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Merge pull request #66 from SAFEHR-data/sk/waveform-dev
Live waveform data in Emap
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| # these settings work on the GAE but if the process is getting OOM killed you can reduce them | ||
| MAX_HEAP_SIZE=4G | ||
| HEAP_NEWSIZE=800M |
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| -- For initialising a local DB in the case where the UDS/IDS does not exist (eg. Emap in a box), | ||
| -- NOT a fake for unit testing | ||
| CREATE SCHEMA IF NOT EXISTS uds_schema; |
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95 changes: 95 additions & 0 deletions
95
...rc/main/java/uk/ac/ucl/rits/inform/datasinks/emapstar/controllers/WaveformController.java
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| package uk.ac.ucl.rits.inform.datasinks.emapstar.controllers; | ||
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| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.stereotype.Component; | ||
| import org.springframework.transaction.annotation.Transactional; | ||
| import uk.ac.ucl.rits.inform.datasinks.emapstar.exceptions.MessageIgnoredException; | ||
| import uk.ac.ucl.rits.inform.datasinks.emapstar.repos.LocationVisitRepository; | ||
| import uk.ac.ucl.rits.inform.datasinks.emapstar.repos.visit_observations.WaveformRepository; | ||
| import uk.ac.ucl.rits.inform.informdb.movement.LocationVisit; | ||
| import uk.ac.ucl.rits.inform.informdb.visit_recordings.VisitObservationType; | ||
| import uk.ac.ucl.rits.inform.informdb.visit_recordings.Waveform; | ||
| import uk.ac.ucl.rits.inform.interchange.InterchangeValue; | ||
| import uk.ac.ucl.rits.inform.interchange.visit_observations.WaveformMessage; | ||
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|
||
| import java.time.Instant; | ||
| import java.util.List; | ||
| import java.util.Optional; | ||
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| /** | ||
| * Controller for Waveform specific information. | ||
| * @author Jeremy Stein | ||
| */ | ||
| @Component | ||
| public class WaveformController { | ||
| private final Logger logger = LoggerFactory.getLogger(getClass()); | ||
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| private final WaveformRepository waveformRepository; | ||
| private final LocationVisitRepository locationVisitRepository; | ||
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| WaveformController( | ||
| WaveformRepository waveformRepository, | ||
| LocationVisitRepository locationVisitRepository | ||
| ) { | ||
| this.waveformRepository = waveformRepository; | ||
| this.locationVisitRepository = locationVisitRepository; | ||
| } | ||
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|
||
| /** | ||
| * Process waveform data message. | ||
| * @param msg the interchange message | ||
| * @param visitObservationType to associate with this waveform data | ||
| * @param storedFrom stored from timestamp | ||
| * @throws MessageIgnoredException if message not processed | ||
| */ | ||
| @Transactional | ||
| public void processWaveform( | ||
| WaveformMessage msg, | ||
| VisitObservationType visitObservationType, | ||
| Instant storedFrom) throws MessageIgnoredException { | ||
| InterchangeValue<List<Double>> interchangeValue = msg.getNumericValues(); | ||
| if (!interchangeValue.isSave()) { | ||
| throw new MessageIgnoredException("Updating/deleting waveform data is not supported"); | ||
| } | ||
| // All given values are put into one new row. It's the responsibility of whoever is | ||
| // generating the message to choose an appropriate size of array. | ||
| List<Double> numericValues = interchangeValue.get(); | ||
| Instant observationTime = msg.getObservationTime(); | ||
| // Try to find the visit. We don't have enough information to create the visit if it doesn't already exist. | ||
| Optional<LocationVisit> inferredLocationVisit = | ||
| locationVisitRepository.findLocationVisitByLocationAndTime(observationTime, msg.getMappedLocationString()); | ||
| // XXX: will have to do some sanity checks here to be sure that the HL7 feed hasn't gone down. | ||
| // See issue #36, and here for discussion: | ||
| // https://github.com/UCLH-DHCT/emap/blob/jeremy/hf-data/docs/dev/features/waveform_hf_data.md#core-processor-logic-orphan-data-problem | ||
| Waveform dataRow = new Waveform( | ||
| observationTime, | ||
| observationTime, | ||
| storedFrom); | ||
| inferredLocationVisit.ifPresent(dataRow::setLocationVisitId); | ||
| Double[] valuesAsArray = numericValues.toArray(new Double[0]); | ||
| dataRow.setSamplingRate(msg.getSamplingRate()); | ||
| dataRow.setSourceLocation(msg.getSourceLocationString()); | ||
| dataRow.setVisitObservationTypeId(visitObservationType); | ||
| dataRow.setUnit(msg.getUnit()); | ||
| dataRow.setValuesArray(valuesAsArray); | ||
| waveformRepository.save(dataRow); | ||
| } | ||
|
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||
| /** | ||
| * Delete waveform data before the cutoff date. | ||
| * @param olderThanCutoff cutoff date | ||
| * @return number of rows deleted | ||
| */ | ||
| @Transactional | ||
| public int deleteOldWaveformData(Instant olderThanCutoff) { | ||
| return waveformRepository.deleteAllInBatchByObservationDatetimeBefore(olderThanCutoff); | ||
| } | ||
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| /** | ||
| * @return Return observation datetime of most recent waveform data. | ||
| */ | ||
| public Instant mostRecentObservationDatatime() { | ||
| return waveformRepository.mostRecentObservationDatatime(); | ||
| } | ||
| } |
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