Replace Standalone Docker Compose with Build-in One

GitHub Actions removed docker-compose: actions/runner-images#9692 Also did some CQL and Dev Docs.
samply · Aug 1, 2024 · e5aece5 · e5aece5
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -577,7 +577,7 @@ jobs:
       if: ${{ matrix.variant == 'standalone' }}
 
     - name: Run Kafka, Cassandra and Blaze
-      run: docker-compose -f .github/distributed-test/docker-compose.yml up -d
+      run: docker compose -f .github/distributed-test/docker-compose.yml up -d
       if: ${{ matrix.variant == 'distributed' }}
 
     - name: Wait for Blaze
@@ -597,23 +597,23 @@ jobs:
       if: ${{ matrix.variant == 'standalone' }}
 
     - name: Docker Logs Kafka
-      run: docker-compose -f .github/distributed-test/docker-compose.yml 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
+      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
+      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
+      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
+      run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-2
       if: ${{ matrix.variant == 'distributed' }}
 
     - name: Docker Stats
@@ -1496,22 +1496,22 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Keycloak
-      run: docker-compose -f .github/openid-auth-test/docker-compose.yml up -d keycloak
+      run: docker compose -f .github/openid-auth-test/docker-compose.yml up -d keycloak
 
     - name: Wait for Keycloak
       run: .github/scripts/wait-for-url.sh http://localhost:8090/health/ready
 
     - name: Run Blaze
-      run: docker-compose -f .github/openid-auth-test/docker-compose.yml up -d blaze
+      run: docker compose -f .github/openid-auth-test/docker-compose.yml up -d blaze
 
     - name: Wait for Blaze
       run: .github/scripts/wait-for-url.sh http://localhost:8080/health
 
     - name: Docker Logs Keycloak
-      run: docker-compose -f .github/openid-auth-test/docker-compose.yml logs keycloak
+      run: docker compose -f .github/openid-auth-test/docker-compose.yml logs keycloak
 
     - name: Docker Logs Blaze
-      run: docker-compose -f .github/openid-auth-test/docker-compose.yml logs blaze
+      run: docker compose -f .github/openid-auth-test/docker-compose.yml logs blaze
 
     - name: Unauthenticated Request
       run: test "MSG_AUTH_REQUIRED" = "$(curl -s http://localhost:8080/fhir | jq -r .issue[0].details.coding[0].code)"
@@ -1537,13 +1537,13 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Keycloak and Blaze
-      run: docker-compose -f .github/custom-search-parameters-test/docker-compose.yml up -d
+      run: docker compose -f .github/custom-search-parameters-test/docker-compose.yml up -d
 
     - name: Wait for Blaze
       run: .github/scripts/wait-for-url.sh http://localhost:8080/health
 
     - name: Docker Logs Blaze
-      run: docker-compose -f .github/custom-search-parameters-test/docker-compose.yml logs blaze
+      run: docker compose -f .github/custom-search-parameters-test/docker-compose.yml logs blaze
 
     - name: Create Patient
       run: .github/custom-search-parameters-test/create-patient.sh
@@ -1572,7 +1572,7 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Test Setup
-      run: docker-compose -f docs/data-sync/copy/docker-compose.yml -f .github/doc-copy-data-test/docker-compose.override.yml up -d
+      run: docker compose -f docs/data-sync/copy/docker-compose.yml -f .github/doc-copy-data-test/docker-compose.override.yml up -d
 
     - name: Wait for Source Blaze
       run: .github/scripts/wait-for-url.sh http://localhost:8080/health
@@ -1677,19 +1677,19 @@ jobs:
       run: make build-ingress
 
     - name: Run Keycloak
-      run: docker-compose -f modules/frontend-e2e/docker-compose.yml up -d keycloak
+      run: docker compose -f modules/frontend-e2e/docker-compose.yml up -d keycloak
 
     - name: Sleep 20 Seconds
       run: sleep 20
 
     - name: Run Everything Else
-      run: docker-compose -f modules/frontend-e2e/docker-compose.yml up -d
+      run: docker compose -f modules/frontend-e2e/docker-compose.yml up -d
 
     - name: Sleep 30 Seconds
       run: sleep 30
 
     - name: Docker Logs
-      run: docker-compose -f modules/frontend-e2e/docker-compose.yml logs
+      run: docker compose -f modules/frontend-e2e/docker-compose.yml logs
 
     - name: Load Data
       run: modules/frontend-e2e/upload.sh
@@ -1851,7 +1851,7 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Kafka, Cassandra and Blaze
-      run: docker-compose -f .github/distributed-test/docker-compose.yml up -d
+      run: docker compose -f .github/distributed-test/docker-compose.yml up -d
 
     - name: Wait for Blaze 1
       run: .github/scripts/wait-for-url.sh http://localhost:8081/metrics
@@ -1860,19 +1860,19 @@ jobs:
       run: .github/scripts/wait-for-url.sh http://localhost:8082/metrics
 
     - name: Docker Logs Kafka
-      run: docker-compose -f .github/distributed-test/docker-compose.yml logs kafka
+      run: docker compose -f .github/distributed-test/docker-compose.yml logs kafka
 
     - name: Docker Logs Cassandra 1
-      run: docker-compose -f .github/distributed-test/docker-compose.yml logs cassandra-1
+      run: docker compose -f .github/distributed-test/docker-compose.yml logs cassandra-1
 
     - name: Docker Logs Cassandra 2
-      run: docker-compose -f .github/distributed-test/docker-compose.yml logs cassandra-2
+      run: docker compose -f .github/distributed-test/docker-compose.yml logs cassandra-2
 
     - name: Docker Logs Blaze 1
-      run: docker-compose -f .github/distributed-test/docker-compose.yml logs blaze-1
+      run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-1
 
     - name: Docker Logs Blaze 2
-      run: docker-compose -f .github/distributed-test/docker-compose.yml logs blaze-2
+      run: docker compose -f .github/distributed-test/docker-compose.yml logs blaze-2
 
     - name: Docker Stats
       run: docker stats --no-stream

diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
@@ -10,13 +10,14 @@ The most reliable way to build Blaze is to use GitHub CI. If you create a PR, a
 
 ### Using a Local Build Environment
 
-* install Java 17
+* install Java 21
 * install nodejs v18
 * install Clojure by following this [guide](https://clojure.org/guides/install_clojure)
 * install Make
 * install cljfmt: `clj -Ttools install io.github.weavejester/cljfmt '{:git/tag "0.11.2"}' :as cljfmt`
+* run `make -C job-ig build` to create the FHIR profiles
 * run `make uberjar` to create the uberjar that will be available under the `target` directory
-* run `docker build .` to build the Docker image
+* run `docker build -t blaze:latest .` to build the Docker image
 
 ## Working with IntelliJ
 

diff --git a/docs/authentication.md b/docs/authentication.md
@@ -9,13 +9,13 @@ If this feature is activated, all FHIR Endpoints will require a valid [JWT][2] i
 In order to test the authentication feature, please start first [Keycloak][4] and then Blaze as defined in the Docker Compose file in the `docs/authentication` directory:
 
 ```sh
-docker-compose up keycloak
+docker compose up keycloak
 ```
 
 wait until keycloak is started
 
 ```sh
-docker-compose up blaze
+docker compose up blaze
 ```
 
 after both services are up, please run:

diff --git a/docs/data-sync.md b/docs/data-sync.md
@@ -7,7 +7,7 @@ If you want to facilitate the CQL engine or other features of Blaze, but you can
 In this example we use [HAPI][2] as our primary FHIR server. In the `docs/data-sync` directory, you can find a Docker Compose file with a setup of a HAPI and a Blaze server. Please start the containers by running:
 
 ```sh
-docker-compose -f docs/data-sync/subscription/docker-compose.yml up
+docker compose -f docs/data-sync/subscription/docker-compose.yml up
 ```
 
 After both servers are up and running, you can create two subscriptions, one for Patient resources and one for Observations. Please run:
@@ -34,7 +34,7 @@ Another use-case would be to copy all data from one Blaze server to another. Tha
 In order to test copying all data from one Blaze server to another, start the following Docker Compose project:
 
 ```sh
-docker-compose -f docs/data-sync/copy/docker-compose.yml up
+docker compose -f docs/data-sync/copy/docker-compose.yml up
 ```
 
 You should see a `src` server started at port 8080 and a `dst` server started at port 8082.

diff --git a/docs/deployment/distributed-backend.md b/docs/deployment/distributed-backend.md
@@ -15,7 +15,7 @@ Please be aware that we **don't recommend** to run Blaze on a single server usin
 You will need about 32 GB of RAM to be able to run the example smoothly. You can start it by going into the `docs/deployment/distributed` directory and run:
 
 ```sh
-docker-compose up -d
+docker compose up -d
 ```
 
 Currently, Blaze uses [Kafka][1] for the Transaction Log and [Cassandra][4] for the Resource Store, so the example uses the same. A walk-through of the components follows:

diff --git a/docs/deployment/full-standalone.md b/docs/deployment/full-standalone.md
@@ -29,19 +29,19 @@ Two certificates and one trust store should be generated in the `modules/ingress
 After you have created the certificates, you can start the system by going into the `docs/deployment/full-standalone` directory and run:
 
 ```sh
-docker-compose up -d keycloak
+docker compose up -d keycloak
 ```
 
 first, because it needs to be fully started before the Blaze components can start to avoid waiting an additional minute for Blaze fetching the Keycloak config again. After Keycloak runs, start the rest of the components:  
 
 ```sh
-docker-compose up -d
+docker compose up -d
 ```
 
 Watch all components to start completely by looking into the log output:
 
 ```sh
-docker-compose logs -f
+docker compose logs -f
 ```
 
 In your browser, please go to `https://blaze.localhost/fhir`. 

diff --git a/docs/implementation/cql.md b/docs/implementation/cql.md
@@ -1,5 +1,54 @@
 # CQL
 
+## Compilation and Evaluation Pipeline
+
+```
+╭───────────────────────╮
+│ CQL → ELM Translation │
+╰───────────┬───────────╯
+╭───────────┴───────────╮
+│    ELM Compilation    │
+╰───────────┬───────────╯
+╭───────────┴───────────╮
+│  Unfiltered Context   │ 
+│      Evaluation       │
+╰───────────┬───────────╯
+╭───────────┴───────────╮
+│ Reference Resolution  │
+╰───────────┬───────────╯
+╭───────────┴───────────╮
+│     Optimization      │
+╰───────────┬───────────╯
+╭───────────┴───────────╮
+│  Bloom filter attach  │
+╰───────────┬───────────╯
+╭───────────┴───────────╮
+│   Parallel Patient    │ 
+│  Context Evaluation   │
+╰───────────────────────╯            
+```
+
+```
+╭──────────────╮   ╭───────────────────────────────╮  ╭────────────────────────╮
+│   Patient    │   │   MedicationAdministration    │  │   Medciation: ATC 1234 │ 
+╰──────────────╯   ╰───────────────────────────────╯  ╰────────────────────────╯ 
+
+╭──────────────╮   ╭───────────────────────────────╮
+│   Patient    │   │   Observation: loinc 788-7    │
+╰──────────────╯   ╰───────────────────────────────╯
+
+```
+
+### CQL → ELM Translation
+
+The Expression Logical Model (ELM) is the abstract syntax tree (AST) form of CQL. Blaze uses the CQL → ELM translator from the [Clinical Quality Framework][1] project. After that translation, the ELM expressions are available in JSON form and are parsed into Clojure data structures. The function doing this is `blaze.cql-translator/translate`.
+
+### ELM Compilation
+
+The ELM expression are compiled into instances of the `blaze.elm.compiler.core/Expression` protocol. During this compilation a first optimization of static values and compilation of database queries is done. The database node is used during that compilation. The function used is `blaze.elm.compiler.library/compile-library`.
+
+### Unfiltered Context Evaluation
+
 ## Expression Cache
 
 * bloom filter
@@ -86,3 +135,5 @@ O C E S
 | |  ^  
 S E C O  
 ```
+
+[1]: <https://github.com/cqframework>
diff --git a/modules/cache-collector/Makefile b/modules/cache-collector/Makefile
@@ -13,6 +13,12 @@ test: prep
 test-coverage: prep
 	clojure -M:test:coverage
 
+cloc-prod:
+	cloc src
+
+cloc-test:
+	cloc test
+
 deps-tree:
 	clojure -X:deps tree
 

diff --git a/modules/frontend/README.md b/modules/frontend/README.md
@@ -7,7 +7,7 @@ First run `make clean build` to install all NPM dependencies and build the front
 Second, start Keycloak:
 
 ```sh
-docker-compose up
+docker compose up
 ```
 
 Third, run the frontend in dev mode: