Add converters for ECG and IRN data, and update exercise data parsing. #202
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| /* | ||
| * Copyright 2026 King's College London | ||
| * | ||
| * 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. | ||
| */ | ||
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| package org.radarbase.googlehealth.converter | ||
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| import com.fasterxml.jackson.databind.JsonNode | ||
| import org.apache.avro.specific.SpecificRecord | ||
| import org.radarbase.googlehealth.user.User | ||
| import org.radarbase.googlehealth.util.googleHealthElectrocardiogram | ||
| import java.time.Instant | ||
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| /** | ||
| * Emits one record per ECG waveform sample. Sample i is timed at the reading start plus | ||
| * i / samplingFrequencyHertz seconds and carries the raw waveform value as reported by the | ||
| * device (an ADC count; divide by millivoltsScalingFactor for millivolts). The reading-level | ||
| * metadata (heart rate, sampling parameters, device info) is repeated on every sample's record, | ||
| * linked by the shared reading id. | ||
| */ | ||
| class ElectrocardiogramGoogleHealthAvroConverter(topic: String) : GoogleHealthAvroConverter(topic) { | ||
| override fun convertDataPoint( | ||
| point: JsonNode, | ||
| user: User, | ||
| ): List<Pair<SpecificRecord, SpecificRecord>> { | ||
| val data = point["electrocardiogram"] ?: return emptyList() | ||
| val start = data["interval"]?.get("startTime")?.asText() | ||
| ?.let { runCatching { Instant.parse(it) }.getOrNull() } ?: return emptyList() | ||
| val id = (point["name"] ?: point["dataPointName"])?.asText()?.substringAfterLast('/') | ||
| ?: run { | ||
| logger.warn("Dropping electrocardiogram data point with no usable id for user={}", user.versionedId) | ||
| return emptyList() | ||
| } | ||
| val samples = data["waveformSamples"]?.takeIf { it.isArray } ?: return emptyList() | ||
| val frequency = data["samplingFrequencyHertz"]?.takeIf { !it.isNull }?.asInt()?.takeIf { it > 0 } | ||
| ?: return emptyList() | ||
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| val device = data["medicalDeviceInfo"] | ||
| val beatsPerMinuteAvg = data["beatsPerMinuteAvg"]?.takeIf { !it.isNull }?.asText()?.toIntOrNull() | ||
| val scalingFactor = data["millivoltsScalingFactor"]?.takeIf { !it.isNull }?.asInt() | ||
| val leadNumber = data["leadNumber"]?.takeIf { !it.isNull }?.asInt() | ||
| val deviceModel = device?.get("deviceModel")?.asText() | ||
| val firmwareVersion = device?.get("firmwareVersion")?.asText() | ||
| val featureVersion = device?.get("featureVersion")?.asText() | ||
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| val startSec = epochSeconds(start) | ||
| val received = nowEpochSeconds() | ||
| return samples.mapIndexed { i, sampleNode -> | ||
| val record = googleHealthElectrocardiogram { | ||
| time = startSec + i.toDouble() / frequency | ||
| timeReceived = received | ||
| this.id = id | ||
| sample = sampleNode.asInt() | ||
| this.beatsPerMinuteAvg = beatsPerMinuteAvg | ||
| this.samplingFrequencyHertz = frequency | ||
| this.millivoltsScalingFactor = scalingFactor | ||
| this.leadNumber = leadNumber | ||
| this.deviceModel = deviceModel | ||
| this.firmwareVersion = firmwareVersion | ||
| this.featureVersion = featureVersion | ||
| } | ||
| user.observationKey to record | ||
| } | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| /* | ||
| * Copyright 2026 King's College London | ||
| * | ||
| * 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. | ||
| */ | ||
|
|
||
| package org.radarbase.googlehealth.converter | ||
|
|
||
| import com.fasterxml.jackson.databind.JsonNode | ||
| import org.apache.avro.specific.SpecificRecord | ||
| import org.radarbase.googlehealth.user.User | ||
| import org.radarbase.googlehealth.util.googleHealthIrregularRhythmNotification | ||
| import java.time.Instant | ||
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| /** | ||
| * Emits one record per heart beat of an Irregular Rhythm Notification, flattening the API's | ||
| * session -> alertWindow -> heartBeat hierarchy. Each record carries the heart beat's own time | ||
| * plus the context of its parent window (start/end, positive) and session (start), with the | ||
| * device metadata repeated, linked by the shared notification id. | ||
| */ | ||
| class IrregularRhythmNotificationGoogleHealthAvroConverter(topic: String) : GoogleHealthAvroConverter(topic) { | ||
| override fun convertDataPoint( | ||
| point: JsonNode, | ||
| user: User, | ||
| ): List<Pair<SpecificRecord, SpecificRecord>> { | ||
| val data = point["irregularRhythmNotification"] ?: return emptyList() | ||
| val id = (point["name"] ?: point["dataPointName"])?.asText()?.substringAfterLast('/') | ||
| ?: run { | ||
| logger.warn("Dropping irregularRhythmNotification data point with no usable id for user={}", user.versionedId) | ||
| return emptyList() | ||
| } | ||
| val windows = data["alertWindows"]?.takeIf { it.isArray } ?: return emptyList() | ||
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| val device = data["medicalDeviceInfo"] | ||
| val sessionStart = data["interval"]?.get("startTime")?.asText() | ||
| ?.let { runCatching { Instant.parse(it) }.getOrNull() } | ||
| val firmwareVersion = device?.get("firmwareVersion")?.asText() | ||
| val featureVersion = device?.get("featureVersion")?.asText() | ||
| val deviceModel = device?.get("deviceModel")?.asText() | ||
| val received = nowEpochSeconds() | ||
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| return windows.flatMap { window -> | ||
| val windowStart = window["startTime"]?.asText() | ||
| ?.let { runCatching { Instant.parse(it) }.getOrNull() } | ||
| val windowEnd = window["endTime"]?.asText() | ||
| ?.let { runCatching { Instant.parse(it) }.getOrNull() } | ||
| if (windowStart == null || windowEnd == null) return@flatMap emptyList() | ||
| val positive = window["positive"]?.takeIf { !it.isNull }?.asBoolean() | ||
| val heartBeats = window["heartBeats"]?.takeIf { it.isArray } ?: return@flatMap emptyList() | ||
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| heartBeats.mapNotNull { beat -> | ||
| val beatTime = (beat["physicalTime"] ?: beat["time"])?.asText() | ||
| ?.let { runCatching { Instant.parse(it) }.getOrNull() } ?: return@mapNotNull null | ||
| val record = googleHealthIrregularRhythmNotification { | ||
| time = epochSeconds(beatTime) | ||
| timeReceived = received | ||
| this.id = id | ||
| sessionStartTime = sessionStart?.let { epochSeconds(it) } | ||
| windowStartTime = epochSeconds(windowStart) | ||
| windowEndTime = epochSeconds(windowEnd) | ||
| this.positive = positive | ||
| beatsPerMinute = beat["beatsPerMinute"]?.takeIf { !it.isNull }?.asText()?.toIntOrNull() | ||
| this.firmwareVersion = firmwareVersion | ||
| this.featureVersion = featureVersion | ||
| this.deviceModel = deviceModel | ||
| } | ||
| user.observationKey to record | ||
| } | ||
| } | ||
| } | ||
| } |
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try using parallel processing here