Merge pull request #36 from medizininformatik-initiative/v3.0.0

V3.0.0

.github/scripts/install-blazectl.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+VERSION="0.13.0"
+
+curl -sLO "https://github.com/samply/blazectl/releases/download/v$VERSION/blazectl-$VERSION-linux-amd64.tar.gz"
+tar xzf "blazectl-$VERSION-linux-amd64.tar.gz"
+rm "blazectl-$VERSION-linux-amd64.tar.gz"
+sudo mv ./blazectl /usr/local/bin/blazectl

.github/scripts/test-consent-queries.sh

@@ -0,0 +1,21 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8081/fhir"
+PERMIT_URI="$BASE/Consent?mii-provision-provision-code-type=2.16.840.1.113883.3.1937.777.24.5.1.1\$permit"
+DENY_URI="$BASE/Consent?mii-provision-provision-code-type=2.16.840.1.113883.3.1937.777.24.5.1.1\$deny"
+
+count() {
+  RESP=$(curl -sH 'Prefer: handling=strict' -H 'Accept: application/fhir+json' "$1")
+
+  if [ "$(echo "$RESP" | jq -r .resourceType)" = "OperationOutcome" ]; then
+    echo "$RESP" | jq -r .issue[].diagnostics
+  else
+    echo "$RESP" | jq -r .total
+  fi
+}
+
+test "permit count" "$(count "$PERMIT_URI")" "1"
+test "permit count" "$(count "$DENY_URI")" "0"

.github/scripts/util.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -e
+
+test() {
+  if [ "$2" = "$3" ]; then
+    echo "OK: the $1 is $3"
+  else
+    echo "Fail: the $1 is $2, expected $3"
+    exit 1
+  fi
+}
+
+test-le() {
+  if [ "$2" -le "$3" ]; then
+    echo "OK: the $1 of $2 is <= $3"
+  else
+    echo "Fail: the $1 is $2, expected <= $3"
+    exit 1
+  fi
+}

.github/scripts/wait-for-url.sh

@@ -0,0 +1,14 @@
+#!/bin/bash -e
+
+URL=$1
+START_EPOCH="$(date +"%s")"
+
+eclipsed() {
+  EPOCH="$(date +"%s")"
+  echo $((EPOCH - START_EPOCH))
+}
+
+# wait at maximum 120 seconds
+while [[ ($(eclipsed) -lt 120) && ("$(curl -s -o /dev/null -w '%{response_code}' "$URL")" != "200") ]]; do
+  sleep 2
+done

.github/workflows/ci.yml

@@ -9,69 +9,39 @@ on:
   pull_request:
     branches:
     - main
-
-env:
-  TEST_DATA_REF: v0.2.0
-  TEST_DATA_PATH: test/data-to-sq
-  AUTH_USERNAME: "codex-developer"
-  AUTH_PASSWORD: "codex"
+    - develop
 
 jobs:
-
-  test:
+  lint:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout Deploy Repo
-      uses: actions/checkout@v2
-
-    - name: Checkout Test Data Repo
-      uses: actions/checkout@v2
-      with:
-        repository: num-codex/codex-testdata-to-sq
-        ref: ${{ env.TEST_DATA_REF }}
-        path: ${{ env.TEST_DATA_PATH }}
+    - name: Check out Git repository
+      uses: actions/checkout@v3
 
-    - name: Cache Test Data
-      id: cache-test-data
-      uses: actions/cache@v2
+    - name: Check shell scripts
+      uses: ludeeus/action-shellcheck@master
       with:
-        path: ${{ env.TEST_DATA_PATH }}/testCases
-        key: testcases-${{ hashFiles('**/*.json') }}
+        ignore_paths: .github/scripts
 
-    - name: Setup Python
-      if: steps.cache-test-data.outputs.cache-hit != 'true'
-      uses: actions/setup-python@v2
+  test-feasibility-triangle-fhir-server:
+    runs-on: ubuntu-latest
 
-    - name: Generate Test Data
-      if: steps.cache-test-data.outputs.cache-hit != 'true'
-      working-directory: ${{ env.TEST_DATA_PATH }}
-      run: python main.py
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@v3
 
-    - name: Setup Base Auth
-      run: bash num-node/setup-base-auth.sh "${{ env.AUTH_USERNAME }}" "${{ env.AUTH_PASSWORD }}"
+    - name: Install Blazectl
+      run: .github/scripts/install-blazectl.sh
 
-    - name: Build the stack
-      env:
-        CODEX_DSF_DIC_FHIR_APP_JVM_ARGS: -Xmx1g
-        CODEX_DSF_DIC_BPE_APP_JVM_ARGS: -Xmx500m
-        CODEX_DSF_ZARS_FHIR_APP_JVM_ARGS: -Xmx1g
-        CODEX_DSF_ZARS_BPE_APP_JVM_ARGS: -Xmx500m
-        CODEX_FEASIBILITY_BACKEND_API_BASE_URL: http://localhost:8091/api/
-      run: ./start-zars-and-num-node.sh --disable-result-obfuscation
+    - name: Start Blaze FHIR Server
+      run: docker-compose -f feasibility-triangle/fhir-server/docker-compose.yml up -d
 
-    - name: Wait for FHIR Server Running
-      uses: ifaxity/wait-on-action@v1
-      with:
-        resource: http://localhost:8081/health
-        timeout: 60000
+    - name: Wait for Blaze FHIR Server
+      run: .github/scripts/wait-for-url.sh  http://localhost:8081/health
 
-    - name: Initialize Test Data
-      run: bash num-node/init-testdata.sh
+    - name: Load Data
+      run: blazectl --no-progress --server http://localhost:8081/fhir upload .github/test-data
 
-    - name: Run tests
-      env:
-        TERM: "xterm"
-        QUERY_ENDPOINT_URL: "http://localhost:8091/api/v1/query-handler/run-query"
-        AUTH_TOKEN_REQUEST_URL: "https://localhost:8443/auth/realms/codex-develop/protocol/openid-connect/token"
-      run: test/run_tests.sh
+    - name: Run Test Queries
+      run: .github/scripts/test-consent-queries.sh

.gitignore

@@ -7,3 +7,8 @@ test/testdata
 num-node/testdata
 !num-node/testdata/test-patient-all.json
 start-zars-and-num-node-all.sh
+.env
+deploy-config.json
+*.pem
+!ca.pem
+.htpasswd

CHANGELOG.md

@@ -0,0 +1,88 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## Component specific changes
+
+Please refer to the respective repositories for a more in depth changelog of single components:
+
+|Component|Link|
+|--|--|
+|UI|<https://github.com/medizininformatik-initiative/feasibility-gui>|
+|Ontology Generation|<https://github.com/medizininformatik-initiative/fhir-ontology-generator>|
+|Backend|<https://github.com/medizininformatik-initiative/feasibility-backend>|
+|AKTIN Broker|<https://github.com/aktin/broker>|
+|AKTIN Feasibility Plugin|<https://github.com/medizininformatik-initiative/feasibility-aktin-plugin>|
+|DSF Feasibility Plugin|<https://github.com/medizininformatik-initiative/feasibility-dsf-process>|
+|FLARE|<https://github.com/medizininformatik-initiative/flare>|
+|Blaze FHIR server|<https://github.com/medizininformatik-initiative/blaze>|
+
+## [3.0.0] - 2023-08-08
+
+### Overall
+
+- Updated all components and underlying libraries to the new versions
+- Updated all components to version compatible with ontology version 2.0
+- Adjusted readme to reflect changes in the underlying components
+
+### Features
+
+| Feature | Affected Components |
+| -- | -- |
+|Added support for referenced criteria|UI, backend, Ontology, Sq2cql, FLARE|
+|Added support for composite search parameters|UI, SQ, Ontology, Sq2cql, FLARE|
+|Updated to new DSF version v1.0.0 compatible with new DSF verison v1.x | Backend, DSF feasibility plugin|
+|Added Dateselection|UI|
+|Update ontology to new ontology generation and added ontology to images directly| Ontology, Backend, FLARE|
+|Added encrypted result logging| Backend|
+|Add support for self-signed certificates| Backend, FLARE, DSF feasibility plugin |
+
+
+## [2.1.0] - 2023-07-25
+
+### Overall
+
+- Updated AKTIN Client to 1.6.0: Fix websocket timeout and improve error handling  - <https://github.com/medizininformatik-initiative/feasibility-aktin-plugin/releases/tag/v1.6.0>
+- Updated FLARE to 1.0: Fix Execution Operation - <https://github.com/medizininformatik-initiative/flare/releases/tag/v1.0.0>
+- Updated Blaze to 0.22: implements $everything, adds basic frontend, Support for Custom Search Parameters <https://github.com/samply/blaze/releases/tag/v0.22.0>
+- Added Troubleshooting specific for triangle
+- Update testdata repo from MII
+
+
+## [2.0.0] - 2023-03-29
+
+### Overall
+
+- Updated all components and underlying libraries to the new versions
+- Updated UI to angular 15
+- Updated keycloak to 21.0
+- Updated nginx to 1.23
+- Refactored deploy repository - removed DSF from this deployment and added reference to DSF deployment in Readme
+- Removed hapi fhir-server from deployment
+
+### Features
+
+| Feature | Affected Components |
+| -- | -- |
+|Added calculated criterion age|Ontology, Sq2cql, FLARE|
+|Improved at site obfuscation|DSF Feasibility Plugin, AKTIN Client|
+|Added SQ query import and export|UI|
+|Improved FHIR query execution and result caching |FLARE|
+|Update Consent to new search params and add central MII consent query|UI, Ontology|
+|Update ontology to newest KDS version| Ontology|
+|Update AKTIN client to new version, move query handling to Java plugin and add query validation|AKTIN client|
+|SQ query validation|Backend, AKTIN client|
+|Add CQL execution to direct broker| Backend|
+
+### Security and Privacy
+
+| Feature | Affected Components |
+| - | - |
+|Added extra security measures, which restrict number queries a user can send and results a user can view|UI, Backend|
+|Improved at site obfuscation|DSF Feasibility Plugin, Aktin Client|
+|Hard rate limit at sites for AKTIN and DSF feasibility plugins|DSF feasibility plugin, AKTIN Client|
+|Query results are no longer persisted and only kept in memory for a configurable amount of time|Backend|
+|Delete query results from central DSF and AKTIN broker on collection|Backend|
+|User blacklisting if too many queries are sent in a given time|Backend|
+
+## [1.6.0] - 2022-09-08