Docker/Development Containers support

.devcontainer/devcontainer.json

@@ -0,0 +1,8 @@
+{
+  "name": "Synthea - synthetic patient data generator",
+  "build": {
+    "context": "..",
+    "dockerfile": "../Dockerfile",
+    "args": { "BASE_IMAGE": "mcr.microsoft.com/devcontainers/base:ubuntu", "USER": "vscode" }
+  }
+}

.dockerignore

@@ -0,0 +1,54 @@
+/.devcontainer
+/.hermit
+
+**/.DS_Store
+.classpath
+.project
+.settings
+.gradle
+/nbproject/**
+/build/**
+
+/.gradle/
+/bin/main
+/bin/test
+
+/failed_exports/
+/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
+src/main/resources/export/snf_pdpm_code_map.json
+src/main/resources/export/snf_pps_code_map.json
+src/main/resources/export/snf_rev_cntr_code_map.json
+src/main/resources/export/hha_rev_cntr_code_map.json
+src/main/resources/export/hha_pps_case_mix_codes.csv
+src/main/resources/export/hha_pps_pdgm_codes.csv
+src/main/resources/export/hospice_rev_cntr_code_map.json
+src/main/resources/export/inpatient_rev_cntr_code_map.json
+src/main/resources/export/outpatient_rev_cntr_code_map.json
+
+# H2 database files
+**/*.mv.db
+**/*.trace.db
+
+# VS Code launch settings
+.vscode/launch.test.json
+.vscode/launch.json
+.vscode/settings.json
+/build/
+
+# VS Code plugin files
+.history

.editorconfig

@@ -0,0 +1,29 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# Top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+# Set default charset
+charset = utf-8
+
+[Makefile]
+indent_style = tab
+
+# 4 space indentation (default)
+indent_style = space
+indent_size = 4
+
+# 2 space indentation
+[*.{bicep,bicepparam,html,js,jsx,ts,tsx,json,sass,yaml,yml}]
+indent_size = 2
+
+# Trim trailing whitespace
+trim_trailing_whitespace = true
+
+# Max line length
+max_line_length = 80

.gitignore

@@ -5,10 +5,10 @@
 .gradle
 /nbproject/**
 /build/**
-bin/**
 
 /.gradle/
-/bin/
+/bin/main
+/bin/test
 
 /failed_exports/
 /output/

Dockerfile

@@ -0,0 +1,52 @@
+ARG BASE_IMAGE=ubuntu:22.04
+FROM ${BASE_IMAGE}
+
+ARG USER=dev
+
+WORKDIR /work
+SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
+
+# setup timezone
+RUN apt-get update;\
+  apt-get install -yq tzdata;\
+  ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime;\
+  dpkg-reconfigure -f noninteractive tzdata;
+
+# Set the locale
+RUN apt-get install -yq locales;
+RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \
+  locale-gen
+ENV LANG en_US.UTF-8  
+ENV LANGUAGE en_US:en  
+ENV LC_ALL en_US.UTF-8 
+
+# install OS deps
+RUN set -eux;\
+  apt-get install -y --no-install-recommends ca-certificates curl git jq make unzip zip;
+RUN set -eux;\
+  apt-get install -y --no-install-recommends libfreetype-dev libfreetype6 fontconfig fonts-dejavu;\
+  rm -rf /var/lib/apt/lists/*;
+
+# run as non-root user
+RUN id -u ${USER} &>/dev/null || useradd -ms /bin/bash ${USER}
+USER ${USER}
+WORKDIR /home/${USER}/work
+
+COPY --chown=${USER}:${USER} ./ ./synthea
+
+# install hermit and binary deps
+COPY --chown=${USER}:${USER} bin/ bin/
+ENV PATH=/home/${USER}/work/bin:${PATH}
+RUN set -eux;\
+  hermit shell-hooks;\
+  hermit install
+
+COPY --chown=${USER}:${USER} ./ ./synthea
+RUN set -eux;\
+  cd synthea;\
+  make install;\
+  make build;
+
+# Synthea repo: https://github.com/synthetichealth/synthea
+# ./synthea/run_synthea -m congestive_heart_failure -c settings-chf.yml -p 10000
+# ./synthea/run_synthea -c settings-chf.yml -p 10000

Makefile

@@ -0,0 +1,20 @@
+.PHONY: build install visualize
+
+SHELL := /bin/bash
+
+export PATH := ./bin:${PATH}
+
+all: install build test visualize
+
+install:
+	hermit shell-hooks
+	hermit install
+
+build:
+	./gradlew build
+
+test:
+	./gradlew check test
+
+visualize:
+	gradle graphviz

README.md

@@ -1,10 +1,13 @@
-# Synthea<sup>TM</sup> Patient Generator ![Build Status](https://github.com/synthetichealth/synthea/workflows/.github/workflows/ci-build-test.yml/badge.svg?branch=master) [![codecov](https://codecov.io/gh/synthetichealth/synthea/branch/master/graph/badge.svg)](https://codecov.io/gh/synthetichealth/synthea)
+# Synthea<sup>TM</sup> Patient Generator
+
+![Build Status](https://github.com/synthetichealth/synthea/workflows/.github/workflows/ci-build-test.yml/badge.svg?branch=master) [![codecov](https://codecov.io/gh/synthetichealth/synthea/branch/master/graph/badge.svg)](https://codecov.io/gh/synthetichealth/synthea) [![Open in Dev Containers](https://img.shields.io/static/v1?label=Dev%20Containers&message=Open&color=blue&logo=visualstudiocode)](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/InnovaSolutions/synthea.git)
 
 Synthea<sup>TM</sup> is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.
 
 Read our [wiki](https://github.com/synthetichealth/synthea/wiki) and [Frequently Asked Questions](https://github.com/synthetichealth/synthea/wiki/Frequently-Asked-Questions) for more information.
 
 Currently, Synthea<sup>TM</sup> features include:
+
 - Birth to Death Lifecycle
 - Configuration-based statistics and demographics (defaults with Massachusetts Census data)
 - Modular Rule System
@@ -30,6 +33,7 @@ These instructions are intended for those wishing to examine the Synthea source
 Synthea<sup>TM</sup> requires Java JDK 11 or newer. We strongly recommend using a Long-Term Support (LTS) release of Java, 11 or 17, as issues may occur with more recent non-LTS versions.
 
 To clone the Synthea<sup>TM</sup> repo, then build and run the test suite:
+
 ```
 git clone https://github.com/synthetichealth/synthea.git
 cd synthea
@@ -38,28 +42,29 @@ cd synthea
 
 ### Changing the default properties
 
-
 The default properties file values can be found at `src/main/resources/synthea.properties`.
 By default, synthea does not generate CCDA, CPCDA, CSV, or Bulk FHIR (ndjson). You'll need to
-adjust this file to activate these features.  See the [wiki](https://github.com/synthetichealth/synthea/wiki)
+adjust this file to activate these features. See the [wiki](https://github.com/synthetichealth/synthea/wiki)
 for more details, or use our [guided customizer tool](https://synthetichealth.github.io/spt/#/customizer).
 
-
-
 ### Generate Synthetic Patients
+
 Generating the population one at a time...
+
 ```
 ./run_synthea
 ```
 
 Command-line arguments may be provided to specify a state, city, population size, or seed for randomization.
+
 ```
 run_synthea [-s seed] [-p populationSize] [state [city]]
 ```
 
 Full usage info can be printed by passing the `-h` option.
+
 ```
-$ ./run_synthea -h     
+$ ./run_synthea -h
 
 > Task :run
 Usage: run_synthea [options] [state [city]]
@@ -97,13 +102,17 @@ Some settings can be changed in `./src/main/resources/synthea.properties`.
 Synthea<sup>TM</sup> will output patient records in C-CDA and FHIR formats in `./output`.
 
 ### Synthea<sup>TM</sup> GraphViz
+
 Generate graphical visualizations of Synthea<sup>TM</sup> rules and modules.
+
 ```
 ./gradlew graphviz
 ```
 
 ### Concepts and Attributes
+
 Generate a list of concepts (used in the records) or attributes (variables on each patient).
+
 ```
 ./gradlew concepts
 ./gradlew attributes

bin/.gradle-8.3.pkg

@@ -0,0 +1 @@
+hermit

bin/.openjdk@17.pkg

@@ -0,0 +1 @@
+hermit

bin/README.hermit.md

@@ -0,0 +1,7 @@
+# Hermit environment
+
+This is a [Hermit](https://github.com/cashapp/hermit) bin directory.
+
+The symlinks in this directory are managed by Hermit and will automatically
+download and install Hermit itself as well as packages. These packages are
+local to this environment.

bin/activate-hermit

@@ -0,0 +1,21 @@
+#!/bin/bash
+# This file must be used with "source bin/activate-hermit" from bash or zsh.
+# You cannot run it directly
+#
+# THIS FILE IS GENERATED; DO NOT MODIFY
+
+if [ "${BASH_SOURCE-}" = "$0" ]; then
+  echo "You must source this script: \$ source $0" >&2
+  exit 33
+fi
+
+BIN_DIR="$(dirname "${BASH_SOURCE[0]:-${(%):-%x}}")"
+if "${BIN_DIR}/hermit" noop > /dev/null; then
+  eval "$("${BIN_DIR}/hermit" activate "${BIN_DIR}/..")"
+
+  if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ]; then
+      hash -r 2>/dev/null
+    fi
+
+    echo "Hermit environment $("${HERMIT_ENV}"/bin/hermit env HERMIT_ENV) activated"
+fi

bin/gradle

@@ -0,0 +1 @@
+.gradle-8.3.pkg

bin/hermit

@@ -0,0 +1,43 @@
+#!/bin/bash
+#
+# THIS FILE IS GENERATED; DO NOT MODIFY
+
+set -eo pipefail
+
+export HERMIT_USER_HOME=~
+
+if [ -z "${HERMIT_STATE_DIR}" ]; then
+  case "$(uname -s)" in
+  Darwin)
+    export HERMIT_STATE_DIR="${HERMIT_USER_HOME}/Library/Caches/hermit"
+    ;;
+  Linux)
+    export HERMIT_STATE_DIR="${XDG_CACHE_HOME:-${HERMIT_USER_HOME}/.cache}/hermit"
+    ;;
+  esac
+fi
+
+export HERMIT_DIST_URL="${HERMIT_DIST_URL:-https://github.com/cashapp/hermit/releases/download/stable}"
+HERMIT_CHANNEL="$(basename "${HERMIT_DIST_URL}")"
+export HERMIT_CHANNEL
+export HERMIT_EXE=${HERMIT_EXE:-${HERMIT_STATE_DIR}/pkg/hermit@${HERMIT_CHANNEL}/hermit}
+
+if [ ! -x "${HERMIT_EXE}" ]; then
+  echo "Bootstrapping ${HERMIT_EXE} from ${HERMIT_DIST_URL}" 1>&2
+  INSTALL_SCRIPT="$(mktemp)"
+  # This value must match that of the install script
+  INSTALL_SCRIPT_SHA256="180e997dd837f839a3072a5e2f558619b6d12555cd5452d3ab19d87720704e38"
+  if [ "${INSTALL_SCRIPT_SHA256}" = "BYPASS" ]; then
+    curl -fsSL "${HERMIT_DIST_URL}/install.sh" -o "${INSTALL_SCRIPT}"
+  else
+    # Install script is versioned by its sha256sum value
+    curl -fsSL "${HERMIT_DIST_URL}/install-${INSTALL_SCRIPT_SHA256}.sh" -o "${INSTALL_SCRIPT}"
+    # Verify install script's sha256sum
+    openssl dgst -sha256 "${INSTALL_SCRIPT}" | \
+      awk -v EXPECTED="$INSTALL_SCRIPT_SHA256" \
+      '$2!=EXPECTED {print "Install script sha256 " $2 " does not match " EXPECTED; exit 1}'
+  fi
+  /bin/bash "${INSTALL_SCRIPT}" 1>&2
+fi
+
+exec "${HERMIT_EXE}" --level=fatal exec "$0" -- "$@"

bin/jar

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jarsigner

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/java

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/javac

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/javadoc

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/javap

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jcmd

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jconsole

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jdb

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jdeprscan

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jdeps

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jfr

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jhsdb

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jimage

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jinfo

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jlink

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jmap

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jmod

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jpackage

@@ -0,0 +1 @@
+.openjdk@17.pkg

bin/jps

@@ -0,0 +1 @@
+.openjdk@17.pkg