# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1538146123 -7200
# Node ID 99863d6245b2adf316e38eca8c3276b5492be9cd
# Parent  4ee3a759afeadcf04775a3cc3d6c9c2ea9dabb85
New URI: "/studies/.../split" to split a study

diff -r 4ee3a759afea -r 99863d6245b2 CMakeLists.txt
--- a/CMakeLists.txt	Thu Sep 27 13:22:57 2018 +0200
+++ b/CMakeLists.txt	Fri Sep 28 16:48:43 2018 +0200
@@ -93,6 +93,7 @@
   OrthancServer/ServerJobs/OrthancJobUnserializer.cpp
   OrthancServer/ServerJobs/OrthancPeerStoreJob.cpp
   OrthancServer/ServerJobs/ResourceModificationJob.cpp
+  OrthancServer/ServerJobs/SplitStudyJob.cpp
   OrthancServer/ServerToolbox.cpp
   OrthancServer/SliceOrdering.cpp
   )
diff -r 4ee3a759afea -r 99863d6245b2 Core/DicomParsing/DicomModification.cpp
--- a/Core/DicomParsing/DicomModification.cpp	Thu Sep 27 13:22:57 2018 +0200
+++ b/Core/DicomParsing/DicomModification.cpp	Fri Sep 28 16:48:43 2018 +0200
@@ -1071,6 +1071,11 @@
 
     for (Json::Value::ArrayIndex i = 0; i < query.size(); i++)
     {
+      if (query[i].type() != Json::stringValue)
+      {
+        throw OrthancException(ErrorCode_BadRequest);
+      }
+      
       std::string name = query[i].asString();
 
       DicomTag tag = FromDcmtkBridge::ParseTag(name);
diff -r 4ee3a759afea -r 99863d6245b2 NEWS
--- a/NEWS	Thu Sep 27 13:22:57 2018 +0200
+++ b/NEWS	Fri Sep 28 16:48:43 2018 +0200
@@ -1,6 +1,12 @@
 Pending changes in the mainline
 ===============================
 
+
+REST API
+--------
+
+* New URI: "/studies/.../split" to split a study
+
 Maintenance
 -----------
 
diff -r 4ee3a759afea -r 99863d6245b2 OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp
--- a/OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp	Thu Sep 27 13:22:57 2018 +0200
+++ b/OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp	Fri Sep 28 16:48:43 2018 +0200
@@ -36,8 +36,10 @@
 
 #include "../../Core/DicomParsing/FromDcmtkBridge.h"
 #include "../../Core/Logging.h"
+#include "../../Core/SerializationToolbox.h"
 #include "../ServerContext.h"
 #include "../ServerJobs/ResourceModificationJob.h"
+#include "../ServerJobs/SplitStudyJob.h"
 
 #include <boost/lexical_cast.hpp>
 #include <boost/algorithm/string/predicate.hpp>
@@ -652,6 +654,93 @@
   }
 
 
+  static void SplitStudy(RestApiPostCall& call)
+  {
+    ServerContext& context = OrthancRestApi::GetContext(call);
+
+    Json::Value request;
+    if (!call.ParseJsonRequest(request))
+    {
+      // Bad JSON request
+      throw OrthancException(ErrorCode_BadFileFormat);
+    }
+
+    const std::string study = call.GetUriComponent("id", "");
+    int priority = Toolbox::GetJsonIntegerField(request, "Priority", 0);
+
+    std::auto_ptr<SplitStudyJob> job(new SplitStudyJob(context, study));    
+    job->SetOrigin(call);
+    job->SetDescription("REST API");
+
+    std::vector<std::string> series;
+    SerializationToolbox::ReadArrayOfStrings(series, request, "Series");
+
+    for (size_t i = 0; i < series.size(); i++)
+    {
+      job->AddSourceSeries(series[i]);
+    }
+
+    static const char* KEEP_SOURCE = "KeepSource";
+    if (request.isMember(KEEP_SOURCE))
+    {
+      job->SetKeepSource(SerializationToolbox::ReadBoolean(request, KEEP_SOURCE));
+    }
+
+    static const char* REMOVE = "Remove";
+    if (request.isMember(REMOVE))
+    {
+      if (request[REMOVE].type() != Json::arrayValue)
+      {
+        throw OrthancException(ErrorCode_BadFileFormat);
+      }
+
+      for (Json::Value::ArrayIndex i = 0; i < request[REMOVE].size(); i++)
+      {
+        if (request[REMOVE][i].type() != Json::stringValue)
+        {
+          throw OrthancException(ErrorCode_BadFileFormat);
+        }
+        else
+        {
+          job->Remove(FromDcmtkBridge::ParseTag(request[REMOVE][i].asCString()));
+        }
+      }
+    }
+
+    static const char* REPLACE = "Replace";
+    if (request.isMember(REPLACE))
+    {
+      if (request[REPLACE].type() != Json::objectValue)
+      {
+        throw OrthancException(ErrorCode_BadFileFormat);
+      }
+
+      Json::Value::Members tags = request[REPLACE].getMemberNames();
+
+      for (size_t i = 0; i < tags.size(); i++)
+      {
+        const Json::Value& value = request[REPLACE][tags[i]];
+        
+        if (value.type() != Json::stringValue)
+        {
+          throw OrthancException(ErrorCode_BadFileFormat);
+        }
+        else
+        {
+          job->Replace(FromDcmtkBridge::ParseTag(tags[i]), value.asString());
+        }
+      }
+    }
+
+    std::string id;
+    context.GetJobsEngine().GetRegistry().Submit(id, job.release(), priority);
+    
+    Json::Value v;
+    v["ID"] = id;
+    call.GetOutput().AnswerJson(v);
+  }
+
+
   void OrthancRestApi::RegisterAnonymizeModify()
   {
     Register("/instances/{id}/modify", ModifyInstance);
@@ -665,5 +754,7 @@
     Register("/patients/{id}/anonymize", AnonymizeResource<ResourceType_Patient>);
 
     Register("/tools/create-dicom", CreateDicom);
+
+    Register("/studies/{id}/split", SplitStudy);
   }
 }
diff -r 4ee3a759afea -r 99863d6245b2 OrthancServer/ServerJobs/SplitStudyJob.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/ServerJobs/SplitStudyJob.cpp	Fri Sep 28 16:48:43 2018 +0200
@@ -0,0 +1,309 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "SplitStudyJob.h"
+
+#include "../../Core/Logging.h"
+#include "../../Core/DicomParsing/FromDcmtkBridge.h"
+
+namespace Orthanc
+{
+  void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
+  {
+    if (allowedTags_.find(tag) == allowedTags_.end())
+    {
+      LOG(ERROR) << "Cannot modify the following tag while splitting a study "
+                 << "(not in the patient/study modules): "
+                 << FromDcmtkBridge::GetTagName(tag, "") << " (" << tag.Format() << ")";
+      throw OrthancException(ErrorCode_ParameterOutOfRange);
+    }
+  }
+
+  
+  void SplitStudyJob::Setup(const std::string& sourceStudy)
+  {
+    SetPermissive(false);
+    
+    keepSource_ = false;
+    sourceStudy_ = sourceStudy;
+    targetStudyUid_ = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study);
+    
+    DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
+    DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
+    allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
+    allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
+
+    ResourceType type;
+    
+    if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
+        type != ResourceType_Study)
+    {
+      LOG(ERROR) << "Cannot split unknown study: " << sourceStudy;
+      throw OrthancException(ErrorCode_UnknownResource);
+    }
+
+    std::list<std::string> children;
+    context_.GetIndex().GetChildren(children, sourceStudy);
+
+    for (std::list<std::string>::const_iterator
+           it = children.begin(); it != children.end(); ++it)
+    {
+      sourceSeries_.insert(*it);
+    }
+  }
+
+  
+  bool SplitStudyJob::HandleInstance(const std::string& instance)
+  {
+    /**
+     * Retrieve the DICOM instance to be modified
+     **/
+    
+    std::auto_ptr<ParsedDicomFile> modified;
+
+    try
+    {
+      ServerContext::DicomCacheLocker locker(context_, instance);
+      modified.reset(locker.GetDicom().Clone(true));
+    }
+    catch (OrthancException&)
+    {
+      LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
+      return false;
+    }
+
+
+    /**
+     * Chose the target UIDs
+     **/
+    
+    std::string series;
+    if (!modified->GetTagValue(series, DICOM_TAG_SERIES_INSTANCE_UID))
+    {
+      throw OrthancException(ErrorCode_BadFileFormat);  // Should never happen
+    }    
+
+    std::string targetSeriesUid;
+    SeriesUidMap::const_iterator found = targetSeries_.find(series);
+
+    if (found == targetSeries_.end())
+    {
+      // Choose a random SeriesInstanceUID for this series
+      targetSeriesUid = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
+      targetSeries_[series] = targetSeriesUid;
+    }
+    else
+    {
+      targetSeriesUid = found->second;
+    }
+
+
+    /**
+     * Apply user-specified modifications
+     **/
+
+    for (Removals::const_iterator it = removals_.begin();
+         it != removals_.end(); ++it)
+    {
+      modified->Remove(*it);
+    }
+    
+    for (Replacements::const_iterator it = replacements_.begin();
+         it != replacements_.end(); ++it)
+    {
+      modified->ReplacePlainString(it->first, it->second);
+    }
+
+
+    /**
+     * Store the new instance into Orthanc
+     **/
+    
+    modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
+    modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid);
+
+    if (targetStudy_.empty())
+    {
+      targetStudy_ = modified->GetHasher().HashStudy();
+    }
+    
+    DicomInstanceToStore toStore;
+    toStore.SetOrigin(origin_);
+    toStore.SetParsedDicomFile(*modified);
+
+    std::string modifiedInstance;
+    if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
+    {
+      LOG(ERROR) << "Error while storing a modified instance " << instance;
+      return false;
+    }
+
+    return true;
+  }
+
+  
+  bool SplitStudyJob::HandleTrailingStep()
+  {
+    if (!keepSource_)
+    {
+      const size_t n = GetInstancesCount();
+
+      for (size_t i = 0; i < n; i++)
+      {
+        Json::Value tmp;
+        context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
+      }
+    }
+
+    return true;
+  }
+
+  
+  SplitStudyJob::SplitStudyJob(ServerContext& context,
+                               const std::string& sourceStudy) :
+    SetOfInstancesJob(true /* with trailing step */),
+    context_(context)
+  {
+    Setup(sourceStudy);
+  }
+  
+
+  SplitStudyJob::SplitStudyJob(ServerContext& context,
+                               const Json::Value& serialized) :
+    SetOfInstancesJob(serialized),
+    context_(context)
+  {
+    //assert(HasTrailingStep());
+    //Setup();
+  }
+
+  
+  void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      origin_ = origin;
+    }
+  }
+
+  
+  void SplitStudyJob::SetOrigin(const RestApiCall& call)
+  {
+    SetOrigin(DicomInstanceOrigin::FromRest(call));
+  }
+
+
+  void SplitStudyJob::AddSourceSeries(const std::string& series)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else if (sourceSeries_.find(series) == sourceSeries_.end())
+    {
+      LOG(ERROR) << "This series does not belong to the study to be split: " << series;
+      throw OrthancException(ErrorCode_UnknownResource);
+    }
+    else
+    {
+      // Add all the instances of the series as to be processed
+      std::list<std::string> instances;
+      context_.GetIndex().GetChildren(instances, series);
+
+      for (std::list<std::string>::const_iterator
+             it = instances.begin(); it != instances.end(); ++it)
+      {
+        AddInstance(*it);
+      }
+    }    
+  }
+
+
+  void SplitStudyJob::SetKeepSource(bool keep)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+
+    keepSource_ = keep;
+  }
+
+
+  void SplitStudyJob::Remove(const DicomTag& tag)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+
+    CheckAllowedTag(tag);
+    removals_.insert(tag);
+  }
+
+  
+  void SplitStudyJob::Replace(const DicomTag& tag,
+                              const std::string& value)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+
+    CheckAllowedTag(tag);
+    replacements_[tag] = value;
+  }
+  
+    
+  void SplitStudyJob::GetPublicContent(Json::Value& value)
+  {
+    SetOfInstancesJob::GetPublicContent(value);
+
+    if (!targetStudy_.empty())
+    {
+      value["TargetStudy"] = targetStudy_;
+    }
+    
+    value["TargetStudyUID"] = targetStudyUid_;
+  }
+  
+
+  bool SplitStudyJob::Serialize(Json::Value& target)
+  {
+    return true;
+  }
+}
diff -r 4ee3a759afea -r 99863d6245b2 OrthancServer/ServerJobs/SplitStudyJob.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/ServerJobs/SplitStudyJob.h	Fri Sep 28 16:48:43 2018 +0200
@@ -0,0 +1,109 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#pragma once
+
+#include "../../Core/JobsEngine/SetOfInstancesJob.h"
+
+#include "../ServerContext.h"
+
+namespace Orthanc
+{
+  class SplitStudyJob : public SetOfInstancesJob
+  {
+  private:
+    typedef std::map<std::string, std::string>  SeriesUidMap;
+    typedef std::map<DicomTag, std::string>     Replacements;
+    typedef std::set<DicomTag>                  Removals;
+    
+    
+    ServerContext&         context_;
+    std::string            sourceStudy_;
+    std::set<std::string>  sourceSeries_;
+    bool                   keepSource_;
+    std::string            targetStudy_;
+    std::string            targetStudyUid_;
+    SeriesUidMap           targetSeries_;
+    std::set<DicomTag>     allowedTags_;
+    DicomInstanceOrigin    origin_;
+    Replacements           replacements_;
+    Removals               removals_;
+
+    void CheckAllowedTag(const DicomTag& tag) const;
+    
+    void Setup(const std::string& sourceStudy);
+    
+  protected:
+    virtual bool HandleInstance(const std::string& instance);
+
+    virtual bool HandleTrailingStep();
+    
+  public:
+    SplitStudyJob(ServerContext& context,
+                  const std::string& sourceStudy);
+
+    SplitStudyJob(ServerContext& context,
+                  const Json::Value& serialized);
+
+    void SetOrigin(const DicomInstanceOrigin& origin);
+
+    void SetOrigin(const RestApiCall& call);
+
+    void AddSourceSeries(const std::string& series);
+
+    bool IsKeepSource() const
+    {
+      return keepSource_;
+    }
+    
+    void SetKeepSource(bool keep);
+
+    void Remove(const DicomTag& tag);
+    
+    void Replace(const DicomTag& tag,
+                 const std::string& value);
+    
+    virtual void Stop(JobStopReason reason)
+    {
+    }
+
+    virtual void GetJobType(std::string& target)
+    {
+      target = "SplitStudyJob";
+    }
+
+    virtual void GetPublicContent(Json::Value& value);
+
+    virtual bool Serialize(Json::Value& target);
+  };
+}