Merge pull request #92 from RADAR-base/release-0.15.0

Release 0.15.0

.github/workflows/main.yml

@@ -16,23 +16,15 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v3
         with:
+          distribution: temurin
           java-version: 11
 
-      - name: Cache
-        uses: actions/cache@v2
-        with:
-          # Cache gradle directories
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          # Key for restoring and saving the cache
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle', 'gradle.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
 
       # Compile the code
       - name: Compile code

.github/workflows/publish_snapshots.yml

@@ -15,27 +15,19 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Has SNAPSHOT version
         id: is-snapshot
         run: grep "version = '.*-SNAPSHOT'" build.gradle
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v3
         with:
+          distribution: temurin
           java-version: 11
 
-      - name: Cache
-        uses: actions/cache@v2
-        with:
-          # Cache gradle directories
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          # Key for restoring and saving the cache
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle', 'gradle.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
 
       - name: Install gpg secret key
         run: |

.github/workflows/release.yml

@@ -13,22 +13,15 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
-      - uses: actions/setup-java@v1
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-java@v3
         with:
+          distribution: temurin
           java-version: 11
 
-      - name: Cache
-        uses: actions/cache@v2
-        with:
-          # Cache gradle directories
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          # Key for restoring and saving the cache
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle', 'gradle.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
 
       # Compile code
       - name: Compile code

.github/workflows/scheduled_snyk.yaml

@@ -8,14 +8,26 @@ jobs:
     env:
       REPORT_FILE: test.json
     steps:
-      - uses: actions/checkout@master
-      - name: Run Snyk to check for vulnerabilities
-        uses: snyk/actions/gradle-jdk11@master
+      - uses: actions/checkout@v3
+      - uses: snyk/actions/setup@master
+
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      - name: Run Snyk
         env:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-        with:
-          command: test
-          args: --json-file-output=${{ env.REPORT_FILE }}
+        run: >
+          snyk test
+          --all-sub-projects
+          --configuration-matching='^runtimeClasspath$'
+          --json-file-output=${{ env.REPORT_FILE }}
+          --org=radar-base
       - name: Report new vulnerabilities
         uses: thehyve/report-vulnerability@master
         with:

.github/workflows/snyk.yaml

@@ -7,10 +7,24 @@ jobs:
   security:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
-    - name: Run Snyk to check for vulnerabilities
-      uses: snyk/actions/gradle-jdk11@master
-      env:
-        SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-      with:
-        args: --severity-threshold=high
+      - uses: actions/checkout@v3
+      - uses: snyk/actions/setup@master
+
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+
+      - 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
+          --severity-threshold=high

README.md

@@ -14,7 +14,7 @@ repositories {
 }
 
 dependencies {
-    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.14.0'
+    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.15.0'
 }
 ```
 
@@ -69,7 +69,7 @@ repositories {
 }
 
 dependencies {
-    implementation group: 'org.radarbase', name: 'radar-commons-server', version: '0.14.0'
+    implementation group: 'org.radarbase', name: 'radar-commons-server', version: '0.15.0'
 }
 ```
 
@@ -82,7 +82,7 @@ repositories {
 }
 
 dependencies {
-    testImplementation group: 'org.radarbase', name: 'radar-commons-testing', version: '0.14.0'
+    testImplementation group: 'org.radarbase', name: 'radar-commons-testing', version: '0.15.0'
 }
 ```
 
@@ -107,7 +107,7 @@ configurations.all {
 }
 
 dependencies {
-    compile group: 'org.radarbase', name: 'radar-commons', version: '0.14.1-SNAPSHOT'
+    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.15.1-SNAPSHOT'
 }
 ```
 

build.gradle

@@ -16,11 +16,11 @@
 plugins {
     id 'com.github.davidmc24.gradle.plugin.avro' version '1.3.0'
     id("io.github.gradle-nexus.publish-plugin") version "1.1.0"
-    id("com.github.ben-manes.versions") version "0.39.0"
+    id("com.github.ben-manes.versions") version "0.42.0"
 }
 
 allprojects {
-    version = '0.14.0'
+    version = '0.15.0'
     group = 'org.radarbase'
 }
 
@@ -69,7 +69,7 @@ subprojects {
         }
 
         onOutput { TestDescriptor td, TestOutputEvent toe ->
-            stdout.addAll(toe.getMessage().split('(?m)$'))
+            stdout.addAll(Arrays.asList(toe.getMessage().split('(?m)$')))
             while (stdout.size() > 100) {
                 stdout.remove()
             }
@@ -99,6 +99,18 @@ subprojects {
     }
 }
 
+def isNonStable = { String version ->
+    def stableKeyword = ["RELEASE", "FINAL", "GA"].any { version.toUpperCase().contains(it) }
+    def regex = /^[0-9,.v-]+(-r)?$/
+    return !stableKeyword && !(version ==~ regex)
+}
+
+tasks.named("dependencyUpdates").configure {
+    rejectVersionIf {
+        isNonStable(it.candidate.version)
+    }
+}
+
 nexusPublishing {
     repositories {
         sonatype {
@@ -109,5 +121,5 @@ nexusPublishing {
 }
 
 wrapper {
-    gradleVersion '7.3.3'
+    gradleVersion '7.4.2'
 }

gradle.properties

@@ -1,12 +1,12 @@
-slf4jVersion=1.7.32
-confluentVersion=7.0.1
-kafkaVersion=7.0.1-ce
+slf4jVersion=1.7.36
+confluentVersion=7.1.1
+kafkaVersion=3.1.0
 avroVersion=1.11.0
-jacksonVersion=2.12.6
-jacksonYamlVersion=2.12.6
+jacksonVersion=2.13.2.20220328
 okhttpVersion=4.9.3
 junitVersion=4.13.2
-mockitoVersion=4.2.0
+mockitoVersion=4.5.1
 hamcrestVersion=1.3
-radarSchemasVersion=0.7.5
-orgJsonVersion=20211205
+radarSchemasVersion=0.7.9
+orgJsonVersion=20220320
+opencsvVersion=5.6

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

radar-commons-server/build.gradle

@@ -22,12 +22,12 @@ dependencies {
     api project(':radar-commons')
 
     // For POJO classes and ConfigLoader
-    implementation group: 'com.fasterxml.jackson.core' , name: 'jackson-databind' , version: jacksonVersion
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: jacksonYamlVersion
+    implementation(platform("com.fasterxml.jackson:jackson-bom:$jacksonVersion"))
+    implementation group: 'com.fasterxml.jackson.core' , name: 'jackson-databind'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml'
 
     api group: 'org.apache.avro', name: 'avro', version: avroVersion
 
-    implementation group: 'com.fasterxml.jackson.core' , name: 'jackson-databind' , version: jacksonVersion
     implementation group: 'org.apache.kafka', name: 'kafka-clients', version: kafkaVersion
 
     testImplementation group: 'org.mockito', name: 'mockito-core', version: mockitoVersion

radar-commons-server/src/main/java/org/radarbase/config/YamlConfigLoader.java

@@ -29,24 +29,32 @@
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.function.Consumer;
 
 /**
  * A YAML Config file loader, to load YAML files into equivalent POJO Objects.
  */
 public class YamlConfigLoader {
     public static final JsonFactory YAML_FACTORY = new YAMLFactory();
-    private static final ObjectMapper YAML_MAPPER = new ObjectMapper(YAML_FACTORY);
 
-    static {
-        YAML_MAPPER.setPropertyNamingStrategy(PropertyNamingStrategies.SNAKE_CASE);
+    private final ObjectMapper yamlMapper = new ObjectMapper(YAML_FACTORY);
+
+    public YamlConfigLoader() {
+        this((mapper) -> { });
+    }
+
+    /** Config loader that does some additional object mapper configuration after initialization. */
+    public YamlConfigLoader(Consumer<ObjectMapper> mapperConfigurator) {
+        yamlMapper.setPropertyNamingStrategy(PropertyNamingStrategies.SNAKE_CASE);
         // only serialize fields, not getters, etc.
-        YAML_MAPPER.setVisibility(YAML_MAPPER.getSerializationConfig().getDefaultVisibilityChecker()
+        yamlMapper.setVisibility(yamlMapper.getSerializationConfig().getDefaultVisibilityChecker()
                 .withFieldVisibility(JsonAutoDetect.Visibility.ANY)
                 .withGetterVisibility(JsonAutoDetect.Visibility.NONE)
                 .withIsGetterVisibility(JsonAutoDetect.Visibility.NONE)
                 .withSetterVisibility(JsonAutoDetect.Visibility.NONE)
                 .withCreatorVisibility(JsonAutoDetect.Visibility.NONE));
-        YAML_MAPPER.addMixIn(ServerConfig.class, ServerConfigMixin.class);
+        yamlMapper.addMixIn(ServerConfig.class, ServerConfigMixin.class);
+        mapperConfigurator.accept(yamlMapper);
     }
 
     /**
@@ -59,22 +67,22 @@ public class YamlConfigLoader {
      */
     public <T> T load(Path file, Class<T> configClass) throws IOException {
         try (Reader reader = Files.newBufferedReader(file, StandardCharsets.UTF_8)) {
-            return YAML_MAPPER.readValue(reader, configClass);
+            return yamlMapper.readValue(reader, configClass);
         }
     }
 
     /** Store config into given YAML file. */
     public void store(Path file, Object config) throws IOException {
         try (Writer writer = Files.newBufferedWriter(file, StandardCharsets.UTF_8)) {
-            YAML_MAPPER.writeValue(writer, config);
+            yamlMapper.writeValue(writer, config);
         }
     }
 
     /**
      * Pretty-print the given object as a YAML string.
      */
     public String prettyString(Object config) {
-        ObjectMapper prettyPrintMapper = YAML_MAPPER.copy();
+        ObjectMapper prettyPrintMapper = yamlMapper.copy();
         // pretty print
         prettyPrintMapper.enable(SerializationFeature.INDENT_OUTPUT);
         // make ConfigRadar the root element

radar-commons-server/src/main/java/org/radarbase/stream/collector/AggregateListCollector.java

@@ -21,6 +21,7 @@
 import java.util.Collections;
 import java.util.List;
 import org.apache.avro.Schema;
+import org.apache.avro.generic.IndexedRecord;
 import org.apache.avro.specific.SpecificRecord;
 import org.radarbase.util.SpecificAvroConvertible;
 
@@ -52,7 +53,7 @@ public AggregateListCollector(String[] fieldNames, Schema schema, boolean useRes
     }
 
     @Override
-    public AggregateListCollector add(SpecificRecord record) {
+    public AggregateListCollector add(IndexedRecord record) {
         for (NumericAggregateCollector collector : collectors) {
             collector.add(record);
         }

radar-commons-server/src/main/java/org/radarbase/stream/collector/NumericAggregateCollector.java

@@ -26,6 +26,7 @@
 import org.apache.avro.Schema;
 import org.apache.avro.Schema.Field;
 import org.apache.avro.Schema.Type;
+import org.apache.avro.generic.IndexedRecord;
 import org.apache.avro.specific.SpecificRecord;
 import org.radarbase.util.SpecificAvroConvertible;
 
@@ -105,7 +106,7 @@ private static Type getType(Field field) {
     }
 
     @Override
-    public NumericAggregateCollector add(SpecificRecord record) {
+    public NumericAggregateCollector add(IndexedRecord record) {
         if (pos == -1) {
             throw new IllegalStateException(
                     "Cannot add record without specifying a schema in the constructor.");

radar-commons-server/src/main/java/org/radarbase/stream/collector/RecordCollector.java

@@ -1,12 +1,12 @@
 package org.radarbase.stream.collector;
 
-import org.apache.avro.specific.SpecificRecord;
+import org.apache.avro.generic.IndexedRecord;
 
 public interface RecordCollector {
     /**
      * Add a sample to the collection.
      * @param record new sample that has to be analysed
      * @throws IllegalStateException if this collector was constructed without a schema.
      */
-    RecordCollector add(SpecificRecord record);
+    RecordCollector add(IndexedRecord record);
 }