Merge pull request #56 from RADAR-base/release-0.3.0

Release 0.3.0

build.gradle.kts

@@ -15,7 +15,7 @@ description = "RADAR Push API Gateway to handle secured data flow to backend."
 
 allprojects {
     group = "org.radarbase"
-    version = "0.2.3"
+    version = "0.3.0"
 
     repositories {
         mavenCentral()
@@ -62,8 +62,8 @@ dependencies {
     runtimeOnly("org.glassfish.grizzly:grizzly-http-server-monitoring:$grizzlyVersion")
 
     val log4j2Version: String by project
-    runtimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:$log4j2Version")
-    runtimeOnly("org.apache.logging.log4j:log4j-api:$log4j2Version")
+    runtimeOnly("org.apache.logging.log4j:log4j-slf4j2-impl:$log4j2Version")
+    runtimeOnly("org.apache.logging.log4j:log4j-core:$log4j2Version")
     runtimeOnly("org.apache.logging.log4j:log4j-jul:$log4j2Version")
 
     val jedisVersion: String by project
@@ -122,7 +122,8 @@ application {
         "-Dcom.sun.management.jmxremote.local.only=false",
         "-Dcom.sun.management.jmxremote.port=9010",
         "-Dcom.sun.management.jmxremote.authenticate=false",
-        "-Dcom.sun.management.jmxremote.ssl=false"
+        "-Dcom.sun.management.jmxremote.ssl=false",
+        "-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager",
     )
 }
 

gradle.properties

@@ -3,13 +3,13 @@ dockerComposeStopContainers=true
 
 kotlinVersion=1.6.10
 okhttp3Version=4.9.3
-radarJerseyVersion=0.8.1
+radarJerseyVersion=0.9.1
 radarCommonsVersion=0.13.2
-radarSchemasVersion=0.7.6
+radarSchemasVersion=0.8.3
 radarOauthClientVersion=0.8.0
-jacksonVersion=2.12.2
-slf4jVersion=1.7.32
-log4j2Version=2.17.0
+jacksonVersion=2.14.1
+slf4jVersion=2.0.7
+log4j2Version=2.20.0
 kafkaVersion=2.8.1
 confluentVersion=6.2.0
 junitVersion=5.7.2

src/main/kotlin/org/radarbase/gateway/Config.kt

@@ -65,9 +65,14 @@ data class GarminConfig(
     val respirationTopicName: String = "push_garmin_respiration",
     val activityDetailsSampleTopicName: String = "push_garmin_activity_detail_sample",
     val bodyBatterySampleTopicName: String = "push_garmin_body_battery_sample",
-    val heartRateSampleConverter: String = "push_garmin_heart_rate_sample",
+    val heartRateSampleTopicName: String = "push_garmin_heart_rate_sample",
     val sleepLevelTopicName: String = "push_garmin_sleep_level",
-    val stressLevelTopicName: String = "push_garmin_stress_level"
+    val stressLevelTopicName: String = "push_garmin_stress_level",
+    val sleepScoreTopicName: String = "push_garmin_sleep_score",
+    val bloodPressureTopicName: String = "push_garmin_blood_pressure",
+    val healthSnapshotTopicName: String = "push_garmin_health_snapshot_summary",
+    val heartRateVariabilityTopicName: String = "push_garmin_heart_rate_variability",
+    val heartRateVariabilitySampleTopicName: String = "push_garmin_heart_rate_variability_sample"
 ) {
     val userRepository: Class<*> = Class.forName(userRepositoryClass)
 

src/main/kotlin/org/radarbase/push/integration/garmin/backfill/GarminRequestGenerator.kt

@@ -68,6 +68,18 @@ class GarminRequestGenerator(
             config.pushIntegration.garmin.consumerKey,
             userRepository
         ),
+        GarminHealthSnapshotRoute(
+            config.pushIntegration.garmin.consumerKey,
+            userRepository
+        ),
+        GarminHrvRoute(
+            config.pushIntegration.garmin.consumerKey,
+            userRepository
+        ),
+        GarminBloodPressureRoute(
+            config.pushIntegration.garmin.consumerKey,
+            userRepository
+        ),
     )
 
     private val userNextRequest: MutableMap<String, Instant> = mutableMapOf()

src/main/kotlin/org/radarbase/push/integration/garmin/backfill/route/GarminBloodPressureRoute.kt

@@ -0,0 +1,13 @@
+package org.radarbase.push.integration.garmin.backfill.route
+
+import org.radarbase.push.integration.garmin.user.GarminUserRepository
+
+class GarminBloodPressureRoute(
+    consumerKey: String,
+    userRepository: GarminUserRepository
+) : GarminRoute(consumerKey, userRepository) {
+
+    override fun subPath(): String = "bloodPressures"
+
+    override fun toString(): String = "garmin_blood_pressures"
+}

src/main/kotlin/org/radarbase/push/integration/garmin/backfill/route/GarminHealthSnapshotRoute.kt

@@ -0,0 +1,13 @@
+package org.radarbase.push.integration.garmin.backfill.route
+
+import org.radarbase.push.integration.garmin.user.GarminUserRepository
+
+class GarminHealthSnapshotRoute(
+    consumerKey: String,
+    userRepository: GarminUserRepository
+) : GarminRoute(consumerKey, userRepository) {
+
+    override fun subPath(): String = "healthSnapshot"
+
+    override fun toString(): String = "garmin_health_snapshot"
+}

src/main/kotlin/org/radarbase/push/integration/garmin/backfill/route/GarminHrvRoute.kt

@@ -0,0 +1,13 @@
+package org.radarbase.push.integration.garmin.backfill.route
+
+import org.radarbase.push.integration.garmin.user.GarminUserRepository
+
+class GarminHrvRoute(
+    consumerKey: String,
+    userRepository: GarminUserRepository
+) : GarminRoute(consumerKey, userRepository) {
+
+    override fun subPath(): String = "hrv"
+
+    override fun toString(): String = "garmin_hrv"
+}

src/main/kotlin/org/radarbase/push/integration/garmin/converter/ActivitiesGarminAvroConverter.kt

@@ -29,6 +29,7 @@ open class ActivitiesGarminAvroConverter(topic: String = "push_integration_garmi
             timeReceived = Instant.now().toEpochMilli() / 1000.0
             startTimeOffset = node["startTimeOffsetInSeconds"]?.asInt()
             activityType = node["activityType"]?.asText()
+            activityId = node["activityId"]?.asText()
             duration = node["durationInSeconds"]?.asInt()
             averageBikeCadence = node["averageBikeCadenceInRoundsPerMinute"]?.floatValue()
             averageHeartRate = node["averageHeartRateInBeatsPerMinute"]?.asInt()

src/main/kotlin/org/radarbase/push/integration/garmin/converter/ActivityDetailsGarminAvroConverter.kt

@@ -29,6 +29,7 @@ class ActivityDetailsGarminAvroConverter(topic: String = "push_integration_garmi
             timeReceived = Instant.now().toEpochMilli() / 1000.0
             startTimeOffset = summary["startTimeOffsetInSeconds"]?.asInt()
             activityType = summary["activityType"]?.asText()
+            activityId = summary["activityId"]?.asText()
             duration = summary["durationInSeconds"]?.asInt()
             averageBikeCadence = summary["averageBikeCadenceInRoundsPerMinute"]?.floatValue()
             averageHeartRate = summary["averageHeartRateInBeatsPerMinute"]?.asInt()

src/main/kotlin/org/radarbase/push/integration/garmin/converter/BloodPressureGarminAvroConverter.kt

@@ -0,0 +1,40 @@
+package org.radarbase.push.integration.garmin.converter
+
+import com.fasterxml.jackson.databind.JsonNode
+import jakarta.ws.rs.BadRequestException
+import org.apache.avro.specific.SpecificRecord
+import org.radarbase.push.integration.common.user.User
+import org.radarcns.push.garmin.GarminBloodPressureSummary
+import java.time.Instant
+
+class BloodPressureGarminAvroConverter(topic: String = "push_integration_garmin_blood_pressure") :
+    GarminAvroConverter(topic) {
+    override fun validate(tree: JsonNode) {
+        val activities = tree[ROOT]
+        if (activities == null || !activities.isArray) {
+            throw BadRequestException("The manual activities data was invalid.")
+        }
+    }
+
+    override fun convert(tree: JsonNode, user: User): List<Pair<SpecificRecord, SpecificRecord>> {
+        return tree[ROOT]
+            .map { node -> Pair(user.observationKey, getRecord(node)) }
+    }
+
+    private fun getRecord(node: JsonNode): SpecificRecord {
+        return GarminBloodPressureSummary.newBuilder().apply {
+            summaryId = node["summaryId"]?.asText()
+            time = node["startTimeInSeconds"].asDouble()
+            timeReceived = Instant.now().toEpochMilli() / 1000.0
+            measurementTimeOffset = node["measurementTimeOffsetInSeconds"]?.asInt()
+            systolic = node["systolic"]?.asInt()
+            diastolic = node["diastolic"]?.asInt()
+            pulse = node["pulse"]?.asInt()
+            sourceType = node["sourceType"]?.asText()
+        }.build()
+    }
+
+    companion object {
+        const val ROOT = "bloodPressures"
+    }
+}

src/main/kotlin/org/radarbase/push/integration/garmin/converter/HealthSnapshotGarminAvroConverter.kt

@@ -0,0 +1,70 @@
+package org.radarbase.push.integration.garmin.converter
+
+import com.fasterxml.jackson.databind.JsonNode
+import jakarta.ws.rs.BadRequestException
+import org.apache.avro.specific.SpecificRecord
+import org.radarbase.push.integration.common.user.User
+import org.radarcns.push.garmin.GarminHealthSnapshotSummary
+import java.time.Instant
+
+class HealthSnapshotGarminAvroConverter(topic: String = "push_integration_garmin_health_snapshot") :
+    GarminAvroConverter(topic) {
+    override fun validate(tree: JsonNode) {
+        val activities = tree[ROOT]
+        if (activities == null || !activities.isArray) {
+            throw BadRequestException("The manual activities data was invalid.")
+        }
+    }
+
+    override fun convert(tree: JsonNode, user: User): List<Pair<SpecificRecord, SpecificRecord>> {
+        return tree[ROOT]
+            .map { node -> Pair(user.observationKey, getRecord(node)) }
+    }
+
+    private fun getRecord(node: JsonNode): SpecificRecord {
+        return GarminHealthSnapshotSummary.newBuilder().apply {
+            summaryId = node["summaryId"]?.asText()
+            time = node["startTimeInSeconds"].asDouble()
+            timeReceived = Instant.now().toEpochMilli() / 1000.0
+            date = node["calendarDate"]?.asText()
+            duration = node["durationInSeconds"]?.asInt()
+            startTimeOffset = node["startTimeOffsetInSeconds"]?.asInt()
+
+            for (summary in node["summaries"]) {
+                when (summary["summaryType"]?.asText()) {
+                    "heart_rate" -> {
+                        heartRateAverage = summary["avgValue"]?.floatValue()
+                        heartRateMax = summary["maxValue"]?.floatValue()
+                        heartRateMin = summary["minValue"]?.floatValue()
+                    }
+
+                    "respiration" -> {
+                        respirationAverage = summary["avgValue"]?.floatValue()
+                        respirationMax = summary["maxValue"]?.floatValue()
+                        respirationMin = summary["minValue"]?.floatValue()
+                    }
+
+                    "stress" -> {
+                        stressAverage = summary["avgValue"]?.floatValue()
+                        stressMax = summary["maxValue"]?.floatValue()
+                        stressMin = summary["minValue"]?.floatValue()
+                    }
+
+                    "spo2" -> {
+                        spo2Average = summary["avgValue"]?.floatValue()
+                        spo2Max = summary["maxValue"]?.floatValue()
+                        spo2Min = summary["minValue"]?.floatValue()
+                    }
+
+                    "rmssd_hrv" -> rmssdHrvAverage = summary["avgValue"]?.floatValue()
+
+                    "sdrr_hrv" -> sdrrHrvAverage = summary["avgValue"]?.floatValue()
+                }
+            }
+        }.build()
+    }
+
+    companion object {
+        const val ROOT = "healthSnapshot"
+    }
+}

src/main/kotlin/org/radarbase/push/integration/garmin/converter/HealthSnapshotHeartRateSampleGarminAvroConverter.kt

@@ -0,0 +1,54 @@
+package org.radarbase.push.integration.garmin.converter
+
+import com.fasterxml.jackson.databind.JsonNode
+import org.apache.avro.specific.SpecificRecord
+import org.radarbase.push.integration.common.user.User
+import org.radarcns.kafka.ObservationKey
+import org.radarcns.push.garmin.GarminHeartRateSample
+import java.time.Instant
+
+class HealthSnapshotHeartRateSampleGarminAvroConverter(
+    topic: String = "push_integration_garmin_heart_rate_sample"
+) :
+    GarminAvroConverter(topic) {
+    override fun validate(tree: JsonNode) = Unit
+
+    override fun convert(tree: JsonNode, user: User): List<Pair<SpecificRecord, SpecificRecord>> {
+        return tree[ROOT].map { node ->
+            getSamples(
+                node[SUB_NODE], node["summaryId"].asText(),
+                user.observationKey, node["startTimeInSeconds"].asDouble()
+            )
+        }.flatten()
+    }
+
+    private fun getSamples(
+        node: JsonNode?,
+        summaryId: String,
+        observationKey: ObservationKey,
+        startTime: Double
+    ): List<Pair<ObservationKey, GarminHeartRateSample>> {
+        if (node == null) {
+            return emptyList()
+        }
+
+        val summary = node.find { it["summaryType"]?.asText() == "heart_rate" } ?: return emptyList()
+
+        return summary["epochSummaries"].fields().asSequence().map { (key, value) ->
+            Pair(
+                observationKey,
+                GarminHeartRateSample.newBuilder().apply {
+                    this.summaryId = summaryId
+                    this.time = startTime + key.toDouble()
+                    this.timeReceived = Instant.now().toEpochMilli() / 1000.0
+                    this.heartRate = value?.floatValue()
+                }.build()
+            )
+        }.toList()
+    }
+
+    companion object {
+        const val ROOT = HealthSnapshotGarminAvroConverter.ROOT
+        const val SUB_NODE = "summaries"
+    }
+}

src/main/kotlin/org/radarbase/push/integration/garmin/converter/HealthSnapshotRespirationSampleGarminAvroConverter.kt

@@ -0,0 +1,53 @@
+package org.radarbase.push.integration.garmin.converter
+
+import com.fasterxml.jackson.databind.JsonNode
+import org.apache.avro.specific.SpecificRecord
+import org.radarbase.push.integration.common.user.User
+import org.radarcns.kafka.ObservationKey
+import org.radarcns.push.garmin.GarminRespiration
+import java.time.Instant
+
+class HealthSnapshotRespirationSampleGarminAvroConverter(
+    topic: String = "push_integration_garmin_respiration"
+) :
+    GarminAvroConverter(topic) {
+    override fun validate(tree: JsonNode) = Unit
+
+    override fun convert(tree: JsonNode, user: User): List<Pair<SpecificRecord, SpecificRecord>> {
+        return tree[ROOT].map { node ->
+            getSamples(
+                node[SUB_NODE], node["summaryId"].asText(),
+                user.observationKey, node["startTimeInSeconds"].asDouble()
+            )
+        }.flatten()
+    }
+
+    private fun getSamples(
+        node: JsonNode?,
+        summaryId: String,
+        observationKey: ObservationKey,
+        startTime: Double
+    ): List<Pair<ObservationKey, GarminRespiration>> {
+        if (node == null) {
+            return emptyList()
+        }
+        val summary = node.find { it["summaryType"]?.asText() == "respiration" } ?: return emptyList()
+
+        return summary["epochSummaries"].fields().asSequence().map { (key, value) ->
+            Pair(
+                observationKey,
+                GarminRespiration.newBuilder().apply {
+                    this.summaryId = summaryId
+                    this.time = startTime + key.toDouble()
+                    this.timeReceived = Instant.now().toEpochMilli() / 1000.0
+                    this.respiration = value?.floatValue()
+                }.build()
+            )
+        }.toList()
+    }
+
+    companion object {
+        const val ROOT = HealthSnapshotGarminAvroConverter.ROOT
+        const val SUB_NODE = "summaries"
+    }
+}