[WIP] Replace Local File Loading with Direct Upload

The local file loading has the security implication that an attacker can load arbitary files located at the server.

Also removed dependencies to lambok, various JSON parsing libs and commons-lang3.

Also migrated to Java 17.

.github/workflows/ci.yml

@@ -15,18 +15,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
 
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v2
       with:
         distribution: 'temurin'
-        java-version: '11'
+        java-version: '17'
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2.1.2
+      uses: actions/cache@v2
       with:
         path: ~/.m2/repository
-        key: maven-repo
+        key: maven-repo-test-${{ hashFiles('pom.xml') }}
 
     - name: Cache SonarCloud packages
       uses: actions/cache@v1
@@ -54,18 +56,17 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v2
       with:
         distribution: 'temurin'
-        java-version: '11'
+        java-version: '17'
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2.1.2
+      uses: actions/cache@v2
       with:
-        path: |
-          ~/.m2/repository
-        key: maven-repo
+        path: ~/.m2/repository
+        key: maven-repo-build-${{ hashFiles('pom.xml') }}
 
     - name: Build with Maven
       run: mvn -B package -DskipTests -Dmaven.javadoc.skip=true

Dockerfile

@@ -1,24 +1,8 @@
-FROM openjdk:14-ea-alpine
+FROM openjdk:17
 
-ENV SPRING_PROFILES_ACTIVE=docker
-ARG JAR_FILE=target/icd10-dictionary.jar
+COPY target/icd10-dictionary.jar /app/
 
-ENV ICD_DB_HOST=localhost
-ENV ICD_DB_PORT=5432
-ENV ICD_DB_NAME=icd10
-ENV ICD_DB_USER=postgres
-ENV ICD_DB_PASSWORD=password
-ENV ICD_POOL_SIZE=30
+WORKDIR /app
+USER 1001
 
-RUN apk update
-RUN apk upgrade
-RUN apk add bash
-RUN apk add gettext
-
-COPY ${JAR_FILE} app.jar
-COPY ./docker/start.sh .
-RUN chmod +x ./start.sh
-RUN mkdir config
-COPY ./docker/docker.template.yml config
-
-CMD ["./start.sh"]
+CMD ["java", "-jar", "icd10-dictionary.jar"]

README.md

@@ -10,28 +10,18 @@ http://localhost:8080/fhir/ValueSet/$expand?url=http://hl7.org/fhir/sid/icd-10-g
 
 ## Default parameters
 
-| variable                  | Docker                    | default value            |
-|---------------------------|---------------------------|--------------------------|
-| application port          |                           | 8080                     |
-| database host             | ICD_DB_HOST               | localhost                |
-| database port             | ICD_DB_PORT               | 5432                     |
-| database name             | ICD_DB_NAME               | icd10                    |
-| database user             | ICD_DB_USER               | postgres                 |
-| database password         | ICD_DB_PASSWORD           | password                 |
-| pool size                 | ICD_POOL_SIZE             | 30                       |
+| Env Var                    | Default Value                          |
+|----------------------------|----------------------------------------|
+|                            | 8080                                   |
+| SPRING_DATASOURCE_URL      | jdbc:postgresql://localhost:5432/icd10 |
+| SPRING_DATASOURCE_USERNAME | icd10                                  |
+| SPRING_DATASOURCE_PASSWORD | icd10                                  |
 
 ## Start postgres
 
-For testing purposes one can start a postgres database with Docker using following comand:
+For testing purposes one can start a postgres database with Docker using following command:
 ```
-docker network create -d bridge icd-net
-docker run --name icd-postgres -d --network=icd-net -e POSTGRES_PASSWORD=password -p 5432:5432 postgres:alpine
-```
-Then create a database by executing a bash and using PSQL
-```
-docker exec -it icd-postgres bin/bash
-psql -U postgres
-CREATE DATABASE icd10;
+docker run -e POSTGRES_DB=icd10 -e POSTGRES_USER=icd10 -e POSTGRES_PASSWORD=icd10 -p 5432:5432 postgres
 ```
 
 ## Preparing data
@@ -56,15 +46,9 @@ java -jar fhir-claml-0.0.1-SNAPSHOT.jar
     -valueset http://hl7.org/fhir/sid/icd-10-gm/vs
 ```
 
-4.) Run the ICD-10 dictionary (as executable jar) and load the data by using the endpoint "/api/v1/icd/load" with the file path to the FHIR .json-file as body - e.g.
-```
-http://localhost:8080/api/v1/icd/load
-
-C:\Users\xyz\icd-service\codesystem-icd10gm-2020.json
+4.) Run the ICD-10 dictionary (as executable jar) and load the data by using the endpoint "/api/v1/icd/load":
 ```
-Remark: When working with Docker the file must be copied to a suitable location inside the container
-```
-docker cp C:\Users\xyz\icd-service\codesystem-icd10gm-2020.json [CONTAINER-ID]:/var/tmp/icd10
+curl -d @codesystem-example.json -H Content-Type:application/json http://localhost:8080/api/v1/icd/load
 ```
 
 ## Docker
@@ -75,16 +59,12 @@ docker build -t icd-dictionary .
 ```
 The command for starting the container is something like
 ```
-docker run --rm -d -e "ICD_DB_HOST=icd-postgres" -p 8080:8080 --network=icd-net --name icd-dictionary icd-dictionary
+docker run --rm -d -p 8080:8080 --name icd-dictionary icd-dictionary
 ```
 
-## Developers
-
-This project uses lombok. Though it is not neccessary it is recomended to install a suitable lombok plugin for your IDE (e.g. for IntelliJ Idea install https://plugins.jetbrains.com/plugin/6317-lombok).
-
 ## License
 
-Copyright 2020 The Samply Development Community
+Copyright 2020 - 2021 The Samply Community
 
 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
 

docker-compose.yml

@@ -0,0 +1,22 @@
+version: '3.2'
+services:
+  postgres:
+    image: "postgres"
+    environment:
+      POSTGRES_DB: icd10
+      POSTGRES_USER: icd10
+      POSTGRES_PASSWORD: icd10
+    volumes:
+      - "data:/var/lib/postgresql/data"
+
+  icd-dictionary:
+    build: .
+    environment:
+      SPRING_DATASOURCE_URL: "jdbc:postgresql://postgres:5432/icd10"
+    ports:
+      - "8080:8080"
+    depends_on:
+      - postgres
+
+volumes:
+  data: