Merge pull request #305 from RADAR-base/release-0.7.9

Release 0.7.9
RADAR-base · Apr 19, 2022 · f64e827 · f64e827
2 parents 26450ba + 48ad0fe
commit f64e827
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Showing 12 changed files with 134 additions and 38 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -28,7 +28,7 @@ jobs:
 
       - uses: actions/setup-java@v2
         with:
-          distribution: zulu
+          distribution: temurin
           java-version: 17
 
       - name: Setup Gradle
@@ -50,7 +50,32 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
+      - name: Docker build parameters
+        id: docker_params
+        run: |
+          echo "::set-output name=has_docker_login::${{ secrets.DOCKERHUB_USERNAME != ''  && secrets.DOCKERHUB_TOKEN != '' }}"
+          if [ "${{ github.event_name == 'pull_request' }}" = "true" ]; then
+            echo "::set-output name=push::false"
+            echo "::set-output name=load::true"
+            echo "::set-output name=platforms::linux/amd64"
+          else
+            echo "::set-output name=push::true"
+            echo "::set-output name=load::false"
+            echo "::set-output name=platforms::linux/amd64,linux/arm64"
+          fi
+
+      - name: Cache Docker layers
+        id: cache_buildx
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ steps.docker_params.outputs.push }}-${{ hashFiles('Dockerfile', 'java-sdk/**/*.gradle', 'java-sdk/gradle.properties', 'java-sdk/*/src/main/**', 'commons/**', 'specifications/**', 'docker/**') }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-${{ steps.docker_params.outputs.push }}-
+            ${{ runner.os }}-buildx-
+
       - name: Login to Docker Hub
+        if: steps.docker_params.outputs.has_docker_login == 'true'
         uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -70,19 +95,10 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v1
 
-      - name: Cache Docker layers
-        id: cache-buildx
-        uses: actions/cache@v2
-        with:
-          path: /tmp/.buildx-cache
-          key: ${{ runner.os }}-buildx-${{ hashFiles('Dockerfile', 'java-sdk/**/*.gradle', 'java-sdk/gradle.properties', 'java-sdk/*/src/main/**', 'commons/**', 'specifications/**', 'docker/**') }}
-          restore-keys: |
-            ${{ runner.os }}-buildx-
-
       - name: Cache parameters
         id: cache-parameters
         run: |
-          if [ "${{ steps.cache-buildx.outputs.cache-hit }}" = "true" ]; then
+          if [ "${{ steps.cache_buildx.outputs.cache-hit }}" = "true" ]; then
             echo "::set-output name=cache-to::"
           else
             echo "::set-output name=cache-to::type=local,dest=/tmp/.buildx-cache-new,mode=max"
@@ -93,7 +109,9 @@ jobs:
         with:
           cache-from: type=local,src=/tmp/.buildx-cache
           cache-to: ${{ steps.cache-parameters.outputs.cache-to }}
-          load: true
+          platforms: ${{ steps.docker_params.outputs.platforms }}
+          load: ${{ steps.docker_params.outputs.load }}
+          push: ${{ steps.docker_params.outputs.push }}
           tags: ${{ steps.docker_meta.outputs.tags }}
           # Use runtime labels from docker_meta as well as fixed labels
           labels: |
@@ -104,6 +122,10 @@ jobs:
             org.opencontainers.image.vendor=RADAR-base
             org.opencontainers.image.licenses=Apache-2.0
 
+      - name: Pull docker image
+        if: steps.docker_params.outputs.load == 'false'
+        run: docker pull ${{ env.DOCKER_IMAGE }}:${{ steps.docker_meta.outputs.version }}
+
       - name: Inspect docker image
         run: docker image inspect ${{ env.DOCKER_IMAGE }}:${{ steps.docker_meta.outputs.version }}
 
@@ -121,7 +143,7 @@ jobs:
       # https://github.com/docker/build-push-action/issues/252
       # https://github.com/moby/buildkit/issues/1896
       - name: Move docker build cache
-        if: steps.cache-buildx.outputs.cache-hit != 'true'
+        if: steps.cache_buildx.outputs.cache-hit != 'true'
         run: |
           rm -rf /tmp/.buildx-cache
           mv /tmp/.buildx-cache-new /tmp/.buildx-cache
diff --git a/.github/workflows/publish_snapshots.yml b/.github/workflows/publish_snapshots.yml
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/setup-java@v2
         with:
-          distribution: zulu
+          distribution: temurin
           java-version: 17
 
       - name: Setup Gradle

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -21,7 +21,7 @@ jobs:
 
       - uses: actions/setup-java@v2
         with:
-          distribution: zulu
+          distribution: temurin
           java-version: 17
 
       - name: Setup Gradle

diff --git a/.github/workflows/scheduled_snyk.yaml b/.github/workflows/scheduled_snyk.yaml
@@ -0,0 +1,34 @@
+name: Snyk scheduled test
+on:
+  schedule:
+    - cron: '0 2 * * 1'
+jobs:
+  security:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: java-sdk
+
+    env:
+      REPORT_FILE: test.json
+    steps:
+      - uses: actions/checkout@master
+      - uses: snyk/actions/setup@master
+
+      - uses: actions/setup-java@v2
+        with:
+          distribution: temurin
+          java-version: 17
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      - name: Run Snyk
+        env:
+          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
+        run: >
+          snyk test
+          --all-sub-projects
+          --configuration-matching='^runtimeClasspath$'
+          --json-file-output=${{ env.REPORT_FILE }}
+          --org=radar-base
diff --git a/.github/workflows/snyk.yaml b/.github/workflows/snyk.yaml
@@ -0,0 +1,34 @@
+name: Snyk test
+on:
+  pull_request:
+    branches:
+      - master
+jobs:
+  security:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        working-directory: java-sdk
+
+    steps:
+      - uses: actions/checkout@master
+      - uses: snyk/actions/setup@master
+
+      - uses: actions/setup-java@v2
+        with:
+          distribution: temurin
+          java-version: 17
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      - name: Run Snyk to check for vulnerabilities
+        env:
+          SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
+        run: >
+          snyk test
+          --all-sub-projects
+          --configuration-matching='^runtimeClasspath$'
+          --fail-on=upgradable
+          --org=radar-base
diff --git a/Dockerfile b/Dockerfile
@@ -24,7 +24,7 @@ COPY java-sdk/radar-catalog-server/src /code/java-sdk/radar-catalog-server/src
 
 RUN gradle jar --no-watch-fs -Pprofile=docker
 
-FROM azul/zulu-openjdk-alpine:17-jre-headless
+FROM eclipse-temurin:17-jre
 
 ENV KAFKA_SCHEMA_REGISTRY=http://schema-registry-1:8081 \
     SCHEMA_REGISTRY_API_KEY="" \
@@ -36,10 +36,9 @@ ENV KAFKA_SCHEMA_REGISTRY=http://schema-registry-1:8081 \
     KAFKA_CONFIG_PATH="" \
     NO_VALIDATE=""
 
-RUN apk add --no-cache \
-		bash \
-		curl \
-		rsync
+RUN apt-get update && apt-get install -y \
+		rsync \
+    && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /schema
 

diff --git a/commons/connector/fitbit/fitbit_resting_heart_rate.avsc b/commons/connector/fitbit/fitbit_resting_heart_rate.avsc
@@ -0,0 +1,11 @@
+{
+  "namespace": "org.radarcns.connector.fitbit",
+  "type": "record",
+  "name": "FitbitRestingHeartRate",
+  "doc": "Heart rate time-series data over a period of time from fitbit device.",
+  "fields": [
+    { "name": "date", "type": "string", "doc": "ISO 8601 formatted local date of device (yyyy-MM-dd)." },
+    { "name": "timeReceived", "type": "double", "doc": "Time that the data was received from the Fitbit API (seconds since the Unix Epoch)." },
+    { "name": "restingHeartRate", "type": "int", "doc": "Resting heart rate value (bpm) for the day. A sleep stage log is required to generate this value. When a classic sleep log is recorded, this value will be missing." }
+  ]
+}
diff --git a/commons/connector/fitbit/fitbit_sleep_classic.avsc b/commons/connector/fitbit/fitbit_sleep_classic.avsc
@@ -9,6 +9,7 @@
     { "name": "duration", "type": "int", "doc": "Duration at this sleep characteristic in seconds." },
     { "name": "level", "type":
       { "name": "FitbitSleepClassicLevel", "type": "enum", "symbols": ["AWAKE", "RESTLESS", "ASLEEP", "UNKNOWN"], "doc": "Level of sleep as computed by Fitbit."},
-      "doc": "Level of sleep as computed by Fitbit.", "default": "UNKNOWN" }
+      "doc": "Level of sleep as computed by Fitbit.", "default": "UNKNOWN" },
+    { "name": "efficiency", "type": ["null", "int"], "doc": "Calculated sleep efficiency score (in percentage). It is a percentage of the amount of time the user was asleep (and not restless) divided by the time they spent in the bed after initially falling asleep.", "default": null }
   ]
 }
diff --git a/commons/connector/fitbit/fitbit_sleep_stage.avsc b/commons/connector/fitbit/fitbit_sleep_stage.avsc
@@ -9,6 +9,7 @@
     { "name": "duration", "type": "int", "doc": "Duration at this sleep characteristic in seconds." },
     { "name": "level", "type":
       {"name": "FitbitSleepStageLevel", "type": "enum", "symbols": ["DEEP", "LIGHT", "REM", "AWAKE", "UNKNOWN"], "doc": "Level of sleep as computed by Fitbit."},
-      "doc": "Level of sleep as computed by Fitbit.", "default": "UNKNOWN" }
+      "doc": "Level of sleep as computed by Fitbit.", "default": "UNKNOWN" },
+    { "name": "efficiency", "type": ["null", "int"], "doc": "Calculated sleep efficiency score (in percentage). It is a percentage of the amount of time the user was asleep (and not restless) divided by the time they spent in the bed after initially falling asleep.", "default": null }
   ]
 }
diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle
@@ -9,7 +9,7 @@ plugins {
 }
 
 allprojects {
-    version = '0.7.8'
+    version = '0.7.9'
     group = 'org.radarbase'
 }
 
@@ -26,8 +26,8 @@ subprojects {
     ext {
         avroVersion = '1.11.0'
         argparseVersion = '0.9.0'
-        jacksonVersion = '2.13.2'
-        radarJerseyVersion = "0.8.2"
+        jacksonVersion = '2.13.2.20220324'
+        radarJerseyVersion = "0.8.3"
 
         junitVersion = '4.13.2'
         confluentVersion = '7.0.1'
@@ -36,16 +36,7 @@ subprojects {
         radarCommonsVersion = '0.13.2'
         slf4jVersion = '1.7.36'
         javaxValidationVersion = '2.0.1.Final'
-        logbackVersion = '1.2.10'
-    }
-
-    configurations.all {
-        resolutionStrategy.eachDependency { DependencyResolveDetails details ->
-            if (details.requested.group == 'com.fasterxml.jackson.module' && details.requested.name == 'jackson-module-kotlin') {
-                details.useVersion jacksonVersion
-                details.because 'Fixes missing kotlin module of latest version'
-            }
-        }
+        logbackVersion = '1.2.11'
     }
 
     repositories {

diff --git a/java-sdk/radar-schemas-core/build.gradle b/java-sdk/radar-schemas-core/build.gradle
@@ -27,9 +27,11 @@ dependencies {
     }
     api group: 'javax.validation', name: 'validation-api', version: javaxValidationVersion
     api project(':radar-schemas-commons')
-    api ("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion")
 
-    implementation ("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:$jacksonVersion")
+    api(platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
+    api("com.fasterxml.jackson.core:jackson-databind")
+
+    implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml")
     implementation(group: 'io.confluent', name: 'kafka-connect-avro-data', version: confluentVersion) {
         exclude group: "org.glassfish.jersey.core", module: "jersey-common"
         exclude group: "jakarta.ws.rs", module: "jakarta.ws.rs-api"

diff --git a/java-sdk/radar-schemas-tools/build.gradle b/java-sdk/radar-schemas-tools/build.gradle
@@ -24,7 +24,8 @@ repositories {
 
 dependencies {
     implementation project(':radar-schemas-registration')
-    implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:$jacksonVersion")
+    implementation(platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
+    implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml")
 
     implementation group: 'net.sourceforge.argparse4j', name: 'argparse4j', version: argparseVersion