From 9376740aa96da853e0e42df83f87594a01e0bde2 Mon Sep 17 00:00:00 2001 From: Alexander Kiel Date: Thu, 28 Mar 2019 18:02:48 +0100 Subject: [PATCH] Initial Commit --- .gitignore | 1 + .travis.yml | 7 ++ LICENSE | 214 +++++++++++++++++++++++++++++++++++ Makefile | 30 +++++ README.md | 46 ++++++++ project.clj | 17 +++ script/life-fhir-gen.tpl.bat | 3 + script/life-fhir-gen.tpl.sh | 5 + src/life_fhir_gen/core.clj | 108 ++++++++++++++++++ 9 files changed, 431 insertions(+) create mode 100644 .gitignore create mode 100644 .travis.yml create mode 100644 LICENSE create mode 100644 Makefile create mode 100644 README.md create mode 100644 project.clj create mode 100644 script/life-fhir-gen.tpl.bat create mode 100644 script/life-fhir-gen.tpl.sh create mode 100644 src/life_fhir_gen/core.clj diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ea8c4bf --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +/target diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..de2866e --- /dev/null +++ b/.travis.yml @@ -0,0 +1,7 @@ +dist: trusty +language: clojure +jdk: + - openjdk8 +lein: 2.8.1 +script: + - lein check diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d921d3d --- /dev/null +++ b/LICENSE @@ -0,0 +1,214 @@ +THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE PUBLIC +LICENSE ("AGREEMENT"). 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Each party waives its rights to a jury trial +in any resulting litigation. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..8a74875 --- /dev/null +++ b/Makefile @@ -0,0 +1,30 @@ +version = 0.1 + +target/life-fhir-gen-$(version)-standalone.jar: + lein clean + lein uberjar + +target/win/life-fhir-gen-$(version)/life-fhir-gen.bat: script/life-fhir-gen.tpl.bat + dirname $@ | xargs mkdir -p + sed -e 's//$(version)/' $< > $@ + +target/win/life-fhir-gen-$(version).zip: target/life-fhir-gen-$(version)-standalone.jar target/win/life-fhir-gen-$(version)/life-fhir-gen.bat + cd target; cp life-fhir-gen-$(version)-standalone.jar win/life-fhir-gen-$(version) + cd target/win; zip life-fhir-gen-$(version).zip life-fhir-gen-$(version)/*.jar + cd target/win; zip --to-crlf life-fhir-gen-$(version).zip life-fhir-gen-$(version)/*.bat + +target/linux/life-fhir-gen-$(version)/life-fhir-gen: script/life-fhir-gen.tpl.sh + dirname $@ | xargs mkdir -p + sed -e 's//$(version)/' $< > $@ + chmod +x $@ + +target/linux/life-fhir-gen-$(version).tar.gz: target/life-fhir-gen-$(version)-standalone.jar target/linux/life-fhir-gen-$(version)/life-fhir-gen + cd target; cp life-fhir-gen-$(version)-standalone.jar linux/life-fhir-gen-$(version) + cd target/linux; tar czf life-fhir-gen-$(version).tar.gz life-fhir-gen-$(version) + +all: target/win/life-fhir-gen-$(version).zip target/linux/life-fhir-gen-$(version).tar.gz + +clean: + lein clean + +.PHONY: clean all diff --git a/README.md b/README.md new file mode 100644 index 0000000..7387383 --- /dev/null +++ b/README.md @@ -0,0 +1,46 @@ +# LIFE FHIR Test Data Generator + +[![Build Status](https://travis-ci.org/life-research/life-fhir-gen.svg?branch=master)](https://travis-ci.org/life-research/life-fhir-gen) +[![Dependencies Status](https://versions.deps.co/life-research/life-fhir-gen/status.svg)](https://versions.deps.co/life-research/life-fhir-gen) + +Generates FHIR Bundles with test data. Currently a fix set of FHIR patient and Observation resources are generated. + +## Install + +Download an archive for your OS: + +* [Windows](https://github.com/life-research/life-fhir-gen/releases/download/v0.1/life-fhir-gen-0.1.zip) +* [Linux](https://github.com/life-research/life-fhir-gen/releases/download/v0.1/life-fhir-gen-0.1.tar.gz) + +Unpack the archive. It will create a directory called `life-fhir-gen-0.1`. Open console in this directory and run `life-fhir-gen`. + +## Usage + +``` +Usage: life-fhir-gen [-n num] [-s start -n num] + -s, --start START Patient index to start. + -n, --num NUM Number of patients to generate. + -v, --version + -h, --help +``` + +The resulting FHIR bundle will be outputted at stdout. You'll have to redirect it into a file. + +## Build + +To create a ZIP for Windows and a tar.gz for Linux run: + +```bash +make all +``` + +The files will be in `target/win` and `target/linux`. You will need [Leiningen][1]. + +## License + +Copyright © 2019 LIFE Research Center (Alexander Kiel) + +Distributed under the Eclipse Public License either version 1.0 or (at +your option) any later version. + +[1]: diff --git a/project.clj b/project.clj new file mode 100644 index 0000000..5737763 --- /dev/null +++ b/project.clj @@ -0,0 +1,17 @@ +(defproject life-fhir-gen "0.1" + :description "FHIR Test Data Generator" + :url "https://github.com/life-research/life-fhir-gen" + + :license {:name "Eclipse Public License" + :url "http://www.eclipse.org/legal/epl-v10.html"} + + :dependencies + [[cheshire "5.8.1"] + [org.clojure/clojure "1.10.0"] + [org.clojure/tools.cli "0.4.1"]] + + :profiles + {:uberjar + {:aot [life-fhir-gen.core]}} + + :main ^:skip-aot life-fhir-gen.core) diff --git a/script/life-fhir-gen.tpl.bat b/script/life-fhir-gen.tpl.bat new file mode 100644 index 0000000..ef61f81 --- /dev/null +++ b/script/life-fhir-gen.tpl.bat @@ -0,0 +1,3 @@ +@echo off + +java -jar "%~dp0life-fhir-gen--standalone.jar" %* diff --git a/script/life-fhir-gen.tpl.sh b/script/life-fhir-gen.tpl.sh new file mode 100644 index 0000000..8688641 --- /dev/null +++ b/script/life-fhir-gen.tpl.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +BASEDIR=$(dirname "$0") + +java -jar "${BASEDIR}/life-fhir-gen--standalone.jar" $@ diff --git a/src/life_fhir_gen/core.clj b/src/life_fhir_gen/core.clj new file mode 100644 index 0000000..fe8c96e --- /dev/null +++ b/src/life_fhir_gen/core.clj @@ -0,0 +1,108 @@ +(ns life-fhir-gen.core + (:require + [cheshire.core :as json] + [clojure.tools.cli :as cli]) + (:import + [java.time OffsetDateTime Instant ZonedDateTime ZoneId LocalDate] + [java.util UUID]) + (:gen-class)) + + +(defn- rand-local-date [^long start-year ^long end-year] + (let [start (.toEpochDay (LocalDate/of start-year 1 1)) + end (.toEpochDay (LocalDate/of end-year 1 1))] + (LocalDate/ofEpochDay (+ start (rand-int (- end start)))))) + + +(defn- rand-date-time [start-year end-year] + (let [zone (ZoneId/of "Europe/Berlin") + start (.toEpochSecond (ZonedDateTime/of start-year 1 1 0 0 0 0 zone)) + end (.toEpochSecond (ZonedDateTime/of end-year 1 1 0 0 0 0 zone))] + (-> (+ start (rand-int (- end start))) + (Instant/ofEpochSecond) + (OffsetDateTime/ofInstant zone)))) + + +(defn gen-patients-with-observations + ([n] + (gen-patients-with-observations 0 n)) + ([start n] + {:resourceType "Bundle" + :id (str (UUID/randomUUID)) + :type "transaction" + :entry + (into + [] + (mapcat + (fn [patient-index] + (into + [{:resource + {:resourceType "Patient" + :id (str patient-index) + :gender (rand-nth ["male" "female"]) + :birthDate (str (rand-local-date 1950 2000))} + :request + {:method "POST" + :url "Patient"}}] + (for [encounter-index (range 10) + observation-index (range 10)] + {:resource + {:resourceType "Observation" + :id (str patient-index "-" encounter-index "-" observation-index) + :status "final" + :subject {:reference (str "Patient/" patient-index)} + :code + {:coding + [{:system "test" + :code (str observation-index)}]} + :valueQuantity + {:value (rand)} + :effectiveDateTime (str (rand-date-time 2000 2010))} + :request + {:method "POST" + :url "Observation"}})))) + (range start (+ start n)))})) + + +(def cli-options + [["-s" "--start START" "Patient index to start." + :parse-fn #(Long/parseLong %)] + ["-n" "--num NUM" "Number of patients to generate." + :parse-fn #(Long/parseLong %)] + ["-v" "--version"] + ["-h" "--help"]]) + + +(defn print-version [] + (println "life-fhir-gen version 0.1") + (System/exit 0)) + + +(defn print-help [summary exit] + (println "Usage: life-fhir-gen [-n num] [-s start -n num]") + (println summary) + (System/exit exit)) + + +(defn -main [& args] + (let [{{:keys [start num version help]} :options :keys [summary]} + (cli/parse-opts args cli-options)] + (when version + (print-version)) + (when help + (print-help summary 0)) + (cond + num + (-> (gen-patients-with-observations (or start 0) num) + (json/generate-string {:pretty true}) + (println)) + :else + (print-help summary 1))) + ) + + +(comment + (str (rand-date-time 2000 2010)) + (gen-patients-with-observations 1) + ) +