Merge pull request #75 from RADAR-base/release-0.12.3

Release 0.12.3

README.md

@@ -14,7 +14,7 @@ repositories {
 }
 
 dependencies {
-    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.12.1'
+    implementation group: 'org.radarbase', name: 'radar-commons', version: '0.12.3'
 }
 ```
 
@@ -65,11 +65,11 @@ For server utilities, include `radar-commons-server`:
 ```gradle
 repositories {
     jcenter()
-    maven { url 'http://packages.confluent.io/maven/' }
+    maven { url 'https://packages.confluent.io/maven/' }
 }
 
 dependencies {
-    implementation group: 'org.radarbase', name: 'radar-commons-server', version: '0.12.1'
+    implementation group: 'org.radarbase', name: 'radar-commons-server', version: '0.12.3'
 }
 ```
 
@@ -78,25 +78,25 @@ For mocking clients of the RADAR-base infrastructure, use that 'radar-commons-te
 ```gradle
 repositories {
     jcenter()
-    maven { url 'http://packages.confluent.io/maven/' }
-    maven { url  'http://dl.bintray.com/radar-base/org.radarbase' }
+    maven { url 'https://packages.confluent.io/maven/' }
+    maven { url  'https://dl.bintray.com/radar-base/org.radarbase' }
 }
 
 dependencies {
-    testImplementation group: 'org.radarbase', name: 'radar-commons-testing', version: '0.12.1'
+    testImplementation group: 'org.radarbase', name: 'radar-commons-testing', version: '0.12.3'
 }
 ```
 
 Finally, if the schema registry is losing old schemas and your code is not recovering, include `radar-commons-unsafe`. Ensure that it comes in the classpath before any Confluent code. This will override the Confluent Avro deserializer to recover from failure when a message with unknown schema ID is passed.
 ```gradle
 repositories {
     jcenter()
-    maven { url 'http://packages.confluent.io/maven/' }
-    maven { url  'http://dl.bintray.com/radar-base/org.radarbase' }
+    maven { url 'https://packages.confluent.io/maven/' }
+    maven { url  'https://dl.bintray.com/radar-base/org.radarbase' }
 }
 
 dependencies {
-    runtimeOnly group: 'org.radarbase', name: 'radar-commons-unsafe', version: '0.12.1'
+    runtimeOnly group: 'org.radarbase', name: 'radar-commons-unsafe', version: '0.12.3'
 }
 ```
 
@@ -121,7 +121,7 @@ configurations.all {
 }
 
 dependencies {
-    compile group: 'org.radarbase', name: 'radar-commons', version: '0.12.2-SNAPSHOT'
+    compile group: 'org.radarbase', name: 'radar-commons', version: '0.12.4-SNAPSHOT'
 }
 ```
 

build.gradle

@@ -15,8 +15,8 @@
  */
 plugins {
     // Get bintray version
-    id 'com.jfrog.bintray' version '1.8.4' apply false
-    id 'com.commercehub.gradle.plugin.avro' version '0.16.0'
+    id 'com.jfrog.bintray' version '1.8.5' apply false
+    id 'com.commercehub.gradle.plugin.avro' version '0.19.1'
 }
 
 subprojects {
@@ -29,35 +29,35 @@ subprojects {
     // Configuration                                                             //
     //---------------------------------------------------------------------------//
 
-    version = '0.12.2'
+    version = '0.12.3'
     group = 'org.radarbase'
     ext.githubRepoName = 'RADAR-base/radar-commons'
 
-    ext.slf4jVersion = '1.7.26'
-    ext.kafkaVersion = '2.3.0'
-    ext.avroVersion = '1.8.2'
-    ext.confluentVersion = '5.3.0'
-    ext.jacksonVersion = '2.9.9.1'
-    ext.jacksonYamlVersion = '2.9.9'
-    ext.okhttpVersion = '4.0.1'
-    ext.junitVersion = '4.12'
-    ext.mockitoVersion = '2.28.2'
+    ext.slf4jVersion = '1.7.30'
+    ext.kafkaVersion = '2.5.0'
+    ext.avroVersion = '1.9.2'
+    ext.confluentVersion = '5.5.0'
+    ext.jacksonVersion = '2.11.0'
+    ext.jacksonYamlVersion = '2.11.0'
+    ext.okhttpVersion = '4.7.2'
+    ext.junitVersion = '4.13'
+    ext.mockitoVersion = '3.3.3'
     ext.hamcrestVersion = '1.3'
-    ext.codacyVersion = '6.0.0'
-    ext.radarSchemasVersion = '0.5.1'
-    ext.orgJsonVersion = '20180813'
+    ext.codacyVersion = '7.9.0'
+    ext.radarSchemasVersion = '0.5.9'
+    ext.orgJsonVersion = '20200518'
 
     ext.githubUrl = "https://github.com/$githubRepoName"
     ext.issueUrl = "https://github.com/$githubRepoName/issues"
-    ext.website = 'http://radar-base.org'
+    ext.website = 'https://radar-base.org'
 
     //---------------------------------------------------------------------------//
     // Dependencies                                                              //
     //---------------------------------------------------------------------------//
     repositories {
         jcenter()
-        maven { url 'http://packages.confluent.io/maven/' }
-        maven { url 'http://dl.bintray.com/typesafe/maven-releases' }
+        maven { url 'https://packages.confluent.io/maven/' }
+        maven { url 'https://dl.bintray.com/typesafe/maven-releases' }
         flatDir {
             dirs "${project.rootDir}/libs"
         }
@@ -111,5 +111,5 @@ subprojects {
 }
 
 wrapper {
-    gradleVersion '5.5.1'
+    gradleVersion '6.3'
 }

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.5.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -125,8 +125,8 @@ if $darwin; then
     GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
     JAVACMD=`cygpath --unix "$JAVACMD"`
@@ -154,19 +154,19 @@ if $cygwin ; then
         else
             eval `echo args$i`="\"$arg\""
         fi
-        i=$((i+1))
+        i=`expr $i + 1`
     done
     case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
     esac
 fi
 
@@ -175,14 +175,9 @@ save () {
     for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
     echo " "
 }
-APP_ARGS=$(save "$@")
+APP_ARGS=`save "$@"`
 
 # Collect all arguments for the java command, following the shell quoting and substitution rules
 eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
-
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -29,6 +29,9 @@ if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 

radar-commons-server/build.gradle

@@ -43,7 +43,7 @@ dependencies {
     testImplementation group: 'org.radarcns', name: 'radar-schemas-commons', version: radarSchemasVersion
     // Direct producer uses KafkaAvroSerializer if initialized
     testImplementation group: 'junit', name: 'junit', version: junitVersion
-    testRuntime group: 'org.slf4j', name: 'slf4j-simple', version: slf4jVersion
+    testRuntimeOnly group: 'org.slf4j', name: 'slf4j-simple', version: slf4jVersion
 }
 
 apply from: '../gradle/publishing.gradle'

radar-commons-testing/build.gradle

@@ -46,7 +46,7 @@ dependencies {
     api group: 'org.apache.avro', name: 'avro', version: avroVersion
     api group: 'org.radarcns', name: 'radar-schemas-commons', version: radarSchemasVersion
 
-    implementation group: 'com.opencsv', name: 'opencsv', version: '4.6'
+    implementation group: 'com.opencsv', name: 'opencsv', version: '5.2'
     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) {

radar-commons-testing/src/main/java/org/radarbase/mock/MockFileSender.java

@@ -16,6 +16,7 @@
 
 package org.radarbase.mock;
 
+import com.opencsv.exceptions.CsvValidationException;
 import java.io.IOException;
 import org.apache.avro.SchemaValidationException;
 import org.radarbase.data.Record;
@@ -50,6 +51,8 @@ public void send() throws IOException {
             }
         } catch (SchemaValidationException e) {
             throw new IOException("Failed to match schemas", e);
+        } catch (CsvValidationException e) {
+            throw new IOException("Failed to read CSV file", e);
         }
     }
 }

radar-commons-testing/src/main/java/org/radarbase/mock/MockProducer.java

@@ -16,11 +16,12 @@
 
 package org.radarbase.mock;
 
-import static io.confluent.kafka.serializers.AbstractKafkaAvroSerDeConfig.SCHEMA_REGISTRY_URL_CONFIG;
+import static io.confluent.kafka.serializers.AbstractKafkaSchemaSerDeConfig.SCHEMA_REGISTRY_URL_CONFIG;
 import static org.apache.kafka.clients.producer.ProducerConfig.BOOTSTRAP_SERVERS_CONFIG;
 import static org.apache.kafka.clients.producer.ProducerConfig.KEY_SERIALIZER_CLASS_CONFIG;
 import static org.apache.kafka.clients.producer.ProducerConfig.VALUE_SERIALIZER_CLASS_CONFIG;
 
+import com.opencsv.exceptions.CsvValidationException;
 import io.confluent.kafka.serializers.KafkaAvroSerializer;
 import java.io.IOException;
 import java.nio.file.Path;
@@ -59,7 +60,7 @@
  * A Mock Producer class that can be used to stream data. It can use MockFileSender and MockDevice
  * for testing purposes, with direct or indirect streaming.
  */
-@SuppressWarnings("PMD.DoNotCallSystemExit")
+@SuppressWarnings("PMD")
 public class MockProducer {
 
     private static final Logger logger = LoggerFactory.getLogger(MockProducer.class);
@@ -120,6 +121,13 @@ public MockProducer(BasicMockConfig mockConfig, Path root) throws IOException {
             for (int i = 0; i < mockFiles.size(); i++) {
                 files.add(new MockFileSender(tmpSenders.get(i + numDevices), mockFiles.get(i)));
             }
+        } catch (CsvValidationException ex) {
+            if (tmpSenders != null) {
+                for (KafkaSender sender : tmpSenders) {
+                    sender.close();
+                }
+            }
+            throw new IOException("Cannot read CSV file", ex);
         } catch (Exception ex) {
             if (tmpSenders != null) {
                 for (KafkaSender sender : tmpSenders) {
@@ -185,7 +193,7 @@ private List<KafkaSender> createRestSenders(int numDevices,
 
     /** Start sending data. */
     public void start() throws IOException {
-        for (MockDevice device : devices) {
+        for (MockDevice<?> device : devices) {
             device.start();
         }
         for (MockFileSender file : files) {
@@ -197,11 +205,11 @@ public void start() throws IOException {
     public void shutdown() throws IOException, InterruptedException, SchemaValidationException {
         if (!devices.isEmpty()) {
             logger.info("Shutting down mock devices");
-            for (MockDevice device : devices) {
+            for (MockDevice<?> device : devices) {
                 device.shutdown();
             }
             logger.info("Waiting for mock devices to finish...");
-            for (MockDevice device : devices) {
+            for (MockDevice<?> device : devices) {
                 device.join(5_000L);
             }
         }
@@ -210,7 +218,7 @@ public void shutdown() throws IOException, InterruptedException, SchemaValidatio
             sender.close();
         }
 
-        for (MockDevice device : devices) {
+        for (MockDevice<?> device : devices) {
             device.checkException();
         }
     }
@@ -345,7 +353,7 @@ private List<RecordGenerator<ObservationKey>> createGenerators(List<MockDataConf
     }
 
     private List<MockCsvParser<ObservationKey>> createMockFiles(List<MockDataConfig> configs,
-            Path dataRoot) throws IOException {
+            Path dataRoot) throws IOException, CsvValidationException {
 
         List<MockCsvParser<ObservationKey>> result = new ArrayList<>(configs.size());
 

radar-commons-testing/src/main/java/org/radarbase/mock/data/MockCsvParser.java

@@ -17,6 +17,7 @@
 package org.radarbase.mock.data;
 
 import com.opencsv.CSVReader;
+import com.opencsv.exceptions.CsvValidationException;
 import java.io.BufferedReader;
 import java.io.Closeable;
 import java.io.IOException;
@@ -55,7 +56,8 @@ public class MockCsvParser<K extends SpecificRecord> implements Closeable {
      * @param root parent directory of the data file.
      * @throws IllegalArgumentException if the second row has the wrong number of columns
      */
-    public MockCsvParser(MockDataConfig config, Path root) throws IOException {
+    public MockCsvParser(MockDataConfig config, Path root)
+            throws IOException, CsvValidationException {
         //noinspection unchecked
         topic = config.parseAvroTopic();
 
@@ -80,7 +82,7 @@ public AvroTopic getTopic() {
      * @throws IllegalStateException if a next row is not available
      * @throws IOException if the next row could not be read
      */
-    public Record<K, SpecificRecord> next() throws IOException {
+    public Record<K, SpecificRecord> next() throws IOException, CsvValidationException {
         if (!hasNext()) {
             throw new IllegalStateException("No next record available");
         }

radar-commons-testing/src/main/java/org/radarbase/mock/data/MockRecordValidator.java

@@ -16,6 +16,7 @@
 
 package org.radarbase.mock.data;
 
+import com.opencsv.exceptions.CsvValidationException;
 import java.io.IOException;
 import java.nio.file.Path;
 import org.apache.avro.specific.SpecificRecord;
@@ -71,7 +72,7 @@ public void validate() {
 
             checkDuration();
             checkFrequency(line);
-        } catch (IOException e) {
+        } catch (IOException | CsvValidationException e) {
             error("Cannot open file", -1, e);
         }
     }

radar-commons-testing/src/main/java/org/radarbase/mock/model/MockAggregator.java

@@ -16,6 +16,7 @@
 
 package org.radarbase.mock.model;
 
+import com.opencsv.exceptions.CsvValidationException;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.util.HashMap;
@@ -81,9 +82,11 @@ public Map<MockDataConfig, ExpectedValue> simulate() throws IOException {
                 }
 
                 expectedValue.put(config, value);
+            } catch (CsvValidationException ex) {
+                throw new IOException(ex);
             }
         }
 
         return expectedValue;
     }
-}
+}