Merge pull request #146 from RADAR-base/release-0.4.1

Release 0.4.1
RADAR-base · Oct 30, 2018 · 9a0f7e8 · 9a0f7e8
2 parents 2d98fc7 + d5281f3
commit 9a0f7e8
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diff --git a/Dockerfile b/Dockerfile
@@ -5,9 +5,11 @@ WORKDIR /code/java-sdk
 
 COPY commons /code/commons
 COPY specifications /code/specifications
-COPY restapi /code/restapi
 COPY java-sdk/gradle /code/java-sdk/gradle
 COPY java-sdk/build.gradle java-sdk/settings.gradle  java-sdk/gradlew /code/java-sdk/
+
+ENV GRADLE_OPTS -Dorg.gradle.daemon=false
+
 RUN ./gradlew tasks
 COPY java-sdk/radar-schemas-commons/build.gradle /code/java-sdk/radar-schemas-commons/
 COPY java-sdk/radar-schemas-commons/src /code/java-sdk/radar-schemas-commons/src

diff --git a/README.md b/README.md
@@ -11,7 +11,6 @@
   - In the `monitor` subdirectory, add schemas for monitoring applications that gather data.
   - In the `passive` subdirectory, add schemas for passive data collection, like wearables.
   - In the `stream` subdirectory, add schemas used in Kafka Streams.
-- The `restapi` directory contains schemas used to get data from the RADAR-CNS REST API.
 - The `specifications` directory contains specifications of what data types are collected through which devices.
 - Java SDKs for each of the components are provided in the `java-sdk` folder, see installation instructions there. They are automatically generated from the Avro schemas using the Avro 1.8.2 specification.
 

diff --git a/commons/active/questionnaire/questionnaire.avsc b/commons/active/questionnaire/questionnaire.avsc
@@ -4,8 +4,9 @@
   "name": "Questionnaire",
   "doc": "General schema for questionnaire. Check the specification folder to see how the questionnaire has been defined. For each QuestionnaireType there is a JSON file reporting the questions set and possible answers if available.",
   "fields": [
-    { "name": "time", "type": "double", "doc": "Timestamp in UTC (s) when the questionnaire is submitted to the subject." },
-    { "name": "timeCompleted", "type": "double", "doc": "Timestamp in UTC (s) when subject marks the questionnaire as." },
+    { "name": "time", "type": "double", "doc": "Timestamp in UTC (s) when the questionnaire is started by the subject." },
+    { "name": "timeCompleted", "type": "double", "doc": "Timestamp in UTC (s) when the questionnaire is completed by the subject." },
+    { "name": "timeNotification", "type": ["null", "double"], "doc": "Timestamp in UTC (s) when the notification to complete the questionnaire is sent.", "default": null },
     { "name": "name", "type": "string", "doc": "Questionnaire names." },
     { "name": "version", "type": "string", "doc": "It reports the questionnaire version stated in the JSON specification." },
     { "name": "answers", "type": {
@@ -15,7 +16,7 @@
         "type": "record",
         "doc": "Questionnaire answer.",
          "fields": [
-           { "name": "questionId", "type": ["null", "string"], "doc": "Unique identifier for the specific question.", "default": null }, 
+           { "name": "questionId", "type": ["null", "string"], "doc": "Unique identifier for the specific question.", "default": null },
            { "name": "value", "type": ["int", "string", "double"], "doc": "Subject answer." },
            { "name": "startTime", "type": "double", "doc": "Timestamp in UTC (s) when the question is shown." },
            { "name": "endTime", "type": "double", "doc": "Timestamp in UTC (s)  when the question is answered." }

diff --git a/commons/passive/ppg/phone_camera_ppg.avsc b/commons/passive/ppg/phone_camera_ppg.avsc
@@ -0,0 +1,14 @@
+{
+    "namespace": "org.radarcns.passive.ppg",
+    "name": "PhoneCameraPpg",
+    "type": "record",
+    "doc": "PPG collected using a phone camera. This ranges over a sample of the image in a camera preview. The number of pixels in the preview image may have been determined by Android and/or the hardware vendor by downsampling from the number of pixels provided by the hardware sensor.",
+    "fields": [
+        { "name": "time", "type": "double", "doc": "Phone time since the Unix Epoch (seconds)." },
+        { "name": "timeReceived", "type": "double", "doc": "Processed time since the Unix Epoch (seconds)." },
+        { "name": "sampleSize", "type": "int", "doc": "Number of pixels that were evaluated to get the current value." },
+        { "name": "red", "type": "float", "doc": "Red component detected in a sample of the camera preview. The range is 0 (no saturation) to 1 (full saturation)." },
+        { "name": "green", "type": "float", "doc": "Green component detected in a sample of the camera preview. The range is 0 (no saturation) to 1 (full saturation)." },
+        { "name": "blue", "type": "float", "doc": "Blue component detected in a sample of the camera preview. The range is 0 (no saturation) to 1 (full saturation)." }
+    ]
+}
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -6,7 +6,7 @@ services:
   # Zookeeper Cluster                                                         #
   #---------------------------------------------------------------------------#
   zookeeper-1:
-    image: confluentinc/cp-zookeeper:3.3.0
+    image: confluentinc/cp-zookeeper:5.0.0
     environment:
       ZOOKEEPER_SERVER_ID: 1
       ZOOKEEPER_CLIENT_PORT: 2181
@@ -19,7 +19,7 @@ services:
   # Kafka Cluster                                                             #
   #---------------------------------------------------------------------------#
   kafka-1:
-    image: confluentinc/cp-kafka:3.3.0
+    image: confluentinc/cp-kafka:5.0.0
     depends_on:
       - zookeeper-1
     environment:
@@ -40,7 +40,7 @@ services:
   # Schema Registry                                                           #
   #---------------------------------------------------------------------------#
   schema-registry-1:
-    image: confluentinc/cp-schema-registry:3.3.0
+    image: confluentinc/cp-schema-registry:5.0.0
     depends_on:
       - zookeeper-1
       - kafka-1

diff --git a/java-sdk/README.md b/java-sdk/README.md
@@ -9,10 +9,10 @@ repositories {
 
 dependencies {
     // Commons schemas (backend, passive remote monitoring app)
-    compile 'org.radarcns:radar-schemas-commons:0.4.0'
+    compile 'org.radarcns:radar-schemas-commons:0.4.1'
 
     // Questionnaire schemas (active remote monitoring app)
-    compile 'org.radarcns:radar-schemas-tools:0.4.0'
+    compile 'org.radarcns:radar-schemas-tools:0.4.1'
 }
 ```
 Usually, you only need to include the schemas you actually need in your dependencies.

diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle
@@ -17,7 +17,7 @@ subprojects {
     apply plugin: 'idea'
 
     // Configuration
-    version = '0.4.0'
+    version = '0.4.1'
     group = 'org.radarcns'
     ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 
@@ -133,5 +133,5 @@ subprojects {
 }
 
 wrapper {
-    gradleVersion '4.9'
+    gradleVersion '4.10.2'
 }
diff --git a/java-sdk/gradle/wrapper/gradle-wrapper.jar b/java-sdk/gradle/wrapper/gradle-wrapper.jar
diff --git a/java-sdk/gradle/wrapper/gradle-wrapper.properties b/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-4.9-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/registration/KafkaTopics.java b/java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/registration/KafkaTopics.java
@@ -127,8 +127,18 @@ public boolean createTopics(Stream<String> topics, int partitions, short replica
         try {
             Set<String> existingTopics = kafkaClient.listTopics().names().get();
 
+            logger.info("Creating topics. Topics marked with [*] already exist.");
+
             List<NewTopic> newTopics = topics
-                    .filter(t -> !existingTopics.contains(t))
+                    .filter(t -> {
+                        if (existingTopics.contains(t)) {
+                            logger.info("[*] {}", t);
+                            return false;
+                        } else {
+                            logger.info("[ ] {}", t);
+                            return true;
+                        }
+                    })
                     .map(t -> new NewTopic(t, partitions, replication))
                     .collect(Collectors.toList());
 
@@ -222,7 +232,7 @@ public void addParser(ArgumentParser parser) {
             parser.addArgument("-r", "--replication")
                     .help("number of replicas per data packet")
                     .type(Short.class)
-                    .setDefault(3);
+                    .setDefault((short) 3);
             parser.addArgument("-b", "--brokers")
                     .help("number of brokers that are expected to be available.")
                     .type(Integer.class)

diff --git a/specifications/active/aRMT-1.2.0.yml → specifications/active/aRMT-1.3.0.yml b/specifications/active/aRMT-1.2.0.yml → specifications/active/aRMT-1.3.0.yml
@@ -1,7 +1,7 @@
 name: aRMT
 vendor: RADAR
 model: aRMT-App
-version: 1.2.0
+version: 1.3.0
 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:
@@ -39,3 +39,11 @@ data:
   - type: COMPLETION_LOG
     topic: questionnaire_completion_log
     value_schema: .monitor.questionnaire.QuestionnaireCompletionLog
+  - type: PDQ
+    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: PDDS
+    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
diff --git a/specifications/active/aRMT-1.4.0.yml b/specifications/active/aRMT-1.4.0.yml
@@ -0,0 +1,54 @@
+name: aRMT
+vendor: RADAR
+model: aRMT-App
+version: 1.4.0
+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.notification.Notification
+    questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/thinc_it/thinc_it_armt.json
+  - type: ROMBERG_TEST
+    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
+    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
+    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.opensmile.OpenSmile2AudioRecording
+  - 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: PDQ
+    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: PDDS
+    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
diff --git a/specifications/passive/android_phone-1.0.0.yml b/specifications/passive/android_phone-1.0.0.yml
@@ -150,13 +150,3 @@ data:
     value_schema: .passive.phone.PhoneUserInteraction
     sample_rate:
       dynamic: true
-  # Weather
-  - type: WEATHER
-    app_provider: .weather.WeatherApiProvider
-    unit: NON_DIMENSIONAL
-    processing_state: RAW
-    topic: android_local_weather
-    value_schema: .passive.weather.LocalWeather
-    sample_rate:
-      interval: 10800
-      configurable: true
diff --git a/specifications/passive/openweathermap_api-0.1.0.yml b/specifications/passive/openweathermap_api-0.1.0.yml
@@ -0,0 +1,15 @@
+#====================================== Android Phone Sensors =====================================#
+vendor: OPENWEATHERMAP
+model: API
+version: 0.1.0
+data:
+  # Weather
+  - type: WEATHER
+    app_provider: .weather.WeatherApiProvider
+    unit: NON_DIMENSIONAL
+    processing_state: RAW
+    topic: android_local_weather
+    value_schema: .passive.weather.LocalWeather
+    sample_rate:
+      interval: 10800
+      configurable: true
diff --git a/specifications/passive/rateaf_ppg-0.1.0.yml b/specifications/passive/rateaf_ppg-0.1.0.yml
@@ -0,0 +1,17 @@
+#====================================== Android Phone Sensors =====================================#
+vendor: RATE-AF
+model: PPG
+version: 0.1.0
+data:
+  #Phone sensors
+  - type: PPG
+    app_provider: org.radarbase.passive.ppg.PhonePpgProvider
+    fields:
+      - name: red
+      - name: green
+      - name: blue
+    sample_rate:
+      dynamic: true
+    processing_state: RADAR
+    topic: android_phone_ppg
+    value_schema: .passive.ppg.PhoneCameraPpg