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build.yml
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name: Build
on:
schedule:
- cron: '0 10 * * *' # every day at 10am
push:
tags:
- 'v*.*.*'
pull_request:
branches:
- main
merge_group:
permissions: read-all
jobs:
fmt:
runs-on: ubuntu-24.04
steps:
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@cc67f8308550d0f18b0ba445c2476f84626a5d6a # 13.1
with:
cljfmt: 0.13.0
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Check Formatting
run: make fmt
lint:
runs-on: ubuntu-24.04
steps:
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@cc67f8308550d0f18b0ba445c2476f84626a5d6a # 13.1
with:
clj-kondo: '2024.09.27'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Lint
run: make lint
job-ig:
runs-on: ubuntu-24.04
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Setup Node
uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
with:
node-version-file: .nvmrc
- name: Build
working-directory: job-ig
run: make build
- name: Validate
working-directory: job-ig
run: make validate
- name: Upload Profiles
uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources/*.json
test:
strategy:
matrix:
module:
- admin-api
- anomaly
- async
- byte-buffer
- byte-string
- cache-collector
- cassandra
- coll
- cql
- db
- db-resource-store
- db-resource-store-cassandra
- db-tx-log
- db-tx-log-kafka
- executor
- extern-terminology-service
- fhir-client
- fhir-path
- fhir-structure
- http-client
- interaction
- jepsen
- job-async-interaction
- job-compact
- job-re-index
- job-scheduler
- job-util
- kv
- luid
- metrics
- module-base
- openid-auth
- operation-code-system-validate-code
- operation-compact
- operation-graphql
- operation-measure-evaluate-measure
- operation-patient-everything
- operation-patient-purge
- operation-totals
- operation-value-set-expand
- operation-value-set-validate-code
- page-id-cipher
- page-store
- page-store-cassandra
- rest-api
- rest-util
- rocksdb
- scheduler
- server
- terminology-service
- thread-pool-executor-collector
java-version:
- '17'
- '21'
exclude:
- module: jepsen
java-version: '17'
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
with:
distribution: 'temurin'
java-version: ${{ matrix.java-version }}
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@cc67f8308550d0f18b0ba445c2476f84626a5d6a # 13.1
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ matrix.module }}-${{ hashFiles(format('modules/{0}/deps.edn', matrix.module)) }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Test
run: make -C modules/${{ matrix.module }} test
- name: Test Coverage
if: ${{ matrix.java-version == '21' && matrix.module != 'db' && matrix.module != 'jepsen' }}
run: make -C modules/${{ matrix.module }} test-coverage
- name: Upload Coverage Report
if: ${{ matrix.java-version == '21' && matrix.module != 'db' && matrix.module != 'jepsen' }}
uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
with:
name: coverage-report-${{ matrix.module }}
path: modules/${{ matrix.module }}/target/coverage/codecov.json
# Special treatment, because it runs much longer as the other modules.
test-coverage-db:
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
with:
distribution: 'temurin'
java-version: '21'
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@cc67f8308550d0f18b0ba445c2476f84626a5d6a # 13.1
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-21-maven-db-coverage-${{ hashFiles('modules/db/deps.edn') }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Test Coverage
run: make -C modules/db test-coverage
- name: Upload Coverage Report
uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
with:
name: coverage-report-db
path: modules/db/target/coverage/codecov.json
test-root:
strategy:
matrix:
java-version:
- '17'
- '21'
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
with:
distribution: 'temurin'
java-version: ${{ matrix.java-version }}
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@cc67f8308550d0f18b0ba445c2476f84626a5d6a # 13.1
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ hashFiles('deps.edn') }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Test
run: make test-root
upload-coverage:
needs: [ test, test-coverage-db ]
runs-on: ubuntu-24.04
steps:
- name: Download Coverage Reports
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
pattern: coverage-report-*
- name: Codecov Upload
uses: codecov/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303 # v5
with:
name: codecov-umbrella
token: ${{ secrets.CODECOV_TOKEN }}
fail_ci_if_error: true
build:
needs: job-ig
runs-on: ubuntu-24.04
steps:
- name: Setup Java
uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
with:
distribution: 'temurin'
java-version: '21'
- name: Setup Clojure
uses: DeLaGuardo/setup-clojure@cc67f8308550d0f18b0ba445c2476f84626a5d6a # 13.1
with:
cli: '1.12.0.1479'
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Cache Local Maven Repo
uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
with:
path: ~/.m2/repository
key: ${{ runner.os }}-temurin-21-maven-build-${{ hashFiles('**/deps.edn') }}
- name: Download Job IG Profiles
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: job-ig-profiles
path: job-ig/fsh-generated/resources
- name: Build Uberjar
run: make uberjar
- name: Upload Blaze Uberjar
uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
with:
name: blaze-uberjar
path: target/blaze-*-standalone.jar
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3
- name: Build and Export to Docker
uses: docker/build-push-action@48aba3b46d1b1fec4febb7c5d0c644b249a11355 # v6
with:
context: .
tags: blaze:latest
outputs: type=docker,dest=/tmp/blaze.tar
- name: Upload Blaze Image
uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
with:
name: blaze-image
path: /tmp/blaze.tar
build-frontend:
runs-on: ubuntu-24.04
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Setup Node
uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
with:
node-version-file: .nvmrc
- name: Build Frontend
run: make build-frontend
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3
- name: Build and Export to Docker
uses: docker/build-push-action@48aba3b46d1b1fec4febb7c5d0c644b249a11355 # v6
with:
context: modules/frontend
tags: blaze-frontend:latest
outputs: type=docker,dest=/tmp/blaze-frontend.tar
- name: Upload Blaze Image
uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
with:
name: blaze-frontend-image
path: /tmp/blaze-frontend.tar
image-scan:
needs: [ build, build-frontend ]
runs-on: ubuntu-24.04
permissions:
security-events: write
strategy:
matrix:
image:
- blaze
- blaze-frontend
steps:
- name: Download Image
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: ${{ matrix.image }}-image
path: /tmp
- name: Load Image
run: docker load --input /tmp/${{ matrix.image }}.tar
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Run Trivy Vulnerability Scanner
uses: aquasecurity/trivy-action@18f2510ee396bbf400402947b394f2dd8c87dbb0 # 0.29.0
with:
image-ref: ${{ matrix.image }}:latest
format: sarif
output: trivy-results.sarif
severity: 'CRITICAL,HIGH'
timeout: '15m0s'
env:
TRIVY_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-db:2
TRIVY_JAVA_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-java-db:1
- name: Upload Trivy Scan Results to GitHub Security Tab
if: ${{ (github.repository_owner == 'samply') || (vars.IMAGE_SCAN_UPLOAD == 'true') }}
uses: github/codeql-action/upload-sarif@48ab28a6f5dbc2a99bf1e0131198dd8f1df78169 # v3
with:
sarif_file: trivy-results.sarif
cql-expr-cache-test:
needs: build
runs-on: ubuntu-24.04
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install Blazectl
run: .github/scripts/install-blazectl.sh
- name: Download Blaze Image
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: blaze-image
path: /tmp
- name: Load Blaze Image
run: docker load --input /tmp/blaze.tar
- name: Run Blaze
run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENABLE_ADMIN_API=true -e CQL_EXPR_CACHE_SIZE=1000 -p 8080:8080 -p 8081:8081 -v blaze-data:/app/data blaze:latest
- name: Wait for Blaze
run: .github/scripts/wait-for-url.sh http://localhost:8080/health
- name: Docker Logs
run: docker logs blaze
- name: Check Capability Statement
run: .github/scripts/check-capability-statement.sh
- name: Ensure that the State of PatientLastChange Index is Current
run: .github/scripts/check-patient-last-change-index-state.sh current
- name: Load Data
run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea
- name: Prometheus Metrics
run: .github/scripts/test-cql-expr-cache-metrics.sh
- name: Check Total-Number of Resources are 92114
run: .github/scripts/check-total-number-of-resources.sh 92114
- name: Evaluate CQL Query 1
run: .github/scripts/evaluate-measure.sh q1 56
- name: Evaluate CQL Query 1 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q1 56
- name: Evaluate CQL Query 1 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q1 56
- name: Evaluate CQL Query 1 on Individual Patients
run: .github/scripts/evaluate-patient-q1-measure.sh
- name: Evaluate CQL Query 2
run: .github/scripts/evaluate-measure.sh q2 42
- name: Evaluate CQL Query 2 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q2 42
- name: Evaluate CQL Query 2 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q2 42
- name: Evaluate CQL Query 4
run: .github/scripts/evaluate-measure.sh q4 0
- name: Evaluate CQL Query 4 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q4 0
- name: Evaluate CQL Query 4 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q4 0
- name: Evaluate CQL Query 7
run: .github/scripts/evaluate-measure.sh q7 81
- name: Evaluate CQL Query 7 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q7 81
- name: Evaluate CQL Query 7 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q7 81
- name: Evaluate CQL Query 14
run: .github/scripts/evaluate-measure.sh q14 96
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh a08d0235112a8033c36c5d33564aaa00f4190281e4db8f7ec1d8d55cd7f4c56f 96
- name: Evaluate CQL Query 14 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q14 96
- name: Evaluate CQL Query 14 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q14 96
- name: Evaluate CQL Query 17
run: .github/scripts/evaluate-measure.sh q17 120
- name: Evaluate CQL Query 17 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q17 120
- name: Evaluate CQL Query 17 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q17 120
- name: Evaluate CQL Query 20 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q20-stratifier-city 120
- name: Evaluate CQL Query 21 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q21-stratifier-city-of-only-women 64
- name: Evaluate CQL Query 26 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q26-stratifier-bmi 120
- name: Evaluate CQL Query 27 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q27-stratifier-calculated-bmi 120
- name: Evaluate CQL Query 32 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q32-stratifier-underweight 120
- name: Evaluate CQL Query 36
run: .github/scripts/evaluate-measure.sh q36-parameter 86
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh fbb79d85457069c8e1926c949690deecd60d751942d5b0cd0b61c08e6029224c 86
- name: Evaluate CQL Query 36 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86
- name: Evaluate CQL Query 37
run: .github/scripts/evaluate-measure.sh q37-overlaps 24
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh 9fe779d821d7647831331b490939aa0cdf314d76c9b2a9518ffaf559353db043 24
- name: Evaluate CQL Query 37 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24
- name: Evaluate CQL Query 37 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q37-overlaps 24
- name: Evaluate CQL Query 46
run: .github/scripts/evaluate-measure.sh q46-between-date 19
- name: Check Bloom Filter
run: .github/scripts/check-bloom-filter.sh 237bcfac3e879272f508e143095e4a0025e1b54505bbb2cf36fbda83dec237f2 19
- name: Evaluate CQL Query 46 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q46-between-date 19
integration-test:
needs: build
runs-on: ubuntu-24.04
strategy:
matrix:
variant:
- standalone
- distributed
steps:
- name: Check out Git repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Install Blazectl
run: .github/scripts/install-blazectl.sh
- name: Install xq
run: .github/scripts/install-xq.sh
- name: Download Blaze Image
uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
with:
name: blaze-image
path: /tmp
- name: Load Blaze Image
run: docker load --input /tmp/blaze.tar
- name: Run Blaze
run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ALLOW_MULTIPLE_DELETE=true -e ENABLE_INTERACTION_DELETE_HISTORY=true -e ENABLE_OPERATION_PATIENT_PURGE=true -p 8080:8080 -p 8081:8081 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
if: ${{ matrix.variant == 'standalone' }}
- name: Run Kafka, Cassandra and Blaze
run: docker compose -f .github/distributed-test/docker-compose.yml up -d
if: ${{ matrix.variant == 'distributed' }}
- name: Wait for Blaze
run: .github/scripts/wait-for-url.sh http://localhost:8080/health
if: ${{ matrix.variant == 'standalone' }}
- name: Wait for Blaze 1
run: .github/scripts/wait-for-url.sh http://localhost:8081/metrics
if: ${{ matrix.variant == 'distributed' }}
- name: Wait for Blaze 2
run: .github/scripts/wait-for-url.sh http://localhost:8082/metrics
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs
run: docker logs blaze
if: ${{ matrix.variant == 'standalone' }}
- name: Docker Logs Kafka
run: docker compose -f .github/distributed-test/docker-compose.yml logs kafka
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Cassandra 1
run: docker compose -f .github/distributed-test/docker-compose.yml logs cassandra-1
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Cassandra 2
run: docker compose -f .github/distributed-test/docker-compose.yml logs cassandra-2
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Blaze 1
run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-1
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Logs Blaze 2
run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-2
if: ${{ matrix.variant == 'distributed' }}
- name: Docker Stats
run: docker stats --no-stream
- name: Check Capability Statement
run: .github/scripts/check-capability-statement.sh
- name: Check Capability Statement Filtered by _elements
run: .github/scripts/check-capability-statement-filtered.sh
- name: Check Capability Statement Caching
run: .github/scripts/check-capability-statement-caching.sh
- name: Check Referential Integrity Enforced
run: .github/scripts/check-referential-integrity-enforced.sh
- name: Load Data
run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea
- name: Check Total-Number of Resources are 92114
run: .github/scripts/check-total-number-of-resources.sh 92114
- name: Check Resource Totals
run: .github/scripts/check-resource-totals.sh
- name: Count Resources
run: blazectl count-resources --server http://localhost:8080/fhir
- name: Download All Resources
run: .github/scripts/download-all-resources.sh
- name: Download Patient Resources
run: .github/scripts/download-resources.sh Patient
- name: Download Male Patient Resources
run: .github/scripts/download-resources-query.sh Patient "gender=male" 56
- name: Download Female Patient Resources
run: .github/scripts/download-resources-query.sh Patient "gender=female" 64
- name: Download Patient Resources - Including Observation, Condition, Encounter and Procedure
run: .github/scripts/revinclude.sh
- name: Download Observation Resources
run: .github/scripts/download-resources.sh Observation
- name: Download Observation Resources with special LOINC Codes
run: .github/scripts/download-resources-query.sh Observation "code=http://loinc.org|10230-1,http://loinc.org|10480-2,http://loinc.org|10834-0,http://loinc.org|14804-9,http://loinc.org|14959-1,http://loinc.org|1742-6,http://loinc.org|1751-7,http://loinc.org|17861-6,http://loinc.org|18262-6,http://loinc.org|19123-9" 2399
- name: Download Observation Resources with all LOINC Codes
run: .github/scripts/download-resources-query.sh Observation "_count=500&code=http://loinc.org|10230-1,http://loinc.org|10480-2,http://loinc.org|10834-0,http://loinc.org|14804-9,http://loinc.org|14959-1,http://loinc.org|1742-6,http://loinc.org|1751-7,http://loinc.org|17861-6,http://loinc.org|18262-6,http://loinc.org|19123-9,http://loinc.org|1920-8,http://loinc.org|1960-4,http://loinc.org|1975-2,http://loinc.org|1988-5,http://loinc.org|19926-5,http://loinc.org|19994-3,http://loinc.org|2019-8,http://loinc.org|2028-9,http://loinc.org|20454-5,http://loinc.org|20505-4,http://loinc.org|20565-8,http://loinc.org|20570-8,http://loinc.org|2069-3,http://loinc.org|2075-0,http://loinc.org|2085-9,http://loinc.org|2093-3,http://loinc.org|21000-5,http://loinc.org|2157-6,http://loinc.org|2160-0,http://loinc.org|21905-5,http://loinc.org|21906-3,http://loinc.org|21907-1,http://loinc.org|21908-9,http://loinc.org|2276-4,http://loinc.org|2339-0,http://loinc.org|2345-7,http://loinc.org|2498-4,http://loinc.org|2500-7,http://loinc.org|2502-3,http://loinc.org|2514-8,http://loinc.org|2532-0,http://loinc.org|25428-4,http://loinc.org|2571-8,http://loinc.org|26881-3,http://loinc.org|2703-7,http://loinc.org|2708-6,http://loinc.org|2713-6,http://loinc.org|2744-1,http://loinc.org|2823-3,http://loinc.org|28245-9,http://loinc.org|2857-1,http://loinc.org|2885-2,http://loinc.org|29463-7,http://loinc.org|2947-0,http://loinc.org|2951-2,http://loinc.org|3094-0,http://loinc.org|32167-9,http://loinc.org|32207-3,http://loinc.org|32465-7,http://loinc.org|32623-1,http://loinc.org|33728-7,http://loinc.org|33756-8,http://loinc.org|33762-6,http://loinc.org|33914-3,http://loinc.org|33959-8,http://loinc.org|38208-5,http://loinc.org|38265-5,http://loinc.org|38483-4,http://loinc.org|39156-5,http://loinc.org|44667-4,http://loinc.org|44963-7,http://loinc.org|4544-3,http://loinc.org|4548-4,http://loinc.org|46240-8,http://loinc.org|46288-7,http://loinc.org|48065-7,http://loinc.org|49765-1,http://loinc.org|55277-8,http://loinc.org|5767-9,http://loinc.org|5770-3,http://loinc.org|5778-6,http://loinc.org|57905-2,http://loinc.org|5792-7,http://loinc.org|5794-3,http://loinc.org|5797-6,http://loinc.org|5799-2,http://loinc.org|5802-4,http://loinc.org|5803-2,http://loinc.org|5804-0,http://loinc.org|5811-5,http://loinc.org|5902-2,http://loinc.org|59032-3,http://loinc.org|5905-5,http://loinc.org|59408-5,http://loinc.org|59557-9,http://loinc.org|59576-9,http://loinc.org|6075-6,http://loinc.org|6082-2,http://loinc.org|6085-5,http://loinc.org|6095-4,http://loinc.org|6106-9,http://loinc.org|6158-0,http://loinc.org|6189-5,http://loinc.org|6206-7,http://loinc.org|6246-3,http://loinc.org|6248-9,http://loinc.org|6273-7,http://loinc.org|6276-0,http://loinc.org|6298-4,http://loinc.org|6299-2,http://loinc.org|6301-6,http://loinc.org|63513-6,http://loinc.org|65750-2,http://loinc.org|66519-0,http://loinc.org|66524-0,http://loinc.org|66529-9,http://loinc.org|66534-9,http://loinc.org|6690-2,http://loinc.org|6768-6,http://loinc.org|6833-8,http://loinc.org|6844-5,http://loinc.org|69453-9,http://loinc.org|704-7,http://loinc.org|706-2,http://loinc.org|711-2,http://loinc.org|713-8,http://loinc.org|718-7,http://loinc.org|71802-3,http://loinc.org|72106-8,http://loinc.org|72166-2,http://loinc.org|72514-3,http://loinc.org|7258-7,http://loinc.org|731-0,http://loinc.org|736-9,http://loinc.org|742-7,http://loinc.org|751-8,http://loinc.org|75325-1,http://loinc.org|76690-7,http://loinc.org|770-8,http://loinc.org|77606-2,http://loinc.org|777-3,http://loinc.org|785-6,http://loinc.org|786-4,http://loinc.org|787-2,http://loinc.org|788-0,http://loinc.org|789-8,http://loinc.org|80382-5,http://loinc.org|80383-3,http://loinc.org|8302-2,http://loinc.org|8310-5,http://loinc.org|8331-1,http://loinc.org|8478-0,http://loinc.org|85318-4,http://loinc.org|85319-2,http://loinc.org|85337-4,http://loinc.org|85339-0,http://loinc.org|85352-3,http://loinc.org|85354-9,http://loinc.org|88020-3,http://loinc.org|88021-1,http://loinc.org|88040-1,http://loinc.org|88262-1,http://loinc.org|8867-4,http://loinc.org|89579-7,http://loinc.org|91148-7,http://loinc.org|92130-4,http://loinc.org|92131-2,http://loinc.org|92134-6,http://loinc.org|92138-7,http://loinc.org|92139-5,http://loinc.org|92140-3,http://loinc.org|92141-1,http://loinc.org|92142-9,http://loinc.org|9279-1,http://loinc.org|94040-3,http://loinc.org|94531-1,http://loinc.org|9843-4,http://loinc.org|99999-0" 42929
- name: Download Observation Resources of male Patients
run: .github/scripts/download-resources-query.sh Observation "patient.gender=male" 20466
- name: Download Observation Resources of male Patients Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_id" 20466
- name: Download Observation Resources of male Patients Sorted Ascending by Last Updated
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_lastUpdated" 20466
- name: Download Observation Resources of male Patients Sorted Descending by Last Updated
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "-_lastUpdated" 20466
- name: Download Laboratory Observation Resources Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "category=laboratory" "_id" 29206
- name: Download Laboratory Observation Resources Sorted Ascending by Last Updated
run: .github/scripts/download-resources-query-sort.sh Observation "category=laboratory" "_lastUpdated" 29206
- name: Download Observation Resources of female Patients
run: .github/scripts/download-resources-query.sh Observation "_count=500&patient.gender=female" 22463
- name: Download Observation Resources of the year 1970
run: .github/scripts/download-resources-query.sh Observation "date=1970" 59
- name: Download Observation Resources of the year 1970 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=1970" "_id" 59
- name: Download Observation Resources of the year 1980
run: .github/scripts/download-resources-query.sh Observation "date=1980" 0
- name: Download Observation Resources of the year 1980 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=1980" "_id" 0
- name: Download Observation Resources of the year 1990
run: .github/scripts/download-resources-query.sh Observation "date=1990" 19
- name: Download Observation Resources of the year 2000
run: .github/scripts/download-resources-query.sh Observation "date=2000" 101
- name: Download Observation Resources of the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=2010" 995
- name: Download Observation Resources of the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=2020" 17419
- name: Download Observation Resources of the year 2020 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=2020" "_id" 17419
- name: Download Observation Resources not of the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=ne2020" 25510
- name: Download Observation Resources not of the year 2020 Sorted by ID
run: .github/scripts/download-resources-query-sort.sh Observation "date=ne2020" "_id" 25510
- name: Download Observation Resources greater than the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=gt2010" 38486
- name: Download Observation Resources greater than the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=gt2020" 983
- name: Download Observation Resources less than the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=lt2010" 3448
- name: Download Observation Resources less than the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=lt2020" 24527
- name: Download Observation Resources greater equal the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=ge2010" 39481
- name: Download Observation Resources greater equal the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=ge2020" 18402
- name: Download Observation Resources less equal the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=le2010" 4443
- name: Download Observation Resources less equal the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=le2020" 41946
- name: Download Observation Resources that start after the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=sa2010" 38486
- name: Download Observation Resources that start after the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=sa2020" 983
- name: Download Observation Resources that end before the year 2010
run: .github/scripts/download-resources-query.sh Observation "date=eb2010" 3448
- name: Download Observation Resources that end before the year 2020
run: .github/scripts/download-resources-query.sh Observation "date=eb2020" 24527
- name: Check Observation Date Search
run: .github/scripts/check-date-search.sh "Observation"
- name: Check Encounter Date Search
run: .github/scripts/check-date-search.sh "Encounter"
- name: Check DiagnosticReport Date Search
run: .github/scripts/check-date-search.sh "DiagnosticReport"
- name: Download Observation Resources of female Patients Sorted Ascending
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "_lastUpdated" 22463
- name: Download Observation Resources of female Patients Sorted Descending
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "-_lastUpdated" 22463
- name: Download Observation Resources - Including Patients
run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:patient' -o Observation-Patient.ndjson
- name: Download Observation Resources - Including Encounters and Patients
run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:encounter&_include=Observation:patient' -o Observation-Encounter-Patient.ndjson
- name: Download Observation Resources - Including Encounters and Encounter Patients
run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:encounter&_include:iterate=Encounter:patient' -o Observation-Encounter-Encounter-Patient.ndjson
- name: Download Condition Resources
run: .github/scripts/download-resources.sh Condition
- name: Download Condition Resources - Including Subjects
run: blazectl --no-progress --server http://localhost:8080/fhir download Condition -q '_include=Condition:subject' -o Condition-Subject.ndjson
- name: Download Condition Resources - Including Encounters
run: blazectl --no-progress --server http://localhost:8080/fhir download Condition -q '_include=Condition:encounter' -o Condition-Encounter.ndjson
- name: Download DiagnosticReport Resources
run: .github/scripts/download-resources.sh DiagnosticReport
- name: Download MedicationRequest Resources of Medications with code 854235
run: .github/scripts/download-resources-query.sh MedicationRequest "medication.code=1736854" 112
- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Ascending
run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "_lastUpdated" 112
- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Descending
run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "-_lastUpdated" 112
- name: Download MedicationRequest Resources - Including Medications
run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson
- name: Download male Patient Resources having inpatient Encounters in 2010
run: .github/scripts/download-resources-query.sh Patient "gender=male&_has:Encounter:patient:class=IMP&_has:Encounter:patient:date=2010" 8
- name: Download female Patient Resources having inpatient Encounters in 2010
run: .github/scripts/download-resources-query.sh Patient "gender=female&_has:Encounter:patient:class=IMP&_has:Encounter:patient:date=2010" 11
- name: Download Observations using _elements=subject
run: .github/scripts/download-observations-elements.sh
- name: Download Observations of all Encounters using ID's
run: .github/scripts/download-observations-of-all-encounters.sh
- name: Search Observation _lastUpdated
run: .github/scripts/search-patient-last-updated.sh
- name: Search Observation _profile
run: .github/scripts/search-observation-profile.sh
- name: Search Compartment
run: .github/scripts/search-compartment.sh
- name: Evaluate CQL Query 1
run: .github/scripts/evaluate-measure.sh q1 56
- name: Evaluate CQL Query 1 as Batch
run: .github/scripts/evaluate-measure-as-batch.sh q1 56
- name: Evaluate CQL Query 1 async
run: .github/scripts/evaluate-measure-async.sh q1 56
- name: Evaluate CQL Query 1 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q1 56
- name: Evaluate CQL Query 1 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q1 56
- name: Evaluate CQL Query 1 - Subject List as Batch
run: .github/scripts/evaluate-measure-subject-list-as-batch.sh q1 56
- name: Evaluate CQL Query 1 on Individual Patients
run: .github/scripts/evaluate-patient-q1-measure.sh
- name: Evaluate CQL Query 2
run: .github/scripts/evaluate-measure.sh q2 42
- name: Evaluate CQL Query 2 as Batch
run: .github/scripts/evaluate-measure-as-batch.sh q2 42
- name: Evaluate CQL Query 2 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q2 42
- name: Evaluate CQL Query 2 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q2 42
- name: Evaluate CQL Query 2 - Subject List as Batch
run: .github/scripts/evaluate-measure-subject-list-as-batch.sh q2 42
- name: Evaluate CQL Query 4
run: .github/scripts/evaluate-measure.sh q4 0
- name: Evaluate CQL Query 4 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q4 0
- name: Evaluate CQL Query 4 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q4 0
- name: Evaluate CQL Query 7
run: .github/scripts/evaluate-measure.sh q7 81
- name: Evaluate CQL Query 7 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q7 81
- name: Evaluate CQL Query 7 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q7 81
- name: Evaluate CQL Query 14
run: .github/scripts/evaluate-measure.sh q14 96
- name: Evaluate CQL Query 14 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q14 96
- name: Evaluate CQL Query 14 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q14 96
- name: Evaluate CQL Query 15 using Blazectl
run: .github/scripts/evaluate-measure.sh q15 31
- name: Evaluate CQL Query 17
run: .github/scripts/evaluate-measure.sh q17 120
- name: Evaluate CQL Query 17 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q17 120
- name: Evaluate CQL Query 17 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q17 120
- name: Evaluate CQL Query 20 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q20-stratifier-city 120
- name: Evaluate CQL Query 21 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q21-stratifier-city-of-only-women 64
- name: Evaluate CQL Query 26 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q26-stratifier-bmi 120
- name: Evaluate CQL Query 27 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q27-stratifier-calculated-bmi 120
- name: Evaluate CQL Query 32 using Blazectl
run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q32-stratifier-underweight 120
- name: Evaluate CQL Query 36
run: .github/scripts/evaluate-measure.sh q36-parameter 86
- name: Evaluate CQL Query 36 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86
- name: Evaluate CQL Query 34
run: .github/scripts/evaluate-measure.sh q37-overlaps 24
- name: Evaluate CQL Query 34 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24
- name: Evaluate CQL Query 34 - Subject List
run: .github/scripts/evaluate-measure-subject-list.sh q37-overlaps 24
- name: Evaluate CQL Query 46
run: .github/scripts/evaluate-measure.sh q46-between-date 19
- name: Evaluate CQL Query 46 using Blazectl
run: .github/scripts/evaluate-measure-blazectl.sh q46-between-date 19
- name: Forwarded Header HTTPS
run: .github/scripts/forwarded-header.sh https
- name: Forwarded Header HTTP
run: .github/scripts/forwarded-header.sh http
- name: X-Forwarded Headers HTTPS
run: .github/scripts/x-forwarded-headers.sh https
- name: X-Forwarded Headers HTTP
run: .github/scripts/x-forwarded-headers.sh http
- name: Delete
run: .github/scripts/delete.sh
- name: Delete Violating Referential Integrity
run: .github/scripts/check-referential-integrity-for-delete.sh 409
- name: Delete After Referring Resource is Deleted Succeeds
run: .github/scripts/check-delete-succeeds-after-referring-resource-is-deleted.sh
- name: Batch
run: .github/scripts/batch.sh
- name: Batch Metadata
run: .github/scripts/batch-metadata.sh
- name: Transaction
run: .github/scripts/transaction.sh
- name: Transaction Read/Write
run: .github/scripts/transaction-rw.sh
- name: Transactional Delete Preserving Referential Integrity
run: .github/scripts/transactional-delete.sh
- name: Transaction with Invalid (Null) Resource
run: .github/scripts/transaction-null-resource.sh
- name: OPTIONS
run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata
- name: Health
run: curl -f http://localhost:8080/health
- name: Health - HEAD
run: curl -f --head http://localhost:8080/health
- name: Not Acceptable
run: .github/scripts/not-acceptable.sh