Merge pull request #1043 from samply/release-v0.22.0

Release v0.22.0

.github/scripts/check-capability-statement.sh

@@ -8,3 +8,7 @@ CAPABILITY_STATEMENT=$(curl -sH 'Accept: application/fhir+json' "$BASE/metadata"
 
 test "software name" "$(echo "$CAPABILITY_STATEMENT" | jq -r .software.name)" "Blaze"
 test "URL" "$(echo "$CAPABILITY_STATEMENT" | jq -r .implementation.url)" "http://localhost:8080/fhir"
+
+test "Operation Measure \$evaluate-measure Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Measure") .operation[] | select(.name == "evaluate-measure") | .definition')" "http://hl7.org/fhir/OperationDefinition/Measure-evaluate-measure"
+test "Operation Patient \$everything Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Patient") .operation[] | select(.name == "everything") | .definition')" "http://hl7.org/fhir/OperationDefinition/Patient-everything"
+test "Operation Patient \$everything Documentation" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Patient") .operation[] | select(.name == "everything") | .documentation')" "Returns all resources from the patient compartment of one concrete patient including the patient. Has a fix limit of 10,000 resources. Paging ist not supported. No params are supported."

.github/scripts/check-frontend.sh

@@ -0,0 +1,36 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+
+echo "checking index.html using the Accept header..."
+HEADERS=$(curl -s -H 'Accept: text/html' -o /dev/null -D - "$BASE")
+CONTENT_TYPE_HEADER=$(echo "$HEADERS" | grep -i 'Content-Type' | tr -d '\r' | cut -d' ' -f2)
+
+test "Content-Type header" "$CONTENT_TYPE_HEADER" "text/html"
+
+echo "checking index.html using the _format query param..."
+HEADERS=$(curl -s -o /dev/null -D - "$BASE?_format=html")
+CONTENT_TYPE_HEADER=$(echo "$HEADERS" | grep -i 'Content-Type' | tr -d '\r' | cut -d' ' -f2)
+
+test "Content-Type header" "$CONTENT_TYPE_HEADER" "text/html"
+
+echo "checking version.json..."
+HEADERS=$(curl -s -H 'Accept: text/html' -o /dev/null -D - "$BASE/__frontend/version.json")
+CONTENT_TYPE_HEADER=$(echo "$HEADERS" | grep -i 'Content-Type' | tr -d '\r' | cut -d' ' -f2)
+
+test "Content-Type header" "$CONTENT_TYPE_HEADER" "application/json"
+
+echo "checking system-search using the Accept header..."
+HEADERS=$(curl -s -H 'Accept: application/fhir+json' -o /dev/null -D - "$BASE")
+CONTENT_TYPE_HEADER=$(echo "$HEADERS" | grep -i 'Content-Type' | tr -d '\r' | cut -d' ' -f2)
+
+test "Content-Type header" "$CONTENT_TYPE_HEADER" "application/fhir+json;charset=utf-8"
+
+echo "checking system-search using the _format query param..."
+HEADERS=$(curl -s -o /dev/null -D - "$BASE?_format=json")
+CONTENT_TYPE_HEADER=$(echo "$HEADERS" | grep -i 'Content-Type' | tr -d '\r' | cut -d' ' -f2)
+
+test "Content-Type header" "$CONTENT_TYPE_HEADER" "application/fhir+json;charset=utf-8"

.github/scripts/patient-everything.sh

@@ -0,0 +1,14 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+PATIENT_IDENTIFIER="X79746011X"
+PATIENT_ID=$(curl -s "$BASE/Patient?identifier=$PATIENT_IDENTIFIER" | jq -r '.entry[0].resource.id')
+BUNDLE=$(curl -s "$BASE/Patient/$PATIENT_ID/\$everything")
+ACTUAL_SIZE=$(echo "$BUNDLE" | jq -r .total)
+
+test "size" "$ACTUAL_SIZE" "3424"
+
+test "type counts" "$(echo "$BUNDLE" | jq -r '.entry | group_by(.resource.resourceType)[] | [.[0].resource.resourceType, length] | @csv')" "$(cat "$SCRIPT_DIR/patient-everything/$PATIENT_IDENTIFIER-type-counts.csv")"

.github/scripts/patient-everything/X79746011X-type-counts.csv

@@ -0,0 +1,16 @@
+"CarePlan",5
+"CareTeam",10
+"Claim",176
+"Condition",15
+"DiagnosticReport",231
+"DocumentReference",78
+"Encounter",78
+"ExplanationOfBenefit",78
+"ImagingStudy",45
+"Immunization",13
+"MedicationAdministration",180
+"MedicationRequest",98
+"Observation",2265
+"Patient",1
+"Procedure",150
+"Provenance",1

.github/scripts/patient-identical-update.sh

@@ -0,0 +1,49 @@
+#!/bin/bash -e
+
+#
+# This script tests that an update without changes of the resource content
+# doesn't create a new history entry.
+#
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+bundle() {
+cat <<END
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "resource": $1,
+      "request": {
+        "method": "PUT",
+        "url": "Patient/$2"
+      }
+    }
+  ]
+}
+END
+}
+
+BASE="http://localhost:8080/fhir"
+PATIENT_IDENTIFIER="X79746011X"
+PATIENT=$(curl -sH "Accept: application/fhir+json" "$BASE/Patient?identifier=$PATIENT_IDENTIFIER" | jq -cM '.entry[0].resource')
+ID="$(echo "$PATIENT" | jq -r .id)"
+VERSION_ID="$(echo "$PATIENT" | jq -r .meta.versionId)"
+
+# Update Interaction
+RESULT=$(curl -sXPUT -H "Content-Type: application/fhir+json" -d "$PATIENT" "$BASE/Patient/$ID")
+RESULT_VERSION_ID="$(echo "$RESULT" | jq -r .meta.versionId)"
+
+test "update versionId" "$RESULT_VERSION_ID" "$VERSION_ID"
+
+# Transaction Interaction
+RESULT=$(curl -sH "Content-Type: application/fhir+json" -H "Prefer: return=representation" -d "$(bundle "$PATIENT" "$ID")" "$BASE")
+RESULT_VERSION_ID="$(echo "$RESULT" | jq -r '.entry[0].resource.meta.versionId')"
+
+test "transaction versionId" "$RESULT_VERSION_ID" "$VERSION_ID"
+
+HISTORY_TOTAL=$(curl -sH "Accept: application/fhir+json" "$BASE/Patient/$ID/_history" | jq -r '.total')
+
+test "history total" "$HISTORY_TOTAL" "1"

.github/workflows/build.yml

@@ -58,6 +58,7 @@ jobs:
         - kv
         - luid
         - metrics
+        - module-base
         - openid-auth
         - operation-graphql
         - operation-measure-evaluate-measure
@@ -617,6 +618,12 @@ jobs:
     - name: Read Ignores T
       run: .github/scripts/read-ignores-t.sh
 
+    - name: Patient Everything
+      run: .github/scripts/patient-everything.sh
+
+    - name: Patient Identical Update
+      run:  .github/scripts/patient-identical-update.sh
+
   not-enforcing-referential-integrity-test:
     needs: build
     runs-on: ubuntu-22.04
@@ -1060,6 +1067,32 @@ jobs:
     - name: Download Both Resources
       run:  test "2" = "$(curl -s http://localhost:8080/fhir/Binary | jq .total)"
 
+  frontend-test:
+    needs: build
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@v3
+
+    - name: Download Blaze Image
+      uses: actions/download-artifact@v3
+      with:
+        name: blaze-image
+        path: /tmp
+
+    - name: Load Blaze Image
+      run: docker load --input /tmp/blaze.tar
+
+    - name: Run Blaze
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENABLE_FRONTEND=true -p 8080:8080 -v blaze-data:/app/data blaze:latest
+
+    - name: Wait for Blaze
+      run: .github/scripts/wait-for-url.sh  http://localhost:8080/health
+
+    - name: Check Frontend
+      run:  .github/scripts/check-frontend.sh
+
   missing-resource-content-test:
     needs: build
     runs-on: ubuntu-22.04
@@ -1487,6 +1520,12 @@ jobs:
     - name: Read Ignores T
       run: .github/scripts/read-ignores-t.sh
 
+    - name: Patient Everything
+      run: .github/scripts/patient-everything.sh
+
+    - name: Patient Identical Update
+      run:  .github/scripts/patient-identical-update.sh
+
     - name: Docker Stats
       run: docker stats --no-stream
 
@@ -1586,9 +1625,11 @@ jobs:
     - openid-auth-test
     - doc-copy-data-test
     - big-binary-test
+    - frontend-test
     - missing-resource-content-test
     - distributed-test
     - jepsen-distributed-test
+    - custom-search-parameters-test
     runs-on: ubuntu-22.04
     permissions:
       packages: write

.gitignore

@@ -2,5 +2,4 @@ target
 classes
 .cpcache
 .cache
-blaze-load-tests/node_modules
 .nrepl-port

CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## v0.22.0
+
+It's not recommended to downgrade from this version to an older version because [#1041](https://github.com/samply/blaze/pull/1041) introduces a new transaction command called `keep` that would be ignored by older versions. However the transaction log is only read at the moment transactions happen or if the index is rebuild. So it will be ok to downgrade in emergency without rebuilding the index.
+
+### New Features
+
+* Implement Operation Patient $everything ([#1037](https://github.com/samply/blaze/pull/1037))
+* Add Basic Frontend ([#951](https://github.com/samply/blaze/pull/951))
+
+### Enhancements
+
+* Ensure History Changes only if Resource Changes ([#1041](https://github.com/samply/blaze/pull/1041))
+
+### Performance
+
+* Improve Database Sync Efficiency ([#1039](https://github.com/samply/blaze/pull/1039))
+
+### Bugfixes
+
+* Fix Evaluate Measure Generating Duplicate List IDs ([#1036](https://github.com/samply/blaze/pull/1036))
+* Fix Comparison of Length Result not Possible in CQL ([#1035](https://github.com/samply/blaze/pull/1035))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/68?closed=1).
+
 ## v0.21.0
 
 ### New Features

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17-jre
+FROM eclipse-temurin:17.0.7_7-jre-jammy
 
 RUN apt-get update && apt-get upgrade -y && \
     apt-get install libjemalloc2 -y && \
@@ -7,14 +7,15 @@ RUN apt-get update && apt-get upgrade -y && \
     rm -rf /var/lib/apt/lists/
 
 RUN mkdir -p /app/data && chown 1001:1001 /app/data
-COPY target/blaze-0.21.0-standalone.jar /app/
+COPY target/blaze-0.22.0-standalone.jar /app/
 
 WORKDIR /app
 USER 1001
 
+ENV LD_PRELOAD="libjemalloc.so.2"
 ENV STORAGE="standalone"
 ENV INDEX_DB_DIR="/app/data/index"
 ENV TRANSACTION_DB_DIR="/app/data/transaction"
 ENV RESOURCE_DB_DIR="/app/data/resource"
 
-CMD ["sh", "-c", "LD_PRELOAD=/usr/lib/$(arch)-linux-gnu/libjemalloc.so.2 exec java -jar blaze-0.21.0-standalone.jar"]
+CMD ["java", "-jar",  "blaze-0.22.0-standalone.jar"]

Makefile

@@ -23,7 +23,10 @@ clean-root:
 
 clean: $(MODULES) clean-root
 
-uberjar: prep
+build-frontend:
+	$(MAKE) -C modules/frontend build
+
+uberjar: prep build-frontend
 	clojure -T:build uber
 
 outdated:
@@ -35,4 +38,4 @@ deps-tree:
 deps-list:
 	clojure -X:deps list
 
-.PHONY: $(MODULES) lint-root lint prep test-root test test-coverage clean-root clean uberjar outdated deps-tree deps-list
+.PHONY: $(MODULES) lint-root lint prep test-root test test-coverage clean-root clean build-frontend uberjar outdated deps-tree deps-list

README.md

@@ -15,7 +15,7 @@ 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: [v0.21.0][5]
+Latest release: [v0.22.0][5]
 
 ## Quick Start
 
@@ -25,7 +25,7 @@ In order to run Blaze just execute the following:
 
 ```sh
 docker volume create blaze-data
-docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.21
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.22
 ```
 
 Blaze will create multiple directories inside the `blaze-data` volume on its first start and use the same directories on subsequent starts.
@@ -74,7 +74,7 @@ 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/v0.21.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.22.0>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

build.clj

@@ -2,7 +2,7 @@
   (:require [clojure.tools.build.api :as b]))
 
 (def lib 'samply/blaze)
-(def version "0.21.0")
+(def version "0.22.0")
 (def class-dir "target/classes")
 (def basis (b/create-basis {:project "deps.edn"}))
 (def uber-file (format "target/%s-%s-standalone.jar" (name lib) version))

deps.edn

@@ -1,12 +1,18 @@
 {:paths ["src" "resources"]
 
  :deps
- {blaze/db-resource-store-cassandra
+ {blaze/admin-api
+  {:local/root "modules/admin-api"}
+
+  blaze/db-resource-store-cassandra
   {:local/root "modules/db-resource-store-cassandra"}
 
   blaze/db-tx-log-kafka
   {:local/root "modules/db-tx-log-kafka"}
 
+  blaze/frontend
+  {:local/root "modules/frontend"}
+
   blaze/interaction
   {:local/root "modules/interaction"}
 
@@ -16,6 +22,9 @@
   blaze.operation/measure-evaluate-measure
   {:local/root "modules/operation-measure-evaluate-measure"}
 
+  blaze.operation/patient-everything
+  {:local/root "modules/operation-patient-everything"}
+
   blaze/openid-auth
   {:local/root "modules/openid-auth"}
 
@@ -69,7 +78,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.71.1119"}}
+    {:mvn/version "1.85.1342"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 
@@ -83,7 +92,7 @@
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "2.4.1070"}
+    {:mvn/version "2.5.1095"}
 
     org.slf4j/slf4j-nop
     {:mvn/version "2.0.7"}}
@@ -133,5 +142,4 @@
     "--exclude" "com.taoensso/timbre"
     "--exclude" "org.antlr/antlr4"
     "--exclude" "org.clojure/alpha.spec"
-    "--exclude" "com.walmartlabs/lacinia"
-    "--exclude" "lambdaisland/kaocha"]}}}
+    "--exclude" "com.walmartlabs/lacinia"]}}}

dev/blaze/dev.clj

@@ -14,9 +14,7 @@
     [clojure.spec.test.alpha :as st]
     [clojure.tools.namespace.repl :refer [refresh]]
     [java-time.api :as time]
-    [taoensso.timbre :as log])
-  (:import
-    [com.github.benmanes.caffeine.cache Cache]))
+    [taoensso.timbre :as log]))
 
 
 ;; Spec Instrumentation

dev/blaze/dev/rocksdb.clj

@@ -38,4 +38,7 @@
        :db (.getDbName status)
        :cf (.getCfName status)})
     (.getThreadList (Env/getDefault)))
+
+  (rocksdb/table-properties (index-kv-store) :resource-as-of-index)
+
   )