Improvements on the MID reject list

- Correctly build the reject list even for runs where the issue happens at the very last sampled QC object, just before EOR
- Search for switched off boards at the end of the period with bad quality instead of the beginning. This should make sure that we do not miss additional boards that stops sending data
- Remove additional time margin at the beginning and end of the run
- Get run number from QC metadata

Author: dstocco

Detectors/MUON/MID/Calibration/macros/build_rejectlist.C

@@ -1,3 +1,4 @@
+
 // Copyright 2019-2020 CERN and copyright holders of ALICE O2.
 // See https://alice-o2.web.cern.ch/copyright for details of the copyright holders.
 // All rights not expressly granted are reserved.
@@ -50,6 +51,17 @@ struct RejectListStruct {
   std::vector<o2::mid::ColumnData> rejectList{}; /// Bad channels
 };
 
+/// @brief Useful metadata
+struct MDStruct {
+  long start = 0;      /// Start validity
+  long end = 0;        /// End validity
+  int runNumber = 0;   /// Run number
+  std::string runType; /// Run Type
+
+  bool operator<(const MDStruct& other) const { return start < other.start; }
+  bool operator==(const MDStruct& other) const { return start == other.start; }
+};
+
 /// @brief Get timestamp in milliseconds
 /// @param timestamp Input timestamp (in s or ms)
 /// @return Timestamp in ms
@@ -96,23 +108,33 @@ std::string timeRangeToString(long start, long end)
 /// @param end Query objects created not after
 /// @param api CDB api
 /// @param path CDB path
-/// @return Vector of start validity of each object sorted in ascending way
-std::vector<long> findObjectsTSInPeriod(long start, long end, const o2::ccdb::CcdbApi& api, const char* path)
+/// @return Vector of metadata in ascending order
+std::vector<MDStruct> findObjectsMDInPeriod(long start, long end, const o2::ccdb::CcdbApi& api, const char* path)
 {
-  std::vector<long> ts;
-  auto out = api.list(path, false, "text/plain", getTSMS(end), getTSMS(start));
-  std::stringstream ss(out);
-  std::string token;
-  while (ss >> token) {
-    if (token.find("Validity") != std::string::npos) {
-      ss >> token;
-      ts.emplace_back(std::atol(token.c_str()));
-    }
+  std::vector<MDStruct> mds;
+  auto out = api.list(path, false, "application/json", getTSMS(end), getTSMS(start));
+  rapidjson::Document doc;
+  doc.Parse(out.c_str());
+  for (auto& obj : doc["objects"].GetArray()) {
+    MDStruct md;
+    md.start = obj["validFrom"].GetInt64();
+    md.end = obj["validUntil"].GetInt64();
+    md.runNumber = std::atoi(obj["RunNumber"].GetString());
+    md.runType = obj["RunType"].GetString();
+    mds.emplace_back(md);
   }
-  ts.erase(std::unique(ts.begin(), ts.end()), ts.end());
+  mds.erase(std::unique(mds.begin(), mds.end()), mds.end());
   // Sort timestamps in ascending order
-  std::sort(ts.begin(), ts.end());
-  return ts;
+  std::sort(mds.begin(), mds.end());
+  return mds;
+}
+
+/// @brief Gets the quality trend graph from the quality canvas
+/// @param qcQuality MID QC quality canvas
+/// @return Quality trend graph
+TGraph* getQualityTrend(const TCanvas* qcQuality)
+{
+  return static_cast<TGraph*>(qcQuality->GetListOfPrimitives()->FindObject("Graph"));
 }
 
 /// @brief Find the first and last time when the quality was good or bad
@@ -121,7 +143,13 @@ std::vector<long> findObjectsTSInPeriod(long start, long end, const o2::ccdb::Cc
 /// @return Pair with first and last time
 std::pair<uint64_t, uint64_t> findTSRange(TCanvas* qcQuality, bool selectBad = true)
 {
-  auto* gr = static_cast<TGraph*>(qcQuality->GetListOfPrimitives()->FindObject("Graph"));
+  // Gets the plot with the quality flags
+  // The flag values are:
+  // Good: 3.5
+  // Medium: 2.5
+  // Bad: 1.5
+  // Null: 0.5
+  auto* gr = getQualityTrend(qcQuality);
   double xp, yp;
   std::pair<uint64_t, uint64_t> range{std::numeric_limits<uint64_t>::max(), 0};
   for (int ip = 0; ip < gr->GetN(); ++ip) {
@@ -138,6 +166,32 @@ std::pair<uint64_t, uint64_t> findTSRange(TCanvas* qcQuality, bool selectBad = t
   return range;
 }
 
+/// @brief Gets the first and last timestamp in the quality
+/// @param qcQuality MID QC quality canvas
+/// @return Pair with the first and last timestamp in the quality trend
+std::pair<uint64_t, uint64_t> getFirstLast(const TCanvas* qcQuality)
+{
+  auto* gr = getQualityTrend(qcQuality);
+  double xp1, xp2, yp;
+  gr->GetPoint(0, xp1, yp);
+  gr->GetPoint(gr->GetN() - 1, xp2, yp);
+  return {static_cast<uint64_t>(xp1 * 1000), static_cast<uint64_t>(xp2 * 1000)};
+}
+
+/// @brief Update the selected range of timestamp
+/// @param selectedTSRange Reference to the selected range to be modified
+/// @param qcTSRange Range of the MID quality trend
+/// @param runRange Run range
+void updateRange(std::pair<uint64_t, uint64_t>& selectedTSRange, const std::pair<uint64_t, uint64_t> qcTSRange, const std::pair<uint64_t, uint64_t> runRange)
+{
+  if (selectedTSRange.first == qcTSRange.first) {
+    selectedTSRange.first = runRange.first;
+  }
+  if (selectedTSRange.second == qcTSRange.second) {
+    selectedTSRange.second = runRange.second;
+  }
+}
+
 /// @brief Find bad channels from the occupancy histograms
 /// @param hits Occupancy histogram
 /// @param infos Mapping
@@ -180,72 +234,61 @@ std::vector<o2::mid::ColumnData> getRejectList(std::vector<o2::mid::ColumnData>
   return badChannels;
 }
 
-/// @brief Gets the run duration with a safety marging
-/// @param ccdbApi CCDB api
-/// @param marging margin in milliseconds
-/// @return Pair with the timestamps of start-margin and end+margin for the run
-std::pair<int64_t, int64_t> getRunDuration(const o2::ccdb::CcdbApi& ccdbApi, int runNumber, int64_t margin = 120000)
-{
-  auto runRange = o2::ccdb::BasicCCDBManager::getRunDuration(ccdbApi, runNumber);
-  runRange.first -= margin;  // Subtract margin
-  runRange.second += margin; // Add margin
-  return runRange;
-}
-
 /// @brief Builds the reject list for the selected timestamp
-/// @param timestamp Timestamp for query
+/// @param md MD structure
 /// @param qcdbApi QCDB api
 /// @param ccdbApi CCDB api
 /// @param outCCDBApi api of the CCDB where the reject list will be uploaded
 /// @return Reject list
-RejectListStruct build_rejectlist(long timestamp, const o2::ccdb::CcdbApi& qcdbApi, const o2::ccdb::CcdbApi& ccdbApi)
+RejectListStruct build_rejectlist(const MDStruct& md, const o2::ccdb::CcdbApi& qcdbApi, const o2::ccdb::CcdbApi& ccdbApi)
 {
-  std::map<std::string, std::string> metadata;
   RejectListStruct rl;
-  auto* qcQuality = qcdbApi.retrieveFromTFileAny<TCanvas>(sPathQCQuality, metadata, getTSMS(timestamp));
+  if (md.runType != "PHYSICS") {
+    std::cout << "Run " << md.runNumber << " is of type " << md.runType << ": skip" << std::endl;
+    return rl;
+  }
+
+  std::map<std::string, std::string> metadata;
+  auto* qcQuality = qcdbApi.retrieveFromTFileAny<TCanvas>(sPathQCQuality, metadata, getTSMS(md.start));
   if (!qcQuality) {
-    std::cerr << "Cannot find QC quality for " << tsToString(timestamp) << std::endl;
+    std::cerr << "Cannot find QC quality for " << tsToString(md.start) << std::endl;
     return rl;
   }
+
   // Find the first and last timestamp where the quality was bad (if any)
   auto badTSRange = findTSRange(qcQuality);
   if (badTSRange.second == 0) {
     std::cout << "All good" << std::endl;
     return rl;
   }
+
+  // Find the first and last timestamp where the quality flag was set
+  auto qualityTSRange = getFirstLast(qcQuality);
   // Search for the last timestamp for which the run quality was good
   auto goodTSRange = findTSRange(qcQuality, false);
-  // Query the CCDB to see to which run the timestamp corresponds
-  auto oldestTSInQCQuality = (goodTSRange.first == 0) ? badTSRange.first : goodTSRange.first;
-  auto grpecs = *ccdbApi.retrieveFromTFileAny<o2::parameters::GRPECSObject>("GLO/Config/GRPECS", metadata, getTSMS(oldestTSInQCQuality));
-  if (!grpecs.isDetReadOut(o2::detectors::DetID::MID)) {
-    std::cout << "Error: we are probably reading a parallel run" << std::endl;
-    grpecs.print();
-    return rl;
-  }
-  if (grpecs.getRunType() != o2::parameters::GRPECS::PHYSICS) {
-    std::cout << "This is not a physics run: skip" << std::endl;
-    grpecs.print();
-    return rl;
-  }
 
-  auto runRange = getRunDuration(ccdbApi, grpecs.getRun());
+  auto runRange = o2::ccdb::BasicCCDBManager::getRunDuration(ccdbApi, md.runNumber);
+  updateRange(badTSRange, qualityTSRange, runRange);
+  updateRange(goodTSRange, qualityTSRange, runRange);
 
   // Search for hits histogram in the period where the QC quality was bad
-  auto tsVector = findObjectsTSInPeriod(badTSRange.first, badTSRange.second, qcdbApi, "qc/MID/MO/QcTaskMIDDigits/Hits");
-  if (tsVector.empty()) {
+  auto mdVector = findObjectsMDInPeriod(badTSRange.first, badTSRange.second, qcdbApi, "qc/MID/MO/QcTaskMIDDigits/Hits");
+  if (mdVector.empty()) {
     std::cerr << "Cannot find hits in period " << tsToString(badTSRange.first) << " - " << tsToString(badTSRange.second) << std::endl;
     return {};
   }
-  // Focus on the first object found
-  TH1* occupancy = qcdbApi.retrieveFromTFileAny<TH1F>("qc/MID/MO/QcTaskMIDDigits/Hits", metadata, getTSMS(tsVector.front()));
+  // Focus on the last object found
+  // We chose the last instead of the first because it might happen that
+  // we lose additional boards before the EOR
+  // If we build the reject list for the first object, we would therefore miss some boards
+  TH1* occupancy = qcdbApi.retrieveFromTFileAny<TH1F>("qc/MID/MO/QcTaskMIDDigits/Hits", metadata, getTSMS(mdVector.back().start));
   o2::mid::GlobalMapper gm;
   auto infos = gm.buildStripsInfo();
   auto badChannels = findBadChannels(occupancy, infos);
-  auto badChannelsCCDB = *ccdbApi.retrieveFromTFileAny<std::vector<o2::mid::ColumnData>>("MID/Calib/BadChannels", metadata, getTSMS(timestamp));
+  auto badChannelsCCDB = *ccdbApi.retrieveFromTFileAny<std::vector<o2::mid::ColumnData>>("MID/Calib/BadChannels", metadata, getTSMS(md.start));
   rl.rejectList = getRejectList(badChannels, badChannelsCCDB);
   if (rl.rejectList.empty()) {
-    std::cout << "Warning: reject list was empty. It probably means that an entire board is already masked in calibration for run " << grpecs.getRun() << std::endl;
+    std::cout << "Warning: reject list was empty. It probably means that an entire board is already masked in calibration for run " << md.runNumber << std::endl;
     return rl;
   }
 
@@ -254,21 +297,15 @@ RejectListStruct build_rejectlist(long timestamp, const o2::ccdb::CcdbApi& qcdbA
   for (auto& col : rl.rejectList) {
     std::cout << col << std::endl;
   }
-  std::cout << "Run number: " << grpecs.getRun() << std::endl;
-  std::cout << "SOR - EOR: " << timeRangeToString(grpecs.getTimeStart(), grpecs.getTimeEnd()) << std::endl;
+  std::cout << "Run number: " << md.runNumber << std::endl;
   std::cout << "SOT - EOT: " << timeRangeToString(runRange.first, runRange.second) << std::endl;
   std::cout << "Good:      " << timeRangeToString(goodTSRange.first, goodTSRange.second) << std::endl;
   std::cout << "Bad:       " << timeRangeToString(badTSRange.first, badTSRange.second) << std::endl;
+  std::cout << "Fraction bad: " << static_cast<double>(badTSRange.second - badTSRange.first) / static_cast<double>(runRange.second - runRange.first) << std::endl;
 
   // Set the start of the reject list to the last timestamp in which the occupancy was ok
   rl.start = goodTSRange.second;
-  if (goodTSRange.first == 0) {
-    // If the quality was bad for the full run, set the start of the reject list to the SOR
-    std::cout << "CAVEAT: no good TS found. Will use SOT instead" << std::endl;
-    rl.start = runRange.first;
-  }
-  // Set the end of the reject list to the end of run
-  rl.end = runRange.second;
+  rl.end = badTSRange.second;
   return rl;
 }
 
@@ -295,8 +332,8 @@ RejectListStruct load_from_json(const o2::ccdb::CcdbApi& ccdbApi, const char* fi
     std::cerr << "Problem parsing " << filename << std::endl;
     return rl;
   }
-  auto startRange = getRunDuration(ccdbApi, doc["startRun"].GetInt());
-  auto endRange = getRunDuration(ccdbApi, doc["endRun"].GetInt());
+  auto startRange = o2::ccdb::BasicCCDBManager::getRunDuration(ccdbApi, doc["startRun"].GetInt());
+  auto endRange = o2::ccdb::BasicCCDBManager::getRunDuration(ccdbApi, doc["endRun"].GetInt());
   rl.start = startRange.first;
   rl.end = endRange.second;
   std::cout << "Manual RL validity: " << timeRangeToString(rl.start, rl.end) << std::endl;
@@ -377,7 +414,7 @@ std::vector<RejectListStruct> merge_rejectlists(const RejectListStruct& manualRL
   return merged;
 }
 
-/// @brief Builds the reject list iin a time range
+/// @brief Builds the reject list in a time range
 /// @param start Start time for query
 /// @param end End time for query
 /// @param qcdbUrl QCDB URL
@@ -391,9 +428,9 @@ void build_rejectlist(long start, long end, const char* qcdbUrl = "http://ali-qc
   o2::ccdb::CcdbApi ccdbApi;
   ccdbApi.init(ccdbUrl);
   std::vector<RejectListStruct> rls;
-  auto objectsTS = findObjectsTSInPeriod(start, end, qcdbApi, sPathQCQuality.c_str());
-  for (auto ts : objectsTS) {
-    auto rl = build_rejectlist(ts, qcdbApi, ccdbApi);
+  auto objectsMD = findObjectsMDInPeriod(start, end, qcdbApi, sPathQCQuality.c_str());
+  for (auto md : objectsMD) {
+    auto rl = build_rejectlist(md, qcdbApi, ccdbApi);
     if (rl.start != rl.end) {
       rls.emplace_back(rl);
     }
@@ -417,4 +454,4 @@ void build_rejectlist(long start, long end, const char* qcdbUrl = "http://ali-qc
       outCCDBApi.storeAsTFileAny(&rl.rejectList, "MID/Calib/RejectList", metadata, rl.start, rl.end);
     }
   }
-}
+}