Merge pull request #901 from samply/release-v0.19.1

Release v0.19.1
samply · Feb 10, 2023 · b3207cc · b3207cc
2 parents 5a2b8d5 + d44780d
commit b3207cc
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diff --git a/.github/scripts/wait-for-url.sh b/.github/scripts/wait-for-url.sh
@@ -1,5 +1,14 @@
 #!/bin/bash -e
 
 URL=$1
+START_EPOCH="$(date +"%s")"
 
-while [[ "$(curl -s -o /dev/null -w ''%{http_code}'' $URL)" != "200" ]]; do sleep 2; done
+eclipsed() {
+  EPOCH="$(date +"%s")"
+  echo $((EPOCH - START_EPOCH))
+}
+
+# wait at maximum 120 seconds
+while [[ ($(eclipsed) -lt 120) && ("$(curl -s -o /dev/null -w ''%{http_code}'' "$URL")" != "200") ]]; do
+  sleep 2
+done
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -210,7 +210,7 @@ jobs:
       uses: docker/setup-buildx-action@v2
 
     - name: Build and Export to Docker
-      uses: docker/build-push-action@v3
+      uses: docker/build-push-action@v4
       with:
         context: .
         tags: blaze:latest
@@ -1305,7 +1305,7 @@ jobs:
           type=semver,pattern={{major}}.{{minor}}
 
     - name: Build and push
-      uses: docker/build-push-action@v3
+      uses: docker/build-push-action@v4
       with:
         context: .
         platforms: linux/amd64,linux/arm64

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,17 @@
 # Changelog
 
+## v0.19.1
+
+### Security
+
+* Update Dependencies ([#898](https://github.com/samply/blaze/pull/898))
+* Update Dependencies ([#899](https://github.com/samply/blaze/pull/899))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/58?closed=1).
+
 ## v0.19.0
 
-### Documentation
+### New Features
 
 * Add Evaluate Measure Timeout ([#888](https://github.com/samply/blaze/pull/888))
 

diff --git a/Dockerfile b/Dockerfile
@@ -6,7 +6,7 @@ RUN apt-get update && apt-get upgrade -y && \
     rm -rf /var/lib/apt/lists/
 
 RUN mkdir -p /app/data && chown 1001:1001 /app/data
-COPY target/blaze-0.19.0-standalone.jar /app/
+COPY target/blaze-0.19.1-standalone.jar /app/
 
 WORKDIR /app
 USER 1001
@@ -16,4 +16,4 @@ ENV INDEX_DB_DIR="/app/data/index"
 ENV TRANSACTION_DB_DIR="/app/data/transaction"
 ENV RESOURCE_DB_DIR="/app/data/resource"
 
-CMD ["java", "-jar", "blaze-0.19.0-standalone.jar"]
+CMD ["java", "-jar", "blaze-0.19.1-standalone.jar"]
diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ The goal of this project is to provide a FHIR® Store with an internal CQL Evalu
 
 Blaze passes all [Touchstone FHIR 4.0.1 Basic Tests][12] and almost all [CQL Tests][3]. Please refer to the [Conformance](docs/conformance.md) section and report any issues you encounter during evaluation.
 
-Latest release: [v0.19.0][5]
+Latest release: [v0.19.1][5]
 
 ## Quick Start
 
@@ -73,7 +73,7 @@ Unless required by applicable law or agreed to in writing, software distributed
 
 [3]: <https://cql.hl7.org/tests.html>
 [4]: <https://alexanderkiel.gitbook.io/blaze/deployment>
-[5]: <https://github.com/samply/blaze/releases/tag/v0.19.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.19.1>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

diff --git a/build.clj b/build.clj
@@ -2,7 +2,7 @@
   (:require [clojure.tools.build.api :as b]))
 
 (def lib 'samply/blaze)
-(def version "0.19.0")
+(def version "0.19.1")
 (def class-dir "target/classes")
 (def basis (b/create-basis {:project "deps.edn"}))
 (def uber-file (format "target/%s-%s-standalone.jar" (name lib) version))

diff --git a/deps.edn b/deps.edn
@@ -47,7 +47,7 @@
  {:build
   {:deps
    {io.github.clojure/tools.build
-    {:git/tag "v0.9.2" :git/sha "fe6b140"}}
+    {:git/tag "v0.9.3" :git/sha "e537cd1"}}
    :ns-default build}
 
   :test
@@ -80,7 +80,7 @@
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "2.2.970"}
+    {:mvn/version "2.2.992"}
 
     org.slf4j/slf4j-nop
     {:mvn/version "2.0.6"}}

diff --git a/docs/conformance/cql.md b/docs/conformance/cql.md
@@ -53,6 +53,8 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 5.1. | Library             | ✓          |                                      |       |
 | 5.2. | IncludeDef          | !          | no custom includes, only FHIRHelpers |       |
 | 5.3. | VersionedIdentifier | ✗          |                                      |       |
+| 5.4. | ContextDef          | ✗          |                                      |       |
+
 
 ### 6. Data Model
 
@@ -87,6 +89,7 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 9.2. | ExpressionRef | !          | only inside same library                    |       |
 | 9.3. | FunctionDef   | ✓          |                                             |       |
 | 9.4. | FunctionRef   | !          | hard coded implementation of some functions |       |
+| 9.5. | OperandRef    | ✓          |                                             |       |
 
 ### 10. Queries
 
@@ -98,19 +101,22 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 10.4.  | ByColumn           | ✓          |                    |       |
 | 10.5.  | ByDirection        | ✓          |                    |       |
 | 10.6.  | ByExpression       | ✓          |                    |       |
-| 10.7.  | LetClause          | ✗          |                    |       |
-| 10.8.  | QueryLetRef        | ✗          |                    |       |
-| 10.9.  | RelationshipClause | ✓          |                    |       |
-| 10.10. | ReturnClause       | !          | always distinct    |       |
-| 10.11. | SortClause         | ✓          |                    |       |
-| 10.12. | With               | !          | only equiv version |       |
-| 10.13. | Without            | ✗          |                    |       |
+| 10.7.  | IdentifierRef      | ✓          |                    |       |
+| 10.8.  | LetClause          | ✗          |                    |       |
+| 10.9.  | QueryLetRef        | ✗          |                    |       |
+| 10.10. | RelationshipClause | ✓          |                    |       |
+| 10.11. | ReturnClause       | !          | always distinct    |       |
+| 10.12. | AggregateClause    | ✗          |                    |       |
+| 10.13. | SortClause         | ✓          |                    |       |
+| 10.14. | With               | !          | only equiv version |       |
+| 10.15. | Without            | ✗          |                    |       |
 
 ### 11. External Data
 
-| Num   | Group    | Expression | State          | Notes |
-|-------|----------|------------|----------------|-------|
-| 11.1. | Retrieve | !          | no date ranges |       |
+| Num   | Group          | Expression | State          | Notes |
+|-------|----------------|------------|----------------|-------|
+| 11.1. | Retrieve       | !          | no date ranges |       |
+| 11.2. | IncludeElement | ✗          |                |       |
 
 ### 12. Comparison Operators
 
@@ -176,7 +182,7 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 16.19. | Round           | ✓          |
 | 16.20. | Subtract        | ✓          |
 | 16.21. | Successor       | ✓          |
-| 16.12. | Truncate        | ✓          |
+| 16.22. | Truncate        | ✓          |
 | 16.23. | TruncatedDivide | ✓          |
 
 ### 17. String Operators
@@ -260,10 +266,11 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 19.25. | ProperIn         | ✓          |
 | 19.26. | ProperIncludes   | ✓          |
 | 19.27. | ProperIncludedIn | ✓          |
-| 19.28. | Start            | ✓          |
-| 19.29. | Starts           | ✓          |
+| 19.28. | Size             | ✗          |
+| 19.29. | Start            | ✓          |
+| 19.30. | Starts           | ✓          |
 | 19.31. | Union            | ✓          |
-| 19.31. | Width            | ✓          |
+| 19.32. | Width            | ✓          |
 
 ### 20. List Operators
 
@@ -296,7 +303,7 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 20.25. | SingletonFrom    | ✓          |            |       |
 | 20.26. | Slice            | ✓          |            |       |
 | 20.27. | Sort             | ✓          |            |       |
-| 20.28. | Times            | ✗          |            |       |
+| 20.28. | Times            | ✓          |            |       |
 | 20.29. | Union            | ✓          |            |       |
 
 ### 21. Aggregate Operators
@@ -367,9 +374,10 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 23.6.  | Equivalent      | ✗          |
 | 23.7.  | InCodeSystem    | ✗          |
 | 23.8.  | InValueSet      | ✗          |
-| 23.9.  | Not Equal       | ✓          |
-| 23.10. | SubsumedBy      | ✗          |
-| 23.11. | Subsumes        | ✗          |
+| 23.9.  | ExpandValueSet  | ✗          |
+| 23.10. | Not Equal       | ✓          |
+| 23.11. | SubsumedBy      | ✗          |
+| 23.12. | Subsumes        | ✗          |
 
 ### 24. Errors and Messages
 

diff --git a/docs/deployment/docker-deployment.md b/docs/deployment/docker-deployment.md
@@ -27,7 +27,7 @@ Blaze should log something like this:
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:64] - JVM version: 16.0.2
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:65] - Maximum available memory: 1738 MiB
 2021-06-27T11:02:37.835Z ee086ef908c1 main INFO [blaze.core:66] - Number of available processors: 8
-2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.19.0 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.19.1 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.19.0"
+  "version": "0.19.1"
 }
 ```
 

diff --git a/docs/deployment/manual-deployment.md b/docs/deployment/manual-deployment.md
@@ -2,12 +2,12 @@
 
 The installation works under Windows, Linux and macOS. The only dependency is an installed OpenJDK 11 or 17 with 17 recommended. Blaze is tested with [Eclipse Temurin][1].
 
-Blaze runs on the JVM and comes as single JAR file. Download the most recent version [here](https://github.com/samply/blaze/releases/tag/v0.19.0). Look for `blaze-0.19.0-standalone.jar`.
+Blaze runs on the JVM and comes as single JAR file. Download the most recent version [here](https://github.com/samply/blaze/releases/tag/v0.19.1). Look for `blaze-0.19.1-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.19.0-standalone.jar
+java -jar blaze-0.19.1-standalone.jar
 ```
 
 Blaze will run with an in-memory, volatile database for testing and demo purposes.
@@ -17,14 +17,14 @@ Blaze can be run with durable storage by setting the environment variables `STOR
 Under Linux/macOS:
 
 ```sh
-STORAGE=standalone java -jar blaze-0.19.0-standalone.jar
+STORAGE=standalone java -jar blaze-0.19.1-standalone.jar
 ```
 
 Under Windows, you need to set the Environment variables in the PowerShell before starting Blaze:
 
 ```powershell
 $Env:STORAGE="standalone"
-java -jar blaze-0.19.0-standalone.jar
+java -jar blaze-0.19.1-standalone.jar
 ```
 
 This will create three directories called `index`, `transaction` and `resource` inside the current working directory, one for each database part used.
@@ -42,7 +42,7 @@ The output should look like this:
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:64] - JVM version: 16.0.2
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:65] - Maximum available memory: 1738 MiB
 2021-06-27T11:02:37.835Z ee086ef908c1 main INFO [blaze.core:66] - Number of available processors: 8
-2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.19.0 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.19.1 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.19.0"
+  "version": "0.19.1"
 }
 ```
 

diff --git a/modules/byte-string/deps.edn b/modules/byte-string/deps.edn
@@ -8,4 +8,4 @@
   {:mvn/version "3.21.12"}
 
   com.fasterxml.jackson.core/jackson-databind
-  {:mvn/version "2.14.1"}}}
+  {:mvn/version "2.14.2"}}}
diff --git a/modules/cassandra/deps.edn b/modules/cassandra/deps.edn
@@ -7,7 +7,7 @@
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   com.fasterxml.jackson.core/jackson-databind
-  {:mvn/version "2.14.1"}
+  {:mvn/version "2.14.2"}
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   io.netty/netty-handler

diff --git a/modules/cql/deps.edn b/modules/cql/deps.edn
@@ -5,23 +5,23 @@
   {:local/root "../db"}
 
   com.fasterxml.jackson.module/jackson-module-jaxb-annotations
-  {:mvn/version "2.14.1"}
+  {:mvn/version "2.14.2"}
 
   com.fasterxml.jackson.dataformat/jackson-dataformat-xml
-  {:mvn/version "2.14.1"}
+  {:mvn/version "2.14.2"}
 
   info.cqframework/cql-to-elm
-  {:mvn/version "2.4.0"
+  {:mvn/version "2.5.0"
    :exclusions [xpp3/xpp3_xpath]}
 
   info.cqframework/elm-jackson
-  {:mvn/version "2.4.0"}
+  {:mvn/version "2.5.0"}
 
   info.cqframework/model-jackson
-  {:mvn/version "2.4.0"}
+  {:mvn/version "2.5.0"}
 
   info.cqframework/quick
-  {:mvn/version "2.4.0"}
+  {:mvn/version "2.5.0"}
 
   org.apache.commons/commons-text
   {:mvn/version "1.10.0"}

diff --git a/modules/cql/src/blaze/cql_translator_spec.clj b/modules/cql/src/blaze/cql_translator_spec.clj
@@ -8,5 +8,5 @@
 
 
 (s/fdef cql-translator/translate
-  :args (s/cat :cql string? :opts (s/* some?))
+  :args (s/cat :cql string?)
   :ret (s/or :library :elm/library :anomaly ::anom/anomaly))
diff --git a/modules/cql/src/blaze/elm/compiler/list_operators.clj b/modules/cql/src/blaze/elm/compiler/list_operators.clj
@@ -7,7 +7,7 @@
     [blaze.anomaly :as ba]
     [blaze.coll.core :as coll]
     [blaze.elm.compiler.core :as core]
-    [blaze.elm.compiler.macros :refer [defunop]]
+    [blaze.elm.compiler.macros :refer [defbinop defunop]]
     [blaze.elm.compiler.queries :as queries]
     [blaze.elm.protocols :as p]
     [cognitect.anomalies :as anom])
@@ -220,3 +220,12 @@
           (->SortByDirectionExpression source (queries/comparator direction))))
       source
       sort-by-items)))
+
+
+;; 20.28. Times
+(defbinop times [list1 list2]
+  (transduce
+    (mapcat #(eduction (map (partial merge %)) list1))
+    (completing (fnil conj []))
+    nil
+    list2))
diff --git a/modules/cql/src/blaze/elm/compiler/queries.clj b/modules/cql/src/blaze/elm/compiler/queries.clj
@@ -239,10 +239,6 @@
 
 
 ;; 10.1. Query
-;;
-;; The Query operator represents a clause-based query. The result of the query
-;; is determined by the type of sources included, as well as the clauses used in
-;; the query.
 (defmulti compile-sort-by-item (fn [_ {:keys [type]}] type))
 
 
@@ -304,9 +300,6 @@
 
 
 ;; 10.3. AliasRef
-;;
-;; The AliasRef expression allows for the reference of a specific source within
-;; the context of a query.
 (defrecord AliasRefExpression [key]
   core/Expression
   (-eval [_ _ _ scopes]
@@ -327,10 +320,6 @@
 
 
 ;; 10.14. With
-;;
-;; The With clause restricts the elements of a given source to only those
-;; elements that have elements in the related source that satisfy the suchThat
-;; condition. This operation is known as a semi-join in database languages.
 (defn- find-operand-with-alias
   "Finds the operand in `expression` that accesses entities with `alias`."
   [operands alias]

diff --git a/modules/cql/src/blaze/elm/normalizer.clj b/modules/cql/src/blaze/elm/normalizer.clj
@@ -407,6 +407,10 @@
 (derive :elm.normalizer.type/singleton-from :elm.normalizer.type/unary-expression)
 
 
+;; 20.28. Times
+(derive :elm.normalizer.type/times :elm.normalizer.type/binary-expression)
+
+
 
 ;; 22. Type Operators