Implement Operation $graphql

Currently only very view fields of Patient and Observation are
supported.

.github/scripts/graphql.sh

@@ -0,0 +1,11 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+TYPE=$1
+EXPECTED_SIZE=$(curl -s "$BASE/${TYPE}?_summary=count" | jq -r .total)
+ACTUAL_SIZE=$(curl -s -H "Content-Type: application/graphql" -d "{ ${TYPE}List { id } }" "$BASE/\$graphql" | jq ".data.${TYPE}List | length")
+
+test "size" "$ACTUAL_SIZE" "$EXPECTED_SIZE"

.github/workflows/build.yml

@@ -59,6 +59,7 @@ jobs:
         - luid
         - metrics
         - openid-auth
+        - operation-graphql
         - operation-measure-evaluate-measure
         - page-store
         - page-store-cassandra
@@ -531,6 +532,12 @@ jobs:
     - name: Conditional Update If-None-Match
       run: .github/scripts/conditional-update-if-none-match.sh
 
+    - name: GraphQL Patient
+      run: .github/scripts/graphql.sh Patient
+
+    - name: GraphQL Observation
+      run: .github/scripts/graphql.sh Observation
+
   not-enforcing-referential-integrity-test:
     needs: build
     runs-on: ubuntu-22.04
@@ -1238,6 +1245,12 @@ jobs:
     - name: Conditional Update If-None-Match
       run: .github/scripts/conditional-update-if-none-match.sh
 
+    - name: GraphQL Patient
+      run: .github/scripts/graphql.sh Patient
+
+    - name: GraphQL Observation
+      run: .github/scripts/graphql.sh Observation
+
     - name: Docker Stats
       run: docker stats --no-stream
 

deps.edn

@@ -10,6 +10,9 @@
   blaze/interaction
   {:local/root "modules/interaction"}
 
+  blaze.operation/graphql
+  {:local/root "modules/operation-graphql"}
+
   blaze.operation/measure-evaluate-measure
   {:local/root "modules/operation-measure-evaluate-measure"}
 
@@ -80,7 +83,7 @@
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "2.2.992"}
+    {:mvn/version "2.2.999"}
 
     org.slf4j/slf4j-nop
     {:mvn/version "2.0.6"}}
@@ -114,6 +117,7 @@
     "-d" "modules/metrics"
     "-d" "modules/module-base"
     "-d" "modules/openid-auth"
+    "-d" "modules/operation-graphql"
     "-d" "modules/operation-measure-evaluate-measure"
     "-d" "modules/page-store"
     "-d" "modules/page-store-cassandra"
@@ -127,6 +131,8 @@
     "-d" "modules/test-util"
     "-d" "modules/thread-pool-executor-collector"
     "--exclude" "com.taoensso/timbre"
+    "--exclude" "org.antlr/antlr4"
     "--exclude" "org.eclipse.jetty/jetty-server"
     "--exclude" "org.clojure/alpha.spec"
+    "--exclude" "com.walmartlabs/lacinia"
     "--exclude" "lambdaisland/kaocha"]}}}

docs/performance.md

@@ -4,6 +4,10 @@
 
 A section about FHIR Search performance can be found [here](performance/fhir-search.md).
 
+## GraphQL
+
+A section about GraphQL performance can be found [here](performance/graphql.md).
+
 ## Transaction Bundle Upload - Summary
 
 | CPU         | # Cores | RAM (GB) | Xmx | MBJ³ | -c¹ | # Resources | Disk Util.² | Duration (s) | Resources/s |

docs/performance/graphql.md

@@ -0,0 +1,32 @@
+# GraphQL
+
+## Simple Code Search
+
+In this section, GraphQL for selecting Observation resources with a certain code is used.
+
+### Download of Resources
+
+All measurements are done after Blaze is in a steady state with all resources to download in it's resource cache in order to cancel out resource load times from disk or file system cache.
+
+Download is done using the following `curl` command:
+
+```sh
+curl -s -H "Content-Type: application/graphql" -d "{ ObservationList { subject { reference } } }" "http://localhost:8080/\$graphql" > /dev/null"
+```
+
+| CPU        | Heap Mem | Block Cache | # Res. ¹ | # Obs. ² | Code    | # Hits | Time (s) | T / 1M ³ |
+|------------|---------:|------------:|---------:|---------:|---------|-------:|---------:|---------:|
+| EPYC 7543P |     8 GB |        1 GB |     29 M |     28 M | 17861-6 |  171 k |    1.045 |     6.11 |
+| EPYC 7543P |     8 GB |        1 GB |     29 M |     28 M | 39156-5 |  967 k |    5.740 |     5.94 |
+| EPYC 7543P |     8 GB |        1 GB |     29 M |     28 M | 29463-7 |  1.3 M |    8.057 |     6.20 |
+| EPYC 7543P |    30 GB |       10 GB |    292 M |    278 M | 17861-6 |  1.7 M |   10.744 |     6.32 |
+| EPYC 7543P |    30 GB |       10 GB |    292 M |    278 M | 39156-5 |  9.7 M |   70.122 |     7.23 |
+| EPYC 7543P |    30 GB |       10 GB |    292 M |    278 M | 29463-7 |   13 M |   96.735 |     7.44 |
+
+¹ Number of Resources, ² Number of Observations, ³ Time in seconds per 1 million resources, The amount of system memory was 128 GB in all cases.
+
+According to the measurements, the time needed by Blaze to deliver Observations containing only the subject reference is about **twice as fast** as returning the same information via [Subsetted FHIR Search](fhir-search.md#download-of-resources-with-subsetting) and **4 times as fast** as downloading the whole Observation Resources using [FHIR Search](fhir-search.md#download-of-resources).
+
+## Used Dataset
+
+The dataset was the same as in [FHIR Search](fhir-search.md) performance tests.

modules/interaction/.clj-kondo/config.edn

@@ -4,27 +4,16 @@
   blaze.async.comp/do-sync clojure.core/let
   blaze.db.api-stub/with-system-data clojure.core/with-open
   blaze.interaction.create-test/with-handler clojure.core/fn
-  blaze.interaction.create-test/with-handler-data clojure.core/fn
   blaze.interaction.delete-test/with-handler clojure.core/fn
-  blaze.interaction.delete-test/with-handler-data clojure.core/fn
   blaze.interaction.history.instance-test/with-handler clojure.core/fn
-  blaze.interaction.history.instance-test/with-handler-data clojure.core/fn
   blaze.interaction.history.system-test/with-handler clojure.core/fn
-  blaze.interaction.history.system-test/with-handler-data clojure.core/fn
   blaze.interaction.history.type-test/with-handler clojure.core/fn
-  blaze.interaction.history.type-test/with-handler-data clojure.core/fn
   blaze.interaction.read-test/with-handler clojure.core/fn
-  blaze.interaction.read-test/with-handler-data clojure.core/fn
   blaze.interaction.search-compartment-test/with-handler clojure.core/fn
-  blaze.interaction.search-compartment-test/with-handler-data clojure.core/fn
   blaze.interaction.search-system-test/with-handler clojure.core/fn
-  blaze.interaction.search-system-test/with-handler-data clojure.core/fn
   blaze.interaction.search-type-test/with-handler clojure.core/fn
-  blaze.interaction.search-type-test/with-handler-data clojure.core/fn
   blaze.interaction.transaction-test/with-handler clojure.core/fn
-  blaze.interaction.transaction-test/with-handler-data clojure.core/fn
   blaze.interaction.update-test/with-handler clojure.core/fn
-  blaze.interaction.update-test/with-handler-data clojure.core/fn
   blaze.test-util/with-system clojure.core/with-open}
 
  :linters

modules/interaction/test/blaze/interaction/create_test.clj

@@ -12,7 +12,7 @@
     [blaze.fhir.response.create-spec]
     [blaze.fhir.spec.type]
     [blaze.interaction.create]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.interaction.util-spec]
     [blaze.test-util :as tu :refer [given-thrown with-system]]
     [clojure.spec.alpha :as s]
@@ -95,7 +95,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{handler# :blaze.interaction/create} system]
        ~txs
        (let [~handler-binding (-> handler# wrap-defaults wrap-error)]

modules/interaction/test/blaze/interaction/delete_test.clj

@@ -6,7 +6,6 @@
     [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.executors :as ex]
     [blaze.interaction.delete]
-    [blaze.interaction.test-util :as itu]
     [blaze.test-util :as tu :refer [given-thrown]]
     [clojure.spec.alpha :as s]
     [clojure.spec.test.alpha :as st]
@@ -55,7 +54,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{handler# :blaze.interaction/delete} system]
        ~txs
        (let [~handler-binding handler#]

modules/interaction/test/blaze/interaction/history/instance_test.clj

@@ -9,7 +9,7 @@
     [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.interaction.history.instance]
     [blaze.interaction.history.util-spec]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.test-util :as tu :refer [given-thrown]]
@@ -91,7 +91,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction.history/instance} system]
        ~txs

modules/interaction/test/blaze/interaction/history/system_test.clj

@@ -8,7 +8,6 @@
     [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.interaction.history.system]
     [blaze.interaction.history.util-spec]
-    [blaze.interaction.test-util :as itu]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.test-util :as tu :refer [given-thrown]]
@@ -93,7 +92,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction.history/system} system]
        ~txs

modules/interaction/test/blaze/interaction/history/type_test.clj

@@ -8,7 +8,6 @@
     [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.interaction.history.type]
     [blaze.interaction.history.util-spec]
-    [blaze.interaction.test-util :as itu]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.test-util :as tu :refer [given-thrown]]
@@ -94,7 +93,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction.history/type} system]
        ~txs

modules/interaction/test/blaze/interaction/read_test.clj

@@ -9,7 +9,7 @@
     [blaze.db.api-stub :refer [mem-node-system with-system-data]]
     [blaze.db.spec]
     [blaze.interaction.read]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.test-util :as tu]
@@ -43,7 +43,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction/read} system]
        ~txs

modules/interaction/test/blaze/interaction/search_compartment_test.clj

@@ -9,7 +9,7 @@
     [blaze.interaction.search.nav-spec]
     [blaze.interaction.search.params-spec]
     [blaze.interaction.search.util-spec]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.page-store-spec]
@@ -99,7 +99,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction/search-compartment} system]
        ~txs

modules/interaction/test/blaze/interaction/search_system_test.clj

@@ -8,7 +8,7 @@
     [blaze.interaction.search.nav-spec]
     [blaze.interaction.search.params-spec]
     [blaze.interaction.search.util-spec]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.page-store-spec]
@@ -101,7 +101,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction/search-system} system]
        ~txs

modules/interaction/test/blaze/interaction/search_type_test.clj

@@ -10,7 +10,7 @@
     [blaze.interaction.search.nav-spec]
     [blaze.interaction.search.params-spec]
     [blaze.interaction.search.util-spec]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.middleware.fhir.db :refer [wrap-db]]
     [blaze.middleware.fhir.db-spec]
     [blaze.page-store-spec]
@@ -171,7 +171,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{node# :blaze.db/node
                          handler# :blaze.interaction/search-type} system]
        ~txs

modules/interaction/test/blaze/interaction/test_util.clj

@@ -8,9 +8,3 @@
   (fn [request]
     (-> (handler request)
         (ac/exceptionally handler-util/error-response))))
-
-
-(defn extract-txs-body [more]
-  (if (vector? (first more))
-    [(first more) (next more)]
-    [[] more]))

modules/interaction/test/blaze/interaction/transaction_test.clj

@@ -14,7 +14,7 @@
     [blaze.interaction.delete]
     [blaze.interaction.read]
     [blaze.interaction.search-type]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.interaction.transaction]
     [blaze.interaction.update]
     [blaze.interaction.util-spec]
@@ -177,7 +177,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{handler# :blaze.interaction/transaction
                          router# ::router} system]
        ~txs

modules/interaction/test/blaze/interaction/update_test.clj

@@ -11,7 +11,7 @@
     [blaze.executors :as ex]
     [blaze.fhir.response.create-spec]
     [blaze.fhir.spec.type]
-    [blaze.interaction.test-util :as itu :refer [wrap-error]]
+    [blaze.interaction.test-util :refer [wrap-error]]
     [blaze.interaction.update]
     [blaze.test-util :as tu :refer [given-thrown with-system]]
     [clojure.spec.alpha :as s]
@@ -98,7 +98,7 @@
 
 
 (defmacro with-handler [[handler-binding] & more]
-  (let [[txs body] (itu/extract-txs-body more)]
+  (let [[txs body] (tu/extract-txs-body more)]
     `(with-system-data [{handler# :blaze.interaction/update} system]
        ~txs
        (let [~handler-binding (-> handler# wrap-defaults wrap-error)]

modules/operation-graphql/.clj-kondo/config.edn

@@ -0,0 +1,22 @@
+{:lint-as
+ {blaze.anomaly/when-ok clojure.core/let
+  blaze.fhir.operation.graphql-test/with-handler clojure.core/fn
+  blaze.test-util/with-system clojure.core/with-open}
+
+ :linters
+ {:unsorted-required-namespaces
+  {:level :error}
+
+  :single-key-in
+  {:level :warning}
+
+  :keyword-binding
+  {:level :error}
+
+  :reduce-without-init
+  {:level :warning}
+
+  :warn-on-reflection
+  {:level :warning :warn-only-on-interop true}}
+
+ :skip-comments true}