Use Integrant to Build Systems under Test

samply · Jul 31, 2021 · f5d3185 · f5d3185
1 parent 02b360e
commit f5d3185
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diff --git a/modules/anomaly/src/blaze/anomaly.clj b/modules/anomaly/src/blaze/anomaly.clj
@@ -1,7 +1,21 @@
 (ns blaze.anomaly
-  (:refer-clojure :exclude [map])
+  (:refer-clojure :exclude [map map-indexed])
   (:require
-    [cognitect.anomalies :as anom]))
+    [cognitect.anomalies :as anom])
+  (:import
+    [java.util.concurrent CompletableFuture]))
+
+
+(defn anomaly? [x]
+  (some? (::anom/category x)))
+
+
+(defn incorrect [msg & kvs]
+  (apply assoc {::anom/category ::anom/incorrect ::anom/message msg} kvs))
+
+
+(defn unsupported [msg & kvs]
+  (apply assoc {::anom/category ::anom/unsupported ::anom/message msg} kvs))
 
 
 (defn ex-anom
@@ -11,6 +25,12 @@
   (ex-info (::anom/message anom "") anom))
 
 
+(defn completion-stage [x]
+  (if (anomaly? x)
+    (CompletableFuture/failedFuture (ex-anom x))
+    (CompletableFuture/completedFuture x)))
+
+
 (defn throw-anom
   "Throws an ExceptionInfo build with `ex-anom`."
   [category message & {:as kvs}]
@@ -68,3 +88,7 @@
 
 (defn exceptionally [x f]
   (if (::anom/category x) (f x) x))
+
+
+(defn map-indexed [f]
+  (comp (clojure.core/map-indexed f) (halt-when anomaly?)))
diff --git a/modules/cql/.clj-kondo/config.edn b/modules/cql/.clj-kondo/config.edn
@@ -1,5 +1,7 @@
 {:lint-as
  {blaze.anomaly/when-ok clojure.core/let
+  blaze.db.api-stub/with-system-data clojure.core/with-open
+  blaze.test-util/with-system clojure.core/with-open
   blaze.elm.compiler.macros/defunop clojure.core/defn
   blaze.elm.compiler.macros/defbinop clojure.core/defn
   blaze.elm.compiler.macros/defternop clojure.core/defn

diff --git a/modules/cql/deps.edn b/modules/cql/deps.edn
@@ -36,12 +36,12 @@
    {blaze/db-stub
     {:local/root "../db-stub"}
 
+    blaze/test-util
+    {:local/root "../test-util"}
+
     lambdaisland/kaocha
     {:mvn/version "1.0.861"}
 
-    org.clojars.akiel/iota
-    {:mvn/version "0.1"}
-
     org.clojure/data.xml
     {:mvn/version "0.2.0-alpha6"}
 
@@ -57,12 +57,12 @@
    {blaze/db-stub
     {:local/root "../db-stub"}
 
+    blaze/test-util
+    {:local/root "../test-util"}
+
     cloverage/cloverage
     {:mvn/version "1.2.2"}
 
-    org.clojars.akiel/iota
-    {:mvn/version "0.1"}
-
     org.clojure/data.xml
     {:mvn/version "0.2.0-alpha6"}
 

diff --git a/modules/cql/test/blaze/elm/compiler/external_data_test.clj b/modules/cql/test/blaze/elm/compiler/external_data_test.clj
@@ -1,14 +1,15 @@
 (ns blaze.elm.compiler.external-data-test
   (:require
     [blaze.db.api :as d]
-    [blaze.db.api-stub :refer [mem-node-with]]
+    [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.elm.compiler :as c]
     [blaze.elm.compiler.core :as core]
     [blaze.elm.compiler.external-data]
     [blaze.elm.compiler.test-util :as tu]
     [blaze.elm.literal :as elm]
     [blaze.fhir.spec :as fhir-spec]
     [blaze.fhir.spec.type]
+    [blaze.test-util :refer [with-system]]
     [clojure.spec.test.alpha :as st]
     [clojure.test :as test :refer [deftest is testing]]
     [cognitect.anomalies :as anom]
@@ -59,8 +60,9 @@
 (deftest compile-retrieve-test
   (testing "Patient context"
     (testing "Patient"
-      (with-open [node (mem-node-with
-                         [[[:put {:fhir/type :fhir/Patient :id "0"}]]])]
+      (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+        [[[:put {:fhir/type :fhir/Patient :id "0"}]]]
+
         (let [context
               {:node node
                :eval-context "Patient"
@@ -74,11 +76,12 @@
             [0 :id] := "0"))))
 
     (testing "Observation"
-      (with-open [node (mem-node-with
-                         [[[:put {:fhir/type :fhir/Patient :id "0"}]
-                           [:put {:fhir/type :fhir/Observation :id "1"
-                                  :subject
-                                  #fhir/Reference{:reference "Patient/0"}}]]])]
+      (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+        [[[:put {:fhir/type :fhir/Patient :id "0"}]
+          [:put {:fhir/type :fhir/Observation :id "1"
+                 :subject
+                 #fhir/Reference{:reference "Patient/0"}}]]]
+
         (let [context
               {:node node
                :eval-context "Patient"
@@ -92,20 +95,21 @@
             [0 :id] := "1")))
 
       (testing "with one code"
-        (with-open [node (mem-node-with
-                           [[[:put {:fhir/type :fhir/Patient :id "0"}]
-                             [:put {:fhir/type :fhir/Observation :id "0"
-                                    :subject
-                                    #fhir/Reference{:reference "Patient/0"}}]
-                             [:put {:fhir/type :fhir/Observation :id "1"
-                                    :code
-                                    #fhir/CodeableConcept
-                                        {:coding
-                                         [#fhir/Coding
-                                             {:system #fhir/uri"system-192253"
-                                              :code #fhir/code"code-192300"}]}
-                                    :subject
-                                    #fhir/Reference{:reference "Patient/0"}}]]])]
+        (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+          [[[:put {:fhir/type :fhir/Patient :id "0"}]
+            [:put {:fhir/type :fhir/Observation :id "0"
+                   :subject
+                   #fhir/Reference{:reference "Patient/0"}}]
+            [:put {:fhir/type :fhir/Observation :id "1"
+                   :code
+                   #fhir/CodeableConcept
+                       {:coding
+                        [#fhir/Coding
+                            {:system #fhir/uri"system-192253"
+                             :code #fhir/code"code-192300"}]}
+                   :subject
+                   #fhir/Reference{:reference "Patient/0"}}]]]
+
           (let [context
                 {:node node
                  :eval-context "Patient"
@@ -128,29 +132,30 @@
               [0 :id] := "1"))))
 
       (testing "with two codes"
-        (with-open [node (mem-node-with
-                           [[[:put {:fhir/type :fhir/Patient :id "0"}]
-                             [:put {:fhir/type :fhir/Observation :id "0"
-                                    :subject
-                                    #fhir/Reference{:reference "Patient/0"}}]
-                             [:put {:fhir/type :fhir/Observation :id "1"
-                                    :code
-                                    #fhir/CodeableConcept
-                                        {:coding
-                                         [#fhir/Coding
-                                             {:system #fhir/uri"system-192253"
-                                              :code #fhir/code"code-192300"}]}
-                                    :subject
-                                    #fhir/Reference{:reference "Patient/0"}}]
-                             [:put {:fhir/type :fhir/Observation :id "2"
-                                    :code
-                                    #fhir/CodeableConcept
-                                        {:coding
-                                         [#fhir/Coding
-                                             {:system #fhir/uri"system-192253"
-                                              :code #fhir/code"code-140541"}]}
-                                    :subject
-                                    #fhir/Reference{:reference "Patient/0"}}]]])]
+        (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+          [[[:put {:fhir/type :fhir/Patient :id "0"}]
+            [:put {:fhir/type :fhir/Observation :id "0"
+                   :subject
+                   #fhir/Reference{:reference "Patient/0"}}]
+            [:put {:fhir/type :fhir/Observation :id "1"
+                   :code
+                   #fhir/CodeableConcept
+                       {:coding
+                        [#fhir/Coding
+                            {:system #fhir/uri"system-192253"
+                             :code #fhir/code"code-192300"}]}
+                   :subject
+                   #fhir/Reference{:reference "Patient/0"}}]
+            [:put {:fhir/type :fhir/Observation :id "2"
+                   :code
+                   #fhir/CodeableConcept
+                       {:coding
+                        [#fhir/Coding
+                            {:system #fhir/uri"system-192253"
+                             :code #fhir/code"code-140541"}]}
+                   :subject
+                   #fhir/Reference{:reference "Patient/0"}}]]]
+
           (let [context
                 {:node node
                  :eval-context "Patient"
@@ -177,11 +182,12 @@
 
   (testing "Specimen context"
     (testing "Patient"
-      (with-open [node (mem-node-with
-                         [[[:put {:fhir/type :fhir/Patient :id "0"}]
-                           [:put {:fhir/type :fhir/Specimen :id "0"
-                                  :subject
-                                  #fhir/Reference{:reference "Patient/0"}}]]])]
+      (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+        [[[:put {:fhir/type :fhir/Patient :id "0"}]
+          [:put {:fhir/type :fhir/Specimen :id "0"
+                 :subject
+                 #fhir/Reference{:reference "Patient/0"}}]]]
+
         (let [context
               {:node node
                :eval-context "Specimen"
@@ -196,14 +202,15 @@
 
   (testing "Unfiltered context"
     (testing "Medication"
-      (with-open [node (mem-node-with
-                         [[[:put {:fhir/type :fhir/Medication :id "0"
-                                  :code
-                                  #fhir/CodeableConcept
-                                      {:coding
-                                       [#fhir/Coding
-                                           {:system #fhir/uri"system-225806"
-                                            :code #fhir/code"code-225809"}]}}]]])]
+      (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+        [[[:put {:fhir/type :fhir/Medication :id "0"
+                 :code
+                 #fhir/CodeableConcept
+                     {:coding
+                      [#fhir/Coding
+                          {:system #fhir/uri"system-225806"
+                           :code #fhir/code"code-225809"}]}}]]]
+
         (let [context
               {:node node
                :eval-context "Unfiltered"
@@ -226,7 +233,7 @@
 
   (testing "with related context"
     (testing "with pre-compiled database query"
-      (with-open [node (mem-node-with [])]
+      (with-system [{:blaze.db/keys [node]} mem-node-system]
         (let [library {:codeSystems
                        {:def [{:name "sys-def-174848" :id "system-174915"}]}
                        :statements
@@ -244,4 +251,3 @@
   (testing "with unsupported type namespace"
     (let [elm {:type "Retrieve" :dataType "{foo}Bar"}]
       (is (thrown-anom? ::anom/unsupported (c/compile {} elm))))))
-
diff --git a/modules/cql/test/blaze/elm/compiler/library_test.clj b/modules/cql/test/blaze/elm/compiler/library_test.clj
@@ -1,9 +1,10 @@
 (ns blaze.elm.compiler.library-test
   (:require
     [blaze.cql-translator :as t]
-    [blaze.db.api-stub :refer [mem-node]]
+    [blaze.db.api-stub :refer [mem-node-system]]
     [blaze.elm.compiler.library :as library]
     [blaze.elm.compiler.library-spec]
+    [blaze.test-util :refer [with-system]]
     [clojure.spec.test.alpha :as st]
     [clojure.test :as test :refer [deftest testing]]
     [cognitect.anomalies :as anom]
@@ -25,13 +26,13 @@
 (deftest compile-library-test
   (testing "empty library"
     (let [library (t/translate "library Test")]
-      (with-open [node (mem-node)]
+      (with-system [{:blaze.db/keys [node]} mem-node-system]
         (given (library/compile-library node library {})
           :life/compiled-expression-defs := {}))))
 
   (testing "one static expression"
     (let [library (t/translate "library Test define Foo: true")]
-      (with-open [node (mem-node)]
+      (with-system [{:blaze.db/keys [node]} mem-node-system]
         (given (library/compile-library node library {})
           :life/compiled-expression-defs := {"Foo" true}))))
 
@@ -40,15 +41,15 @@
     using FHIR version '4.0.0'
     context Patient
     define Gender: Patient.gender")]
-      (with-open [node (mem-node)]
+      (with-system [{:blaze.db/keys [node]} mem-node-system]
         (given (library/compile-library node library {})
           [:life/compiled-expression-defs "Gender" :key] := :gender
           [:life/compiled-expression-defs "Gender" :source :name] := "Patient"))))
 
   (testing "one static expression"
     (let [library (t/translate "library Test
     define Error: singleton from {1, 2}")]
-      (with-open [node (mem-node)]
+      (with-system [{:blaze.db/keys [node]} mem-node-system]
         (given (library/compile-library node library {})
           ::anom/category := ::anom/conflict
           ::anom/message := "More than one element in `SingletonFrom` expression.")))))
diff --git a/modules/cql/test/blaze/elm/compiler/queries_test.clj b/modules/cql/test/blaze/elm/compiler/queries_test.clj
@@ -1,7 +1,7 @@
 (ns blaze.elm.compiler.queries-test
   (:require
     [blaze.db.api :as d]
-    [blaze.db.api-stub :refer [mem-node-with]]
+    [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.elm.code :as code]
     [blaze.elm.code-spec]
     [blaze.elm.compiler :as c]
@@ -113,7 +113,9 @@
         (is (not (instance? IPersistentCollection res))))))
 
   (testing "Retrieve queries"
-    (with-open [node (mem-node-with [[[:put {:fhir/type :fhir/Patient :id "0"}]]])]
+    (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+      [[[:put {:fhir/type :fhir/Patient :id "0"}]]]
+
       (let [db (d/db node)
             retrieve {:type "Retrieve" :dataType "{http://hl7.org/fhir}Patient"}
             where {:type "Equal"
@@ -171,11 +173,12 @@
 ;; 10.12. With
 (deftest compile-with-clause-test
   (testing "Equiv With with two Observations comparing there subjects."
-    (with-open [node (mem-node-with
-                       [[[:put {:fhir/type :fhir/Patient :id "0"}]
-                         [:put {:fhir/type :fhir/Observation :id "0"
-                                :subject
-                                #fhir/Reference{:reference "Patient/0"}}]]])]
+    (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+      [[[:put {:fhir/type :fhir/Patient :id "0"}]
+        [:put {:fhir/type :fhir/Observation :id "0"
+               :subject
+               #fhir/Reference{:reference "Patient/0"}}]]]
+
       (let [elm {:alias "O1"
                :type "WithEquiv"
                :expression
@@ -204,11 +207,12 @@
       (is (= [lhs-entity] (into [] xform [lhs-entity]))))))
 
   (testing "Equiv With with one Patient and one Observation comparing the patient with the operation subject."
-    (with-open [node (mem-node-with
-                       [[[:put {:fhir/type :fhir/Patient :id "0"}]
-                         [:put {:fhir/type :fhir/Observation :id "0"
-                                :subject
-                                #fhir/Reference{:reference "Patient/0"}}]]])]
+    (with-system-data [{:blaze.db/keys [node]} mem-node-system]
+      [[[:put {:fhir/type :fhir/Patient :id "0"}]
+        [:put {:fhir/type :fhir/Observation :id "0"
+               :subject
+               #fhir/Reference{:reference "Patient/0"}}]]]
+
       (let [elm {:alias "O"
                :type "WithEquiv"
                :expression

diff --git a/modules/db-resource-store-cassandra/.clj-kondo/config.edn b/modules/db-resource-store-cassandra/.clj-kondo/config.edn
@@ -1,5 +1,6 @@
 {:lint-as
  {blaze.anomaly/when-ok clojure.core/let
+  blaze.test-util/with-system clojure.core/with-open
   prometheus.alpha/defhistogram clojure.core/def}
 
  :linters