Merge pull request #770 from samply/release-v0.17.11

Release v0.17.11
samply · Jul 13, 2022 · d8b317e · d8b317e
2 parents ac423e8 + 02f2409
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,13 +1,26 @@
 # Changelog
 
-## v0.17.10
+## v0.17.11
 
 ### Bugfixes
 
-* Fix Reference Resolution on Extended Primitive References
+* Fix Quantity Indexing without Value ([#764](https://github.com/samply/blaze/issues/764))
+* Fix Deserialisation of Primitive Values in Extensions ([#767](https://github.com/samply/blaze/issues/767))
 
 ### Other Improvements ([#758](https://github.com/samply/blaze/issues/758))
 
+* Implement Functions in CQL ([#766](https://github.com/samply/blaze/pull/766))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/50?closed=1).
+
+## v0.17.10
+
+### Bugfixes
+
+* Fix Reference Resolution on Extended Primitive References ([#758](https://github.com/samply/blaze/issues/758))
+
+### Other Improvements
+
 * Implement CQL ConvertsToTime ([#759](https://github.com/samply/blaze/pull/759))
 
 The full changelog can be found [here](https://github.com/samply/blaze/milestone/48?closed=1).

diff --git a/README.md b/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: [v0.17.10][5]
+Latest release: [v0.17.11][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/v0.17.10>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.17.11>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

diff --git a/docs/conformance/cql.md b/docs/conformance/cql.md
@@ -85,7 +85,7 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 |------|---------------|------------|---------------------------------------------|-------|
 | 9.1. | ExpressionDef | ✓          |                                             |       |
 | 9.2. | ExpressionRef | !          | only inside same library                    |       |
-| 9.3. | FunctionDef   | ✗          |                                             |       |
+| 9.3. | FunctionDef   | ✓          |                                             |       |
 | 9.4. | FunctionRef   | !          | hard coded implementation of some functions |       |
 
 ### 10. Queries
@@ -322,38 +322,38 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 ### 22. Type Operators
 
 | Num    | Group              | Expression | State         | Notes |
-|--------|--------------------|-----------|---------------|-------|
-| 22.1.  | As                 | !         | no strictness |       |
-| 22.2.  | CanConvert         | ✗         |               |       |
-| 22.3.  | CanConvertQuantity | ✓         |               |       |
-| 22.4.  | Children           | ✓         |               |       |
-| 22.5.  | Convert            | ✗         |               |       |
-| 22.6.  | ConvertQuantity    | ✓         |               |       |
-| 22.7.  | ConvertsToBoolean  | ✓         |               |       |
-| 22.8.  | ConvertsToDate     | ✓         |               |       |
-| 22.9.  | ConvertsToDateTime | ✓         |               |       |
-| 22.10. | ConvertsToDecimal  | ✓         |               |       |
-| 22.11. | ConvertsToLong     | ✓         |               |       |
-| 22.12. | ConvertsToInteger  | ✓         |               |       |
-| 22.13. | ConvertsToQuantity | ✓         |               |       |
-| 22.14. | ConvertsToRatio    | ✗         |               |       |
-| 22.15. | ConvertsToString   | ✓         |               |       |
-| 22.16. | ConvertsToTime     | ✓         |               |       |
-| 22.17. | Descendents        | ✓         |               |       |
-| 22.18. | Is                 | ✗         |               |       |
-| 22.19. | ToBoolean          | ✓         |               |       |
-| 22.20. | ToChars            | ✓         |               |       |
-| 22.21. | ToConcept          | ✗         |               |       |
-| 22.22. | ToDate             | ✓         |               |       |
-| 22.23. | ToDateTime         | ✓         |               |       |
-| 22.24. | ToDecimal          | ✓         |               |       |
-| 22.25. | ToInteger          | ✓         |               |       |
-| 22.26. | ToList             | ✓         |               |       |
-| 22.27. | ToLong             | ✓         |               |       |
-| 22.28. | ToQuantity         | ✓         |               |       |
-| 22.29. | ToRatio            | ✗         |               |       |
-| 22.30. | ToString           | ✓         |               |       |
-| 22.31. | ToTime             | ✓         |               |       |
+|--------|--------------------|------------|---------------|-------|
+| 22.1.  | As                 | !          | no strictness |       |
+| 22.2.  | CanConvert         | ✗          |               |       |
+| 22.3.  | CanConvertQuantity | ✓          |               |       |
+| 22.4.  | Children           | ✓          |               |       |
+| 22.5.  | Convert            | ✗          |               |       |
+| 22.6.  | ConvertQuantity    | ✓          |               |       |
+| 22.7.  | ConvertsToBoolean  | ✓          |               |       |
+| 22.8.  | ConvertsToDate     | ✓          |               |       |
+| 22.9.  | ConvertsToDateTime | ✓          |               |       |
+| 22.10. | ConvertsToDecimal  | ✓          |               |       |
+| 22.11. | ConvertsToLong     | ✓          |               |       |
+| 22.12. | ConvertsToInteger  | ✓          |               |       |
+| 22.13. | ConvertsToQuantity | ✓          |               |       |
+| 22.14. | ConvertsToRatio    | ✗          |               |       |
+| 22.15. | ConvertsToString   | ✓          |               |       |
+| 22.16. | ConvertsToTime     | ✓          |               |       |
+| 22.17. | Descendents        | ✓          |               |       |
+| 22.18. | Is                 | ✗          |               |       |
+| 22.19. | ToBoolean          | ✓          |               |       |
+| 22.20. | ToChars            | ✓          |               |       |
+| 22.21. | ToConcept          | ✗          |               |       |
+| 22.22. | ToDate             | ✓          |               |       |
+| 22.23. | ToDateTime         | ✓          |               |       |
+| 22.24. | ToDecimal          | ✓          |               |       |
+| 22.25. | ToInteger          | ✓          |               |       |
+| 22.26. | ToList             | ✓          |               |       |
+| 22.27. | ToLong             | ✓          |               |       |
+| 22.28. | ToQuantity         | ✓          |               |       |
+| 22.29. | ToRatio            | ✗          |               |       |
+| 22.30. | ToString           | ✓          |               |       |
+| 22.31. | ToTime             | ✓          |               |       |
 
 ### 23. Clinical Operators
 

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 0.17.10 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.17.11 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.17.10"
+  "version": "0.17.11"
 }
 ```
 

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. 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/v0.17.10). Look for `blaze-0.17.10-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/v0.17.11). Look for `blaze-0.17.11-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.17.10-standalone.jar -m blaze.core
+java -jar blaze-0.17.11-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-0.17.10-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.17.11-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-0.17.10-standalone.jar -m blaze.core
+java -jar blaze-0.17.11-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 0.17.10 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.17.11 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.17.10"
+  "version": "0.17.11"
 }
 ```
 

diff --git a/modules/cql/src/blaze/elm/compiler/core.clj b/modules/cql/src/blaze/elm/compiler/core.clj
@@ -41,7 +41,11 @@
 
 
 (defmulti compile*
-  "Compiles `expression` in `context`."
+  "Compiles `expression` in `context`.
+
+  Context consists of:
+  * :library - the library in it's ELM form
+  * :node - the database node"
   {:arglists '([context expression])}
   (fn [_ {:keys [type] :as expr}]
     (assert (string? type) (format "Missing :type in expression `%s`." (pr-str expr)))

diff --git a/modules/cql/src/blaze/elm/compiler/external_data.clj b/modules/cql/src/blaze/elm/compiler/external_data.clj
@@ -18,7 +18,9 @@
 (defrecord CompartmentListRetrieveExpression [context data-type]
   core/Expression
   (-eval [_ {:keys [db]} {:keys [id]} _]
-    (d/list-compartment-resource-handles db context id data-type)))
+    (d/list-compartment-resource-handles db context id data-type))
+  (-form [_]
+    `(~'compartment-list-retrieve ~data-type)))
 
 
 (defrecord CompartmentQueryRetrieveExpression [query data-type clauses]
@@ -93,7 +95,9 @@
 (defrecord ResourceRetrieveExpression []
   core/Expression
   (-eval [_ _ resource _]
-    [resource]))
+    [resource])
+  (-form [_]
+    (list 'retrieve-resource)))
 
 
 (def ^:private resource-expr

diff --git a/modules/cql/src/blaze/elm/compiler/function.clj b/modules/cql/src/blaze/elm/compiler/function.clj
@@ -0,0 +1,12 @@
+(ns blaze.elm.compiler.function
+  (:require
+    [blaze.elm.compiler.core :as core]))
+
+
+(defn arity-n [name fn-expr operand-names operands]
+  (reify core/Expression
+    (-eval [_ context resource scope]
+      (let [values (map #(core/-eval % context resource scope) operands)]
+        (core/-eval fn-expr context resource (merge scope (zipmap operand-names values)))))
+    (-form [_]
+      `(~'call ~name ~@(map core/-form operands)))))
diff --git a/modules/cql/src/blaze/elm/compiler/library.clj b/modules/cql/src/blaze/elm/compiler/library.clj
@@ -1,39 +1,57 @@
 (ns blaze.elm.compiler.library
   (:require
-    [blaze.anomaly :as ba :refer [when-ok]]
+    [blaze.anomaly :as ba :refer [if-ok when-ok]]
     [blaze.elm.compiler :as compiler]
+    [blaze.elm.compiler.function :as function]
     [blaze.elm.deps-infer :as deps-infer]
     [blaze.elm.equiv-relationships :as equiv-relationships]
     [blaze.elm.normalizer :as normalizer]))
 
 
 (defn- compile-expression-def
-  "Compiles the expression of `expression-def` in `context` and associates the
-  resulting compiled expression under ::compiler/expression to the
-  `expression-def` which itself is returned.
-
-  Returns an anomaly on errors."
-  {:arglists '([context expression-def])}
-  [context {:keys [expression] :as expression-def}]
-  (let [context (assoc context :eval-context (:context expression-def))]
-    (-> (ba/try-anomaly
-          (assoc expression-def
-            ::compiler/expression (compiler/compile context expression)))
+  "Compiles the expression of `def` in `context` and returns a tuple of
+  `[name compiled-expression]` or an anomaly on errors."
+  [context {:keys [name expression] :as def}]
+  (let [context (assoc context :eval-context (:context def))]
+    (-> (ba/try-anomaly [name (compiler/compile context expression)])
         (ba/exceptionally
           #(assoc % :context context :elm/expression expression)))))
 
 
-(defn- expr-defs [context library]
+(defn- compile-function-def
+  "Compiles the function of `def` in `context`.
+
+  Returns the compiled function or an anomaly on errors."
+  [context {:keys [name operand] :as def}]
+  (when-ok [[_ expression] (compile-expression-def context def)]
+    (partial function/arity-n name expression (mapv :name operand))))
+
+
+(defn- compile-function-defs [context library]
   (transduce
-    (comp (map (partial compile-expression-def context))
-          (halt-when ba/anomaly?))
+    (filter (comp #{"FunctionDef"} :type))
     (completing
-      (fn [r {:keys [name] ::compiler/keys [expression]}]
-        (assoc r name expression)))
-    {}
+      (fn [context {:keys [name] :as def}]
+        (if-ok [function (compile-function-def context def)]
+          (assoc-in context [:functions name] function)
+          reduced)))
+    context
     (-> library :statements :def)))
 
 
+(defn- expression-defs [context library]
+  (when-ok [context (compile-function-defs context library)]
+    (transduce
+      (comp (filter (comp nil? :type))
+            (map (partial compile-expression-def context))
+            (halt-when ba/anomaly?))
+      (completing
+        (fn [r [name expression]]
+          (assoc r name expression)))
+      {}
+      (-> library :statements :def))))
+
+
 (defn- compile-parameter-def
   "Compiles the default value of `parameter-def` in `context` and associates the
   resulting compiled default value under :default to the `parameter-def` which
@@ -71,7 +89,7 @@
                     equiv-relationships/find-equiv-rels-library
                     deps-infer/infer-library-deps)
         context (assoc opts :node node :library library)]
-    (when-ok [expr-defs (expr-defs context library)
+    (when-ok [expression-defs (expression-defs context library)
               parameter-default-values (parameter-default-values context library)]
-      {:compiled-expression-defs expr-defs
+      {:compiled-expression-defs expression-defs
        :parameter-default-values parameter-default-values})))
diff --git a/modules/cql/src/blaze/elm/compiler/queries.clj b/modules/cql/src/blaze/elm/compiler/queries.clj
@@ -298,18 +298,6 @@
     (throw (Exception. (str "Unsupported number of " (count sources) " sources in query.")))))
 
 
-;; ?.? IdentifierRef
-;;
-;; The IdentifierRef type defines an expression that references an identifier
-;; that is either unresolved, or has been resolved to an attribute in an
-;; unambiguous iteration scope such as a sort. Implementations should attempt to
-;; resolve the identifier, only throwing an error at compile-time (or run-time
-;; for an interpretive system) if the identifier reference cannot be resolved.
-(defmethod core/compile* :elm.compiler.type/identifier-ref
-  [_ {:keys [name]}]
-  (structured-values/->SingleScopePropertyExpression (keyword name)))
-
-
 ;; 10.3. AliasRef
 ;;
 ;; The AliasRef expression allows for the reference of a specific source within
@@ -336,7 +324,13 @@
     (->AliasRefExpression name)))
 
 
-;; 10.12. With
+;; 10.7 IdentifierRef
+(defmethod core/compile* :elm.compiler.type/identifier-ref
+  [_ {:keys [name]}]
+  (structured-values/->SingleScopePropertyExpression (keyword name)))
+
+
+;; 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
@@ -386,4 +380,4 @@
         (format "Unsupported call without single query scope.")))))
 
 
-;; TODO 10.13. Without
+;; TODO 10.15. Without