Merge pull request #83 from RADAR-base/release-0.13.2

Release 0.13.2
RADAR-base · Apr 15, 2021 · 6b9755e · 6b9755e
2 parents 53a8bec + 0d852d8
commit 6b9755e
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Showing 11 changed files with 72 additions and 44 deletions.
diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@ repositories {
 }
 
 dependencies {
-    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.13.1'
+    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.13.2'
 }
 ```
 
@@ -69,7 +69,7 @@ repositories {
 }
 
 dependencies {
-    implementation group: 'org.radarbase', name: 'radar-commons-server', version: '0.13.1'
+    implementation group: 'org.radarbase', name: 'radar-commons-server', version: '0.13.2'
 }
 ```
 
@@ -82,7 +82,7 @@ repositories {
 }
 
 dependencies {
-    testImplementation group: 'org.radarbase', name: 'radar-commons-testing', version: '0.13.1'
+    testImplementation group: 'org.radarbase', name: 'radar-commons-testing', version: '0.13.2'
 }
 ```
 
@@ -94,7 +94,7 @@ repositories {
 }
 
 dependencies {
-    runtimeOnly group: 'org.radarbase', name: 'radar-commons-unsafe', version: '0.13.1'
+    runtimeOnly group: 'org.radarbase', name: 'radar-commons-unsafe', version: '0.13.2'
 }
 ```
 
@@ -119,7 +119,7 @@ configurations.all {
 }
 
 dependencies {
-    compile group: 'org.radarbase', name: 'radar-commons', version: '0.13.2-SNAPSHOT'
+    compile group: 'org.radarbase', name: 'radar-commons', version: '0.13.3-SNAPSHOT'
 }
 ```
 

diff --git a/build.gradle b/build.gradle
@@ -15,35 +15,38 @@
  */
 plugins {
     id 'com.commercehub.gradle.plugin.avro' version '0.19.1'
+    id("io.github.gradle-nexus.publish-plugin") version "1.0.0"
+    id("com.github.ben-manes.versions") version "0.38.0"
 }
 
 subprojects {
     // Apply the plugins
     apply plugin: 'java'
     apply plugin: 'java-library'
     apply plugin: 'idea'
+    apply plugin: 'com.github.ben-manes.versions'
 
     //---------------------------------------------------------------------------//
     // Configuration                                                             //
     //---------------------------------------------------------------------------//
 
-    version = '0.13.1'
+    version = '0.13.2'
     group = 'org.radarbase'
     ext.githubRepoName = 'RADAR-base/radar-commons'
 
     ext.slf4jVersion = '1.7.30'
-    ext.kafkaVersion = '2.7.0'
+    ext.kafkaVersion = '6.1.1-ce'
     ext.avroVersion = '1.9.2'
-    ext.confluentVersion = '5.5.3'
-    ext.jacksonVersion = '2.12.1'
-    ext.jacksonYamlVersion = '2.12.1'
+    ext.confluentVersion = '6.1.1'
+    ext.jacksonVersion = '2.12.3'
+    ext.jacksonYamlVersion = '2.12.3'
     ext.okhttpVersion = '4.9.1'
     ext.junitVersion = '4.13.2'
-    ext.mockitoVersion = '3.7.7'
+    ext.mockitoVersion = '3.9.0'
     ext.hamcrestVersion = '1.3'
-    ext.codacyVersion = '7.9.0'
-    ext.radarSchemasVersion = '0.5.15'
-    ext.orgJsonVersion = '20201115'
+    ext.codacyVersion = '11.15.0'
+    ext.radarSchemasVersion = '0.6.0'
+    ext.orgJsonVersion = '20210307'
 
     ext.githubUrl = "https://github.com/$githubRepoName"
     ext.issueUrl = "https://github.com/$githubRepoName/issues"
@@ -53,9 +56,8 @@ subprojects {
     // Dependencies                                                              //
     //---------------------------------------------------------------------------//
     repositories {
-        jcenter()
+        mavenCentral()
         maven { url 'https://packages.confluent.io/maven/' }
-        maven { url 'https://dl.bintray.com/typesafe/maven-releases' }
         flatDir {
             dirs "${project.rootDir}/libs"
         }
@@ -108,6 +110,15 @@ subprojects {
     }
 }
 
+nexusPublishing {
+    repositories {
+        sonatype {
+            username = project.hasProperty("ossrh.user") ? project.property("ossrh.user") : System.getenv("OSSRH_USER")
+            password = project.hasProperty("ossrh.password") ? project.property("ossrh.password") : System.getenv("OSSRH_PASSWORD")
+        }
+    }
+}
+
 wrapper {
-    gradleVersion '6.8.3'
+    gradleVersion '7.0'
 }
diff --git a/gradle/publishing.gradle b/gradle/publishing.gradle
@@ -72,20 +72,6 @@ publishing {
             }
         }
     }
-
-    repositories {
-        maven {
-            name = "OSSRH"
-            credentials {
-                username = project.hasProperty("ossrh.user") ? project.property("ossrh.user") : System.getenv("OSSRH_USER")
-                password = project.hasProperty("ossrh.password") ? project.property("ossrh.password") : System.getenv("OSSRH_PASSWORD")
-            }
-
-            def releasesRepoUrl = uri("https://oss.sonatype.org/service/local/staging/deploy/maven2/")
-            def snapshotsRepoUrl = uri("https://oss.sonatype.org/content/repositories/snapshots/")
-            url = version.toString().endsWith("SNAPSHOT") ? snapshotsRepoUrl : releasesRepoUrl
-        }
-    }
 }
 
 signing {

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.8.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.0-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/radar-commons-server/build.gradle b/radar-commons-server/build.gradle
@@ -40,7 +40,7 @@ dependencies {
     testImplementation group: 'org.mockito', name: 'mockito-core', version: mockitoVersion
     // Direct producer uses KafkaAvroSerializer if initialized
     testImplementation group: 'io.confluent', name: 'kafka-avro-serializer', version: confluentVersion
-    testImplementation group: 'org.radarcns', name: 'radar-schemas-commons', version: radarSchemasVersion
+    testImplementation group: 'org.radarbase', name: 'radar-schemas-commons', version: radarSchemasVersion
     // Direct producer uses KafkaAvroSerializer if initialized
     testImplementation group: 'junit', name: 'junit', version: junitVersion
     testRuntimeOnly group: 'org.slf4j', name: 'slf4j-simple', version: slf4jVersion

diff --git a/radar-commons-testing/build.gradle b/radar-commons-testing/build.gradle
@@ -44,9 +44,9 @@ dependencies {
     api project(':radar-commons')
     api project(':radar-commons-server')
     api group: 'org.apache.avro', name: 'avro', version: avroVersion
-    api group: 'org.radarcns', name: 'radar-schemas-commons', version: radarSchemasVersion
+    api group: 'org.radarbase', name: 'radar-schemas-commons', version: radarSchemasVersion
 
-    implementation group: 'com.opencsv', name: 'opencsv', version: '5.3'
+    implementation group: 'com.opencsv', name: 'opencsv', version: '5.4'
     implementation group: 'com.fasterxml.jackson.core' , name: 'jackson-databind' , version: jacksonVersion
     implementation group: 'org.apache.kafka', name: 'kafka-clients', version: kafkaVersion
     implementation (group: 'io.confluent', name: 'kafka-avro-serializer', version: confluentVersion) {

diff --git a/radar-commons-testing/src/main/java/org/radarbase/mock/data/MockCsvParser.java b/radar-commons-testing/src/main/java/org/radarbase/mock/data/MockCsvParser.java
@@ -22,9 +22,12 @@
 import java.io.Closeable;
 import java.io.IOException;
 import java.lang.reflect.Method;
+import java.nio.ByteBuffer;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Base64;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -59,7 +62,6 @@ public class MockCsvParser<K extends SpecificRecord> implements Closeable {
      */
     public MockCsvParser(MockDataConfig config, Path root)
             throws IOException, CsvValidationException {
-        //noinspection unchecked
         topic = config.parseAvroTopic();
 
         bufferedReader = Files.newBufferedReader(config.getDataFile(root));
@@ -72,7 +74,7 @@ public MockCsvParser(MockDataConfig config, Path root)
         currentLine = csvReader.readNext();
     }
 
-    public AvroTopic getTopic() {
+    public AvroTopic<K, SpecificRecord> getTopic() {
         return topic;
     }
 
@@ -111,15 +113,21 @@ private <V extends SpecificRecord> V parseRecord(String[] rawValues,
         V record = (V) SpecificData.newInstance(recordClass, schema);
 
         for (Field field : schema.getFields()) {
-            String fieldString = rawValues[header.get(field.name())];
+            Integer fieldHeader = header.get(field.name());
+            if (fieldHeader == null) {
+                throw new IllegalArgumentException(
+                        "Cannot map record field " + field.name()
+                                + ": no corresponding header in " + header.keySet());
+            }
+            String fieldString = rawValues[fieldHeader];
             Object fieldValue = parseValue(field.schema(), fieldString);
             record.put(field.pos(), fieldValue);
         }
 
         return record;
     }
 
-    private static Object parseValue(Schema schema, String fieldString) {
+    public static Object parseValue(Schema schema, String fieldString) {
         switch (schema.getType()) {
             case INT:
                 return Integer.parseInt(fieldString);
@@ -139,12 +147,20 @@ private static Object parseValue(Schema schema, String fieldString) {
                 return parseUnion(schema, fieldString);
             case ENUM:
                 return parseEnum(schema, fieldString);
+            case BYTES:
+                return parseBytes(fieldString);
             default:
                 throw new IllegalArgumentException("Cannot handle schemas of type "
                         + schema.getType());
         }
     }
 
+    private static ByteBuffer parseBytes(String fieldString) {
+        byte[] result = Base64.getDecoder()
+                .decode(fieldString.getBytes(StandardCharsets.UTF_8));
+        return ByteBuffer.wrap(result);
+    }
+
     private static Object parseUnion(Schema schema, String fieldString) {
         if (schema.getTypes().size() != 2) {
             throw new IllegalArgumentException(

diff --git a/radar-commons-testing/src/test/java/org/radarbase/mock/data/MockCsvParserTest.java b/radar-commons-testing/src/test/java/org/radarbase/mock/data/MockCsvParserTest.java
@@ -0,0 +1,16 @@
+package org.radarbase.mock.data;
+
+import static org.junit.Assert.assertArrayEquals;
+
+import java.nio.ByteBuffer;
+import org.apache.avro.Schema;
+import org.junit.Test;
+
+public class MockCsvParserTest {
+    @Test
+    public void parseValue() {
+        Schema schema = new Schema.Parser().parse("{\"type\":\"bytes\"}");
+        ByteBuffer buffer = (ByteBuffer) MockCsvParser.parseValue(schema, "ab");
+        assertArrayEquals(new byte[] { 105 }, buffer.array());
+    }
+}
diff --git a/radar-commons-testing/src/test/java/org/radarbase/mock/data/MockRecordValidatorTest.java b/radar-commons-testing/src/test/java/org/radarbase/mock/data/MockRecordValidatorTest.java
@@ -152,7 +152,7 @@ public void validateMissingKeyField() throws Exception {
             writer.append("test,a,1,2,1\n");
         }
 
-        assertValidateThrows(NullPointerException.class, config);
+        assertValidateThrows(IllegalArgumentException.class, config);
     }
 
     @Test
@@ -165,7 +165,7 @@ public void validateMissingValueField() throws Exception {
             writer.append("test,a,b,1,2\n");
         }
 
-        assertValidateThrows(NullPointerException.class, config);
+        assertValidateThrows(IllegalArgumentException.class, config);
     }
 
     @Test

diff --git a/radar-commons-unsafe/build.gradle b/radar-commons-unsafe/build.gradle
@@ -7,14 +7,13 @@ sourceCompatibility = '1.8'
 // Sources and classpath configurations                                      //
 //---------------------------------------------------------------------------//
 
-configurations.compile {
+configurations.implementation {
     resolutionStrategy.cacheChangingModulesFor 0, 'SECONDS'
 }
 
 // In this section you declare where to find the dependencies of your project
 repositories {
     maven { url 'https://jitpack.io' }
-    maven { url 'https://oss.jfrog.org/artifactory/oss-snapshot-local' }
 }
 
 // In this section you declare the dependencies for your production and test code

diff --git a/radar-commons/build.gradle b/radar-commons/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     implementation group: 'org.slf4j', name:'slf4j-api', version: slf4jVersion
 
     testImplementation group: 'com.fasterxml.jackson.core' , name: 'jackson-databind' , version: jacksonVersion
-    testImplementation group: 'org.radarcns', name: 'radar-schemas-commons', version: radarSchemasVersion
+    testImplementation group: 'org.radarbase', name: 'radar-schemas-commons', version: radarSchemasVersion
     testImplementation group: 'junit', name: 'junit', version: junitVersion
     testImplementation group: 'org.mockito', name: 'mockito-core', version: mockitoVersion
     testImplementation group: 'com.squareup.okhttp3', name: 'mockwebserver', version: okhttpVersion