Merge pull request #723 from samply/release-v0.17.5

Release v0.17.5

.github/workflows/build.yml

@@ -397,12 +397,6 @@ jobs:
     - name: Evaluate CQL Query 14 - Subject List
       run: .github/scripts/evaluate-measure-subject-list.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q14-query.cql 96
 
-    - name: Evaluate CQL Query 15
-      run: .github/scripts/evaluate-measure.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q15-query.cql 31
-
-    - name: Evaluate CQL Query 15 - Subject List
-      run: .github/scripts/evaluate-measure-subject-list.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q15-query.cql 31
-
     - name: Evaluate CQL Query 17
       run: .github/scripts/evaluate-measure.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q17-query.cql 120
 
@@ -823,12 +817,6 @@ jobs:
     - name: Evaluate CQL Query 14 - Subject List
       run: .github/scripts/evaluate-measure-subject-list.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q14-query.cql 96
 
-    - name: Evaluate CQL Query 15
-      run: .github/scripts/evaluate-measure.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q15-query.cql 31
-
-    - name: Evaluate CQL Query 15 - Subject List
-      run: .github/scripts/evaluate-measure-subject-list.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q15-query.cql 31
-
     - name: Evaluate CQL Query 17
       run: .github/scripts/evaluate-measure.sh modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q17-query.cql 120
 

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## v0.17.5
+
+### Bugfixes
+
+* Allow Extensions on Date Data Type ([#371](https://github.com/samply/blaze/issues/371))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/43?closed=1).
+
 ## v0.17.4
 
 ### Bugfixes

README.md

@@ -14,7 +14,7 @@ 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: [v0.17.4][5]
+Latest release: [v0.17.5][5]
 
 ## Quick Start
 
@@ -72,7 +72,7 @@ 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/v0.17.4>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.17.5>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

deps.edn

@@ -80,7 +80,7 @@
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "1.6.2"}
+    {:mvn/version "1.6.774"}
 
     org.slf4j/slf4j-nop
     {:mvn/version "1.7.36"}}

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 0.17.4 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.17.5 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.17.4"
+  "version": "0.17.5"
 }
 ```
 

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. Blaze is tested with [AdoptOpenJDK][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/v0.17.4). Look for `blaze-0.17.4-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/v0.17.5). Look for `blaze-0.17.5-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.17.4-standalone.jar -m blaze.core
+java -jar blaze-0.17.5-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-0.17.4-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.17.5-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-0.17.4-standalone.jar -m blaze.core
+java -jar blaze-0.17.5-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 0.17.4 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.17.5 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.17.4"
+  "version": "0.17.5"
 }
 ```
 

modules/db-stub/src/blaze/db/api_stub.clj

@@ -26,7 +26,7 @@
       :resource-handle-cache (ig/ref :blaze.db/resource-handle-cache)
       :tx-cache (ig/ref :blaze.db/tx-cache)
       :indexer-executor (ig/ref :blaze.db.node/indexer-executor)
-      :resource-store (ig/ref :blaze.db/resource-store)
+      :resource-store (ig/ref ::rs/kv)
       :kv-store (ig/ref :blaze.db/index-kv-store)
       :resource-indexer (ig/ref :blaze.db.node/resource-indexer)
       :search-param-registry (ig/ref :blaze.db/search-param-registry)}

modules/db/deps.edn

@@ -37,6 +37,7 @@
   blaze/spec
   {:local/root "../spec"}
 
+  ;; Warning: version 0.4.1 is from 2017 but has no dependencies
   clj-fuzzy/clj-fuzzy
   {:mvn/version "0.4.1"}}
 

modules/db/test-perf/blaze/db/api_test_perf.clj

@@ -31,7 +31,7 @@
     :resource-handle-cache (ig/ref :blaze.db/resource-handle-cache)
     :tx-cache (ig/ref :blaze.db/tx-cache)
     :indexer-executor (ig/ref :blaze.db.node/indexer-executor)
-    :resource-store (ig/ref :blaze.db/resource-store)
+    :resource-store (ig/ref ::rs/kv)
     :kv-store (ig/ref :blaze.db/index-kv-store)
     :resource-indexer (ig/ref :blaze.db.node/resource-indexer)
     :search-param-registry (ig/ref :blaze.db/search-param-registry)

modules/db/test/blaze/db/api_test.clj

@@ -63,7 +63,7 @@
 
 (def slow-resource-store-system
   (-> (assoc-in system [:blaze.db/node :resource-store] (ig/ref ::slow-resource-store))
-      (assoc ::slow-resource-store {:resource-store (ig/ref :blaze.db/resource-store)})))
+      (assoc ::slow-resource-store {:resource-store (ig/ref ::rs/kv)})))
 
 
 (defmethod ig/init-key ::resource-store-failing-on-put [_ _]
@@ -245,6 +245,24 @@
             [:meta :versionId] := #fhir/id"1"
             [meta :blaze.db/op] := :put))))
 
+    (testing "one Patient with an Extension on birthDate"
+      (with-system-data [{:blaze.db/keys [node]} system]
+        [[[:put {:fhir/type :fhir/Patient :id "0"
+                 :birthDate
+                 #fhir/date
+                         {:extension [#fhir/Extension{:url "foo" :value #fhir/code"bar"}]
+                          :value "2022"}}]]]
+
+        (testing "the Patient was created"
+          (given @(d/pull node (d/resource-handle (d/db node) "Patient" "0"))
+            :fhir/type := :fhir/Patient
+            :id := "0"
+            [:meta :versionId] := #fhir/id"1"
+            [meta :blaze.db/op] := :put
+            [:birthDate :extension 0 :url] := "foo"
+            [:birthDate :extension 0 :value] := #fhir/code"bar"
+            [:birthDate :value] := #fhir/date"2022"))))
+
     (testing "one Patient with one Observation"
       (with-system-data [{:blaze.db/keys [node]} system]
         ;; the create ops are purposely disordered in order to test the

modules/db/test/blaze/db/node_test.clj

@@ -78,7 +78,7 @@
   (-> (assoc-in system [:blaze.db/node :resource-store]
                 (ig/ref ::resource-store-slow-on-put))
       (assoc ::resource-store-slow-on-put
-             {:resource-store (ig/ref :blaze.db/resource-store)})))
+             {:resource-store (ig/ref ::rs/kv)})))
 
 
 (deftest init-test

modules/db/test/blaze/db/test_util.clj

@@ -22,7 +22,7 @@
     :resource-handle-cache (ig/ref :blaze.db/resource-handle-cache)
     :tx-cache (ig/ref :blaze.db/tx-cache)
     :indexer-executor (ig/ref :blaze.db.node/indexer-executor)
-    :resource-store (ig/ref :blaze.db/resource-store)
+    :resource-store (ig/ref ::rs/kv)
     :kv-store (ig/ref :blaze.db/index-kv-store)
     :resource-indexer (ig/ref :blaze.db.node/resource-indexer)
     :search-param-registry (ig/ref :blaze.db/search-param-registry)
@@ -31,8 +31,10 @@
    ::tx-log/local
    {:kv-store (ig/ref :blaze.db/transaction-kv-store)
     :clock (ig/ref :blaze.test/clock)}
+
    [::kv/mem :blaze.db/transaction-kv-store]
    {:column-families {}}
+
    :blaze.test/clock {}
 
    :blaze.db/resource-handle-cache {}
@@ -61,8 +63,10 @@
    ::rs/kv
    {:kv-store (ig/ref :blaze.db/resource-kv-store)
     :executor (ig/ref ::rs-kv/executor)}
+
    [::kv/mem :blaze.db/resource-kv-store]
    {:column-families {}}
+
    ::rs-kv/executor {}
 
    :blaze.db.node/resource-indexer

modules/fhir-path/src/blaze/fhir_path.clj

@@ -541,13 +541,13 @@
   fhirpathParser$DateLiteralContext
   (-compile [ctx]
     (let [text (subs (.getText (.getSymbol (.DATE ctx))) 1)]
-      [(type/->Date text)]))
+      [(type/date text)]))
 
   fhirpathParser$DateTimeLiteralContext
   (-compile [ctx]
     (let [text (subs (.getText (.getSymbol (.DATETIME ctx))) 1)
           text (if (str/ends-with? text "T") (subs text 0 (dec (count text))) text)]
-      [(type/->DateTime text)]))
+      [(type/dateTime text)]))
 
   fhirpathParser$MemberInvocationContext
   (-compile [ctx]

modules/fhir-structure/.clj-kondo/config.edn

@@ -1,10 +1,11 @@
 {:lint-as
- {blaze.fhir.spec.type.macros/defprimitivetype clojure.core/deftype
+ {blaze.fhir.spec.type.macros/def-primitive-type clojure.core/deftype
+  blaze.fhir.spec.type.macros/defextended clojure.core/defrecord
   blaze.test-util/with-system clojure.core/with-open}
 
  :hooks
  {:macroexpand
-  {blaze.fhir.spec.type.macros/defcomplextype macros/defcomplextype}}
+  {blaze.fhir.spec.type.macros/def-complex-type macros/def-complex-type}}
 
  :linters
  {:unsorted-required-namespaces

modules/fhir-structure/.clj-kondo/macros.clj

@@ -1,7 +1,7 @@
 (ns macros)
 
 
-(defmacro defcomplextype
+(defmacro def-complex-type
   [name [& fields] & {:keys [fhir-type hash-num interned references field-serializers]
                       :or {interned false}}]
   `(defrecord ~name [~@fields]

modules/fhir-structure/deps.edn

@@ -44,13 +44,7 @@
 
    :extra-deps
    {blaze/test-util
-    {:local/root "../test-util"}
-
-    criterium/criterium
-    {:mvn/version "0.4.6"}
-
-    org.openjdk.jol/jol-core
-    {:mvn/version "0.16"}}}
+    {:local/root "../test-util"}}}
 
   :kaocha
   {:extra-deps
@@ -77,4 +71,5 @@
    {cloverage/cloverage
     {:mvn/version "1.2.3"}}
 
-   :main-opts ["-m" "cloverage.coverage" "--codecov" "-p" "src" "-s" "test"]}}}
+   :main-opts ["-m" "cloverage.coverage" "--codecov" "-p" "src" "-s" "test"
+               "-e" ".*spec$"]}}}

modules/fhir-structure/resources/data_readers.clj

@@ -1,22 +1,25 @@
 {blaze/hash blaze.fhir.hash/from-hex
  blaze/hash-prefix blaze.fhir.hash/prefix-from-hex
- fhir/integer clojure.core/int
- fhir/long clojure.core/long
+ fhir/boolean blaze.fhir.spec.type/boolean
+ fhir/integer blaze.fhir.spec.type/integer
+ fhir/long blaze.fhir.spec.type/long
+ fhir/string blaze.fhir.spec.type/string
+ fhir/decimal blaze.fhir.spec.type/decimal
  fhir/uri blaze.fhir.spec.type/uri
- fhir/url blaze.fhir.spec.type/->Url
+ fhir/url blaze.fhir.spec.type/url
  fhir/canonical blaze.fhir.spec.type/canonical
- fhir/base64Binary blaze.fhir.spec.type/->Base64Binary
- fhir/instant blaze.fhir.spec.type/->Instant
- fhir/date blaze.fhir.spec.type/->Date
- fhir/dateTime blaze.fhir.spec.type/->DateTime
- fhir/time blaze.fhir.spec.type/->Time
+ fhir/base64Binary blaze.fhir.spec.type/base64Binary
+ fhir/instant blaze.fhir.spec.type/instant
+ fhir/date blaze.fhir.spec.type/date
+ fhir/dateTime blaze.fhir.spec.type/dateTime
+ fhir/time blaze.fhir.spec.type/time
  fhir/code blaze.fhir.spec.type/code
- fhir/oid blaze.fhir.spec.type/->Oid
- fhir/id blaze.fhir.spec.type/->Id
- fhir/markdown blaze.fhir.spec.type/->Markdown
- fhir/unsignedInt blaze.fhir.spec.type/->UnsignedInt
- fhir/positiveInt blaze.fhir.spec.type/->PositiveInt
- fhir/uuid blaze.fhir.spec.type/->Uuid
+ fhir/oid blaze.fhir.spec.type/oid
+ fhir/id blaze.fhir.spec.type/id
+ fhir/markdown blaze.fhir.spec.type/markdown
+ fhir/unsignedInt blaze.fhir.spec.type/unsignedInt
+ fhir/positiveInt blaze.fhir.spec.type/positiveInt
+ fhir/uuid blaze.fhir.spec.type/uuid
  fhir/xhtml blaze.fhir.spec.type/->Xhtml
  fhir/Attachment blaze.fhir.spec.type/map->Attachment
  fhir/Extension blaze.fhir.spec.type/extension

modules/fhir-structure/src/blaze/fhir/spec.clj

@@ -12,7 +12,7 @@
     [cognitect.anomalies :as anom]
     [jsonista.core :as j])
   (:import
-    [com.fasterxml.jackson.databind DeserializationFeature]
+    [com.fasterxml.jackson.databind DeserializationFeature ObjectMapper]
     [com.fasterxml.jackson.dataformat.cbor CBORFactory]
     [java.util.regex Pattern]))
 
@@ -22,11 +22,10 @@
 
 
 (def ^:private json-object-mapper
-  (-> (j/object-mapper
-        {:decode-key-fn true
-         :bigdecimals true
-         :modules [type/fhir-module]})
-      (.enable DeserializationFeature/FAIL_ON_TRAILING_TOKENS)))
+  (doto (ObjectMapper.)
+    (.registerModule type/fhir-module)
+    (.enable DeserializationFeature/USE_BIG_DECIMAL_FOR_FLOATS)
+    (.enable DeserializationFeature/FAIL_ON_TRAILING_TOKENS)))
 
 
 (defn parse-json
@@ -44,10 +43,8 @@
 
 
 (def ^:private cbor-object-mapper
-  (j/object-mapper
-    {:factory (CBORFactory.)
-     :decode-key-fn true
-     :modules [type/fhir-module]}))
+  (doto (ObjectMapper. (CBORFactory.))
+    (.registerModule type/fhir-module)))
 
 
 (defn parse-cbor
@@ -290,7 +287,7 @@
           (when-not (s2/invalid? resource)
             resource))))
     (ba/incorrect
-      "Invalid intermediate representation of a resource."
+      "Invalid JSON representation of a resource."
       :x x
       :fhir/issues (:fhir/issues (explain-data-json x)))))
 
@@ -309,6 +306,6 @@
           (when-not (s2/invalid? resource)
             resource))))
     (ba/incorrect
-      "Invalid intermediate representation of a resource."
+      "Invalid XML representation of a resource."
       :x x
       :fhir/issues (:fhir/issues (explain-data-xml x)))))