Pass Validation Simple Terminology Tests

Closes: #2292

.clj-kondo/root/config.edn

@@ -74,6 +74,7 @@
     blaze.fhir.spec.references fsr
     blaze.fhir.spec.type type
     blaze.fhir.structure-definition-repo sdr
+    blaze.handler.fhir.util fhir-util
     blaze.job-scheduler js
     blaze.job.async-interaction job-async
     blaze.job.compact job-compact

.github/scripts/install-validator.sh

@@ -1,5 +1,5 @@
 #!/bin/bash -e
 
-VERSION="1.0.60"
+VERSION="1.0.61"
 
 curl -sLO "https://github.com/hapifhir/org.hl7.fhir.validator-wrapper/releases/download/$VERSION/validator_cli.jar"

.github/terminology-tests/all.sh

@@ -1,7 +1,6 @@
 #!/bin/bash -e
 
-java -jar validator_cli.jar -txTests -version 4.0.1 \
+java -jar validator_cli.jar -txTests -version current \
   -tx http://localhost:8080/fhir \
-  -source fhir-tx-ecosystem-ig/tests \
   -output .github/terminology-tests/output \
   -mode flat

.github/terminology-tests/good.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+java -jar validator_cli.jar -txTests -version current \
+  -tx http://localhost:8080/fhir \
+  -output .github/terminology-tests/output \
+  -mode flat \
+  -filter good

.github/terminology-tests/parameters-expand.sh

@@ -1,16 +1,7 @@
 #!/bin/bash
 
-SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
-
-# remove test cases that need the R5 representation of the ValueSet resource
-jq -f "$SCRIPT_DIR/remove-r5-tests.jq" fhir-tx-ecosystem-ig/tests/test-cases.json > fhir-tx-ecosystem-ig/tests/test-cases-new.json
-mv fhir-tx-ecosystem-ig/tests/test-cases-new.json fhir-tx-ecosystem-ig/tests/test-cases.json
-
-java -jar validator_cli.jar -txTests -version 4.0.1 \
+java -jar validator_cli.jar -txTests -version current \
   -tx http://localhost:8080/fhir \
-  -source fhir-tx-ecosystem-ig/tests \
   -output .github/terminology-tests/output \
   -mode flat \
   -filter parameters-expand
-
-exit $((! $?))

.github/terminology-tests/simple-expand.sh

@@ -1,10 +1,7 @@
 #!/bin/bash
 
-java -jar validator_cli.jar -txTests -version 4.0.1 \
+java -jar validator_cli.jar -txTests -version current \
   -tx http://localhost:8080/fhir \
-  -source fhir-tx-ecosystem-ig/tests \
   -output .github/terminology-tests/output \
   -mode flat \
   -filter simple-expand
-
-exit $((! $?))

.github/terminology-tests/validation-simple.sh

@@ -1,10 +1,7 @@
 #!/bin/bash
 
-java -jar validator_cli.jar -txTests -version 4.0.1 \
+java -jar validator_cli.jar -txTests -version current \
   -tx http://localhost:8080/fhir \
-  -source fhir-tx-ecosystem-ig/tests \
   -output .github/terminology-tests/output \
   -mode flat \
   -filter validation-simple
-
-exit $((! $?))

.github/validation/Makefile

@@ -5,10 +5,7 @@ kds-test-data: kds-testdata-2024.0.1.zip
 	unzip kds-testdata-2024.0.1.zip
 	rm kds-testdata-2024.0.1.zip
 
-validate-medication:
-	./validate-medication.sh
-
 clean:
 	rm -rf kds-testdata-2024.0.1
 
-.PHONY: kds-test-data validate clean
+.PHONY: kds-test-data clean

.github/workflows/build.yml

@@ -1351,6 +1351,7 @@ jobs:
       with:
         repository: HL7/fhir-tx-ecosystem-ig
         path: fhir-tx-ecosystem-ig
+        ref: c000bbc79078938c980df74afeac3c80cb9deffd
 
     - name: Setup Node
       uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
@@ -1384,8 +1385,8 @@ jobs:
     - name: Check Simple Expand
       run: .github/terminology-tests/simple-expand.sh
 
-    - name: Check Parameters Expand
-      run: .github/terminology-tests/parameters-expand.sh
+    - name: Check Good
+      run: .github/terminology-tests/good.sh
 
   not-enforcing-referential-integrity-test:
     needs: build

cljfmt.edn

@@ -16,4 +16,7 @@
   satisfies-prop [[:block 1]]
   clojure.test.check.properties/for-all [[:block 1]]
   blaze.metrics.core/collector [[:block 0]]
-  reify-expr [[:inner 0] [:inner 1]]}}
+  reify-expr [[:inner 0] [:inner 1]]
+  code-system-validate-code [[:block 1]]
+  expand-value-set [[:block 1]]
+  value-set-validate-code [[:block 1]]}}

job-ig/package.json

@@ -1,5 +1,5 @@
 {
   "dependencies": {
-    "fsh-sushi": "^3.13.1"
+    "fsh-sushi": "^3.14.0"
   }
 }

modules/extern-terminology-service/src/blaze/terminology_service/extern.clj

@@ -2,6 +2,7 @@
   (:require
    [blaze.async.comp :as ac]
    [blaze.fhir-client :as fhir-client]
+   [blaze.fhir.spec.type :as type]
    [blaze.http-client.spec]
    [blaze.module :as m :refer [reg-collector]]
    [blaze.terminology-service :as ts]
@@ -28,18 +29,22 @@
                                 {:http-client http-client
                                  :query-params {:url url}}))
 
-(defn- expand-value-set [base-uri http-client url]
+(defn- extract-url [{parameters :parameter}]
+  (some #(when (= "url" (type/value (:name %))) (type/value (:value %)))
+        parameters))
+
+(defn- expand-value-set [base-uri http-client params]
   (let [timer (prom/timer request-duration-seconds)]
-    (-> (expand-value-set* base-uri http-client url)
+    (-> (expand-value-set* base-uri http-client (extract-url params))
         (ac/when-complete
          (fn [_ _] (prom/observe-duration! timer))))))
 
 (defn- cache [base-uri http-client]
   (-> (Caffeine/newBuilder)
       (.maximumSize 1000)
       (^[AsyncCacheLoader] Caffeine/.buildAsync
-       (fn [request _]
-         (expand-value-set base-uri http-client (:url request))))))
+       (fn [params _]
+         (expand-value-set base-uri http-client params)))))
 
 (defmethod m/pre-init-spec ::ts/extern [_]
   (s/keys :req-un [::base-uri :blaze/http-client]))
@@ -49,8 +54,8 @@
   (log/info (str "Init terminology server connection: " base-uri))
   (let [cache (cache base-uri http-client)]
     (reify p/TerminologyService
-      (-expand-value-set [_ request]
-        (.get ^AsyncLoadingCache cache request)))))
+      (-expand-value-set [_ params]
+        (.get ^AsyncLoadingCache cache params)))))
 
 (derive ::ts/extern :blaze/terminology-service)
 

modules/extern-terminology-service/test/blaze/terminology_service/extern_test.clj

@@ -1,6 +1,7 @@
 (ns blaze.terminology-service.extern-test
   (:require
    [blaze.fhir.test-util]
+   [blaze.fhir.util :as u]
    [blaze.http-client.spec :refer [http-client?]]
    [blaze.module.test-util :refer [with-system]]
    [blaze.terminology-service :as ts]
@@ -62,13 +63,17 @@
       [:cause-data ::s/problems 1 :pred] := `http-client?
       [:cause-data ::s/problems 1 :val] := ::invalid)))
 
+(defn- expand-value-set [ts & nvs]
+  (ts/expand-value-set ts (apply u/parameters nvs)))
+
 (deftest terminology-service-test
   (with-system [{ts ::ts/extern ::keys [http-client]} config]
 
     (-> (.onGet ^HttpClientMock http-client "http://localhost:8080/fhir/ValueSet/$expand?url=http://hl7.org/fhir/ValueSet/administrative-gender")
         (.doReturn (j/write-value-as-string {:resourceType "ValueSet" :id "0"}))
         (.withHeader "content-type" "application/fhir+json"))
 
-    (given @(ts/expand-value-set ts {:url "http://hl7.org/fhir/ValueSet/administrative-gender"})
+    (given @(expand-value-set ts
+              "url" #fhir/uri"http://hl7.org/fhir/ValueSet/administrative-gender")
       :fhir/type := :fhir/ValueSet
       :id := "0")))

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

@@ -81,3 +81,6 @@
 
 (s/def :fhir/Parameters
   #(s2/valid? :fhir/Parameters %))
+
+(s/def :fhir.OperationOutcome/issue
+  #(s2/valid? :fhir.OperationOutcome/issue %))

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

@@ -0,0 +1,16 @@
+(ns blaze.fhir.util
+  (:require
+   [blaze.fhir.spec.type :as type]))
+
+(defn parameters [& nvs]
+  {:fhir/type :fhir/Parameters
+   :parameter
+   (into
+    []
+    (keep
+     (fn [[name value]]
+       (when (some? value)
+         {:fhir/type :fhir.Parameters/parameter
+          :name (type/string name)
+          (if (:fhir/type value) :resource :value) value})))
+    (partition 2 nvs))})

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

@@ -0,0 +1,30 @@
+(ns blaze.fhir.util-test
+  (:require
+   [blaze.fhir.util :as u]
+   [blaze.test-util :as tu]
+   [clojure.spec.test.alpha :as st]
+   [clojure.test :as test :refer [deftest]]
+   [juxt.iota :refer [given]]))
+
+(st/instrument)
+
+(test/use-fixtures :each tu/fixture)
+
+(deftest parameters-test
+  (given (u/parameters)
+    :fhir/type := :fhir/Parameters
+    :parameter :? empty?)
+
+  (given (u/parameters "foo" #fhir/string"bar")
+    :fhir/type := :fhir/Parameters
+    [:parameter 0 :name] := #fhir/string"foo"
+    [:parameter 0 :value] := #fhir/string"bar")
+
+  (given (u/parameters "foo" nil)
+    :fhir/type := :fhir/Parameters
+    :parameter :? empty?)
+
+  (given (u/parameters "foo" {:fhir/type :fhir/ValueSet})
+    :fhir/type := :fhir/Parameters
+    [:parameter 0 :name] := #fhir/string"foo"
+    [:parameter 0 :resource] := {:fhir/type :fhir/ValueSet}))