons-io', version: '2.5'
-    // note that commons-io is already a dependency
-    // of commons-csv in the primary dependencies above
-  }
-}
+
 
 jacocoTestReport {
   reports {
@@ -324,22 +328,6 @@ run {
   }
 }
 
-task sourceJar(type: Jar) {
-    classifier "sources"
-    from sourceSets.main.allJava
-}
-
-task javadocJar(type: Jar, dependsOn: javadoc) {
-    classifier "javadoc"
-    from javadoc.destinationDir
-}
-
-artifacts {
-    archives jar
-    archives sourceJar
-    archives javadocJar
-}
-
 def mavenGroup = 'org.mitre.synthea'
 def mavenVersion = '3.2.1-SNAPSHOT'
 
@@ -350,12 +338,6 @@ publishing {
             version mavenVersion
             from components.java
 
-            artifact(sourceJar) {
-                classifier = 'sources'
-            }
-            artifact(javadocJar) {
-                classifier = 'javadoc'
-            }
             pom {
                 name = 'Synthea'
                 description = 'Synthetic Patient Population Simulator'

src/main/java/org/mitre/synthea/export/Exporter.java

@@ -225,6 +225,8 @@
         writeNewFile(outFilePath, bundleJson);
       }
     }
+
+
     if (Config.getAsBoolean("exporter.fhir.export")) {
       File outDirectory = getOutputFolder("fhir", person);
       if (Config.getAsBoolean("exporter.fhir.bulk_data")) {
@@ -236,13 +238,28 @@
           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);
@@ -255,6 +272,17 @@
       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);

src/main/resources/synthea.properties

@@ -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 = false
 # 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.
@@ -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 = true
 exporter.csv.export = false
+exporter.ndjson.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