Merge pull request #173 from RADAR-base/release-0.5.1

Release 0.5.1

commons/active/opensmile/open_smile_2_audio_analysis.avsc

@@ -2,7 +2,7 @@
   "namespace": "org.radarcns.active.opensmile",
   "type": "record",
   "name": "OpenSmile2AudioAnalysis",
-  "doc": "Audio data collected by aRMT app and processed using openSMILE.",
+  "doc": "NOTE: THIS SCHEMA IS DEPRACATED. PLEASE USE org.radarcns.active.questionnaire.Questionnaire. Audio data collected by aRMT app and processed using openSMILE.",
   "fields": [
     {"name": "time", "type": "double", "doc": "Device timestamp in UTC (s)."},
     { "name": "timeCompleted", "type": "double", "doc": "Timestamp in UTC (s) when subject completed the audio questionnaire." },

commons/active/opensmile/open_smile_2_audio_recording.avsc

@@ -2,7 +2,7 @@
   "namespace": "org.radarcns.active.opensmile",
   "name": "OpenSmile2AudioRecording",
   "type": "record",
-  "doc": "Audio recording part of the RADAR aRMT app.",
+  "doc": "NOTE: THIS SCHEMA IS DEPRACATED. PLEASE USE org.radarcns.active.questionnaire.Questionnaire. Audio recording part of the RADAR aRMT app.",
   "fields": [
     { "name": "time", "type": "double", "doc": "Device timestamp when the audio recording was started (s since the Unix Epoch)." },
     { "name": "timeCompleted", "type": "double", "doc": "Device timestamp when the audio recording was completed (s since the Unix Epoch)." },

java-sdk/build.gradle

@@ -4,8 +4,8 @@
 
 plugins {
     id 'com.commercehub.gradle.plugin.avro-base' version '0.16.0'
-    id 'com.jfrog.bintray' version '1.8.4'
-    id 'com.jfrog.artifactory' version '4.9.1'
+    id 'com.jfrog.bintray' version '1.8.4' apply false
+    id 'com.jfrog.artifactory' version '4.9.5' apply false
 }
 
 subprojects {
@@ -17,7 +17,7 @@ subprojects {
     apply plugin: 'idea'
 
     // Configuration
-    version = '0.5.0'
+    version = '0.5.1'
     group = 'org.radarcns'
     ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 
@@ -27,6 +27,9 @@ subprojects {
     ext.issueUrl = "https://github.com/${githubRepoName}/issues"
     ext.website = 'http://radar-cns.org'
 
+    targetCompatibility = '1.8'
+    sourceCompatibility = '1.8'
+
     // dependencies
 
     dependencies {
@@ -125,5 +128,5 @@ subprojects {
 }
 
 wrapper {
-    gradleVersion '5.2.1'
+    gradleVersion '5.4'
 }

java-sdk/gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-5.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

java-sdk/gradlew

@@ -1,5 +1,21 @@
 #!/usr/bin/env sh
 
+#
+# Copyright 2015 the original author or authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 ##############################################################################
 ##
 ##  Gradle start up script for UN*X
@@ -28,7 +44,7 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m"'
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"

java-sdk/gradlew.bat

@@ -1,3 +1,19 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      http://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
 @if "%DEBUG%" == "" @echo off
 @rem ##########################################################################
 @rem
@@ -14,7 +30,7 @@ set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
 @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"
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome

java-sdk/radar-schemas-commons/build.gradle

@@ -1,8 +1,5 @@
 apply plugin: 'com.jfrog.artifactory'
 
-targetCompatibility = '1.7'
-sourceCompatibility = '1.7'
-
 ext.artifactName = 'radar-schemas-commons'
 ext.description = 'RADAR Schemas Commons SDK'
 

java-sdk/radar-schemas-tools/build.gradle

@@ -31,31 +31,33 @@ ext {
     description = 'RADAR Schemas specification and validation tools.'
 
     argparseVersion = '0.8.1'
-    jacksonVersion = '2.9.8'
+    jacksonVersion = '2.9.9'
     jerseyVersion = '2.28'
-    jettyVersion = '9.4.15.v20190215'
+    jettyVersion = '9.4.17.v20190418'
     junitVersion = '4.12'
-    confluentVersion = '5.1.2'
-    kafkaVersion = '2.1.1'
-    okHttpVersion = '3.13.1'
-    radarCommonsVersion = '0.12.0-SNAPSHOT'
+    confluentVersion = '5.2.1'
+    kafkaVersion = '2.2.0-cp2'
+    okHttpVersion = '3.14.1'
+    radarCommonsVersion = '0.12.1'
     slf4jVersion = '1.7.26'
 }
 
 repositories {
     jcenter()
     maven { url 'http://packages.confluent.io/maven/' }
+    maven { url  "https://dl.bintray.com/radar-base/org.radarbase" }
     maven { url 'https://oss.jfrog.org/artifactory/oss-snapshot-local' }
 }
 
 dependencies {
     api group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: jacksonVersion
     api group: 'javax.validation', name: 'validation-api', version: '2.0.0.Final'
     api group: 'org.apache.kafka', name: 'kafka_2.12', version: kafkaVersion
+
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: jacksonVersion
     implementation project(':radar-schemas-commons')
-    implementation group: 'org.radarcns', name: 'radar-commons', version: radarCommonsVersion
-    implementation group: 'org.radarcns', name: 'radar-commons-server', version: radarCommonsVersion
+    implementation group: 'org.radarbase', name: 'radar-commons', version: radarCommonsVersion
+    implementation group: 'org.radarbase', name: 'radar-commons-server', version: radarCommonsVersion
     implementation group: 'net.sourceforge.argparse4j', name: 'argparse4j', version: argparseVersion
     implementation group: 'com.squareup.okhttp3', name: 'okhttp', version: okHttpVersion
     implementation group: 'org.eclipse.jetty', name: 'jetty-server', version: jettyVersion

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/registration/SchemaRegistry.java

@@ -34,15 +34,15 @@
 import okhttp3.ResponseBody;
 import okio.BufferedSink;
 import org.apache.avro.Schema;
-import org.radarcns.config.ServerConfig;
-import org.radarcns.producer.rest.ParsedSchemaMetadata;
-import org.radarcns.producer.rest.RestClient;
-import org.radarcns.producer.rest.SchemaRetriever;
+import org.radarbase.config.ServerConfig;
+import org.radarbase.producer.rest.ParsedSchemaMetadata;
+import org.radarbase.producer.rest.RestClient;
+import org.radarbase.producer.rest.SchemaRetriever;
 import org.radarcns.schema.CommandLineApp;
 import org.radarcns.schema.specification.DataProducer;
 import org.radarcns.schema.specification.SourceCatalogue;
 import org.radarcns.schema.util.SubCommand;
-import org.radarcns.topic.AvroTopic;
+import org.radarbase.topic.AvroTopic;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/specification/DataProducer.java

@@ -10,7 +10,7 @@
 import javax.validation.constraints.NotBlank;
 import javax.validation.constraints.NotNull;
 import org.radarcns.schema.Scope;
-import org.radarcns.topic.AvroTopic;
+import org.radarbase.topic.AvroTopic;
 
 /**
  * A producer of data to Kafka, generally mapping to a source.

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/specification/DataTopic.java

@@ -15,9 +15,9 @@
 import java.util.Map;
 import java.util.stream.Stream;
 import org.radarcns.catalogue.Unit;
-import org.radarcns.config.AvroTopicConfig;
+import org.radarbase.config.AvroTopicConfig;
 import org.radarcns.kafka.ObservationKey;
-import org.radarcns.topic.AvroTopic;
+import org.radarbase.topic.AvroTopic;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/specification/SourceCatalogue.java

@@ -39,7 +39,7 @@
 import org.radarcns.schema.specification.monitor.MonitorSource;
 import org.radarcns.schema.specification.passive.PassiveSource;
 import org.radarcns.schema.specification.stream.StreamGroup;
-import org.radarcns.topic.AvroTopic;
+import org.radarbase.topic.AvroTopic;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/specification/stream/StreamDataTopic.java

@@ -10,12 +10,12 @@
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Stream;
-import org.radarcns.config.AvroTopicConfig;
+import org.radarbase.config.AvroTopicConfig;
 import org.radarcns.kafka.AggregateKey;
 import org.radarcns.kafka.ObservationKey;
 import org.radarcns.schema.specification.DataTopic;
 import org.radarcns.stream.TimeWindowMetadata;
-import org.radarcns.topic.AvroTopic;
+import org.radarbase.topic.AvroTopic;
 
 /**
  * Topic used for Kafka Streams.

specifications/active/aRMT-1.4.3.yml

@@ -0,0 +1,63 @@
+name: aRMT
+vendor: RADAR
+model: aRMT-App
+version: 1.4.3
+assessment_type: QUESTIONNAIRE
+doc: aRMT Questionnaires definition. Includes Personal Health Questionnaire Depression Scale (PHQ-8), Experience sampling method (ESM) and RSES and other data.
+data:
+  - type: THINC_IT
+    topic: notification_thinc_it
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/thinc_it/thinc_it_armt.json
+  - type: ROMBERG_TEST
+    doc: The value of the task is in milliseconds (ms).
+    topic: task_romberg_test
+    value_schema: .active.task.Task
+    questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/romberg_test/romberg_test_armt.json
+  - type: 2MW_TEST
+    doc: The value of the task is in milliseconds (ms).
+    topic: task_2MW_test
+    value_schema: .active.task.Task
+    questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/2MW_test/2MW_test_armt.json
+  - type: TANDEM_WALKING_TEST
+    doc: The value of the task is in milliseconds (ms).
+    topic: task_tandem_walking_test
+    value_schema: .active.task.Task
+    questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/tandem_walking_test/tandem_walking_test_armt.json
+  - type: PHQ8
+    topic: questionnaire_phq8
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/phq8/phq8_armt.json
+  - type: ESM
+    topic: questionnaire_esm
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/esm/esm_armt.json
+  - type: AUDIO
+    topic: questionnaire_audio
+    value_schema: .active.questionnaire.Questionnaire
+  - type: AUDIO_2
+    topic: questionnaire_audio
+    value_schema: .active.questionnaire.Questionnaire
+  - type: AUDIO_3
+    topic: questionnaire_audio
+    value_schema: .active.questionnaire.Questionnaire
+  - type: RSES
+    topic: questionnaire_rses
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/rses/rses_armt.json
+  - type: PERCEIVED_DEFICITS_QUESTIONNAIRE
+    topic: questionnaire_perceived_deficits_questionnaire
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/perceived_deficits_questionnaire/perceived_deficits_questionnaire_armt.json
+  - type: PATIENT_DETERMINED_DISEASE_STEP
+    topic: questionnaire_patient_determined_disease_step
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/patient_determined_disease_step/patient_determined_disease_step_armt.json
+  - type: COMPLETION_LOG
+    doc: Information about the completeness of each questionnaire.
+    topic: questionnaire_completion_log
+    value_schema: .monitor.questionnaire.QuestionnaireCompletionLog
+  - type: TIMEZONE
+    doc: Timezone information sent along with each questionnaire.
+    topic: questionnaire_timezone
+    value_schema: .monitor.application.ApplicationTimeZone