Merge pull request #600 from samply/release-v0.15.5

Release v0.15.5

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## v0.15.5
+
+### New Features
+
+* Implement FHIRPath Function extension ([#598](https://github.com/samply/blaze/pull/598))
+
+### Bugfixes
+
+* Fix NPE in Reference Resolution ([#599](https://github.com/samply/blaze/pull/599))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/28?closed=1).
+
 ## v0.15.4
 
 ### 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: [v0.15.4][5]
+Latest release: [v0.15.5][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/v0.15.4>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.15.5>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

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 0.15.4 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.15.5 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.15.4"
+  "version": "0.15.5"
 }
 ```
 

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/v0.15.4). Look for `blaze-0.15.4-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/v0.15.5). Look for `blaze-0.15.5-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.15.4-standalone.jar -m blaze.core
+java -jar blaze-0.15.5-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-0.15.4-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.15.5-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-0.15.4-standalone.jar -m blaze.core
+java -jar blaze-0.15.5-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 0.15.4 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.15.5 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.15.4"
+  "version": "0.15.5"
 }
 ```
 

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

@@ -1,5 +1,5 @@
 (ns blaze.fhir-path
-  (:refer-clojure :exclude [eval compile resolve])
+  (:refer-clojure :exclude [compile eval resolve])
   (:require
     [blaze.anomaly :as ba :refer [throw-anom]]
     [blaze.anomaly-spec]
@@ -16,30 +16,30 @@
     [org.antlr.v4.runtime.tree TerminalNode]
     [org.cqframework.cql.gen
      fhirpathLexer fhirpathParser
-     fhirpathParser$TermExpressionContext
-     fhirpathParser$InvocationExpressionContext
-     fhirpathParser$IndexerExpressionContext
      fhirpathParser$AdditiveExpressionContext
-     fhirpathParser$TypeExpressionContext
-     fhirpathParser$UnionExpressionContext
-     fhirpathParser$EqualityExpressionContext
      fhirpathParser$AndExpressionContext
-     fhirpathParser$InvocationTermContext
-     fhirpathParser$LiteralTermContext
-     fhirpathParser$ParenthesizedTermContext
-     fhirpathParser$NullLiteralContext
      fhirpathParser$BooleanLiteralContext
-     fhirpathParser$StringLiteralContext
-     fhirpathParser$NumberLiteralContext
      fhirpathParser$DateLiteralContext
      fhirpathParser$DateTimeLiteralContext
-     fhirpathParser$MemberInvocationContext
-     fhirpathParser$FunctionInvocationContext
+     fhirpathParser$EqualityExpressionContext
      fhirpathParser$FunctionContext
+     fhirpathParser$FunctionInvocationContext
+     fhirpathParser$IdentifierContext
+     fhirpathParser$IndexerExpressionContext
+     fhirpathParser$InvocationExpressionContext
+     fhirpathParser$InvocationTermContext
+     fhirpathParser$LiteralTermContext
+     fhirpathParser$MemberInvocationContext
+     fhirpathParser$NullLiteralContext
+     fhirpathParser$NumberLiteralContext
      fhirpathParser$ParamListContext
-     fhirpathParser$TypeSpecifierContext
+     fhirpathParser$ParenthesizedTermContext
      fhirpathParser$QualifiedIdentifierContext
-     fhirpathParser$IdentifierContext]))
+     fhirpathParser$StringLiteralContext
+     fhirpathParser$TermExpressionContext
+     fhirpathParser$TypeExpressionContext
+     fhirpathParser$TypeSpecifierContext
+     fhirpathParser$UnionExpressionContext]))
 
 
 (set! *warn-on-reflection* true)
@@ -279,35 +279,6 @@
       (throw-anom (ba/incorrect (as-type-specifier-msg coll))))))
 
 
-;; See: http://hl7.org/fhirpath/#wherecriteria-expression-collection
-(defn- non-boolean-result-msg [x]
-  (format "non-boolean result `%s` of type `%s` while evaluating where function criteria"
-          (pr-str x) (fhir-spec/fhir-type x)))
-
-
-(defn- multiple-result-msg [x]
-  (format "multiple result items `%s` while evaluating where function criteria"
-          (pr-str x)))
-
-
-(defrecord WhereFunctionExpression [criteria]
-  Expression
-  (-eval [_ context coll]
-    (filterv
-      (fn [item]
-        (let [coll (-eval criteria context [item])]
-          (case (.count ^Counted coll)
-            0 false
-
-            1 (let [first (nth coll 0)]
-                (if (identical? :system/boolean (system/type first))
-                  first
-                  (throw-anom (ba/incorrect (non-boolean-result-msg first)))))
-
-            (throw-anom (ba/incorrect (multiple-result-msg coll))))))
-      coll)))
-
-
 (defrecord OfTypeFunctionExpression [type-specifier]
   Expression
   (-eval [_ _ coll]
@@ -368,6 +339,40 @@
     (throw-anom (ba/incorrect "missing type specifier in `as` function"))))
 
 
+
+;; 5.2. Filtering and projection
+
+;; 5.2.1. where(criteria : expression) : collection
+
+;; See: http://hl7.org/fhirpath/#wherecriteria-expression-collection
+(defn- non-boolean-result-msg [x]
+  (format "non-boolean result `%s` of type `%s` while evaluating where function criteria"
+          (pr-str x) (fhir-spec/fhir-type x)))
+
+
+(defn- multiple-result-msg [x]
+  (format "multiple result items `%s` while evaluating where function criteria"
+          (pr-str x)))
+
+
+(defrecord WhereFunctionExpression [criteria]
+  Expression
+  (-eval [_ context coll]
+    (filterv
+      (fn [item]
+        (let [coll (-eval criteria context [item])]
+          (case (.count ^Counted coll)
+            0 false
+
+            1 (let [first (nth coll 0)]
+                (if (identical? :system/boolean (system/type first))
+                  first
+                  (throw-anom (ba/incorrect (non-boolean-result-msg first)))))
+
+            (throw-anom (ba/incorrect (multiple-result-msg coll))))))
+      coll)))
+
+
 (defmethod function-expression "where"
   [_ ^fhirpathParser$ParamListContext paramsCtx]
   (if-let [criteria-ctx (some-> paramsCtx (.expression 0))]
@@ -389,7 +394,22 @@
     (->ExistsFunctionExpression)))
 
 
-;; See: https://hl7.org/fhir/fhirpath.html#functions
+
+;; Additional functions (https://www.hl7.org/fhir/fhirpath.html#functions)
+
+(defrecord ExtensionFunctionExpression [xf]
+  Expression
+  (-eval [_ _ coll]
+    (into [] xf coll)))
+
+
+(defmethod function-expression "extension"
+  [_ ^fhirpathParser$ParamListContext paramsCtx]
+  (let [url-pred (set (some-> paramsCtx (.expression 0) -compile))
+        xf (comp (mapcat :extension) (filter (comp url-pred :url)))]
+    (->ExtensionFunctionExpression xf)))
+
+
 (defmethod function-expression "resolve"
   [_ _]
   (->ResolveFunctionExpression))