Merge pull request #287 from samply/develop

Develop

Makefile

@@ -1,4 +1,4 @@
-VERSION := "0.10.0"
+VERSION := "0.10.1"
 MODULES := $(wildcard modules/*)
 
 $(MODULES):

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 report any issues you encounter during evaluation.
 
-Latest release: [v0.10.0][5]
+Latest release: [v0.10.1][5]
 
 ## Quick Start
 
@@ -24,7 +24,7 @@ In order to run Blaze just execute the following:
 
 ```bash
 docker volume create blaze-data
-docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.10.0
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.10.1
 ```
 
 Blaze will create multiple directories inside the `blaze-data` volume on its first start and use the same directories on subsequent starts.
@@ -63,7 +63,7 @@ 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/v0.10.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.10.1>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

docker-compose.yml

@@ -1,7 +1,7 @@
 version: '3.2'
 services:
   blaze:
-    image: "samply/blaze:0.10.0"
+    image: "samply/blaze:0.10.1"
     environment:
       BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"

docs/cql-queries.md

@@ -9,7 +9,7 @@ The most accessible way to create and execute CQL queries is to use the Quality
 If you don't already have Blaze running, you can read about how to do it in [Deployment](deployment/). If you have Docker available just run:
 
 ```
-docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.10.0
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.10.1
 ```
 
 Start the Quality Reporting UI. You should see an empty measure list.

docs/deployment/docker-deployment.md

@@ -11,7 +11,7 @@ docker volume create blaze-data
 ## Blaze
 
 ```bash
-docker run -d --name blaze -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.10.0
+docker run -d --name blaze -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.10.1
 ```
 
 Blaze should log something like this:
@@ -29,7 +29,7 @@ Blaze should log something like this:
 2020-06-23 08:06:49.235+0000 73c1e4c03d80 INFO [blaze.core:60] - JVM version: 11.0.6
 2020-06-23 08:06:49.236+0000 73c1e4c03d80 INFO [blaze.core:61] - Maximum available memory: 1488 MiB
 2020-06-23 08:06:49.236+0000 73c1e4c03d80 INFO [blaze.core:62] - Number of available processors: 4
-2020-06-23 08:06:49.238+0000 73c1e4c03d80 INFO [blaze.core:63] - Successfully started Blaze version 0.10.0 in 24.9 seconds
+2020-06-23 08:06:49.238+0000 73c1e4c03d80 INFO [blaze.core:63] - Successfully started Blaze version 0.10.1 in 24.9 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -49,7 +49,7 @@ that should return:
 ```javascript
 {
   "name": "Blaze",
-  "version": "0.10.0"
+  "version": "0.10.1"
 }
 ```
 
@@ -63,7 +63,7 @@ A Docker Compose file looks like this:
 version: '3.2'
 services:
   blaze:
-    image: "samply/blaze:0.10.0"
+    image: "samply/blaze:0.10.1"
     environment:
       BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"

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/v0.9.0). Look for `blaze-0.10.0-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/v0.9.0). Look for `blaze-0.10.1-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```bash
-java -jar blaze-0.10.0-standalone.jar -m blaze.core
+java -jar blaze-0.10.1-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:
 
 ```bash
-STORAGE=standalone java -jar blaze-0.10.0-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.10.1-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-0.10.0-standalone.jar -m blaze.core
+java -jar blaze-0.10.1-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.
@@ -76,7 +76,7 @@ The output should look like this:
 2020-06-23 06:45:06.858+0000 my-server INFO [blaze.core:60] - JVM version: 11.0.7
 2020-06-23 06:45:06.859+0000 my-server INFO [blaze.core:61] - Maximum available memory: 4070 MiB
 2020-06-23 06:45:06.859+0000 my-server INFO [blaze.core:62] - Number of available processors: 4
-2020-06-23 06:45:06.860+0000 my-server INFO [blaze.core:63] - Successfully started Blaze version 0.10.0 in 25,5 seconds
+2020-06-23 06:45:06.860+0000 my-server INFO [blaze.core:63] - Successfully started Blaze version 0.10.1 in 25,5 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -96,7 +96,7 @@ that should return:
 ```javascript
 {
   "name": "Blaze",
-  "version": "0.10.0"
+  "version": "0.10.1"
 }
 ```
 

modules/db-resource-store-cassandra/src/blaze/db/resource_store/cassandra.clj

@@ -127,7 +127,7 @@
 
 
 (defn- execute-multi-get [session get-statement hashes]
-  (map #(ac/->completable-future (execute-get session get-statement %)) hashes))
+  (mapv #(ac/->completable-future (execute-get session get-statement %)) hashes))
 
 
 (defn- bind-put [^PreparedStatement statement hash resource]

modules/db-resource-store/src/blaze/db/resource_store/kv.clj

@@ -33,7 +33,7 @@
 (def ^:private entry-thawer
   (map
     (fn [[k v]]
-      [(bs/from-byte-array k) (fhir-spec/conform-json (parse-cbor v hash))])))
+      [(bs/from-byte-array k) (fhir-spec/conform-cbor (parse-cbor v hash))])))
 
 
 (def ^:private entry-freezer

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

@@ -418,7 +418,7 @@
                             (new-kv-resource-store)
                             (new-random-slow-resource-store))})]
       (let [db-futures
-            (map
+            (mapv
               #(d/transact node [[:create {:fhir/type :fhir/Patient :id (str %)}]])
               (range 10))]
 

modules/fhir-structure/README.md

@@ -0,0 +1,18 @@
+# FHIR Structure
+
+This module provides [specs][1] for the [FHIR Data Model][2] and functions to conform und unform JSON and XML representation to and from the internal representation used by Blaze.
+
+## Examples
+
+### Conforming a JSON Representation to the Internal Representation
+
+```clojure
+(use 'blaze.fhir.spec)
+
+(conform-json {:resourceType "Patient" :id "0"})
+;;=> {:id "0", :fhir/type :fhir/Patient}
+```
+
+
+[1]: <https://clojure.org/guides/spec>
+[2]: <../../docs/implementation/fhir-data-model.md>

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

@@ -10,14 +10,15 @@
     [cuerdas.core :as str])
   (:import
     [java.net URLEncoder]
+    [java.nio.charset StandardCharsets]
     [clojure.data.xml.node Element]))
 
 
 (xml-name/alias-uri 'f "http://hl7.org/fhir")
 
 
 (def ^:const fhir-namespace
-  (str "xmlns." (URLEncoder/encode "http://hl7.org/fhir")))
+  (str "xmlns." (URLEncoder/encode "http://hl7.org/fhir" StandardCharsets/UTF_8)))
 
 
 (defn- find-fhir-type [{:keys [extension]}]
@@ -689,16 +690,15 @@
 
 
 ;; Resource Spec
-(defn conform-json-resource [{type :resourceType :as resource}]
-  (s/conform (keyword "fhir.json" type) resource))
+(defmulti json-resource identity)
 
 
-(defn unform-json-resource [{:fhir/keys [type] :as resource}]
-  (s/unform (keyword "fhir.json" (name type)) resource))
+(defmethod json-resource :default [{json-type :resourceType :fhir/keys [type]}]
+  (keyword "fhir.json" (or json-type (name type))))
 
 
 (s/def :fhir.json/Resource
-  (s/conformer conform-json-resource unform-json-resource))
+  (s/multi-spec json-resource (fn [value tag] (assoc value :resourceType tag))))
 
 
 (defn conform-cbor-resource [{type :resourceType :as resource}]
@@ -713,25 +713,24 @@
   (s/conformer conform-cbor-resource unform-cbor-resource))
 
 
-(def ^:const invalid ::s/invalid)
+(defmulti xml-resource identity)
 
 
-(defn conform-xml-resource
-  {:arglists '([element])}
-  [{:keys [content]}]
-  (if-let [{:keys [tag] :as element} (some #(when (element? %) %) content)]
-    (if-let [spec-key (some->> tag name (keyword "fhir.xml"))]
-      (s/conform spec-key element)
-      invalid)
-    invalid))
+(defmethod xml-resource :default [{:keys [tag] :fhir/keys [type]}]
+  (->> (or tag type) name (keyword "fhir.xml")))
 
 
-(defn unform-xml-resource [{:fhir/keys [type] :as resource}]
-  (xml-node/element ::f/resource {} (s/unform (keyword "fhir.xml" (name type)) resource)))
+(defn conform-xml-resource [{:keys [content]}]
+  (some #(when (element? %) %) content))
+
+
+(defn unform-xml-resource [resource]
+  (xml-node/element ::f/resource {} resource))
 
 
 (s/def :fhir.xml/Resource
-  (s/conformer conform-xml-resource unform-xml-resource))
+  (s/and (s/conformer conform-xml-resource unform-xml-resource)
+         (s/multi-spec xml-resource (fn [value _] value))))
 
 
 ;; register all resource specs

modules/fhir-structure/test/blaze/fhir/spec/impl_test.clj

@@ -481,20 +481,6 @@
 (def sexp prxml/sexp-as-element)
 
 
-(deftest conform-xml-test
-  (testing "patient resource with mixed character content"
-    (given (impl/conform-xml :fhir/Patient (sexp [::f/Patient "" [::f/id {:value "0"}]]))
-      :fhir/type := :fhir/Patient
-      :id (sexp [::f/id {:value "0"}]))))
-
-
-(deftest conform-xml-resource-test
-  (testing "patient resource with mixed character content"
-    (given (impl/conform-xml-resource (sexp [::f/resource "" [::f/Patient [::f/id {:value "0"}]]]))
-      :fhir/type := :fhir/Patient
-      :id "0")))
-
-
 (deftest elem-def->spec-def
   (testing "normal type"
     (is (= (impl/elem-def->spec-def

modules/fhir-structure/test/blaze/fhir/spec_test.clj

@@ -340,7 +340,14 @@
 
   (testing "Patient with multipleBirthInteger"
     (let [json {:resourceType "Patient" :multipleBirthInteger 2}]
-      (is (= json (fhir-spec/unform-json {:fhir/type :fhir/Patient :multipleBirth (int 2)}))))))
+      (is (= json (fhir-spec/unform-json {:fhir/type :fhir/Patient :multipleBirth (int 2)})))))
+
+  (testing "Bundle with Patient"
+    (let [json {:resourceType "Bundle"
+                :entry
+                [{:resource
+                  {:resourceType "Patient" :id "0"}}]}]
+      (is (= json (fhir-spec/unform-json (fhir-spec/conform-json json)))))))
 
 
 (deftest unform-primitives-test
@@ -508,7 +515,20 @@
       [:fhir/issues 0 :fhir.issues/code] := "invariant"
       [:fhir/issues 0 :fhir.issues/diagnostics] :=
       "Error on value `1`. Expected type is `HumanName`."
-      [:fhir/issues 0 :fhir.issues/expression] := "name[0]")))
+      [:fhir/issues 0 :fhir.issues/expression] := "name[0]"))
+
+  (testing "Bundle with invalid Patient gender"
+    (given (fhir-spec/explain-data-json
+             {:resourceType "Bundle"
+              :entry
+              [{:resource
+                {:resourceType "Patient"
+                 :gender 1}}]})
+      [:fhir/issues 0 :fhir.issues/severity] := "error"
+      [:fhir/issues 0 :fhir.issues/code] := "invariant"
+      [:fhir/issues 0 :fhir.issues/diagnostics] :=
+      "Error on value `1`. Expected type is `code`."
+      [:fhir/issues 0 :fhir.issues/expression] := "entry[0].resource.gender")))
 
 
 (deftest explain-data-xml
@@ -528,7 +548,8 @@
     (given (fhir-spec/explain-data-xml {:tag "<unknown>"})
       [:fhir/issues 0 :fhir.issues/severity] := "error"
       [:fhir/issues 0 :fhir.issues/code] := "value"
-      [:fhir/issues 0 :fhir.issues/diagnostics] := "Unknown resource type `<unknown>`."))
+      [:fhir/issues 0 :fhir.issues/diagnostics] :=
+      "Unknown resource type `<unknown>`."))
 
   (testing "invalid resource"
     (given (fhir-spec/explain-data-xml
@@ -538,7 +559,23 @@
       [:fhir/issues 0 :fhir.issues/diagnostics] :=
       "Error on value ``. Expected type is `code`, regex `[^\\s]+(\\s[^\\s]+)*`."
       ;; TODO: implement expression for XML
-      (comment [:fhir/issues 0 :fhir.issues/expression] := "name[0].use"))))
+      (comment [:fhir/issues 0 :fhir.issues/expression] := "name[0].use")))
+
+  (testing "Bundle with invalid Patient gender"
+    (given (fhir-spec/explain-data-xml
+             (sexp
+               [::f/Bundle
+                [::f/entry
+                 [::f/resource
+                  [::f/Patient [::f/gender {:value " "}]]]]]))
+      [:fhir/issues 0 :fhir.issues/severity] := "error"
+      [:fhir/issues 0 :fhir.issues/code] := "invariant"
+      [:fhir/issues 0 :fhir.issues/diagnostics] :=
+      "Error on value ` `. Expected type is `code`, regex `[^\\s]+(\\s[^\\s]+)*`."
+      ;; TODO: implement expression for XML
+      (comment
+        [:fhir/issues 0 :fhir.issues/expression] :=
+        "entry[0].resource.gender"))))
 
 
 (deftest primitive?

modules/interaction/src/blaze/interaction/create.clj

@@ -6,6 +6,7 @@
     [blaze.anomaly :refer [throw-anom]]
     [blaze.async.comp :as ac]
     [blaze.db.api :as d]
+    [blaze.db.spec]
     [blaze.fhir.response.create :as response]
     [blaze.handler.util :as handler-util]
     [blaze.interaction.create.spec]
@@ -50,9 +51,8 @@
       (-> (ac/supply (validate-resource type body))
           (ac/then-apply #(assoc % :id id))
           (ac/then-compose #(d/transact node [[:create %]]))
-          ;; it's important to switch to the transaction executor here, because
-          ;; otherwise the central indexing thread would execute response
-          ;; building.
+          ;; it's important to switch to the executor here, because otherwise
+          ;; the central indexing thread would execute response building.
           (ac/then-apply-async identity executor)
           (ac/then-compose
             #(response/build-created-response

modules/interaction/src/blaze/interaction/delete.clj

@@ -5,6 +5,7 @@
   (:require
     [blaze.async.comp :as ac]
     [blaze.db.api :as d]
+    [blaze.db.spec]
     [blaze.handler.util :as handler-util]
     [blaze.interaction.delete.spec]
     [blaze.middleware.fhir.metrics :refer [wrap-observe-request-duration]]
@@ -50,7 +51,7 @@
           (-> (build-response* (d/tx db t))
               (ac/completed-future))
           (-> (d/transact node [[:delete type id]])
-              ;; it's important to switch to the transaction executor here,
+              ;; it's important to switch to the executor here,
               ;; because otherwise the central indexing thread would execute
               ;; response building.
               (ac/then-apply-async build-response executor)))