--- a/NEWS	Wed Apr 27 16:56:53 2022 +0200
+++ b/NEWS	Sat Apr 30 19:40:52 2022 +0200
@@ -12,7 +12,7 @@
     the storage might still contain dicom-as-json files that are not needed
     anymore -> it will remove them
   - if "ExtraMainDicomTags" has changed.
-  - if "StorageCompression" has chagned.
+  - if "StorageCompression" or "IngestTranscoding" has chagned.
 * New configuration "Warnings" to enable/disable individual warnings that can
   be identified by a W0XX prefix in the logs.
   These warnings have been added:
@@ -38,9 +38,20 @@
   - /studies, /studies/../series, /studies/../instances
   - /series, /series/../instances
   - /instances
-* new field "MainDicomTags" in the /system route response to list the tags that
-  are saved in DB
-* new field "StorageCompression" reported in the /system route response
+* /reconstruct routes:
+  - new options "ReconstructFiles" (false by default to keep backward compatibility) to 
+    potentialy compress/uncompress the files or transcode them if "StorageCompression"
+    or "IngestTranscoding" has changed since the file has been ingested.
+  POSSIBLE BREAKING-CHANGES:
+  - the /reconstruct routes now preserve all metadata
+  - the /reconstruct routes now skip the IncomingInstanceFilter
+  - the /reconstruct routes won't generate new events like NewStudy, StableStudy, ...
+    therefore, the corresponding callbacks won't be called anymore
+  - the /reconstruct routes won't affect the patient recycling anymore
+* new fields reported in the /system route:
+  - "MainDicomTags" to list the tags that are saved in DB
+  - "StorageCompression", "OverwriteInstances", "IngestTranscoding" reported from the 
+    configuration file
 * New option "filename" in "/.../{id}/archive" and "/.../{id}/media" to
   manually set the filename in the "Content-Disposition" HTTP header
 

--- a/OrthancServer/Plugins/Samples/Housekeeper/Plugin.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Plugins/Samples/Housekeeper/Plugin.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -25,6 +25,7 @@
 
 #include <boost/thread.hpp>
 #include <boost/algorithm/string.hpp>
+#include <boost/date_time/posix_time/posix_time.hpp>
 #include <json/value.h>
 #include <json/writer.h>
 #include <string.h>
@@ -42,6 +43,7 @@
 static bool triggerOnStorageCompressionChange_ = true;
 static bool triggerOnMainDicomTagsChange_ = true;
 static bool triggerOnUnnecessaryDicomAsJsonFiles_ = true;
+static bool triggerOnIngestTranscodingChange_ = true;
 
 
 struct RunningPeriod
@@ -112,6 +114,7 @@
   }
 };
 
+
 struct RunningPeriods
 {
   std::list<RunningPeriod> runningPeriods_;
@@ -153,6 +156,7 @@
 
 RunningPeriods runningPeriods_;
 
+
 struct DbConfiguration
 {
   std::string orthancVersion;
@@ -160,6 +164,7 @@
   std::string studiesMainDicomTagsSignature;
   std::string seriesMainDicomTagsSignature;
   std::string instancesMainDicomTagsSignature;
+  std::string ingestTranscoding;
   bool storageCompressionEnabled;
 
   DbConfiguration()
@@ -179,6 +184,7 @@
     studiesMainDicomTagsSignature.clear();
     seriesMainDicomTagsSignature.clear();
     instancesMainDicomTagsSignature.clear();
+    ingestTranscoding.clear();
   }
 
   void ToJson(Json::Value& target)
@@ -202,6 +208,7 @@
       target["MainDicomTagsSignature"] = signatures;
       target["OrthancVersion"] = orthancVersion;
       target["StorageCompressionEnabled"] = storageCompressionEnabled;
+      target["IngestTranscoding"] = ingestTranscoding;
     }
   }
 
@@ -218,15 +225,18 @@
       instancesMainDicomTagsSignature = signatures["Instance"].asString();
 
       storageCompressionEnabled = source["StorageCompressionEnabled"].asBool();
+      ingestTranscoding = source["IngestTranscoding"].asString();
     }
   }
 };
 
+
 struct PluginStatus
 {
   int statusVersion;
   int64_t lastProcessedChange;
   int64_t lastChangeToProcess;
+  boost::posix_time::ptime lastTimeStarted;
 
   DbConfiguration currentlyProcessingConfiguration; // last configuration being processed (has not reached last change yet)
   DbConfiguration lastProcessedConfiguration;       // last configuration that has been fully processed (till last change)
@@ -234,7 +244,8 @@
   PluginStatus()
   : statusVersion(1),
     lastProcessedChange(-1),
-    lastChangeToProcess(-1)
+    lastChangeToProcess(-1),
+    lastTimeStarted(boost::date_time::special_values::not_a_date_time)
   {
   }
 
@@ -245,6 +256,15 @@
     target["Version"] = statusVersion;
     target["LastProcessedChange"] = Json::Value::Int64(lastProcessedChange);
     target["LastChangeToProcess"] = Json::Value::Int64(lastChangeToProcess);
+    
+    if (lastTimeStarted == boost::posix_time::special_values::not_a_date_time)
+    {
+      target["LastTimeStarted"] = Json::Value::null;  
+    }
+    else
+    {
+      target["LastTimeStarted"] = boost::posix_time::to_iso_string(lastTimeStarted);
+    }
 
     currentlyProcessingConfiguration.ToJson(target["CurrentlyProcessingConfiguration"]);
     lastProcessedConfiguration.ToJson(target["LastProcessedConfiguration"]);
@@ -255,6 +275,14 @@
     statusVersion = source["Version"].asInt();
     lastProcessedChange = source["LastProcessedChange"].asInt64();
     lastChangeToProcess = source["LastChangeToProcess"].asInt64();
+    if (source["LastTimeStarted"].isNull())
+    {
+      lastTimeStarted = boost::posix_time::special_values::not_a_date_time;
+    }
+    else
+    {
+      lastTimeStarted = boost::posix_time::from_iso_string(source["LastTimeStarted"].asString());
+    }
 
     Json::Value& current = source["CurrentlyProcessingConfiguration"];
     Json::Value& last = source["LastProcessedConfiguration"];
@@ -264,9 +292,13 @@
   }
 };
 
+static PluginStatus pluginStatus_;
+static boost::recursive_mutex pluginStatusMutex_;
 
-static void ReadStatusFromDb(PluginStatus& pluginStatus)
+static void ReadStatusFromDb()
 {
+  boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+
   OrthancPlugins::OrthancString globalPropertyContent;
 
   globalPropertyContent.Assign(OrthancPluginGetGlobalProperty(OrthancPlugins::GetGlobalContext(),
@@ -277,29 +309,32 @@
   {
     Json::Value jsonStatus;
     globalPropertyContent.ToJson(jsonStatus);
-    pluginStatus.FromJson(jsonStatus);
+    pluginStatus_.FromJson(jsonStatus);
   }
   else
   {
     // default config
-    pluginStatus.statusVersion = 1;
-    pluginStatus.lastProcessedChange = -1;
-    pluginStatus.lastChangeToProcess = -1;
+    pluginStatus_.statusVersion = 1;
+    pluginStatus_.lastProcessedChange = -1;
+    pluginStatus_.lastChangeToProcess = -1;
+    pluginStatus_.lastTimeStarted = boost::date_time::special_values::not_a_date_time;
     
-    pluginStatus.currentlyProcessingConfiguration.orthancVersion = "1.9.0"; // when we don't know, we assume some files were stored with Orthanc 1.9.0 (last version saving the dicom-as-json files)
+    pluginStatus_.lastProcessedConfiguration.orthancVersion = "1.9.0"; // when we don't know, we assume some files were stored with Orthanc 1.9.0 (last version saving the dicom-as-json files)
 
     // default main dicom tags signature are the one from Orthanc 1.4.2 (last time the list was changed):
-    pluginStatus.currentlyProcessingConfiguration.patientsMainDicomTagsSignature = "0010,0010;0010,0020;0010,0030;0010,0040;0010,1000";
-    pluginStatus.currentlyProcessingConfiguration.studiesMainDicomTagsSignature = "0008,0020;0008,0030;0008,0050;0008,0080;0008,0090;0008,1030;0020,000d;0020,0010;0032,1032;0032,1060";
-    pluginStatus.currentlyProcessingConfiguration.seriesMainDicomTagsSignature = "0008,0021;0008,0031;0008,0060;0008,0070;0008,1010;0008,103e;0008,1070;0018,0010;0018,0015;0018,0024;0018,1030;0018,1090;0018,1400;0020,000e;0020,0011;0020,0037;0020,0105;0020,1002;0040,0254;0054,0081;0054,0101;0054,1000";
-    pluginStatus.currentlyProcessingConfiguration.instancesMainDicomTagsSignature = "0008,0012;0008,0013;0008,0018;0020,0012;0020,0013;0020,0032;0020,0037;0020,0100;0020,4000;0028,0008;0054,1330"; 
+    pluginStatus_.lastProcessedConfiguration.patientsMainDicomTagsSignature = "0010,0010;0010,0020;0010,0030;0010,0040;0010,1000";
+    pluginStatus_.lastProcessedConfiguration.studiesMainDicomTagsSignature = "0008,0020;0008,0030;0008,0050;0008,0080;0008,0090;0008,1030;0020,000d;0020,0010;0032,1032;0032,1060";
+    pluginStatus_.lastProcessedConfiguration.seriesMainDicomTagsSignature = "0008,0021;0008,0031;0008,0060;0008,0070;0008,1010;0008,103e;0008,1070;0018,0010;0018,0015;0018,0024;0018,1030;0018,1090;0018,1400;0020,000e;0020,0011;0020,0037;0020,0105;0020,1002;0040,0254;0054,0081;0054,0101;0054,1000";
+    pluginStatus_.lastProcessedConfiguration.instancesMainDicomTagsSignature = "0008,0012;0008,0013;0008,0018;0020,0012;0020,0013;0020,0032;0020,0037;0020,0100;0020,4000;0028,0008;0054,1330"; 
   }
 }
 
-static void SaveStatusInDb(PluginStatus& pluginStatus)
+static void SaveStatusInDb()
 {
+  boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+
   Json::Value jsonStatus;
-  pluginStatus.ToJson(jsonStatus);
+  pluginStatus_.ToJson(jsonStatus);
 
   Json::StreamWriterBuilder builder;
   builder.settings_["indentation"] = "   ";
@@ -321,26 +356,29 @@
   configuration.seriesMainDicomTagsSignature = systemInfo["MainDicomTags"]["Series"].asString();
   configuration.instancesMainDicomTagsSignature = systemInfo["MainDicomTags"]["Instance"].asString();
   configuration.storageCompressionEnabled = systemInfo["StorageCompression"].asBool();
+  configuration.ingestTranscoding = systemInfo["IngestTranscoding"].asString();
 
   configuration.orthancVersion = OrthancPlugins::GetGlobalContext()->orthancVersion;
 }
 
-static bool NeedsProcessing(const DbConfiguration& current, const DbConfiguration& last)
+static void CheckNeedsProcessing(bool& needsReconstruct, bool& needsReingest, const DbConfiguration& current, const DbConfiguration& last)
 {
+  needsReconstruct = false;
+  needsReingest = false;
+
   if (!last.IsDefined())
   {
-    return true;
+    return;
   }
 
   const char* lastVersion = last.orthancVersion.c_str();
-  bool needsProcessing = false;
 
   if (!OrthancPlugins::CheckMinimalVersion(lastVersion, 1, 9, 1))
   {
     if (triggerOnUnnecessaryDicomAsJsonFiles_)
     {
       OrthancPlugins::LogWarning("Housekeeper: your storage might still contain some dicom-as-json files -> will perform housekeeping");
-      needsProcessing = true;
+      needsReconstruct = true;  // the default reconstruct removes the dicom-as-json
     }
     else
     {
@@ -353,7 +391,7 @@
     if (triggerOnMainDicomTagsChange_)
     {
       OrthancPlugins::LogWarning("Housekeeper: Patient main dicom tags have changed, -> will perform housekeeping");
-      needsProcessing = true;
+      needsReconstruct = true;
     }
     else
     {
@@ -366,7 +404,7 @@
     if (triggerOnMainDicomTagsChange_)
     {
       OrthancPlugins::LogWarning("Housekeeper: Study main dicom tags have changed, -> will perform housekeeping");
-      needsProcessing = true;
+      needsReconstruct = true;
     }
     else
     {
@@ -379,7 +417,7 @@
     if (triggerOnMainDicomTagsChange_)
     {
       OrthancPlugins::LogWarning("Housekeeper: Series main dicom tags have changed, -> will perform housekeeping");
-      needsProcessing = true;
+      needsReconstruct = true;
     }
     else
     {
@@ -392,7 +430,7 @@
     if (triggerOnMainDicomTagsChange_)
     {
       OrthancPlugins::LogWarning("Housekeeper: Instance main dicom tags have changed, -> will perform housekeeping");
-      needsProcessing = true;
+      needsReconstruct = true;
     }
     else
     {
@@ -413,7 +451,7 @@
         OrthancPlugins::LogWarning("Housekeeper: storage compression is now disabled -> will perform housekeeping");
       }
       
-      needsProcessing = true;
+      needsReingest = true;
     }
     else
     {
@@ -421,16 +459,33 @@
     }
   }
 
-  return needsProcessing;
+  if (current.ingestTranscoding != last.ingestTranscoding)
+  {
+    if (triggerOnIngestTranscodingChange_)
+    {
+      OrthancPlugins::LogWarning("Housekeeper: ingest transcoding has changed -> will perform housekeeping");
+      
+      needsReingest = true;
+    }
+    else
+    {
+      OrthancPlugins::LogWarning("Housekeeper: ingest transcoding has changed but the trigger is disabled");
+    }
+  }
+
 }
 
-static bool ProcessChanges(PluginStatus& pluginStatus, const DbConfiguration& currentDbConfiguration)
+static bool ProcessChanges(bool needsReconstruct, bool needsReingest, const DbConfiguration& currentDbConfiguration)
 {
   Json::Value changes;
 
-  pluginStatus.currentlyProcessingConfiguration = currentDbConfiguration;
+  {
+    boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
 
-  OrthancPlugins::RestApiGet(changes, "/changes?since=" + boost::lexical_cast<std::string>(pluginStatus.lastProcessedChange) + "&limit=100", false);
+    pluginStatus_.currentlyProcessingConfiguration = currentDbConfiguration;
+
+    OrthancPlugins::RestApiGet(changes, "/changes?since=" + boost::lexical_cast<std::string>(pluginStatus_.lastProcessedChange) + "&limit=100", false);
+  }
 
   for (Json::ArrayIndex i = 0; i < changes["Changes"].size(); i++)
   {
@@ -440,16 +495,29 @@
     if (change["ChangeType"] == "NewStudy") // some StableStudy might be missing if orthanc was shutdown during a StableAge -> consider only the NewStudy events that can not be missed
     {
       Json::Value result;
-      OrthancPlugins::RestApiPost(result, "/studies/" + change["ID"].asString() + "/reconstruct", std::string(""), false);
-      boost::this_thread::sleep(boost::posix_time::milliseconds(throttleDelay_ * 1000));
+      Json::Value request;
+      if (needsReingest)
+      {
+        request["ReconstructFiles"] = true;
+      }
+      OrthancPlugins::RestApiPost(result, "/studies/" + change["ID"].asString() + "/reconstruct", request, false);
     }
 
-    if (seq >= pluginStatus.lastChangeToProcess)  // we are done !
     {
-      return true;
+      boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+
+      pluginStatus_.lastProcessedChange = seq;
+
+      if (seq >= pluginStatus_.lastChangeToProcess)  // we are done !
+      {
+        return true;
+      }
     }
 
-    pluginStatus.lastProcessedChange = seq;
+    if (change["ChangeType"] == "NewStudy")
+    {
+      boost::this_thread::sleep(boost::posix_time::milliseconds(throttleDelay_ * 1000));
+    }
   }
 
   return false;
@@ -458,21 +526,31 @@
 
 static void WorkerThread()
 {
-  PluginStatus pluginStatus;
   DbConfiguration currentDbConfiguration;
 
   OrthancPluginLogWarning(OrthancPlugins::GetGlobalContext(), "Starting Housekeeper worker thread");
 
-  ReadStatusFromDb(pluginStatus);
+  ReadStatusFromDb();
+
   GetCurrentDbConfiguration(currentDbConfiguration);
 
-  if (!NeedsProcessing(currentDbConfiguration, pluginStatus.lastProcessedConfiguration))
+  bool needsReconstruct = false;
+  bool needsReingest = false;
+
+  {
+    boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+    CheckNeedsProcessing(needsReconstruct, needsReingest, currentDbConfiguration, pluginStatus_.lastProcessedConfiguration);
+  }
+
+  bool needsProcessing = needsReconstruct || needsReingest;
+
+  if (!needsProcessing)
   {
     OrthancPlugins::LogWarning("Housekeeper: everything has been processed already !");
     return;
   }
 
-  if (force_ || NeedsProcessing(currentDbConfiguration, pluginStatus.currentlyProcessingConfiguration))
+  if (force_ || needsProcessing)
   {
     if (force_)
     {
@@ -486,29 +564,41 @@
     Json::Value changes;
     OrthancPlugins::RestApiGet(changes, "/changes?last", false);
 
-    pluginStatus.lastProcessedChange = 0;
-    pluginStatus.lastChangeToProcess = changes["Last"].asInt64();  // the last change is the last change at the time we start.  We assume that every new ingested file will be constructed correctly
+    {
+      boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+
+      pluginStatus_.lastProcessedChange = 0;
+      pluginStatus_.lastChangeToProcess = changes["Last"].asInt64();  // the last change is the last change at the time we start.  We assume that every new ingested file will be constructed correctly
+      pluginStatus_.lastTimeStarted = boost::posix_time::microsec_clock::universal_time();
+    }
   }
   else
   {
     OrthancPlugins::LogWarning("Housekeeper: the DB configuration has not changed since last run, will continue processing changes");
   }
 
-  bool completed = pluginStatus.lastChangeToProcess == 0;  // if the DB is empty at start, no need to process anyting
+  bool completed = false;
+  {
+    boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+    completed = pluginStatus_.lastChangeToProcess == 0;  // if the DB is empty at start, no need to process anyting
+  }
+
   bool loggedNotRightPeriodChangeMessage = false;
 
   while (!workerThreadShouldStop_ && !completed)
   {
     if (runningPeriods_.isInPeriod())
     {
-      completed = ProcessChanges(pluginStatus, currentDbConfiguration);
-      SaveStatusInDb(pluginStatus);
+      completed = ProcessChanges(needsReconstruct, needsReingest, currentDbConfiguration);
+      SaveStatusInDb();
       
       if (!completed)
       {
+        boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+    
         OrthancPlugins::LogInfo("Housekeeper: processed changes " + 
-                                boost::lexical_cast<std::string>(pluginStatus.lastProcessedChange) + 
-                                " / " + boost::lexical_cast<std::string>(pluginStatus.lastChangeToProcess));
+                                boost::lexical_cast<std::string>(pluginStatus_.lastProcessedChange) + 
+                                " / " + boost::lexical_cast<std::string>(pluginStatus_.lastChangeToProcess));
         
         boost::this_thread::sleep(boost::posix_time::milliseconds(throttleDelay_ * 100));  // wait 1/10 of the delay between changes
       }
@@ -527,13 +617,15 @@
 
   if (completed)
   {
-    pluginStatus.lastProcessedConfiguration = currentDbConfiguration;
-    pluginStatus.currentlyProcessingConfiguration.Clear();
+    boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+
+    pluginStatus_.lastProcessedConfiguration = currentDbConfiguration;
+    pluginStatus_.currentlyProcessingConfiguration.Clear();
 
-    pluginStatus.lastProcessedChange = -1;
-    pluginStatus.lastChangeToProcess = -1;
+    pluginStatus_.lastProcessedChange = -1;
+    pluginStatus_.lastChangeToProcess = -1;
     
-    SaveStatusInDb(pluginStatus);
+    SaveStatusInDb();
 
     OrthancPluginLogWarning(OrthancPlugins::GetGlobalContext(), "Housekeeper: finished processing all changes");
   }
@@ -541,6 +633,28 @@
 
 extern "C"
 {
+  OrthancPluginErrorCode GetPluginStatus(OrthancPluginRestOutput* output,
+                                         const char* url,
+                                         const OrthancPluginHttpRequest* request)
+  {
+    if (request->method != OrthancPluginHttpMethod_Get)
+    {
+      OrthancPlugins::AnswerMethodNotAllowed(output, "GET");
+    }
+    else
+    {
+      boost::recursive_mutex::scoped_lock lock(pluginStatusMutex_);
+
+      Json::Value status;
+      pluginStatus_.ToJson(status);
+
+      OrthancPlugins::AnswerJson(status, output);
+    }
+
+    return OrthancPluginErrorCode_Success;
+  }
+
+
   OrthancPluginErrorCode OnChangeCallback(OrthancPluginChangeType changeType,
                                           OrthancPluginResourceType resourceType,
                                           const char* resourceId)
@@ -581,10 +695,10 @@
     OrthancPlugins::LogWarning("Housekeeper plugin is initializing");
     OrthancPluginSetDescription(c, "Optimizes your DB and storage.");
 
-    OrthancPlugins::OrthancConfiguration configuration;
+    OrthancPlugins::OrthancConfiguration orthancConfiguration;
 
     OrthancPlugins::OrthancConfiguration housekeeper;
-    configuration.GetSection(housekeeper, "Housekeeper");
+    orthancConfiguration.GetSection(housekeeper, "Housekeeper");
 
     bool enabled = housekeeper.GetBooleanValue("Enable", false);
     if (enabled)
@@ -644,8 +758,10 @@
       if (housekeeper.GetJson().isMember("Triggers"))
       {
         triggerOnStorageCompressionChange_ = housekeeper.GetBooleanValue("StorageCompressionChange", true);
+
         triggerOnMainDicomTagsChange_ = housekeeper.GetBooleanValue("MainDicomTagsChange", true);
         triggerOnUnnecessaryDicomAsJsonFiles_ = housekeeper.GetBooleanValue("UnnecessaryDicomAsJsonFiles", true);
+        triggerOnIngestTranscodingChange_ = housekeeper.GetBooleanValue("IngestTranscodingChange", true);
       }
 
       if (housekeeper.GetJson().isMember("Schedule"))
@@ -654,6 +770,7 @@
       }
 
       OrthancPluginRegisterOnChangeCallback(c, OnChangeCallback);
+      OrthancPluginRegisterRestCallback(c, "/housekeeper/status", GetPluginStatus);
     }
     else
     {

--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -2850,7 +2850,8 @@
                                                  bool hasPixelDataOffset,
                                                  uint64_t pixelDataOffset,
                                                  uint64_t maximumStorageSize,
-                                                 unsigned int maximumPatients)
+                                                 unsigned int maximumPatients,
+                                                 bool isReconstruct)
   {
     class Operations : public IReadWriteOperations
     {
@@ -2868,6 +2869,7 @@
       uint64_t                             pixelDataOffset_;
       uint64_t                             maximumStorageSize_;
       unsigned int                         maximumPatientCount_;
+      bool                                 isReconstruct_;
 
       // Auto-computed fields
       bool          hasExpectedInstances_;
@@ -2955,7 +2957,8 @@
                  bool hasPixelDataOffset,
                  uint64_t pixelDataOffset,
                  uint64_t maximumStorageSize,
-                 unsigned int maximumPatientCount) :
+                 unsigned int maximumPatientCount,
+                 bool isReconstruct) :
         storeStatus_(StoreStatus_Failure),
         instanceMetadata_(instanceMetadata),
         dicomSummary_(dicomSummary),
@@ -2968,7 +2971,8 @@
         hasPixelDataOffset_(hasPixelDataOffset),
         pixelDataOffset_(pixelDataOffset),
         maximumStorageSize_(maximumStorageSize),
-        maximumPatientCount_(maximumPatientCount)
+        maximumPatientCount_(maximumPatientCount),
+        isReconstruct_(isReconstruct)
       {
         hasExpectedInstances_ = ComputeExpectedNumberOfInstances(expectedInstances_, dicomSummary);
     
@@ -3022,31 +3026,33 @@
           }
 
 
-          // Warn about the creation of new resources. The order must be
-          // from instance to patient.
-
-          // NB: In theory, could be sped up by grouping the underlying
-          // calls to "transaction.LogChange()". However, this would only have an
-          // impact when new patient/study/series get created, which
-          // occurs far less often that creating new instances. The
-          // positive impact looks marginal in practice.
-          transaction.LogChange(instanceId, ChangeType_NewInstance, ResourceType_Instance, hashInstance_);
-
-          if (status.isNewSeries_)
+          if (!isReconstruct_)  // don't signal new resources if this is a reconstruction
           {
-            transaction.LogChange(status.seriesId_, ChangeType_NewSeries, ResourceType_Series, hashSeries_);
-          }
-      
-          if (status.isNewStudy_)
-          {
-            transaction.LogChange(status.studyId_, ChangeType_NewStudy, ResourceType_Study, hashStudy_);
-          }
-      
-          if (status.isNewPatient_)
-          {
-            transaction.LogChange(status.patientId_, ChangeType_NewPatient, ResourceType_Patient, hashPatient_);
-          }
-      
+            // Warn about the creation of new resources. The order must be
+            // from instance to patient.
+
+            // NB: In theory, could be sped up by grouping the underlying
+            // calls to "transaction.LogChange()". However, this would only have an
+            // impact when new patient/study/series get created, which
+            // occurs far less often that creating new instances. The
+            // positive impact looks marginal in practice.
+            transaction.LogChange(instanceId, ChangeType_NewInstance, ResourceType_Instance, hashInstance_);
+
+            if (status.isNewSeries_)
+            {
+              transaction.LogChange(status.seriesId_, ChangeType_NewSeries, ResourceType_Series, hashSeries_);
+            }
+        
+            if (status.isNewStudy_)
+            {
+              transaction.LogChange(status.studyId_, ChangeType_NewStudy, ResourceType_Study, hashStudy_);
+            }
+        
+            if (status.isNewPatient_)
+            {
+              transaction.LogChange(status.patientId_, ChangeType_NewPatient, ResourceType_Patient, hashPatient_);
+            }
+          }      
       
           // Ensure there is enough room in the storage for the new instance
           uint64_t instanceSize = 0;
@@ -3056,9 +3062,11 @@
             instanceSize += it->GetCompressedSize();
           }
 
-          transaction.Recycle(maximumStorageSize_, maximumPatientCount_,
-                              instanceSize, hashPatient_ /* don't consider the current patient for recycling */);
-      
+          if (!isReconstruct_)  // reconstruction should not affect recycling
+          {
+            transaction.Recycle(maximumStorageSize_, maximumPatientCount_,
+                                instanceSize, hashPatient_ /* don't consider the current patient for recycling */);
+          }  
      
           // Attach the files to the newly created instance
           for (Attachments::const_iterator it = attachments_.begin();
@@ -3070,33 +3078,9 @@
       
           {
             ResourcesContent content(true /* new resource, metadata can be set */);
-      
-            // Populate the tags of the newly-created resources
-
-            content.AddResource(instanceId, ResourceType_Instance, dicomSummary_);
-            content.AddMetadata(instanceId, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Instance));  // New in Orthanc 1.11.0
-
-            if (status.isNewSeries_)
-            {
-              content.AddResource(status.seriesId_, ResourceType_Series, dicomSummary_);
-              content.AddMetadata(status.seriesId_, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Series));  // New in Orthanc 1.11.0
-            }
-
-            if (status.isNewStudy_)
-            {
-              content.AddResource(status.studyId_, ResourceType_Study, dicomSummary_);
-              content.AddMetadata(status.studyId_, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Study));  // New in Orthanc 1.11.0
-            }
-
-            if (status.isNewPatient_)
-            {
-              content.AddResource(status.patientId_, ResourceType_Patient, dicomSummary_);
-              content.AddMetadata(status.patientId_, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Patient));  // New in Orthanc 1.11.0
-            }
-
-
-            // Attach the user-specified metadata
-
+
+
+            // Attach the user-specified metadata (in case of reconstruction, metadata_ contains all past metadata, including the system ones we want to keep)
             for (MetadataMap::const_iterator 
                    it = metadata_.begin(); it != metadata_.end(); ++it)
             {
@@ -3124,7 +3108,29 @@
               }
             }
 
-        
+            // Populate the tags of the newly-created resources
+
+            content.AddResource(instanceId, ResourceType_Instance, dicomSummary_);
+            SetInstanceMetadata(content, instanceMetadata_, instanceId, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Instance));  // New in Orthanc 1.11.0
+
+            if (status.isNewSeries_)
+            {
+              content.AddResource(status.seriesId_, ResourceType_Series, dicomSummary_);
+              content.AddMetadata(status.seriesId_, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Series));  // New in Orthanc 1.11.0
+            }
+
+            if (status.isNewStudy_)
+            {
+              content.AddResource(status.studyId_, ResourceType_Study, dicomSummary_);
+              content.AddMetadata(status.studyId_, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Study));  // New in Orthanc 1.11.0
+            }
+
+            if (status.isNewPatient_)
+            {
+              content.AddResource(status.patientId_, ResourceType_Patient, dicomSummary_);
+              content.AddMetadata(status.patientId_, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(ResourceType_Patient));  // New in Orthanc 1.11.0
+            }
+
             // Attach the auto-computed metadata for the patient/study/series levels
             std::string now = SystemToolbox::GetNowIsoString(true /* use UTC time (not local time) */);
             content.AddMetadata(status.seriesId_, MetadataType_LastUpdate, now);
@@ -3144,17 +3150,6 @@
                                   origin_.GetRemoteAetC());
             }
 
-        
-            // Attach the auto-computed metadata for the instance level,
-            // reflecting these additions into the input metadata map
-            SetInstanceMetadata(content, instanceMetadata_, instanceId,
-                                MetadataType_Instance_ReceptionDate, now);
-            SetInstanceMetadata(content, instanceMetadata_, instanceId, MetadataType_RemoteAet,
-                                origin_.GetRemoteAetC());
-            SetInstanceMetadata(content, instanceMetadata_, instanceId, MetadataType_Instance_Origin, 
-                                EnumerationToString(origin_.GetRequestOrigin()));
-
-
             if (hasTransferSyntax_)
             {
               // New in Orthanc 1.2.0
@@ -3163,7 +3158,17 @@
                                   GetTransferSyntaxUid(transferSyntax_));
             }
 
-            {
+            if (!isReconstruct_) // don't change origin metadata
+            {        
+              // Attach the auto-computed metadata for the instance level,
+              // reflecting these additions into the input metadata map
+              SetInstanceMetadata(content, instanceMetadata_, instanceId,
+                                  MetadataType_Instance_ReceptionDate, now);
+              SetInstanceMetadata(content, instanceMetadata_, instanceId, MetadataType_RemoteAet,
+                                  origin_.GetRemoteAetC());
+              SetInstanceMetadata(content, instanceMetadata_, instanceId, MetadataType_Instance_Origin, 
+                                  EnumerationToString(origin_.GetRequestOrigin()));
+
               std::string s;
 
               if (origin_.LookupRemoteIp(s))
@@ -3270,7 +3275,7 @@
 
     Operations operations(instanceMetadata, dicomSummary, attachments, metadata, origin,
                           overwrite, hasTransferSyntax, transferSyntax, hasPixelDataOffset,
-                          pixelDataOffset, maximumStorageSize, maximumPatients);
+                          pixelDataOffset, maximumStorageSize, maximumPatients, isReconstruct);
     Apply(operations);
     return operations.GetStoreStatus();
   }

--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.h	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.h	Sat Apr 30 19:40:52 2022 +0200
@@ -659,7 +659,8 @@
                       bool hasPixelDataOffset,
                       uint64_t pixelDataOffset,
                       uint64_t maximumStorageSize,
-                      unsigned int maximumPatients);
+                      unsigned int maximumPatients,
+                      bool isReconstruct);
 
     StoreStatus AddAttachment(int64_t& newRevision /*out*/,
                               const FileInfo& attachment,

--- a/OrthancServer/Sources/DicomInstanceToStore.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/DicomInstanceToStore.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -300,4 +300,14 @@
   {
     return GetParsedDicomFile().DecodeFrame(frame);
   }
+
+  void DicomInstanceToStore::CopyMetadata(const DicomInstanceToStore::MetadataMap& metadata)
+  {
+    for (MetadataMap::const_iterator it = metadata.begin(); 
+         it != metadata.end(); ++it)
+    {
+      AddMetadata(it->first.first, it->first.second, it->second);
+    }
+  }
+
 }

--- a/OrthancServer/Sources/DicomInstanceToStore.h	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/DicomInstanceToStore.h	Sat Apr 30 19:40:52 2022 +0200
@@ -94,6 +94,8 @@
       metadata_[std::make_pair(level, metadata)] = value;
     }
 
+    void CopyMetadata(const MetadataMap& metadata);
+
     bool LookupTransferSyntax(DicomTransferSyntax& result) const;
 
     virtual ParsedDicomFile& GetParsedDicomFile() const = 0;

--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -57,6 +57,7 @@
 static const std::string CHECK_REVISIONS = "CheckRevisions";
 
 static const char* const IGNORE_LENGTH = "ignore-length";
+static const char* const RECONSTRUCT_FILES = "ReconstructFiles";
 
 
 namespace Orthanc
@@ -3379,6 +3380,32 @@
     call.GetOutput().AnswerBuffer("", MimeType_PlainText);
   }
 
+  void DocumentReconstructFilesField(RestApiPostCall& call)
+  {
+    call.GetDocumentation()
+      .SetRequestField(RECONSTRUCT_FILES, RestApiCallDocumentation::Type_Boolean,
+                       "Also reconstruct the files of the resources (e.g: apply IngestTranscoding, StorageCompression). "
+                       "'false' by default. (New in Orthanc 1.11.0)", false);
+  }
+
+  bool GetReconstructFilesField(RestApiPostCall& call)
+  {
+    bool reconstructFiles = false;
+    Json::Value request;
+
+    if (call.GetBodySize() > 0 && call.ParseJsonRequest(request) && request.isMember(RECONSTRUCT_FILES)) // allow "" payload to keep backward compatibility
+    {
+      if (!request[RECONSTRUCT_FILES].isBool())
+      {
+        throw OrthancException(ErrorCode_BadFileFormat,
+                               "The field " + std::string(RECONSTRUCT_FILES) + " must contain a Boolean");
+      }
+
+      reconstructFiles = request[RECONSTRUCT_FILES].asBool();
+    }
+
+    return reconstructFiles;
+  }
 
   template <enum ResourceType type>
   static void ReconstructResource(RestApiPostCall& call)
@@ -3388,18 +3415,20 @@
       const std::string resource = GetResourceTypeText(type, false /* plural */, false /* lower case */);
       call.GetDocumentation()
         .SetTag(GetResourceTypeText(type, true /* plural */, true /* upper case */))
-        .SetSummary("Reconstruct tags of " + resource)
-        .SetDescription("Reconstruct the main DICOM tags of the " + resource + " whose Orthanc identifier is provided "
+        .SetSummary("Reconstruct tags & optionally files of " + resource)
+        .SetDescription("Reconstruct the main DICOM tags in DB of the " + resource + " whose Orthanc identifier is provided "
                         "in the URL. This is useful if child studies/series/instances have inconsistent values for "
                         "higher-level tags, in order to force Orthanc to use the value from the resource of interest. "
                         "Beware that this is a time-consuming operation, as all the children DICOM instances will be "
                         "parsed again, and the Orthanc index will be updated accordingly.")
         .SetUriArgument("id", "Orthanc identifier of the " + resource + " of interest");
+        DocumentReconstructFilesField(call);
+
       return;
     }
 
     ServerContext& context = OrthancRestApi::GetContext(call);
-    ServerToolbox::ReconstructResource(context, call.GetUriComponent("id", ""));
+    ServerToolbox::ReconstructResource(context, call.GetUriComponent("id", ""), GetReconstructFilesField(call));
     call.GetOutput().AnswerBuffer("", MimeType_PlainText);
   }
 
@@ -3414,7 +3443,11 @@
         .SetDescription("Reconstruct the index of all the tags of all the DICOM instances that are stored in Orthanc. "
                         "This is notably useful after the deletion of resources whose children resources have inconsistent "
                         "values with their sibling resources. Beware that this is a highly time-consuming operation, "
-                        "as all the DICOM instances will be parsed again, and as all the Orthanc index will be regenerated.");
+                        "as all the DICOM instances will be parsed again, and as all the Orthanc index will be regenerated. "
+                        "If you have a large database to process, it is advised to use the Housekeeper plugin to perform "
+                        "this action resource by resource");
+        DocumentReconstructFilesField(call);
+
       return;
     }
 
@@ -3422,11 +3455,12 @@
 
     std::list<std::string> studies;
     context.GetIndex().GetAllUuids(studies, ResourceType_Study);
+    bool reconstructFiles = GetReconstructFilesField(call);
 
     for (std::list<std::string>::const_iterator 
            study = studies.begin(); study != studies.end(); ++study)
     {
-      ServerToolbox::ReconstructResource(context, *study);
+      ServerToolbox::ReconstructResource(context, *study, reconstructFiles);
     }
     
     call.GetOutput().AnswerBuffer("", MimeType_PlainText);

--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestSystem.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestSystem.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -74,6 +74,8 @@
     static const char* const VERSION = "Version";
     static const char* const MAIN_DICOM_TAGS = "MainDicomTags";
     static const char* const STORAGE_COMPRESSION = "StorageCompression";
+    static const char* const OVERWRITE_INSTANCES = "OverwriteInstances";
+    static const char* const INGEST_TRANSCODING = "IngestTranscoding";
     
     if (call.IsDocumentation())
     {
@@ -104,6 +106,10 @@
                         "The list of MainDicomTags saved in DB for each resource level (new in Orthanc 1.11.0)")
         .SetAnswerField(STORAGE_COMPRESSION, RestApiCallDocumentation::Type_Boolean,
                         "Whether storage compression is enabled (new in Orthanc 1.11.0)")
+        .SetAnswerField(OVERWRITE_INSTANCES, RestApiCallDocumentation::Type_Boolean,
+                        "Whether instances are overwritten when re-ingested (new in Orthanc 1.11.0)")
+        .SetAnswerField(INGEST_TRANSCODING, RestApiCallDocumentation::Type_String,
+                        "Whether instances are transcoded when ingested into Orthanc (`""` if no transcoding is performed) (new in Orthanc 1.11.0)")
         .SetHttpGetSample("https://demo.orthanc-server.com/system", true);
       return;
     }
@@ -125,6 +131,8 @@
       result[NAME] = lock.GetConfiguration().GetStringParameter(NAME, "");
       result[CHECK_REVISIONS] = lock.GetConfiguration().GetBooleanParameter(CHECK_REVISIONS, false);  // New in Orthanc 1.9.2
       result[STORAGE_COMPRESSION] = lock.GetConfiguration().GetBooleanParameter(STORAGE_COMPRESSION, false); // New in Orthanc 1.11.0
+      result[OVERWRITE_INSTANCES] = lock.GetConfiguration().GetBooleanParameter(OVERWRITE_INSTANCES, false); // New in Orthanc 1.11.0
+      result[INGEST_TRANSCODING] = lock.GetConfiguration().GetStringParameter(INGEST_TRANSCODING, ""); // New in Orthanc 1.11.0
     }
 
     result[STORAGE_AREA_PLUGIN] = Json::nullValue;

--- a/OrthancServer/Sources/ServerContext.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/ServerContext.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -495,7 +495,8 @@
 
   ServerContext::StoreResult ServerContext::StoreAfterTranscoding(std::string& resultPublicId,
                                                                   DicomInstanceToStore& dicom,
-                                                                  StoreInstanceMode mode)
+                                                                  StoreInstanceMode mode,
+                                                                  bool isReconstruct)
   {
     bool overwrite;
     switch (mode)
@@ -544,6 +545,7 @@
       // Test if the instance must be filtered out
       StoreResult result;
 
+      if (!isReconstruct) // skip all filters if this is a reconstruction
       {
         boost::shared_lock<boost::shared_mutex> lock(listenersMutex_);
 
@@ -615,7 +617,7 @@
       InstanceMetadata  instanceMetadata;
       result.SetStatus(index_.Store(
         instanceMetadata, summary, attachments, dicom.GetMetadata(), dicom.GetOrigin(), overwrite,
-        hasTransferSyntax, transferSyntax, hasPixelDataOffset, pixelDataOffset));
+        hasTransferSyntax, transferSyntax, hasPixelDataOffset, pixelDataOffset, isReconstruct));
 
       // Only keep the metadata for the "instance" level
       dicom.ClearMetadata();
@@ -636,41 +638,47 @@
         }
       }
 
-      switch (result.GetStatus())
+      if (!isReconstruct) // skip logs in case of reconstruction
       {
-        case StoreStatus_Success:
-          LOG(INFO) << "New instance stored";
-          break;
+        switch (result.GetStatus())
+        {
+          case StoreStatus_Success:
+            LOG(INFO) << "New instance stored";
+            break;
 
-        case StoreStatus_AlreadyStored:
-          LOG(INFO) << "Already stored";
-          break;
+          case StoreStatus_AlreadyStored:
+            LOG(INFO) << "Already stored";
+            break;
 
-        case StoreStatus_Failure:
-          LOG(ERROR) << "Store failure";
-          break;
+          case StoreStatus_Failure:
+            LOG(ERROR) << "Store failure";
+            break;
 
-        default:
-          // This should never happen
-          break;
+          default:
+            // This should never happen
+            break;
+        }
       }
 
-      if (result.GetStatus() == StoreStatus_Success ||
-          result.GetStatus() == StoreStatus_AlreadyStored)
+      if (!isReconstruct) // skip all signals if this is a reconstruction
       {
-        boost::shared_lock<boost::shared_mutex> lock(listenersMutex_);
-
-        for (ServerListeners::iterator it = listeners_.begin(); it != listeners_.end(); ++it)
+        if (result.GetStatus() == StoreStatus_Success ||
+            result.GetStatus() == StoreStatus_AlreadyStored)
         {
-          try
+          boost::shared_lock<boost::shared_mutex> lock(listenersMutex_);
+
+          for (ServerListeners::iterator it = listeners_.begin(); it != listeners_.end(); ++it)
           {
-            it->GetListener().SignalStoredInstance(resultPublicId, dicom, simplifiedTags);
-          }
-          catch (OrthancException& e)
-          {
-            LOG(ERROR) << "Error in the " << it->GetDescription() 
-                       << " callback while receiving an instance: " << e.What()
-                       << " (code " << e.GetErrorCode() << ")";
+            try
+            {
+              it->GetListener().SignalStoredInstance(resultPublicId, dicom, simplifiedTags);
+            }
+            catch (OrthancException& e)
+            {
+              LOG(ERROR) << "Error in the " << it->GetDescription() 
+                        << " callback while receiving an instance: " << e.What()
+                        << " (code " << e.GetErrorCode() << ")";
+            }
           }
         }
       }
@@ -743,10 +751,19 @@
     }
 #endif
 
+    return TranscodeAndStore(resultPublicId, dicom, mode);
+  }
+
+  ServerContext::StoreResult ServerContext::TranscodeAndStore(std::string& resultPublicId,
+                                                              DicomInstanceToStore* dicom,
+                                                              StoreInstanceMode mode,
+                                                              bool isReconstruct)
+  {
+
     if (!isIngestTranscoding_)
     {
       // No automated transcoding. This was the only path in Orthanc <= 1.6.1.
-      return StoreAfterTranscoding(resultPublicId, *dicom, mode);
+      return StoreAfterTranscoding(resultPublicId, *dicom, mode, isReconstruct);
     }
     else
     {
@@ -782,7 +799,7 @@
       if (!transcode)
       {
         // No transcoding
-        return StoreAfterTranscoding(resultPublicId, *dicom, mode);
+        return StoreAfterTranscoding(resultPublicId, *dicom, mode, isReconstruct);
       }
       else
       {
@@ -801,7 +818,12 @@
           std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*tmp));
           toStore->SetOrigin(dicom->GetOrigin());
 
-          StoreResult result = StoreAfterTranscoding(resultPublicId, *toStore, mode);
+          if (isReconstruct) // the initial instance to store already has its own metadata
+          {
+            toStore->CopyMetadata(dicom->GetMetadata());
+          }
+
+          StoreResult result = StoreAfterTranscoding(resultPublicId, *toStore, mode, isReconstruct);
           assert(resultPublicId == tmp->GetHasher().HashInstance());
 
           return result;
@@ -809,7 +831,7 @@
         else
         {
           // Cannot transcode => store the original file
-          return StoreAfterTranscoding(resultPublicId, *dicom, mode);
+          return StoreAfterTranscoding(resultPublicId, *dicom, mode, isReconstruct);
         }
       }
     }

--- a/OrthancServer/Sources/ServerContext.h	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/ServerContext.h	Sat Apr 30 19:40:52 2022 +0200
@@ -261,7 +261,8 @@
 
     StoreResult StoreAfterTranscoding(std::string& resultPublicId,
                                       DicomInstanceToStore& dicom,
-                                      StoreInstanceMode mode);
+                                      StoreInstanceMode mode,
+                                      bool isReconstruct);
 
     void PublishDicomCacheMetrics();
 
@@ -335,6 +336,11 @@
                       DicomInstanceToStore& dicom,
                       StoreInstanceMode mode);
 
+    StoreResult TranscodeAndStore(std::string& resultPublicId,
+                                  DicomInstanceToStore* dicom,
+                                  StoreInstanceMode mode,
+                                  bool isReconstruct = false);
+
     void AnswerAttachment(RestApiOutput& output,
                           const std::string& resourceId,
                           FileContentType content);

--- a/OrthancServer/Sources/ServerIndex.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/ServerIndex.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -518,7 +518,8 @@
                                  bool hasTransferSyntax,
                                  DicomTransferSyntax transferSyntax,
                                  bool hasPixelDataOffset,
-                                 uint64_t pixelDataOffset)
+                                 uint64_t pixelDataOffset,
+                                 bool isReconstruct)
   {
     uint64_t maximumStorageSize;
     unsigned int maximumPatients;
@@ -531,7 +532,7 @@
 
     return StatelessDatabaseOperations::Store(
       instanceMetadata, dicomSummary, attachments, metadata, origin, overwrite, hasTransferSyntax,
-      transferSyntax, hasPixelDataOffset, pixelDataOffset, maximumStorageSize, maximumPatients);
+      transferSyntax, hasPixelDataOffset, pixelDataOffset, maximumStorageSize, maximumPatients, isReconstruct);
   }
 
   

--- a/OrthancServer/Sources/ServerIndex.h	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/ServerIndex.h	Sat Apr 30 19:40:52 2022 +0200
@@ -84,7 +84,8 @@
                       bool hasTransferSyntax,
                       DicomTransferSyntax transferSyntax,
                       bool hasPixelDataOffset,
-                      uint64_t pixelDataOffset);
+                      uint64_t pixelDataOffset,
+                      bool isResonstruct);
 
     StoreStatus AddAttachment(int64_t& newRevision /*out*/,
                               const FileInfo& attachment,

--- a/OrthancServer/Sources/ServerToolbox.cpp	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/ServerToolbox.cpp	Sat Apr 30 19:40:52 2022 +0200
@@ -254,7 +254,8 @@
 
     
     void ReconstructResource(ServerContext& context,
-                             const std::string& resource)
+                             const std::string& resource,
+                             bool reconstructFiles)
     {
       LOG(WARNING) << "Reconstructing resource " << resource;
       
@@ -271,7 +272,30 @@
                                             -1 /* dummy revision */, "" /* dummy MD5 */);
         
         context.GetIndex().ReconstructInstance(locker.GetDicom());
+
+        if (reconstructFiles)
+        {
+          // preserve metadata from old resource
+          typedef std::map<MetadataType, std::string>  InstanceMetadata;
+          InstanceMetadata  instanceMetadata;
+
+          std::string resultPublicId;  // ignored
+          std::unique_ptr<DicomInstanceToStore> dicomInstancetoStore(DicomInstanceToStore::CreateFromParsedDicomFile(locker.GetDicom()));
+
+          context.GetIndex().GetAllMetadata(instanceMetadata, *it, ResourceType_Instance);
+          
+          for (InstanceMetadata::const_iterator itm = instanceMetadata.begin();
+              itm != instanceMetadata.end(); ++itm)
+          {
+            dicomInstancetoStore->AddMetadata(ResourceType_Instance, itm->first, itm->second);
+          }
+
+          context.TranscodeAndStore(resultPublicId, dicomInstancetoStore.get(), StoreInstanceMode_OverwriteDuplicate, true);
+        }
       }
     }
   }
 }
+
+
+todo: add a status route for the plugin !!!
\ No newline at end of file

--- a/OrthancServer/Sources/ServerToolbox.h	Wed Apr 27 16:56:53 2022 +0200
+++ b/OrthancServer/Sources/ServerToolbox.h	Sat Apr 30 19:40:52 2022 +0200
@@ -54,6 +54,7 @@
     std::string NormalizeIdentifier(const std::string& value);
 
     void ReconstructResource(ServerContext& context,
-                             const std::string& resource);
+                             const std::string& resource,
+                             bool reconstructFiles);
   }
 }