Merge pull request #929 from samply/release-v0.20.0

Release v0.20.0

.github/scripts/download-all-resources.sh

@@ -5,8 +5,6 @@ SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
 
 BASE="http://localhost:8080/fhir"
 EXPECTED_SIZE=$(curl -s "$BASE?_summary=count" | jq -r .total)
+ACTUAL_SIZE=$(blazectl --server "$BASE" download 2>/dev/null | wc -l | xargs)
 
-FILE_NAME=$(uuidgen)
-blazectl --no-progress --server "$BASE" download -o "$FILE_NAME.ndjson"
-
-test "download size" "$(wc -l "$FILE_NAME.ndjson" | xargs | cut -d ' ' -f1)" "$EXPECTED_SIZE"
+test "download size" "$ACTUAL_SIZE" "$EXPECTED_SIZE"

.github/scripts/download-observations-elements.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+NUM_PATIENTS=$(curl -s "$BASE/Patient?_summary=count" | jq -r .total)
+
+NUM_CODES=$(blazectl --server "$BASE" download Observation -q '_elements=subject' 2>/dev/null | jq -rc '.code' | grep -cv null | xargs)
+test "number of codes using GET" "$NUM_CODES" "0"
+
+NUM_SUBJECT_REFS=$(blazectl --server "$BASE" download Observation -q '_elements=subject' 2>/dev/null | jq -rc '.subject.reference' | sort -u | wc -l | xargs)
+test "number of unique subject refs using GET" "$NUM_SUBJECT_REFS" "$NUM_PATIENTS"
+
+NUM_CODES=$(blazectl --server "$BASE" download Observation -p -q '_elements=subject' 2>/dev/null | jq -rc '.code' | grep -cv null | xargs)
+test "number of codes using POST" "$NUM_CODES" "0"
+
+NUM_SUBJECT_REFS=$(blazectl --server "$BASE" download Observation -p -q '_elements=subject' 2>/dev/null | jq -rc '.subject.reference' | sort -u | wc -l | xargs)
+test "number of unique subject refs using POST" "$NUM_SUBJECT_REFS" "$NUM_PATIENTS"

.github/scripts/download-resources.sh

@@ -6,8 +6,6 @@ SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
 BASE="http://localhost:8080/fhir"
 TYPE=$1
 EXPECTED_SIZE=$(curl -s "$BASE/${TYPE}?_summary=count" | jq -r .total)
+ACTUAL_SIZE=$(blazectl --server "$BASE" download "$TYPE" 2>/dev/null | wc -l | xargs)
 
-FILE_NAME=$(uuidgen)
-blazectl --no-progress --server "$BASE" download "$TYPE" -o "$FILE_NAME.ndjson"
-
-test "download size" "$(wc -l "$FILE_NAME.ndjson" | xargs | cut -d ' ' -f1)" "$EXPECTED_SIZE"
+test "download size" "$ACTUAL_SIZE" "$EXPECTED_SIZE"

.github/scripts/evaluate-measure-subject-list.sh

@@ -131,7 +131,7 @@ fi
 
 LIST_ID=$(echo "$REPORT" | jq -r '.group[0].population[0].subjectResults.reference | split("/")[1]')
 PATIENT_BUNDLE=$(fetch-patients "$BASE" "$LIST_ID")
-ID_COUNT=$(echo "$PATIENT_BUNDLE" | jq -r ".entry[].resource.id" | sort -u | wc -l | xargs | cut -d ' ' -f1)
+ID_COUNT=$(echo "$PATIENT_BUNDLE" | jq -r ".entry[].resource.id" | sort -u | wc -l | xargs)
 
 if [ "$ID_COUNT" = "$EXPECTED_COUNT" ]; then
   echo "Success: downloaded patient count ($ID_COUNT) equals the expected count"

.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
@@ -85,7 +86,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1224'
+        cli: '1.11.1.1237'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -116,7 +117,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1224'
+        cli: '1.11.1.1237'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -158,7 +159,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1224'
+        cli: '1.11.1.1237'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -186,7 +187,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1224'
+        cli: '1.11.1.1237'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -372,6 +373,9 @@ jobs:
     - name: Download MedicationRequest Resources - Including Medications
       run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson
 
+    - name: Download Observations using _elements=subject
+      run: .github/scripts/download-observations-elements.sh
+
     - name: Search Observation _lastUpdated
       run: .github/scripts/search-patient-last-updated.sh
 
@@ -528,6 +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
@@ -784,7 +794,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1224'
+        cli: '1.11.1.1237'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -931,7 +941,7 @@ jobs:
       run: .github/scripts/generate-large-binary-resource.sh
 
     - name: Post Large Binary Resource
-      run:  curl -f -H Content-Type:application/fhir+xml -d @large-binary.xml http://localhost:8080/fhir/Binary
+      run:  curl -f -H Content-Type:application/fhir+xml -H Prefer:return=minimal -d @large-binary.xml http://localhost:8080/fhir/Binary
 
   distributed-test:
     needs: build
@@ -1073,6 +1083,9 @@ jobs:
     - name: Download MedicationRequest Resources - Including Medications
       run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson
 
+    - name: Download Observations using _elements=subject
+      run: .github/scripts/download-observations-elements.sh
+
     - name: Search Observation _lastUpdated
       run: .github/scripts/search-patient-last-updated.sh
 
@@ -1232,6 +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
 
@@ -1249,7 +1268,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1224'
+        cli: '1.11.1.1237'
 
     - name: Check out Git repository
       uses: actions/checkout@v3

CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## v0.20.0
+
+### New Features
+
+* Implement Special Search Parameter _elements ([#923](https://github.com/samply/blaze/pull/923))
+
+* Implement First Parts of Operation $graphql ([#924](https://github.com/samply/blaze/pull/924))  
+
+### Bugfixes
+
+* Fix Indexing Error during Soundex Calculation ([#928](https://github.com/samply/blaze/pull/928))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/59?closed=1).
+
 ## v0.19.4
 
 ### Bugfixes

Dockerfile

@@ -6,7 +6,7 @@ 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-0.19.4-standalone.jar /app/
+COPY target/blaze-0.20.0-standalone.jar /app/
 
 WORKDIR /app
 USER 1001
@@ -16,4 +16,4 @@ ENV INDEX_DB_DIR="/app/data/index"
 ENV TRANSACTION_DB_DIR="/app/data/transaction"
 ENV RESOURCE_DB_DIR="/app/data/resource"
 
-CMD ["java", "-jar", "blaze-0.19.4-standalone.jar"]
+CMD ["java", "-jar", "blaze-0.20.0-standalone.jar"]

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: [v0.19.4][5]
+Latest release: [v0.20.0][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:0.19
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.20
 ```
 
 Blaze will create multiple directories inside the `blaze-data` volume on its first start and use the same directories on subsequent starts.
@@ -73,7 +73,7 @@ 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/v0.19.4>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.20.0>
 [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 "0.19.4")
+(def version "0.20.0")
 (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

@@ -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"}
 
@@ -61,7 +64,7 @@
     {:mvn/version "0.4.6"}
 
     org.clojure/tools.namespace
-    {:mvn/version "1.4.1"}}}
+    {:mvn/version "1.4.2"}}}
 
   :kaocha
   {:extra-deps
@@ -75,12 +78,12 @@
 
    :extra-deps
    {org.clojure/tools.namespace
-    {:mvn/version "1.4.1"}}}
+    {:mvn/version "1.4.2"}}}
 
   :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"]}}}

docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   blaze:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     environment:
       BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"

docs/authentication/docker-compose.yml

@@ -10,7 +10,7 @@ services:
     volumes:
     - "../../.github/openid-auth-test/realm.json:/tmp/realm.json"
   blaze:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     environment:
       BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"

docs/consistency/docker-compose.yml

@@ -148,7 +148,7 @@ services:
       HEAP_NEWSIZE: "200M"
 
   blaze-1:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     hostname: "blaze-1"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx4g -Dclojure.server.repl='{:address,\"0.0.0.0\",:port,5555,:accept,clojure.core.server/repl}'"
@@ -178,7 +178,7 @@ services:
     restart: unless-stopped
 
   blaze-2:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     hostname: "blaze-2"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx4g"

docs/cql-queries.md

@@ -22,7 +22,7 @@ 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/README.md). If you have Docker available just run:
 
 ```
-docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.19
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.20
 ```
 
 Start the Quality Reporting UI. You should see an empty measure list.

docs/cql-queries/blazectl.md

@@ -20,7 +20,7 @@ cd blaze
 If you don't already have Blaze running, you can read about how to do it in [Deployment](../deployment/README.md). If you have Docker available just run:
 
 ```sh
-docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.19
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.20
 ```
 
 ## Import some data

docs/cql-queries/command-line.md

@@ -16,7 +16,7 @@ cd blaze
 If you don't already have Blaze running, you can read about how to do it in [Deployment](../deployment/README.md). If you have Docker available just run:
 
 ```sh
-docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.19
+docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.20
 ```
 
 ## Import some data

docs/data-sync/copy/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   src:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     environment:
       BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"
@@ -11,7 +11,7 @@ services:
     - "blaze-data-src:/app/data"
 
   dst:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     environment:
       BASE_URL: "http://localhost:8082"
       SERVER_PORT: "8082"

docs/data-sync/subscription/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   blaze:
-    image: "samply/blaze:0.19"
+    image: "samply/blaze:0.20"
     environment:
       BASE_URL: "http://localhost:8080"
       JAVA_TOOL_OPTIONS: "-Xmx2g"

docs/database/migration.md

@@ -22,7 +22,7 @@ backup of all the data Blaze has written to disk, **plan for a downtime**, delet
 Please start Blaze with a shell assuming that you use the volume `blaze-data`:
 
 ```sh
-docker run -it -v blaze-data:/app/data samply/blaze:0.19 sh
+docker run -it -v blaze-data:/app/data samply/blaze:0.20 sh
 ```
 
 in that shell, go into `/app/data` and list all directories: