Merge

Author: jawalonoski

.github/ISSUE_TEMPLATE/bug-template.yml

@@ -0,0 +1,41 @@
+name: Bug Report
+description: File a bug report
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+
+        Please note that this template is for bugs only. This is a case where Synthea crashes,
+        behaves in an unexpected way or outputs incorrect information.
+
+        If you have a question about how Synthea works, please visit Synthea Discussions.
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+      placeholder: Tell us what you see!
+      value: "A bug happened!"
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Environment
+      description: |
+        examples:
+          - **OS**: macOS 12.2.1
+          - **Java**: openjdk version 17.0.1
+      value: |
+          - OS:
+          - Java:
+      render: markdown
+    validations:
+      required: false
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: shell

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature-template.yml

@@ -0,0 +1,24 @@
+name: Feature Request
+description: Request a new feature in Synthea
+labels: ["feature"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this feature request!
+
+        Prior to filling out a feature request, it is recommended to open a Synthea Discussion
+        to ensure that the desired functionality is something that can't be currently achieved
+        with Synthea and that the idea is something that the Synthea team would be willing to
+        incorporate.
+
+        Also, please check the [Contributions to Avoid](https://github.com/synthetichealth/synthea/wiki/Contributing#contributions-to-avoid)
+        section of the Synthea wiki to ensure your idea is something that fits Synthea's scope.
+  - type: textarea
+    id: feature
+    attributes:
+      label: Requested Feature
+      description: New behavior, simulated information or other item you would like in Synthea
+      placeholder: Synthea should add a feature to...
+    validations:
+      required: true

.github/workflows/ci-build-test.yml

@@ -3,24 +3,24 @@ on: [push, pull_request]
 jobs:
   check_java_latest:
     runs-on: ubuntu-latest
-    name: Java 16
+    name: Java 17
 
     steps:
       - uses: actions/checkout@v2
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:
-          java-version: 16
+          java-version: 17
 
       - name: Gradle cache
         uses: actions/cache@v2
         with:
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-jdk16-${{ hashFiles('**/*.gradle*') }}
+          key: ${{ runner.os }}-gradle-jdk17-${{ hashFiles('**/*.gradle*') }}
           restore-keys: |
-            ${{ runner.os }}-gradle-jdk16
+            ${{ runner.os }}-gradle-jdk17
             
       - name: Compile with Gradle
         run: ./gradlew assemble
@@ -30,8 +30,8 @@ jobs:
         if: env.SLACK_WEBHOOK_URL
         with:
           status: custom
-          job_name: Java 16
-          author_name: Java 16 Build
+          job_name: Java 17
+          author_name: Java 17 Build
           fields: workflow,commit,repo,author,took
           # see https://action-slack.netlify.app/usecase/02-custom for custom payload info
           custom_payload: |

.gitignore

@@ -13,9 +13,20 @@ bin/**
 /output/
 /out/
 
+**/*.log
+
 # don't commit the autobuilt version file
 src/main/resources/version.txt
 
+# don't commit the code maps
+src/main/resources/export/condition_code_map.json
+src/main/resources/export/medication_code_map.json
+src/main/resources/export/drg_code_map.json
+src/main/resources/export/dme_code_map.json
+src/main/resources/export/hcpcs_code_map.json
+src/main/resources/export/betos_code_map.json
+src/main/resources/export/external_codes.csv
+
 # H2 database files
 **/*.mv.db
 **/*.trace.db
@@ -26,5 +37,5 @@ src/main/resources/version.txt
 .vscode/settings.json
 /build/
 
-src/main/resources/map.json
-
+# VS Code plugin files
+.history

NOTICE

@@ -1,5 +1,5 @@
 Synthea
-Copyright 2017-2020 The MITRE Corporation
+Copyright 2017-2022 The MITRE Corporation
 
 This material contains prescribable drug codes from RxNorm that are released by
 the National Library of Medicine and is in the public domain.

README.md

@@ -36,7 +36,7 @@ cd synthea
 ./gradlew build check test
 ```
 
-### Changing the default properties 
+### Changing the default properties
 
 
 The default properties file values can be found at `src/main/resources/synthea.properties`.
@@ -53,19 +53,46 @@ Generating the population one at a time...
 ```
 
 Command-line arguments may be provided to specify a state, city, population size, or seed for randomization.
-
-Usage is 
 ```
-run_synthea [-s seed] [-p populationSize] [-m moduleFilter] [state [city]]
+run_synthea [-s seed] [-p populationSize] [state [city]]
 ```
-For example:
 
- - `run_synthea Massachusetts`
- - `run_synthea Alaska Juneau`
- - `run_synthea -s 12345`
- - `run_synthea -p 1000`
- - `run_synthea -s 987 Washington Seattle`
- - `run_synthea -s 21 -p 100 Utah "Salt Lake City"`
+Full usage info can be printed by passing the `-h` option.
+```
+$ ./run_synthea -h     
+
+> Task :run
+Usage: run_synthea [options] [state [city]]
+Options: [-s seed]
+         [-cs clinicianSeed]
+         [-p populationSize]
+         [-r referenceDate as YYYYMMDD]
+         [-g gender]
+         [-a minAge-maxAge]
+         [-o overflowPopulation]
+         [-m moduleFileWildcardList]
+         [-c localConfigFilePath]
+         [-d localModulesDirPath]
+         [-i initialPopulationSnapshotPath]
+         [-u updatedPopulationSnapshotPath]
+         [-t updateTimePeriodInDays]
+         [-f fixedRecordPath]
+         [-k keepMatchingPatientsPath]
+         [--config* value]
+          * any setting from src/main/resources/synthea.properties
+
+Examples:
+run_synthea Massachusetts
+run_synthea Alaska Juneau
+run_synthea -s 12345
+run_synthea -p 1000
+run_synthea -s 987 Washington Seattle
+run_synthea -s 21 -p 100 Utah "Salt Lake City"
+run_synthea -g M -a 60-65
+run_synthea -p 10 --exporter.fhir.export true
+run_synthea -m moduleFilename:anotherModule:module*
+run_synthea --exporter.baseDirectory "./output_tx/" Texas
+```
 
 Some settings can be changed in `./src/main/resources/synthea.properties`.
 
@@ -86,7 +113,7 @@ Generate a list of concepts (used in the records) or attributes (variables on ea
 
 # License
 
-Copyright 2017-2021 The MITRE Corporation
+Copyright 2017-2022 The MITRE Corporation
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

build.gradle

@@ -25,24 +25,29 @@ repositories {
   }
 }
 
+// Uncomment to see deprecation warnings
+// tasks.withType(JavaCompile) {
+//   options.compilerArgs << "-Xlint:deprecation"
+// }
+
 checkstyle {
   toolVersion '8.4'
   //showViolations = true
 }
 
 jacoco {
-  toolVersion '0.8.6'
+  toolVersion '0.8.7'
 }
 
 dependencies {
   // This dependency is found on compile classpath of this component and consumers.
   implementation 'com.google.code.gson:gson:2.8.7'
   implementation 'com.jayway.jsonpath:json-path:2.4.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:5.2.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:5.2.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:5.2.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:5.2.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:5.2.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:5.7.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:5.7.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:5.7.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:5.7.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:5.7.0'
   // C-CDA export uses Apache FreeMarker templates
   implementation 'org.freemarker:freemarker:2.3.26-incubating'
 
@@ -72,7 +77,14 @@ dependencies {
   // get rid of SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
   // if we switch to a real logging framework we may want to switch this
   implementation "org.slf4j:slf4j-api:1.7.9"
-  // compile "org.slf4j:slf4j-nop:1.6.1" // SLF4J seems to already be provided by org.apache.logging.log4j
+  //implementation "org.slf4j:slf4j-nop:1.7.9" // SLF4J seems to already be provided by org.apache.logging.log4j
+  
+  // ensure transitive dependencies do not use vulnerable log4j 
+  implementation "org.apache.logging.log4j:log4j-core", {
+        version {
+            strictly '2.17.0'
+        }
+    }
 
   // Physiology simulation dependencies
   implementation files('lib/sbscl/SimulationCoreLibrary_v1.5_slim.jar')
@@ -92,12 +104,12 @@ dependencies {
   testImplementation 'org.powermock:powermock-module-junit4:1.7.1'
   testImplementation 'org.powermock:powermock-api-mockito2:1.7.1'
   testImplementation 'com.github.tomakehurst:wiremock-jre8:2.26.3'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation:5.2.0'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:5.2.0'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:5.2.0'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu2:5.2.0'
-  testImplementation 'com.helger:ph-schematron:5.0.4'
-  testImplementation 'com.helger:ph-commons:9.1.1'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation:5.7.0'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:5.7.0'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:5.7.0'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu2:5.7.0'
+  testImplementation 'com.helger:ph-schematron:5.6.5'
+  testImplementation 'com.helger:ph-commons:9.5.4'
 }
 
 // Provide more descriptive test failure output
@@ -110,11 +122,17 @@ test {
     // showStandardStreams = true
   }
   maxHeapSize = "6144m"
+  jacoco {
+    excludes = ["org.hl7.*", "com.google.*"]
+  }
 }
 
 buildscript {
   repositories {
-    jcenter()
+    mavenCentral()
+    maven {
+      url "https://oss.sonatype.org/content/repositories/snapshots"
+    }
   }
   dependencies {
     // commons-io used in getting the version id below
@@ -126,8 +144,8 @@ buildscript {
 
 jacocoTestReport {
   reports {
-    xml.enabled true
-    html.enabled true
+    xml.required = true
+    html.required = true
   }
 }
 
@@ -137,7 +155,7 @@ task graphviz(type: JavaExec) {
   group 'Application'
   description 'Generate rule visualization'
   classpath sourceSets.main.runtimeClasspath
-  main = "Graphviz"
+  mainClass = "Graphviz"
 }
 
 task uberJar(type: Jar) {
@@ -166,30 +184,30 @@ task concepts(type: JavaExec) {
   group 'Application'
   description 'Create a list of simulated concepts'
   classpath sourceSets.main.runtimeClasspath
-  main = "org.mitre.synthea.helpers.Concepts"
+  mainClass = "org.mitre.synthea.helpers.Concepts"
   args 'false'
 }
 
 task conceptswithoutcosts(type: JavaExec) {
   group 'Application'
   description 'Create a list of simulated concepts without costs'
   classpath sourceSets.main.runtimeClasspath
-  main = "org.mitre.synthea.helpers.Concepts"
+  mainClass = "org.mitre.synthea.helpers.Concepts"
   args 'true'
 }
 
 task attributes(type: JavaExec) {
   group 'Application'
   description 'Create a list of patient attributes'
   classpath sourceSets.main.runtimeClasspath
-  main = "org.mitre.synthea.helpers.Attributes"
+  mainClass = "org.mitre.synthea.helpers.Attributes"
 }
 
 task overrides(type: JavaExec) {
   group 'Application'
   description 'Create a list of modules parameters in module override format'
   classpath sourceSets.main.runtimeClasspath
-  main = "org.mitre.synthea.helpers.ModuleOverrides"
+  mainClass = "org.mitre.synthea.helpers.ModuleOverrides"
   doFirst {
     // TODO: is there a way to make this cleaner?
     String includeFields = project.hasProperty('includeFields') ? project.getProperty('includeFields') : ""
@@ -205,7 +223,7 @@ task physiology(type: JavaExec) {
     group 'Application'
     description 'Test a physiology simulation'
     classpath sourceSets.main.runtimeClasspath
-    main = "org.mitre.synthea.engine.PhysiologySimulator"
+    mainClass = "org.mitre.synthea.engine.PhysiologySimulator"
 }
 
 task versionTxt() {
@@ -273,7 +291,7 @@ artifacts {
 }
 
 def mavenGroup = 'org.mitre.synthea'
-def mavenVersion = '3.0.0-SNAPSHOT'
+def mavenVersion = '3.1.0-SNAPSHOT'
 
 publishing {
     publications {

config/checkstyle/checkstyle.xml

@@ -33,8 +33,10 @@
         <property name="eachLine" value="true"/>
     </module>
 
+    <module name="SuppressWarningsFilter" />
     <module name="TreeWalker">
         <module name="OuterTypeFilename"/>
+        <module name="SuppressWarningsHolder" />
         <module name="IllegalTokenText">
             <property name="tokens" value="STRING_LITERAL, CHAR_LITERAL"/>
             <property name="format" value="\\u00(09|0(a|A)|0(c|C)|0(d|D)|22|27|5(C|c))|\\(0(10|11|12|14|15|42|47)|134)"/>