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Merge pull request #53 from RADAR-base/new_garmin_data
New garmin data integration
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40 changes: 40 additions & 0 deletions
40
...otlin/org/radarbase/push/integration/garmin/converter/BloodPressureGarminAvroConverter.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 = "bloodPressure" | ||
| } | ||
| } |
70 changes: 70 additions & 0 deletions
70
...tlin/org/radarbase/push/integration/garmin/converter/HealthSnapshotGarminAvroConverter.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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() | ||
|
|
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| "sdrr_hrv" -> sdrrHrvAverage = summary["avgValue"]?.floatValue() | ||
| } | ||
| } | ||
| }.build() | ||
| } | ||
|
|
||
| companion object { | ||
| const val ROOT = "healthSnapshot" | ||
| } | ||
| } |
54 changes: 54 additions & 0 deletions
54
...ase/push/integration/garmin/converter/HealthSnapshotHeartRateSampleGarminAvroConverter.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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" | ||
| } | ||
| } |
53 changes: 53 additions & 0 deletions
53
...e/push/integration/garmin/converter/HealthSnapshotRespirationSampleGarminAvroConverter.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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" | ||
| } | ||
| } |
58 changes: 58 additions & 0 deletions
58
...adarbase/push/integration/garmin/converter/HealthSnapshotSpO2SampleGarminAvroConverter.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| 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.GarminPulseOx | ||
| import java.time.Instant | ||
|
|
||
| class HealthSnapshotSpO2SampleGarminAvroConverter( | ||
| 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(), | ||
| node["calendarDate"]?.asText() | ||
| ) | ||
| }.flatten() | ||
| } | ||
|
|
||
| private fun getSamples( | ||
| node: JsonNode?, | ||
| summaryId: String, | ||
| observationKey: ObservationKey, | ||
| startTime: Double, | ||
| date: String? | ||
| ): List<Pair<ObservationKey, GarminPulseOx>> { | ||
| if (node == null) { | ||
| return emptyList() | ||
| } | ||
|
|
||
| val summary = node.find { it["summaryType"]?.asText() == "spo2" } ?: return emptyList() | ||
|
|
||
| return summary["epochSummaries"].fields().asSequence().map { (key, value) -> | ||
| Pair( | ||
| observationKey, | ||
| GarminPulseOx.newBuilder().apply { | ||
| this.summaryId = summaryId | ||
| this.time = startTime + key.toDouble() | ||
| this.timeReceived = Instant.now().toEpochMilli() / 1000.0 | ||
| this.date = date | ||
| this.spo2Value = value?.floatValue() | ||
| this.onDemand = true | ||
| }.build() | ||
| ) | ||
| }.toList() | ||
| } | ||
|
|
||
| companion object { | ||
| const val ROOT = HealthSnapshotGarminAvroConverter.ROOT | ||
| const val SUB_NODE = "summaries" | ||
| } | ||
| } |
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