Merge pull request #152 from RADAR-base/release-0.4.2

Release 0.4.2

.gitignore

@@ -8,3 +8,4 @@ out/
 gradle.properties
 exchange.properties
 *.class
+/doc/

commons/connector/fitbit/fitbit_activity_heart_rate.avsc

@@ -0,0 +1,18 @@
+{
+  "namespace": "org.radarcns.connector.fitbit",
+  "name": "FitbitActivityHeartRate",
+  "type": "record",
+  "doc": "Aggregate heart rate as measured over an activity. The heart rates are divided amongst so-called heart rate zones. A heart rate zone is a range of heart rates and it does not overlap with other heart rate zones. These zones are called, in order of increasing heart rate, 'Out of Range', 'Fat Burn', 'Cardio', and 'Peak'. Fitbit uses the common formula of 220 minus your age to estimate your maximum heart rate. The 'Out of Range' zone has heart rates up to 50 percent of maximum heart rate, the 'Fat Burn' has heart rates up to 70 percent of maximum heart rate, 'Cardio' up to 85 percent of maximum heart rate and the 'Peak' range has heart rates higher than that.",
+  "fields": [
+    {"name": "mean", "type": ["null", "int"], "doc": "Mean heart rate over the duration of an activity (bpm). Null if unknown.", "default": null},
+    {"name": "min", "type": ["null", "int"], "doc": "Minimum heart rate for the duration of an activity (bpm). Null if unknown.", "default": null},
+    {"name": "max", "type": ["null", "int"], "doc": "Maximum heart rate for the duration of an activity (bpm). Null if unknown.", "default": null},
+    {"name": "minFatBurn", "type": ["null", "int"], "doc": "Threshold heart rate above which a the heart rate is considered in the heart rate zone 'Fat Burn' (bpm), up to the value of the minCardio field. Null if unknown.", "default": null},
+    {"name": "minCardio", "type": ["null", "int"], "doc": "Threshold heart rate above which a the heart rate is considered in the heart rate zone 'Cardio' (bpm), up to the value of the minPeak field. Null if unknown.", "default": null},
+    {"name": "minPeak", "type": ["null", "int"], "doc": "Threshold heart rate above which a the heart rate is considered in the heart rate zone 'Peak' (bpm). Null if unknown.", "default": null},
+    {"name": "durationOutOfRange", "type": ["null", "int"], "doc": "Duration in the heart rate zone 'Out Of Range', which is the lowest heart rate zone (s). Null if unknown.", "default": null},
+    {"name": "durationFatBurn", "type": ["null", "int"], "doc": "Duration in the heart rate zone 'Fat Burn', which is the second lowest heart rate zone (s). Null if unknown.", "default": null},
+    {"name": "durationCardio", "type": ["null", "int"], "doc": "Duration in the heart rate zone 'Cardio', which is the third lowest heart rate zone (s). Null if unknown.", "default": null},
+    {"name": "durationPeak", "type": ["null", "int"], "doc": "Duration in the heart rate zone 'Peak', which is the highest heart rate zone (s). Null if unknown.", "default": null}
+  ]
+}

commons/connector/fitbit/fitbit_activity_levels.avsc

@@ -0,0 +1,12 @@
+{
+  "namespace": "org.radarcns.connector.fitbit",
+  "name": "FitbitActivityLevels",
+  "type": "record",
+  "doc": "Aggregate activity levels during an activity.",
+  "fields": [
+    {"name": "durationSedentary", "type": ["null", "int"], "doc": "Duration that the activity level was considered sedentary (s). Null if unknown.", "default": null},
+    {"name": "durationLightly", "type": ["null", "int"], "doc": "Duration that the activity level was considered light (s). Null if unknown.", "default": null},
+    {"name": "durationFairly", "type": ["null", "int"], "doc": "Duration that the activity level was considered fair (s). Null if unknown.", "default": null},
+    {"name": "durationVery", "type": ["null", "int"], "doc": "Duration that the activity level was considered very high (s). Null if unknown.", "default": null}
+  ]
+}

commons/connector/fitbit/fitbit_activity_log_record.avsc

@@ -0,0 +1,26 @@
+{
+  "namespace": "org.radarcns.connector.fitbit",
+  "name": "FitbitActivityLogRecord",
+  "type": "record",
+  "doc": "Fitbit Activity Log record, containing the aggregate data of a single activity. This data is preprocessed by Fitbit, using algorithms based on the intraday data.",
+  "fields": [
+    {"name": "time", "type": "double", "doc": "Start time of the activity, time since the Unix Epoch (s)."},
+    {"name": "timeReceived", "type": "double", "doc": "Time that this record was collected by a connector. Start time of the activity, seconds since the Unix Epoch (s)."},
+    {"name": "timeZoneOffset", "type": "int", "doc": "Time zone offset compared to UTC (s)."},
+    {"name": "timeLastModified", "type": "double", "doc": "Time when the record was last modified, time since the Unix Epoch (s)."},
+    {"name": "duration", "type": "float", "doc": "Duration of the activity (s)."},
+    {"name": "durationActive", "type": "float", "doc": "Duration of the part of the activity where the participant was active (s)."},
+    {"name": "id", "type": "long", "doc": "Activity log ID."},
+    {"name": "name", "type": ["null", "string"], "doc": "Activity name. Null if none or unknown.", "default": null},
+    {"name": "logType", "type": ["null", "string"], "doc": "Type of log, e.g. manual. Null if unknown.", "default": null},
+    {"name": "type", "type": "long", "doc": "Fitbit-generated ID of the type of activity."},
+    {"name": "source", "type": ["null", "FitbitSource"], "doc": "Source of the data. Null if unknown.", "default": null},
+    {"name": "manualDataEntry", "type": ["null", "FitbitManualDataEntry"], "doc": "Indicates what values of this record are entered manually. Null if unknown.", "default": null},
+    {"name": "energy", "type": ["null", "float"], "doc": "Estimated of energy expended during the activity (kJ). Null if unknown.", "default": null},
+    {"name": "levels", "type": ["null", "FitbitActivityLevels"], "doc": "Levels of activity. Null if unknown.", "default": null},
+    {"name": "heartRate", "type": ["null", "FitbitActivityHeartRate"], "doc": "Heart rate aggregate information collected during the activity. Null if unknown.", "default": null},
+    {"name": "steps", "type": ["null", "int"], "doc": "Number of steps made during the activity. Null if unknown or if the type of activity is not step-based.", "default": null},
+    {"name": "distance", "type": ["null", "float"], "doc": "Distance covered during the activity (km). Null if unknown or if the type of activity is not distance-based.", "default": null},
+    {"name": "speed", "type": ["null", "double"], "doc": "Mean speed during the activity (km/h). Null if unknown or if the type of activity is not distance-based.", "default": null}
+  ]
+}

commons/connector/fitbit/fitbit_manual_data_entry.avsc

@@ -0,0 +1,11 @@
+{
+  "namespace": "org.radarcns.connector.fitbit",
+  "name": "FitbitManualDataEntry",
+  "type": "record",
+  "doc": "Indicates values in an activity log that are entered manually by the user, instead of being automatically collected by a device.",
+  "fields": [
+    {"name": "distance", "type": ["null", "boolean"], "doc": "Whether the distance field was manually entered. Null if unknown.", "default": null},
+    {"name": "energy", "type": ["null", "boolean"], "doc": "Whether the energy field was manually entered. Null if unknown.", "default": null},
+    {"name": "steps", "type": ["null", "boolean"], "doc": "Whether the steps field was manually entered. Null if unknown.", "default": null}
+  ]
+}

commons/connector/fitbit/fitbit_source.avsc

@@ -0,0 +1,12 @@
+{
+  "namespace": "org.radarcns.connector.fitbit",
+  "name": "FitbitSource",
+  "type": "record",
+  "doc": "A single fitbit source, e.g. a watch or an app.",
+  "fields": [
+    {"name": "id", "type": "string", "doc": "Source id."},
+    {"name": "name", "type": ["null", "string"], "doc": "Source name. Null if unknown.", "default": null},
+    {"name": "type", "type": ["null", "string"], "doc": "Source type. Null if unknown.", "default": null},
+    {"name": "url", "type": ["null", "string"], "doc": "Source URL. Null if unknown.", "default": null}
+  ]
+}

java-sdk/README.md

@@ -9,10 +9,10 @@ repositories {
 
 dependencies {
     // Commons schemas (backend, passive remote monitoring app)
-    compile 'org.radarcns:radar-schemas-commons:0.4.1'
+    compile 'org.radarcns:radar-schemas-commons:0.4.2'
 
     // Questionnaire schemas (active remote monitoring app)
-    compile 'org.radarcns:radar-schemas-tools:0.4.1'
+    compile 'org.radarcns:radar-schemas-tools:0.4.2'
 }
 ```
 Usually, you only need to include the schemas you actually need in your dependencies.

java-sdk/build.gradle

@@ -17,7 +17,7 @@ subprojects {
     apply plugin: 'idea'
 
     // Configuration
-    version = '0.4.1'
+    version = '0.4.2'
     group = 'org.radarcns'
     ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 

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

@@ -74,6 +74,8 @@ public boolean waitForBrokers(int brokers) throws InterruptedException,
             brokersAvailable = brokerList.size() >= brokers;
             if (brokersAvailable) {
                 logger.info("Kafka brokers available. Starting topic creation.");
+                // wait for 5sec before proceeding with topic creation
+                Thread.sleep(5000L);
 
                 String bootstrapServers = brokerList.stream()
                         .map(Broker::endPoints)
@@ -130,6 +132,8 @@ public boolean createTopics(Stream<String> topics, int partitions, short replica
             logger.info("Creating topics. Topics marked with [*] already exist.");
 
             List<NewTopic> newTopics = topics
+                    .sorted()
+                    .distinct()
                     .filter(t -> {
                         if (existingTopics.contains(t)) {
                             logger.info("[*] {}", t);

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

@@ -20,6 +20,7 @@
 
 import java.io.IOException;
 import java.net.MalformedURLException;
+import java.util.Comparator;
 import java.util.Optional;
 import java.util.concurrent.TimeUnit;
 import java.util.regex.Pattern;
@@ -81,21 +82,22 @@ public boolean registerSchemas(SourceCatalogue catalogue) {
         return catalogue.getSources().stream()
                 .filter(DataProducer::doRegisterSchema)
                 .flatMap(DataProducer::getTopics)
+                .sorted(Comparator.comparing(AvroTopic::getName))
+                .distinct()
+                .peek(t -> logger.info("Registering topic {} schemas: {} - {}",
+                        t.getName(), t.getKeySchema().getFullName(),
+                        t.getValueSchema().getFullName()))
                 .allMatch(this::registerSchema);
     }
 
     /** Register the schema of a single topic. */
     public boolean registerSchema(AvroTopic<?, ?> topic) {
         try {
             Schema schema = topic.getKeySchema();
-            logger.info("Registering topic {} key schema: {}",
-                    topic.getName(), schema.getFullName());
             ParsedSchemaMetadata metadata = new ParsedSchemaMetadata(null, null, schema);
             this.schemaClient.addSchemaMetadata(topic.getName(), false, metadata);
 
             schema = topic.getValueSchema();
-            logger.info("Registering topic {} value schema: {}",
-                    topic.getName(), schema.getFullName());
             metadata = new ParsedSchemaMetadata(null, null, schema);
             this.schemaClient.addSchemaMetadata(topic.getName(), true, metadata);
             return true;

specifications/active/aRMT-1.4.0.yml → specifications/active/aRMT-1.4.1.yml

@@ -1,7 +1,7 @@
 name: aRMT
 vendor: RADAR
 model: aRMT-App
-version: 1.4.0
+version: 1.4.1
 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:
@@ -10,14 +10,17 @@ data:
     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
+    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

specifications/connector/radar-fitbit-connector.yml

@@ -19,3 +19,6 @@ data:
   - doc: User profile timezone.
     topic: connect_fitbit_time_zone
     value_schema: .connector.fitbit.FitbitTimeZone
+  - doc: Aggregate activity log.
+    topic: connect_fitbit_activity_log
+    value_schema: .connector.fitbit.FitbitActivityLogRecord

specifications/stream/android_phone.yml

@@ -7,10 +7,11 @@ data:
     windowed: true
   - input_topic: android_phone_usage_event
     value_schema: .passive.phone.PhoneUsageEvent
+    windowed: false
   - topic: android_phone_usage_event_aggregated
     input_topic: android_phone_usage_event_output
     value_schema: .stream.aggregator.PhoneUsageAggregate
-    windowed: true
+    windowed: false
   - input_topic: android_phone_battery_level
     value_schema: .stream.aggregator.NumericAggregate
     windowed: true