Merge pull request #422 from IBM/master

sync with master

Author: albertwang-ibm

.github/workflows/build.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Continuous Integration
 
 on:
   pull_request:
@@ -8,12 +8,16 @@ on:
 jobs:
   build-tools:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ 'openjdk8', 'openjdk11' ]
+      fail-fast: false
     steps:
     - uses: actions/checkout@v1
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+    - name: Set up OpenJDK
+      uses: joschi/setup-jdk@v1
       with:
-        java-version: 1.8
+        java-version: ${{ matrix.java }}
     - name: Build tools
       run: mvn -B install --file fhir-tools/pom.xml
     - name: Build samples
@@ -26,33 +30,80 @@ jobs:
       run: mvn -B package --file fhir-benchmark/pom.xml
   build:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ 'openjdk8', 'openjdk11' ]
+      fail-fast: false
     steps:
     - uses: actions/checkout@v1
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+    - name: Set up OpenJDK
+      uses: joschi/setup-jdk@v1
       with:
-        java-version: 1.8
+        java-version: ${{ matrix.java }}
     - name: Build samples
-      run: mvn -B install --file fhir-examples/pom.xml
+      run: mvn -B install --file fhir-examples/pom.xml --no-transfer-progress
     - name: Build parent with tests
-      run: mvn -B -T2C package --file fhir-parent/pom.xml
+      env:
+        BASE: origin/${{ github['base_ref'] }}
+      run: |
+        jdbc_paths=(
+          fhir-search/src/main
+          fhir-persistence/src/main
+          fhir-persistence-schema/src/main
+          fhir-persistence-jdbc
+        )
+        model_paths=(
+          fhir-model
+        )
+        declare -a PROFILES_ARR
+
+        if [ -n "$(git --no-pager diff --name-only ${BASE} ${GITHUB_SHA} -- ${jdbc_paths[@]})" ]; then
+          echo "Changes affect fhir-persistence-jdbc, running ALL"
+          PROFILES_ARR+=(jdbc-all-tests)
+        else
+          echo "No changes affect fhir-persistence-jdbc, running MINIMAL"
+        fi
+
+        if [ -n "$(git --no-pager diff --name-only ${BASE} ${GITHUB_SHA} -- ${model_paths[@]})" ]; then
+          echo "Changes affect fhir-model, running ALL"
+          PROFILES_ARR+=(model-all-tests)
+        else
+          echo "No changes affect fhir-model, running MINIMAL"
+        fi
+
+        if [ ${#PROFILES[@]} -eq 0 ]; then
+          # Convert the PROFILES_ARR array to a comma-delimited string
+          PROFILES=$(IFS=, ; echo "${PROFILES_ARR[*]}")
+          echo "Using profiles ${PROFILES}"
+          mvn -B -T2C package --file fhir-parent/pom.xml -P "${PROFILES}" --no-transfer-progress
+        else
+          mvn -B -T2C package --file fhir-parent/pom.xml --no-transfer-progress
+        fi
   e2e-tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: [ 'openjdk8', 'openjdk11' ]
+      fail-fast: false
     steps:
     - uses: actions/checkout@v1
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+    - name: Set up OpenJDK
+      uses: joschi/setup-jdk@v1
       with:
-        java-version: 1.8
+        java-version: ${{ matrix.java }}
     - name: Build samples
-      run: mvn -B install --file fhir-examples/pom.xml
+      run: mvn -B install --file fhir-examples/pom.xml --no-transfer-progress
     - name: Build parent without tests
-      run: mvn -B install --file fhir-parent/pom.xml -DskipTests
+      run: mvn -B install --file fhir-parent/pom.xml -DskipTests --no-transfer-progress
     - name: Server Integration Tests
+      env:
+        # debian-based linux uses C.UTF-8 by default and Derby doesn't like that
+        LC_ALL: en_US.UTF-8
       run: |
         export WORKSPACE=${GITHUB_WORKSPACE}
         build/pre-integration-test.sh
-        mvn test -DskipTests=false -f fhir-server-test/pom.xml -DskipWebSocketTest=true
+        env
+        mvn -B test -DskipTests=false -f fhir-server-test/pom.xml -DskipWebSocketTest=true --no-transfer-progress
         build/post-integration-test.sh
     - name: Gather error logs
       if: failure()
@@ -69,5 +120,5 @@ jobs:
       if: always()
       uses: actions/upload-artifact@master
       with:
-        name: integration-test-results
+        name: integration-test-results-${{ matrix.java }}
         path: SIT/integration-test-results

build/pre-integration-test.sh

@@ -75,7 +75,7 @@ tries=0
 status=0
 while [ $status -ne 200 -a $tries -lt ${MAX_TRIES} ]; do
     tries=$((tries + 1))
-    cmd="curl -k -o ${WORKSPACE}/metadata.json -I -w "%{http_code}" -u fhiruser:change-password $metadata_url"
+    cmd="curl -sS -k -o ${WORKSPACE}/metadata.json -I -w %{http_code} -u fhiruser:change-password $metadata_url "
     echo "Executing[$tries]: $cmd"
     status=$($cmd)
     echo "Status code: $status"

docs/.gitattributes

@@ -0,0 +1,2 @@
+#*.zip filter=lfs diff=lfs merge=lfs -text
+#*.tgz filter=lfs diff=lfs merge=lfs -text

docs/.gitignore

@@ -0,0 +1,103 @@
+# Eclipse
+.project
+.settings/
+.classpath
+
+## Annotation processing
+.apt_generated/
+.apt_generated_tests/
+.factorypath
+
+# IntelliJ IDEA
+*.iml
+.idea/
+
+# Mac OS X
+.DS_Store
+
+# Output folders
+target/
+test-output/
+
+# Integration tests
+/SIT/
+/pre-it-logs/
+/pre-it-logs.zip
+/server-logs/
+/integration-test-results/
+/integration-test-results.zip
+
+# avoid LFS problems
+/apidocs/**/*.zip
+/target/
+
+
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (http://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Typescript v1 declaration files
+typings/
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# dotenv environment variables file
+.env
+
+# gatsby files
+.cache/
+public
+
+# Mac files
+.DS_Store
+
+# Yarn
+yarn-error.log
+.pnp/
+.pnp.js
+# Yarn Integrity file
+.yarn-integrity

docs/CHANGELOG.md

@@ -0,0 +1,35 @@
+# Jekyll Configuration for Static Pages
+
+title: IBM FHIR Server
+description: >- 
+  The IBM FHIR Server is a modular Java implementation of version 4 
+  of the <a href="https://www.hl7.org/fhir/r4/http.html">HL7 FHIR specification</a> with 
+  a focus on performance and configurability.
+baseurl: ""
+url: "https://ibm.github.io/fhir" 
+
+# Build settings
+plugins:
+  - jekyll-github-metadata
+  - jekyll-sitemap
+
+source: ./_site/ 
+destination: ./_site/
+show_drafts: false
+future: false
+
+markdown: kramdown
+
+# Remote Theme - https://github.blog/2017-11-29-use-any-theme-with-github-pages/
+theme: jekyll-theme-slate
+
+relative_links:
+  enabled:     true
+  collections: false
+
+include:
+  - public/
+  - _site/
+  - index.html
+
+repository: IBM/FHIR

docs/_config.yml

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+###############################################################################
+# (C) Copyright IBM Corp. 2016, 2019
+#
+# SPDX-License-Identifier: Apache-2.0
+###############################################################################
+set -ex
+
+# Steps that need to be executed
+
+# install gatsby and plugins
+# npm install gatsby-plugin-slug --save
+npm install 
+
+gatsby build --prefix-paths
+
+# Run gatsby serve to see what the site looks like.