Merge pull request #818 from samply/release-v0.18.1

Release v0.18.1
samply · Oct 14, 2022 · 315385a · 315385a
2 parents 867d3e1 + 66da081
commit 315385a
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diff --git a/.github/distributed-test/docker-compose.yml b/.github/distributed-test/docker-compose.yml
@@ -65,7 +65,7 @@ services:
       HEAP_NEWSIZE: "100M"
 
   blaze-1:
-    image: "ghcr.io/samply/blaze:sha-${GITHUB_SHA}"
+    image: "blaze:latest"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx512m"
       STORAGE: "distributed"
@@ -94,7 +94,7 @@ services:
     - cassandra-2
 
   blaze-2:
-    image: "ghcr.io/samply/blaze:sha-${GITHUB_SHA}"
+    image: "blaze:latest"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx512m"
       STORAGE: "distributed"

diff --git a/.github/openid-auth-test/docker-compose.yml b/.github/openid-auth-test/docker-compose.yml
@@ -12,7 +12,7 @@ services:
     - "${GITHUB_WORKSPACE}/.github/openid-auth-test/realm.json:/tmp/realm.json"
 
   blaze:
-    image: "ghcr.io/samply/blaze:sha-${GITHUB_SHA}"
+    image: "blaze:latest"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx2g"
       OPENID_PROVIDER_URL: "http://keycloak:8080/auth/realms/blaze"

diff --git a/.github/scripts/evaluate-patient-q1-measure.sh b/.github/scripts/evaluate-patient-q1-measure.sh
@@ -76,7 +76,7 @@ evaluate-measure() {
 }
 
 BASE="http://localhost:8080/fhir"
-FILE="modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q1-query.cql"
+FILE="modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q1.cql"
 DATA=$(base64 "$FILE" | tr -d '\n')
 LIBRARY_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 MEASURE_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,14 @@
 # Changelog
 
+## v0.18.1
+
+### Security
+
+* Update Dependencies ([#817](https://github.com/samply/blaze/pull/817))
+* Uninstall wget because of CVE-2021-31879 ([#801](https://github.com/samply/blaze/pull/801))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/52?closed=1).
+
 ## v0.18.0
 
 ### New Features

diff --git a/Dockerfile b/Dockerfile
@@ -1,7 +1,7 @@
 FROM eclipse-temurin:17-jre
 
 RUN apt-get update && apt-get upgrade -y && \
-    apt-get purge curl libbinutils libctf0 libctf-nobfd0 libncurses6 -y && \
+    apt-get purge curl wget libbinutils libctf0 libctf-nobfd0 libncurses6 -y && \
     apt-get autoremove -y && apt-get clean
 
 RUN mkdir -p /app/data && chown 1001:1001 /app/data

diff --git a/README.md b/README.md
@@ -2,7 +2,8 @@
 
 [![Build](https://github.com/samply/blaze/actions/workflows/build.yml/badge.svg)](https://github.com/samply/blaze/actions/workflows/build.yml)
 [![Docker Pulls](https://img.shields.io/docker/pulls/samply/blaze.svg)](https://hub.docker.com/r/samply/blaze/)
-[![codecov](https://codecov.io/gh/samply/blaze/branch/develop/graph/badge.svg)](https://codecov.io/gh/samply/blaze)
+[![Code Coverage](https://codecov.io/gh/samply/blaze/branch/develop/graph/badge.svg)](https://codecov.io/gh/samply/blaze)
+[![Latest Release](https://img.shields.io/github/v/release/samply/blaze)][5]
 
 A FHIR® Store with internal, fast CQL Evaluation Engine
 
@@ -14,7 +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: [v0.18.0][5]
+Latest release: [v0.18.1][5]
 
 ## Quick Start
 
@@ -72,7 +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/v0.18.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.18.1>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

diff --git a/deps.edn b/deps.edn
@@ -41,7 +41,7 @@
   {:mvn/version "1.3.6"}
 
   org.slf4j/slf4j-nop
-  {:mvn/version "2.0.2"}}
+  {:mvn/version "2.0.3"}}
 
  :aliases
  {:depstar
@@ -80,10 +80,10 @@
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "2.1.927"}
+    {:mvn/version "2.1.932"}
 
     org.slf4j/slf4j-nop
-    {:mvn/version "2.0.2"}}
+    {:mvn/version "2.0.3"}}
 
    :main-opts
    ["-m" "antq.core"

diff --git a/dev/blaze/dev.clj b/dev/blaze/dev.clj
@@ -13,7 +13,7 @@
     [clojure.repl :refer [pst]]
     [clojure.spec.test.alpha :as st]
     [clojure.tools.namespace.repl :refer [refresh]]
-    [java-time :as time]
+    [java-time.api :as time]
     [taoensso.timbre :as log])
   (:import
     [com.github.benmanes.caffeine.cache Cache]))

diff --git a/dev/blaze/dev/tx_log.clj b/dev/blaze/dev/tx_log.clj
@@ -2,7 +2,7 @@
   (:require
     [blaze.core :refer [system]]
     [blaze.db.tx-log :as tx-log]
-    [java-time :as time]))
+    [java-time.api :as time]))
 
 
 (def tx-log

diff --git a/docs/conformance/cql.md b/docs/conformance/cql.md
@@ -340,7 +340,7 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 22.15. | ConvertsToString   | ✓          |               |       |
 | 22.16. | ConvertsToTime     | ✓          |               |       |
 | 22.17. | Descendents        | ✓          |               |       |
-| 22.18. | Is                 | ✗          |               |       |
+| 22.18. | Is                 | ✓          |               |       |
 | 22.19. | ToBoolean          | ✓          |               |       |
 | 22.20. | ToChars            | ✓          |               |       |
 | 22.21. | ToConcept          | ✗          |               |       |

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 0.18.0 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.18.1 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.18.0"
+  "version": "0.18.1"
 }
 ```
 

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/v0.18.0). Look for `blaze-0.18.0-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/v0.18.1). Look for `blaze-0.18.1-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.18.0-standalone.jar -m blaze.core
+java -jar blaze-0.18.1-standalone.jar -m blaze.core
 ```
 
 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-0.18.0-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.18.1-standalone.jar -m blaze.core
 ```
 
 Under Windows, you need to set the Environment variables in the PowerShell before starting Blaze:
 
 ```powershell
 $Env:STORAGE="standalone"
-java -jar blaze-0.18.0-standalone.jar -m blaze.core
+java -jar blaze-0.18.1-standalone.jar -m blaze.core
 ```
 
 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 0.18.0 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.18.1 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.18.0"
+  "version": "0.18.1"
 }
 ```
 

diff --git a/modules/byte-buffer/deps.edn b/modules/byte-buffer/deps.edn
@@ -1,6 +1,6 @@
 {:deps
  {com.google.protobuf/protobuf-java
-  {:mvn/version "3.21.6"}}
+  {:mvn/version "3.21.7"}}
 
  :aliases
  {:test

diff --git a/modules/byte-string/deps.edn b/modules/byte-string/deps.edn
@@ -5,7 +5,7 @@
   {:mvn/version "31.1-jre"}
 
   com.google.protobuf/protobuf-java
-  {:mvn/version "3.21.6"}
+  {:mvn/version "3.21.7"}
 
   com.fasterxml.jackson.core/jackson-databind
-  {:mvn/version "2.13.4"}}}
+  {:mvn/version "2.13.4.2"}}}
diff --git a/modules/cassandra/deps.edn b/modules/cassandra/deps.edn
@@ -7,11 +7,11 @@
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   com.fasterxml.jackson.core/jackson-databind
-  {:mvn/version "2.13.4"}
+  {:mvn/version "2.13.4.2"}
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   io.netty/netty-handler
-  {:mvn/version "4.1.82.Final"}}
+  {:mvn/version "4.1.84.Final"}}
 
  :aliases
  {:test

diff --git a/modules/cassandra/src/blaze/cassandra/config.clj b/modules/cassandra/src/blaze/cassandra/config.clj
@@ -1,7 +1,7 @@
 (ns blaze.cassandra.config
   (:require
     [clojure.string :as str]
-    [java-time :as time])
+    [java-time.api :as time])
   (:import
     [com.datastax.oss.driver.api.core.config OptionsMap TypedDriverOption]
     [java.net InetSocketAddress]))

diff --git a/modules/cassandra/test/blaze/cassandra/config_test.clj b/modules/cassandra/test/blaze/cassandra/config_test.clj
@@ -3,7 +3,7 @@
     [blaze.cassandra.config :as config]
     [clojure.spec.test.alpha :as st]
     [clojure.test :as test :refer [deftest are testing]]
-    [java-time :as time])
+    [java-time.api :as time])
   (:import
     [com.datastax.oss.driver.api.core.config OptionsMap TypedDriverOption]
     [java.net InetSocketAddress]))

diff --git a/modules/cql/src/blaze/elm/compiler/type_operators.clj b/modules/cql/src/blaze/elm/compiler/type_operators.clj
@@ -228,7 +228,65 @@
     (->DescendentsOperatorExpression source)))
 
 
-;; TODO 22.18. Is
+;; 22.18. Is
+(defrecord IsExpression [operand type pred]
+  core/Expression
+  (-eval [_ context resource scope]
+    (pred (core/-eval operand context resource scope)))
+  (-form [_]
+    `(~'is ~type ~(core/-form operand))))
+
+
+(defn- matches-elm-named-type-is [type-name]
+  (case type-name
+    "Boolean" ['elm/boolean boolean?]
+    "Integer" ['elm/integer int?]
+    "Long" ['elm/long system/long?]
+    "Decimal" ['elm/decimal decimal?]
+    "Date" ['elm/date system/date?]
+    "DateTime" ['elm/date-time date-time/temporal?]
+    "Quantity" ['elm/quantity quantity/quantity?]
+    "String" ['elm/string string?]))
+
+
+(defn- matches-named-type-is [type-name]
+  (let [[type-ns type-name] (elm-util/parse-qualified-name type-name)]
+    (case type-ns
+      "http://hl7.org/fhir"
+      [(symbol "fhir" type-name)
+       (let [fhir-type (keyword "fhir" type-name)]
+         #(identical? fhir-type (fhir-spec/fhir-type %)))]
+      "urn:hl7-org:elm-types:r1"
+      (matches-elm-named-type-is type-name))))
+
+
+(defn- matches-type-specifier-is [is-type-specifier]
+  (case (:type is-type-specifier)
+    "NamedTypeSpecifier"
+    (matches-named-type-is (:name is-type-specifier))
+
+    "ListTypeSpecifier"
+    (let [[type pred] (matches-type-specifier-is (:elementType is-type-specifier))]
+      [`(~'list ~type)
+       (fn matches-type? [x]
+         (every? pred x))])))
+
+
+(defn- matches-type-is
+  [{is-type :isType is-type-specifier :isTypeSpecifier}]
+  (cond
+    is-type
+    (matches-named-type-is is-type)
+
+    is-type-specifier
+    (matches-type-specifier-is is-type-specifier)))
+
+
+(defmethod core/compile* :elm.compiler.type/is
+  [context {:keys [operand] :as expression}]
+  (let [[type pred] (matches-type-is expression)]
+    (->IsExpression (core/compile* context operand) type pred)))
+
 
 ;; 22.19. ToBoolean
 (defunop to-boolean [x]

diff --git a/modules/cql/src/blaze/elm/date_time.clj b/modules/cql/src/blaze/elm/date_time.clj
@@ -8,7 +8,7 @@
     [blaze.elm.protocols :as p]
     [blaze.fhir.spec.type]
     [blaze.fhir.spec.type.system :as system]
-    [java-time :as time])
+    [java-time.api :as time])
   (:import
     [blaze.fhir.spec.type OffsetInstant]
     [blaze.fhir.spec.type.system DateTimeYear DateTimeYearMonth DateTimeYearMonthDay]

diff --git a/modules/cql/src/blaze/elm/expression_spec.clj b/modules/cql/src/blaze/elm/expression_spec.clj
@@ -7,7 +7,7 @@
     [blaze.elm.expression :as expr]
     [blaze.fhir.spec]
     [clojure.spec.alpha :as s]
-    [java-time :as time]))
+    [java-time.api :as time]))
 
 
 (s/def ::now

diff --git a/modules/cql/test/blaze/cql_test.clj b/modules/cql/test/blaze/cql_test.clj
@@ -143,8 +143,6 @@
             "StringToIntegerError"                          ; TODO: implement
             "StringToDateTime"                              ; TODO: implement
             "StringToTime"                                  ; TODO: implement
-            "IntegerIsInteger"                              ; TODO: implement
-            "StringIsInteger"                               ; TODO: implement
             "StringNoToBoolean"                             ; TODO: implement
             "CodeToConcept1"                                ; TODO: implement
             "ToDateTime4"                                   ; time zones don't match

diff --git a/modules/cql/test/blaze/elm/compiler/comparison_operators_test.clj b/modules/cql/test/blaze/elm/compiler/comparison_operators_test.clj
@@ -564,6 +564,10 @@
 
     (tu/testing-binary-null elm/greater-or-equal #elm/date "2013-06-15"))
 
+  (testing "DateTime with mixed precision"
+    (are [x y] (nil? (tu/compile-binop elm/greater-or-equal elm/date-time x y))
+      "2005-06-17" "2005"))
+
   (testing "Time"
     (are [x y res] (= res (tu/compile-binop elm/greater-or-equal elm/time x y))
       "00:00:00" "00:00:00" true

diff --git a/modules/cql/test/blaze/elm/compiler/date_time_operators_test.clj b/modules/cql/test/blaze/elm/compiler/date_time_operators_test.clj
@@ -18,7 +18,7 @@
     [clojure.test :as test :refer [are deftest is testing]]
     [clojure.test.check.properties :as prop]
     [cognitect.anomalies :as anom]
-    [java-time :as time]
+    [java-time.api :as time]
     [juxt.iota :refer [given]])
   (:import
     [java.time Year YearMonth]