KafkaEventStreamDecoder.cpp

#include "MantidLiveData/Kafka/KafkaEventStreamDecoder.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/Logger.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/WarningSuppressions.h"
#include "MantidKernel/make_unique.h"
#include "MantidLiveData/Exception.h"

GCC_DIAG_OFF(conversion)
#include "private/Schema/ba57_run_info_generated.h"
#include "private/Schema/df12_det_spec_map_generated.h"
#include "private/Schema/ev42_events_generated.h"
#include "private/Schema/is84_isis_events_generated.h"
GCC_DIAG_ON(conversion)

#include <boost/make_shared.hpp>

#include <MantidLiveData/Kafka/KafkaTopicSubscriber.h>
#include <cassert>
#include <functional>
#include <map>

namespace {
/// Logger
Mantid::Kernel::Logger g_log("KafkaEventStreamDecoder");

static const std::string PROTON_CHARGE_PROPERTY = "proton_charge";
static const std::string RUN_NUMBER_PROPERTY = "run_number";
static const std::string RUN_START_PROPERTY = "run_start";

// File identifiers from flatbuffers schema
static const std::string RUN_MESSAGE_ID = "ba57";
static const std::string EVENT_MESSAGE_ID = "ev42";

static const std::chrono::seconds MAX_LATENCY(1);
}

namespace Mantid {
namespace LiveData {
using DataObjects::TofEvent;
using Kernel::DateAndTime;

// -----------------------------------------------------------------------------
// Public members
// -----------------------------------------------------------------------------
/**
 * Constructor
 * @param broker A reference to a Broker object for creating topic streams
 * @param eventTopic The name of the topic streaming the event data
 * @param spDetTopic The name of the topic streaming the spectrum-detector
 * run mapping
 */
KafkaEventStreamDecoder::KafkaEventStreamDecoder(
    std::shared_ptr<IKafkaBroker> broker, const std::string &eventTopic,
    const std::string &runInfoTopic, const std::string &spDetTopic)
    : m_broker(broker), m_eventTopic(eventTopic), m_runInfoTopic(runInfoTopic),
      m_spDetTopic(spDetTopic), m_interrupt(false), m_localEvents(),
      m_specToIdx(), m_runStart(), m_runNumber(-1), m_thread(),
      m_capturing(false), m_exception(), m_extractWaiting(false) {}

/**
 * Destructor.
 * Stops capturing from the stream
 */
KafkaEventStreamDecoder::~KafkaEventStreamDecoder() { stopCapture(); }

/**
 * Start capturing from the stream on a separate thread. This is a non-blocking
 * call and will return after the thread has started
 */
void KafkaEventStreamDecoder::startCapture(bool startNow) {

  // If we are not starting now, then we want to start at the start of the run
  if (!startNow) {
    // Get last two messages in run topic to ensure we get a runStart message
    m_runStream =
        m_broker->subscribe({m_runInfoTopic}, subscribeAtOption::LASTTWO);
    std::string rawMsgBuffer;
    auto runStartData = getRunStartMessage(rawMsgBuffer);
    auto startTimeMilliseconds =
        runStartData.startTime * 1000; // seconds to milliseconds
    m_eventStream =
        m_broker->subscribe({m_eventTopic, m_runInfoTopic},
                            startTimeMilliseconds, subscribeAtOption::TIME);
  } else {
    m_eventStream = m_broker->subscribe({m_eventTopic, m_runInfoTopic},
                                        subscribeAtOption::LATEST);
  }

  // Get last two messages in run topic to ensure we get a runStart message
  m_runStream =
      m_broker->subscribe({m_runInfoTopic}, subscribeAtOption::LASTTWO);
  m_spDetStream =
      m_broker->subscribe({m_spDetTopic}, subscribeAtOption::LASTONE);

  auto m_thread = std::thread([this]() { this->captureImpl(); });
  m_thread.detach();
}

/**
 * Stop capturing from the stream. This is a blocking call until the capturing
 * function has completed
 */
void KafkaEventStreamDecoder::stopCapture() noexcept {
  // This will interrupt the "event" loop
  m_interrupt = true;
  // Wait until the function has completed. The background thread
  // will exit automatically
  while (m_capturing) {
    std::this_thread::sleep_for(std::chrono::milliseconds(50));
  };
}

/**
 * Check if there is data available to extract
 * @return True if data has been accumulated so that extractData()
 * can be called, false otherwise
 */
bool KafkaEventStreamDecoder::hasData() const noexcept {
  std::lock_guard<std::mutex> lock(m_mutex);
  return !m_localEvents.empty();
}

/**
 * Check if a message has indicated that end of run has been reached
 * @return  True if end of run has been reached
 */
bool KafkaEventStreamDecoder::hasReachedEndOfRun() noexcept {
  // Notify the decoder that MonitorLiveData knows it has reached end of run
  // and after giving it opportunity to interrupt, decoder can continue with
  // messages of the next run
  if (!m_extractedEndRunData)
    return false;
  if (m_endRun) {
    std::lock_guard<std::mutex> runStatusLock(m_runStatusMutex);
    m_runStatusSeen = true;
    m_cvRunStatus.notify_one();
  }
  return m_endRun;
}

/**
 * Check for an exception thrown by the background thread and rethrow
 * it if necessary. If no error occurred swap the current internal buffer
 * for a fresh one and return the old buffer.
 * @return A pointer to the data collected since the last call to this
 * method
 */
API::Workspace_sptr KafkaEventStreamDecoder::extractData() {
  if (m_exception) {
    throw * m_exception;
  }

  m_extractWaiting = true;
  m_cv.notify_one();

  auto workspace_ptr = extractDataImpl();

  m_extractWaiting = false;
  m_cv.notify_one();

  return workspace_ptr;
}

// -----------------------------------------------------------------------------
// Private members
// -----------------------------------------------------------------------------

API::Workspace_sptr KafkaEventStreamDecoder::extractDataImpl() {
  std::lock_guard<std::mutex> lock(m_mutex);
  if (m_localEvents.size() == 1) {
    auto temp = createBufferWorkspace(m_localEvents.front());
    std::swap(m_localEvents.front(), temp);
    return temp;
  } else if (m_localEvents.size() > 1) {
    auto group = boost::make_shared<API::WorkspaceGroup>();
    size_t index(0);
    for (auto &filledBuffer : m_localEvents) {
      auto temp = createBufferWorkspace(filledBuffer);
      std::swap(m_localEvents[index++], temp);
      group->addWorkspace(temp);
    }
    return group;
  } else {
    throw Exception::NotYet("Local buffers not initialized.");
  }
}

/**
 * Start decoding data from the streams into the internal buffers.
 * Implementation designed to be entry point for new thread of execution.
 * It catches all thrown exceptions.
 */
void KafkaEventStreamDecoder::captureImpl() noexcept {
  m_capturing = true;
  try {
    captureImplExcept();
  } catch (std::exception &exc) {
    m_exception = boost::make_shared<std::runtime_error>(exc.what());
  } catch (...) {
    m_exception = boost::make_shared<std::runtime_error>(
        "KafkaEventStreamDecoder: Unknown exception type caught.");
  }
  m_capturing = false;
}

/**
 * Exception-throwing variant of captureImpl(). Do not call this directly
 */
void KafkaEventStreamDecoder::captureImplExcept() {
  g_log.debug("Event capture starting");
  initLocalCaches();

  m_interrupt = false;
  m_endRun = false;
  m_runStatusSeen = false;
  m_extractedEndRunData = true;
  std::string buffer;
  int64_t offset;
  int32_t partition;
  std::string topicName;
  std::unordered_map<std::string, std::vector<int64_t>> stopOffsets;
  std::unordered_map<std::string, std::vector<bool>> reachedEnd;
  // Set to true when a runStop message has been received and we need to start
  // checking if we have reached the last message in the run for each partition
  bool checkOffsets = false;
  while (!m_interrupt) {
    // If extractData method is waiting for access to the buffer workspace
    // then we wait for it to finish
    std::unique_lock<std::mutex> readyLock(m_waitMutex);
    if (m_extractWaiting) {
      m_cv.wait(readyLock, [&] { return !m_extractWaiting; });
      readyLock.unlock();
      if (m_endRun) {
        m_extractedEndRunData = true;
        // Wait until MonitorLiveData has seen that end of run was
        // reached before setting m_endRun back to false and continuing
        std::unique_lock<std::mutex> runStatusLock(m_runStatusMutex);
        m_cvRunStatus.wait(runStatusLock, [&] { return m_runStatusSeen; });
        m_endRun = false;
        m_runStatusSeen = false;
        runStatusLock.unlock();
        // Give time for MonitorLiveData to act on runStatus information
        // and trigger m_interrupt for next loop iteration if user requested
        // LiveData algorithm to stop at the end of the run
        std::this_thread::sleep_for(std::chrono::milliseconds(100));
      }
    }

    // Pull in events
    m_eventStream->consumeMessage(&buffer, offset, partition, topicName);
    // No events, wait for some to come along...
    if (buffer.empty())
      continue;

    if (checkOffsets) {
      if (offset >= stopOffsets[topicName][partition]) {
        reachedEnd[topicName][partition] = true;
        g_log.debug() << "Reached end-of-run in " << topicName << " topic."
                      << std::endl;
        g_log.debug() << "topic: " << topicName << " offset: " << offset
                      << " stopOffset: " << stopOffsets[topicName][partition]
                      << std::endl;
        // Check if we've reached the stop offset on every partition of every
        // topic
        if (std::all_of(reachedEnd.cbegin(), reachedEnd.cend(),
                        [](std::pair<std::string, std::vector<bool>> kv) {
                          return std::all_of(
                              kv.second.cbegin(), kv.second.cend(),
                              [](bool partitionEnd) { return partitionEnd; });
                        })) {
          m_endRun = true;
          // If we've reached the end of a run then set m_extractWaiting to true
          // so that we wait until the buffer is emptied before continuing.
          // Otherwise we can end up with data from two different runs in the
          // same buffer workspace which is problematic if the user wanted the
          // "Stop" or "Rename" run transition option.
          m_extractWaiting = true;
          m_extractedEndRunData = false;
          g_log.debug() << "Reached end of run in data stream." << std::endl;
        }
      }
    }

    // Check if we have an event message
    // Most will be event messages so we check for this type first
    if (flatbuffers::BufferHasIdentifier(
            reinterpret_cast<const uint8_t *>(buffer.c_str()),
            EVENT_MESSAGE_ID.c_str())) {
      auto eventMsg =
          GetEventMessage(reinterpret_cast<const uint8_t *>(buffer.c_str()));

      DateAndTime pulseTime = static_cast<int64_t>(eventMsg->pulse_time());
      const auto &tofData = *(eventMsg->time_of_flight());
      const auto &detData = *(eventMsg->detector_id());
      auto nEvents = tofData.size();

      if (eventMsg->facility_specific_data_type() != FacilityData_ISISData) {
        throw std::runtime_error("KafkaEventStreamDecoder only knows how to "
                                 "deal with ISIS facility specific data");
      }
      auto ISISMsg =
          static_cast<const ISISData *>(eventMsg->facility_specific_data());

      std::lock_guard<std::mutex> lock(m_mutex);
      auto &periodBuffer =
          *m_localEvents[static_cast<size_t>(ISISMsg->period_number())];
      auto &mutableRunInfo = periodBuffer.mutableRun();
      mutableRunInfo.getTimeSeriesProperty<double>(PROTON_CHARGE_PROPERTY)
          ->addValue(pulseTime, ISISMsg->proton_charge());
      for (decltype(nEvents) i = 0; i < nEvents; ++i) {
        auto &spectrum = periodBuffer.getSpectrum(m_specToIdx[detData[i]]);
        spectrum.addEventQuickly(TofEvent(static_cast<double>(tofData[i]) *
                                              1e-9, // nanoseconds to seconds
                                          pulseTime));
      }
    }

    // Check if we have a runMessage
    if (flatbuffers::BufferHasIdentifier(
            reinterpret_cast<const uint8_t *>(buffer.c_str()),
            RUN_MESSAGE_ID.c_str())) {
      // Check if we have a runStop message
      auto runMsg =
          GetRunInfo(reinterpret_cast<const uint8_t *>(buffer.c_str()));
      if (runMsg->info_type_type() == InfoTypes_RunStop) {
        auto runStopMsg = static_cast<const RunStop *>(runMsg->info_type());
        auto stopTime = runStopMsg->stop_time();
        g_log.debug() << "stopTime is " << stopTime << std::endl;
        // Wait for max latency so that we don't miss any late messages
        std::this_thread::sleep_for(MAX_LATENCY);
        stopOffsets = m_eventStream->getOffsetsForTimestamp(
            (stopTime + 1) * 1000); // Convert seconds to milliseconds
        // Set reachedEnd to false for each topic and partition
        for (auto keyValue : stopOffsets) {
          // Ignore the runInfo topic
          if (keyValue.first.substr(
                  keyValue.first.length() -
                  KafkaTopicSubscriber::RUN_TOPIC_SUFFIX.length()) !=
              KafkaTopicSubscriber::RUN_TOPIC_SUFFIX) {
            g_log.debug() << "TOPIC: " << keyValue.first
                          << "PARTITIONS: " << keyValue.second.size()
                          << std::endl;
            reachedEnd.insert(
                {keyValue.first,
                 std::vector<bool>(keyValue.second.size(), false)});
          }
        }
        checkOffsets = true;
        g_log.debug("Received an end-of-run message");
      }
    }
  }
  g_log.debug("Event capture finished");
}

KafkaEventStreamDecoder::RunStartStruct
KafkaEventStreamDecoder::getRunStartMessage(std::string &rawMsgBuffer) {
  getRunInfoMessage(rawMsgBuffer);
  auto runMsg =
      GetRunInfo(reinterpret_cast<const uint8_t *>(rawMsgBuffer.c_str()));
  if (runMsg->info_type_type() != InfoTypes_RunStart) {
    // We want a runStart message, try the next one
    getRunInfoMessage(rawMsgBuffer);
    runMsg =
        GetRunInfo(reinterpret_cast<const uint8_t *>(rawMsgBuffer.c_str()));
    if (runMsg->info_type_type() != InfoTypes_RunStart) {
      throw std::runtime_error("KafkaEventStreamDecoder::initLocalCaches() - "
                               "Could not find a run start message"
                               "in the run info topic. Unable to continue");
    }
  }
  auto runStartData = static_cast<const RunStart *>(runMsg->info_type());
  KafkaEventStreamDecoder::RunStartStruct runStart = {
      runStartData->instrument_name()->str(), runStartData->run_number(),
      runStartData->start_time(),
      static_cast<size_t>(runStartData->n_periods())};
  return runStart;
}

/**
 * Pull information from the run & detector-spectrum stream and initialize
 * the internal EventWorkspace buffer + other cached information such as run
 * start. This includes loading the instrument.
 * By the end of this method the local event buffer is ready to accept
 * events
 */
void KafkaEventStreamDecoder::initLocalCaches() {
  std::string rawMsgBuffer;

  // Load spectra-detector mapping from stream
  int64_t offset;
  int32_t partition;
  std::string topicName;
  m_spDetStream->consumeMessage(&rawMsgBuffer, offset, partition, topicName);
  if (rawMsgBuffer.empty()) {
    throw std::runtime_error("KafkaEventStreamDecoder::initLocalCaches() - "
                             "Empty message received from spectrum-detector "
                             "topic. Unable to continue");
  }
  auto spDetMsg = GetSpectraDetectorMapping(
      reinterpret_cast<const uint8_t *>(rawMsgBuffer.c_str()));
  auto nspec = spDetMsg->spectrum()->size();
  auto nudet = spDetMsg->detector_id()->size();
  if (nudet != nspec) {
    std::ostringstream os;
    os << "KafkaEventStreamDecoder::initLocalEventBuffer() - Invalid "
          "spectra/detector mapping. Expected matched length arrays but "
          "found nspec=" << nspec << ", ndet=" << nudet;
    throw std::runtime_error(os.str());
  }
  // Create buffer
  auto eventBuffer = createBufferWorkspace(
      static_cast<size_t>(spDetMsg->n_spectra()), spDetMsg->spectrum()->data(),
      spDetMsg->detector_id()->data(), nudet);

  // Load run metadata
  auto runStartData = getRunStartMessage(rawMsgBuffer);
  // Load the instrument if possible but continue if we can't
  auto instName = runStartData.instrumentName;
  if (instName.size() > 0)
    loadInstrument(instName, eventBuffer);
  else
    g_log.warning(
        "Empty instrument name received. Continuing without instrument");

  auto &mutableRun = eventBuffer->mutableRun();
  // Run start. Cache locally for computing frame times
  auto runStartTime = static_cast<time_t>(runStartData.startTime);
  char timeString[32];
  strftime(timeString, 32, "%Y-%m-%dT%H:%M:%S", localtime(&runStartTime));
  m_runStart.setFromISO8601(timeString, false);
  // Run number
  mutableRun.addProperty(RUN_START_PROPERTY, std::string(timeString));
  m_runNumber = runStartData.runNumber;
  mutableRun.addProperty(RUN_NUMBER_PROPERTY, std::to_string(m_runNumber));
  // Create the proton charge property
  mutableRun.addProperty(
      new Kernel::TimeSeriesProperty<double>(PROTON_CHARGE_PROPERTY));

  // Cache spec->index mapping. We assume it is the same across all periods
  m_specToIdx = eventBuffer->getSpectrumToWorkspaceIndexMap();

  // Buffers for each period
  const size_t nperiods = runStartData.nPeriods;
  if (nperiods == 0) {
    throw std::runtime_error(
        "KafkaEventStreamDecoder - Message has n_periods==0. This is "
        "an error by the data producer");
  }
  std::lock_guard<std::mutex> lock(m_mutex);
  m_localEvents.resize(nperiods);
  m_localEvents[0] = eventBuffer;
  for (size_t i = 1; i < nperiods; ++i) {
    // A clone should be cheap here as there are no events yet
    m_localEvents[i] = eventBuffer->clone();
  }
}

/**
 * Try to get a runInfo message from Kafka, throw error if it fails
 * @param rawMsgBuffer : string to use as message buffer
 */
void KafkaEventStreamDecoder::getRunInfoMessage(std::string &rawMsgBuffer) {
  int64_t offset;
  int32_t partition;
  std::string topicName;
  m_runStream->consumeMessage(&rawMsgBuffer, offset, partition, topicName);
  if (rawMsgBuffer.empty()) {
    throw std::runtime_error("KafkaEventStreamDecoder::initLocalCaches() - "
                             "Empty message received from run info "
                             "topic. Unable to continue");
  }
}

/**
 * Create a buffer workspace of the correct size based on the values given.
 * @param nspectra The number of unique spectrum numbers
 * @param spec An array of length ndet specifying the spectrum number of each
 * detector
 * @param udet An array of length ndet specifying the detector ID of each
 * detector
 * @param length The length of the spec/udet arrays
 * @return A new workspace of the appropriate size
 */
DataObjects::EventWorkspace_sptr KafkaEventStreamDecoder::createBufferWorkspace(
    const size_t nspectra, const int32_t *spec, const int32_t *udet,
    const uint32_t length) {
  // Order is important here
  std::map<int32_t, std::set<int32_t>> spdetMap;
  for (uint32_t i = 0; i < length; ++i) {
    auto specNo = spec[i];
    auto detId = udet[i];
    auto search = spdetMap.find(specNo);
    if (search != spdetMap.end()) {
      search->second.insert(detId);
    } else {
      spdetMap.insert({specNo, {detId}});
    }
  }
  assert(nspectra == spdetMap.size());

  // Create event workspace
  auto eventBuffer = boost::static_pointer_cast<DataObjects::EventWorkspace>(
      API::WorkspaceFactory::Instance().create("EventWorkspace", nspectra, 2,
                                               1));
  // Set the units
  eventBuffer->getAxis(0)->unit() =
      Kernel::UnitFactory::Instance().create("TOF");
  eventBuffer->setYUnit("Counts");
  // Setup spectra-detector mapping.
  size_t wsIdx(0);
  for (const auto &spIter : spdetMap) {
    auto &spectrum = eventBuffer->getSpectrum(wsIdx);
    spectrum.setSpectrumNo(spIter.first);
    spectrum.addDetectorIDs(spIter.second);
    ++wsIdx;
  }
  return eventBuffer;
}

/**
 * Create new buffer workspace from an existing copy
 * @param parent A pointer to an existing workspace
 */
DataObjects::EventWorkspace_sptr KafkaEventStreamDecoder::createBufferWorkspace(
    const DataObjects::EventWorkspace_sptr &parent) {
  auto buffer = boost::static_pointer_cast<DataObjects::EventWorkspace>(
      API::WorkspaceFactory::Instance().create(
          "EventWorkspace", parent->getNumberHistograms(), 2, 1));
  // Copy meta data
  API::WorkspaceFactory::Instance().initializeFromParent(*parent, *buffer,
                                                         false);
  // Clear out the old logs, except for the most recent entry
  buffer->mutableRun().clearOutdatedTimeSeriesLogValues();
  return buffer;
}

/**
 * Run LoadInstrument for the given instrument name. If it cannot succeed it
 * does nothing to the internal workspace
 * @param name Name of an instrument to load
 * @param workspace A pointer to the workspace receiving the instrument
 */
void KafkaEventStreamDecoder::loadInstrument(
    const std::string &name, DataObjects::EventWorkspace_sptr workspace) {
  if (name.empty()) {
    g_log.warning("Empty instrument name found");
    return;
  }
  try {
    auto alg =
        API::AlgorithmManager::Instance().createUnmanaged("LoadInstrument");
    // Do not put the workspace in the ADS
    alg->setChild(true);
    alg->initialize();
    alg->setPropertyValue("InstrumentName", name);
    alg->setProperty("Workspace", workspace);
    alg->setProperty("RewriteSpectraMap", Kernel::OptionalBool(false));
    alg->execute();
  } catch (std::exception &exc) {
    g_log.warning() << "Error loading instrument '" << name
                    << "': " << exc.what() << "\n";
  }
}
}

} // namespace Mantid