Merge pull request #38 from samply/release-1.0.0

Release 1.0.0

.dockerignore

@@ -0,0 +1,9 @@
+.github
+.idea
+.mvn
+converter
+output
+templates
+test-templates
+temp-files
+fhir-packages

.github/workflows/build.yml

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+name: Build
+
+on:
+  schedule:
+    - cron: '0 10 * * *' # every day at 10am
+  push:
+    branches:
+      - main
+      - develop
+    tags:
+      - 'v*.*.*'
+  pull_request:
+    branches:
+      - main
+      - develop
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Setup Java
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '20'
+
+      - name: Check out Git repository
+        uses: actions/checkout@v3
+
+      - name: Cache Local Maven Repo
+        uses: actions/cache@v3
+        with:
+          path: ~/.m2/repository
+          key: maven-${{ hashFiles('pom.xml') }}
+
+      - name: Test with Maven
+        run: mvn -B package
+
+
+  build:
+    needs: test
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Setup Java
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '20'
+
+      - name: Check out Git repository
+        uses: actions/checkout@v3
+
+      - name: Cache Local Maven Repo
+        uses: actions/cache@v3
+        with:
+          path: ~/.m2/repository
+          key: maven-${{ hashFiles('pom.xml') }}
+
+      - name: Build with Maven
+        run: mvn -B package -DskipTests
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Docker meta
+        id: docker-meta
+        uses: docker/metadata-action@v3
+        with:
+          images: |
+            samply/exporter
+          tags: |
+            type=schedule
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=sha,format=long
+
+      - name: Build and push image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          platforms: linux/amd64, linux/arm64
+          push: true
+          tags: ${{ steps.docker-meta.outputs.tags }}
+          labels: ${{ steps.docker-meta.outputs.labels }}
+
+      - name: Run Trivy vulnerability scanner
+        uses: aquasecurity/trivy-action@master
+        with:
+          image-ref: samply/exporter:sha-${{ github.sha }}
+          format: sarif
+          output: trivy-results.sarif
+          severity: 'CRITICAL,HIGH'
+
+      - name: Upload Trivy scan results to GitHub Security tab
+        uses: github/codeql-action/upload-sarif@codeql-bundle-20220401
+        with:
+          sarif_file: trivy-results.sarif

.gitignore

@@ -1,23 +1,41 @@
-# Compiled class file
-*.class
+HELP.md
+target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+templates
+test-templates
+output
+converter
+test-converters
+temp-files
+fhir-packages
 
-# Log file
-*.log
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
 
-# BlueJ files
-*.ctxt
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.iml
+*.ipr
 
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
 
-# Package Files #
-*.jar
-*.war
-*.nar
-*.ear
-*.zip
-*.tar.gz
-*.rar
-
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
+### VS Code ###
+.vscode/
+/lib/

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,2 @@
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.8.6/apache-maven-3.8.6-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.0/maven-wrapper-3.1.0.jar

CHANGELOG.md

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+# Change Log
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/)
+and this project adheres to [Semantic Versioning](http://semver.org/).
+
+## [1.0.0 - 2023-08-04]
+### Added
+- Search Controller
+- Blaze Store Client
+- LDM Client
+- Containers and Containers Templates
+- FHIR-Bundle to Containers Converter
+- FHIR Rev Includes in Containers Templates
+- Executor in Fhir Store Client
+- Converter Pattern
+- Converter Manager
+- Converter Template and Conversion Template
+- Input and Output Format in Converter
+- Load converter from application context
+- Converter Selector
+- Get Source Ids and Converter Template Ids
+- Project Version
+- REST API: retrieve-query
+- Docker
+- Timestamp variable for templates
+- Environment variables for templates
+- Parent-fhir-path in attribute template
+- MDR URN in attribute template
+- Child fhir path
+- Spring Boot 3.0.1
+- Anonym Attribute Template
+- Converter Session
+- Apache POI
+- Excel Converter
+- Anonym Attributes
+- Operation in Attribute
+- EXTRACT_RELATIVE_ID attribute operation
+- Api Key
+- Java 19
+- Template in request body
+- Attribute condition fhir path
+- Exporter DB
+- Attribute join fhir path
+- Attribute condition id and value fhir path
+- Excel Format
+- Flyway config
+- Query entity
+- JPA config (Hibernate)
+- Get all queries (paging)
+- Query Execution and Query Execution File
+- Download files (also as zip)
+- Clean Temp and Write Files Jobs
+- GET active, error and archived inquiries
+- Format inquiry timestamp
+- Allow Cors
+- Default value for inquiry label and description
+- Archive Query
+- Send execution file url in inquiry
+- Get Query Execution Status
+- Opal Importer
+- Http relative path
+- Http servlet request scheme
+- Export in JSON format
+- Export in XML format
+- File Filter in Response
+- Validation to bundles
+- FHIR Profile URL
+- Opal permission
+- Validation Utils
+- FHIR Package Loader
+- Converter Template attribute: FHIR Package
+- Explorer, CSV Explorer
+- Deactivate hapi fhir client and hibernate logs (configurable)
+- FHIR Terminology Server
+- Location String and Message for validation
+- Parameter LOG_FHIR_VALIDATION
+- Java 20
+- Buffered Logger
+- Request Logs
+- Csv Explorer
+- Json Explorer
+- XML Exporter
+- Request Page Size
+- Http response header number-of-pages
+
+### Changed
+- Rename Conversion Template as Converter Template
+- First anonym: 1
+- Cors config
+- Bugfix: Allow join-fhir-path parent with many children
+- Rename teiler to exporter
+- Bugfix: Filter paths
+- Bugfix: Change default template
+- Bugfix: Generate filenames only once in session for csv and excel
+- Bugfix: Recognize internal network requests
+- Bugfix: Avoid null resources

Dockerfile

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+FROM eclipse-temurin:20-jre
+
+COPY target/exporter.jar /app/
+
+WORKDIR /app
+
+RUN apt-get update && apt-get upgrade -y && apt-get install python3-pip -y &&  \
+    apt-get install libcurl4-openssl-dev libssl-dev -y && \
+    python3 -m pip install obiba-opal
+
+
+CMD ["java", "-jar", "exporter.jar"]

README.md

@@ -1,2 +1,5 @@
-# teiler
-Teiler
+# exporter
+Exporter
+
+## Opal
+To use the Opal exporter, it is required to have installed the opal python client (https://opaldoc.obiba.org/en/latest/python-user-guide/index.html#installation)