view OrthancServer/DatabaseWrapper.cpp @ 2294:e371519d4ac9

added -U option to gdcmconv to prevent gdcmconv to mess up the files. Without that option, we have seen the SpecificCharSet tag becoming invalid !!! (seen on the VIX samples)
author Alain Mazy <am@osimis.io>
date Tue, 04 Jul 2017 15:36:19 +0000
parents a3a65de1840f
children 878b59270859
line wrap: on
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/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017 Osimis, 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 "PrecompiledHeadersServer.h"
#include "DatabaseWrapper.h"

#include "../Core/DicomFormat/DicomArray.h"
#include "../Core/Logging.h"
#include "EmbeddedResources.h"
#include "ServerToolbox.h"

#include <stdio.h>
#include <boost/lexical_cast.hpp>

namespace Orthanc
{

  namespace Internals
  {
    class SignalFileDeleted : public SQLite::IScalarFunction
    {
    private:
      IDatabaseListener& listener_;

    public:
      SignalFileDeleted(IDatabaseListener& listener) :
        listener_(listener)
      {
      }

      virtual const char* GetName() const
      {
        return "SignalFileDeleted";
      }

      virtual unsigned int GetCardinality() const
      {
        return 7;
      }

      virtual void Compute(SQLite::FunctionContext& context)
      {
        std::string uncompressedMD5, compressedMD5;

        if (!context.IsNullValue(5))
        {
          uncompressedMD5 = context.GetStringValue(5);
        }

        if (!context.IsNullValue(6))
        {
          compressedMD5 = context.GetStringValue(6);
        }

        FileInfo info(context.GetStringValue(0),
                      static_cast<FileContentType>(context.GetIntValue(1)),
                      static_cast<uint64_t>(context.GetInt64Value(2)),
                      uncompressedMD5,
                      static_cast<CompressionType>(context.GetIntValue(3)),
                      static_cast<uint64_t>(context.GetInt64Value(4)),
                      compressedMD5);
        
        listener_.SignalFileDeleted(info);
      }
    };

    class SignalResourceDeleted : public SQLite::IScalarFunction
    {
    private:
      IDatabaseListener& listener_;

    public:
      SignalResourceDeleted(IDatabaseListener& listener) :
        listener_(listener)
      {
      }

      virtual const char* GetName() const
      {
        return "SignalResourceDeleted";
      }

      virtual unsigned int GetCardinality() const
      {
        return 2;
      }

      virtual void Compute(SQLite::FunctionContext& context)
      {
        ResourceType type = static_cast<ResourceType>(context.GetIntValue(1));
        ServerIndexChange change(ChangeType_Deleted, type, context.GetStringValue(0));
        listener_.SignalChange(change);
      }
    };

    class SignalRemainingAncestor : public SQLite::IScalarFunction
    {
    private:
      bool hasRemainingAncestor_;
      std::string remainingPublicId_;
      ResourceType remainingType_;

    public:
      SignalRemainingAncestor() : 
        hasRemainingAncestor_(false)
      {
      }

      void Reset()
      {
        hasRemainingAncestor_ = false;
      }

      virtual const char* GetName() const
      {
        return "SignalRemainingAncestor";
      }

      virtual unsigned int GetCardinality() const
      {
        return 2;
      }

      virtual void Compute(SQLite::FunctionContext& context)
      {
        VLOG(1) << "There exists a remaining ancestor with public ID \""
                << context.GetStringValue(0)
                << "\" of type "
                << context.GetIntValue(1);

        if (!hasRemainingAncestor_ ||
            remainingType_ >= context.GetIntValue(1))
        {
          hasRemainingAncestor_ = true;
          remainingPublicId_ = context.GetStringValue(0);
          remainingType_ = static_cast<ResourceType>(context.GetIntValue(1));
        }
      }

      bool HasRemainingAncestor() const
      {
        return hasRemainingAncestor_;
      }

      const std::string& GetRemainingAncestorId() const
      {
        assert(hasRemainingAncestor_);
        return remainingPublicId_;
      }

      ResourceType GetRemainingAncestorType() const
      {
        assert(hasRemainingAncestor_);
        return remainingType_;
      }
    };
  }



  void DatabaseWrapper::GetChildren(std::list<std::string>& childrenPublicIds,
                                    int64_t id)
  {
    SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE parentId=?");
    s.BindInt64(0, id);

    childrenPublicIds.clear();
    while (s.Step())
    {
      childrenPublicIds.push_back(s.ColumnString(0));
    }
  }


  void DatabaseWrapper::DeleteResource(int64_t id)
  {
    signalRemainingAncestor_->Reset();

    SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Resources WHERE internalId=?");
    s.BindInt64(0, id);
    s.Run();

    if (signalRemainingAncestor_->HasRemainingAncestor() &&
        listener_ != NULL)
    {
      listener_->SignalRemainingAncestor(signalRemainingAncestor_->GetRemainingAncestorType(),
                                         signalRemainingAncestor_->GetRemainingAncestorId());
    }
  }


  bool DatabaseWrapper::GetParentPublicId(std::string& target,
                                          int64_t id)
  {
    SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT a.publicId FROM Resources AS a, Resources AS b "
                        "WHERE a.internalId = b.parentId AND b.internalId = ?");     
    s.BindInt64(0, id);

    if (s.Step())
    {
      target = s.ColumnString(0);
      return true;
    }
    else
    {
      return false;
    }
  }


  int64_t DatabaseWrapper::GetTableRecordCount(const std::string& table)
  {
    char buf[128];
    sprintf(buf, "SELECT COUNT(*) FROM %s", table.c_str());
    SQLite::Statement s(db_, buf);

    if (!s.Step())
    {
      throw OrthancException(ErrorCode_InternalError);
    }

    int64_t c = s.ColumnInt(0);
    assert(!s.Step());

    return c;
  }

    
  DatabaseWrapper::DatabaseWrapper(const std::string& path) : 
    listener_(NULL), 
    base_(db_),
    signalRemainingAncestor_(NULL),
    version_(0)
  {
    db_.Open(path);
  }

  DatabaseWrapper::DatabaseWrapper() : 
    listener_(NULL), 
    base_(db_),
    signalRemainingAncestor_(NULL),
    version_(0)
  {
    db_.OpenInMemory();
  }

  void DatabaseWrapper::Open()
  {
    db_.Execute("PRAGMA ENCODING=\"UTF-8\";");

    // Performance tuning of SQLite with PRAGMAs
    // http://www.sqlite.org/pragma.html
    db_.Execute("PRAGMA SYNCHRONOUS=NORMAL;");
    db_.Execute("PRAGMA JOURNAL_MODE=WAL;");
    db_.Execute("PRAGMA LOCKING_MODE=EXCLUSIVE;");
    db_.Execute("PRAGMA WAL_AUTOCHECKPOINT=1000;");
    //db_.Execute("PRAGMA TEMP_STORE=memory");

    if (!db_.DoesTableExist("GlobalProperties"))
    {
      LOG(INFO) << "Creating the database";
      std::string query;
      EmbeddedResources::GetFileResource(query, EmbeddedResources::PREPARE_DATABASE);
      db_.Execute(query);
    }

    // Check the version of the database
    std::string tmp;
    if (!LookupGlobalProperty(tmp, GlobalProperty_DatabaseSchemaVersion))
    {
      tmp = "Unknown";
    }

    bool ok = false;
    try
    {
      LOG(INFO) << "Version of the Orthanc database: " << tmp;
      version_ = boost::lexical_cast<unsigned int>(tmp);
      ok = true;
    }
    catch (boost::bad_lexical_cast&)
    {
    }

    if (!ok)
    {
      LOG(ERROR) << "Incompatible version of the Orthanc database: " << tmp;
      throw OrthancException(ErrorCode_IncompatibleDatabaseVersion);
    }

    signalRemainingAncestor_ = new Internals::SignalRemainingAncestor;
    db_.Register(signalRemainingAncestor_);
  }


  static void ExecuteUpgradeScript(SQLite::Connection& db,
                                   EmbeddedResources::FileResourceId script)
  {
    std::string upgrade;
    EmbeddedResources::GetFileResource(upgrade, script);
    db.BeginTransaction();
    db.Execute(upgrade);
    db.CommitTransaction();    
  }


  void DatabaseWrapper::Upgrade(unsigned int targetVersion,
                                IStorageArea& storageArea)
  {
    if (targetVersion != 6)
    {
      throw OrthancException(ErrorCode_IncompatibleDatabaseVersion);
    }

    // This version of Orthanc is only compatible with versions 3, 4,
    // 5 and 6 of the DB schema
    if (version_ != 3 &&
        version_ != 4 &&
        version_ != 5 &&
        version_ != 6)
    {
      throw OrthancException(ErrorCode_IncompatibleDatabaseVersion);
    }

    if (version_ == 3)
    {
      LOG(WARNING) << "Upgrading database version from 3 to 4";
      ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_3_TO_4);
      version_ = 4;
    }

    if (version_ == 4)
    {
      LOG(WARNING) << "Upgrading database version from 4 to 5";
      ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_4_TO_5);
      version_ = 5;
    }

    if (version_ == 5)
    {
      LOG(WARNING) << "Upgrading database version from 5 to 6";
      // No change in the DB schema, the step from version 5 to 6 only
      // consists in reconstructing the main DICOM tags information
      // (as more tags got included).
      db_.BeginTransaction();
      ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Patient);
      ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Study);
      ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Series);
      ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Instance);
      db_.Execute("UPDATE GlobalProperties SET value=\"6\" WHERE property=" +
                  boost::lexical_cast<std::string>(GlobalProperty_DatabaseSchemaVersion) + ";");
      db_.CommitTransaction();
      version_ = 6;
    }
  }


  void DatabaseWrapper::SetListener(IDatabaseListener& listener)
  {
    listener_ = &listener;
    db_.Register(new Internals::SignalFileDeleted(listener));
    db_.Register(new Internals::SignalResourceDeleted(listener));
  }


  void DatabaseWrapper::ClearTable(const std::string& tableName)
  {
    db_.Execute("DELETE FROM " + tableName);    
  }


  bool DatabaseWrapper::LookupParent(int64_t& parentId,
                                     int64_t resourceId)
  {
    bool found;
    ErrorCode error = base_.LookupParent(found, parentId, resourceId);

    if (error != ErrorCode_Success)
    {
      throw OrthancException(error);
    }
    else
    {
      return found;
    }
  }


  ResourceType DatabaseWrapper::GetResourceType(int64_t resourceId)
  {
    ResourceType result;
    ErrorCode code = base_.GetResourceType(result, resourceId);

    if (code == ErrorCode_Success)
    {
      return result;
    }
    else
    {
      throw OrthancException(code);
    }
  }


  std::string DatabaseWrapper::GetPublicId(int64_t resourceId)
  {
    std::string id;

    if (base_.GetPublicId(id, resourceId))
    {
      return id;
    }
    else
    {
      throw OrthancException(ErrorCode_UnknownResource);
    }
  }


  void DatabaseWrapper::GetChanges(std::list<ServerIndexChange>& target /*out*/,
                                   bool& done /*out*/,
                                   int64_t since,
                                   uint32_t maxResults)
  {
    ErrorCode code = base_.GetChanges(target, done, since, maxResults);

    if (code != ErrorCode_Success)
    {
      throw OrthancException(code);
    }
  }


  void DatabaseWrapper::GetLastChange(std::list<ServerIndexChange>& target /*out*/)
  {
    ErrorCode code = base_.GetLastChange(target);

    if (code != ErrorCode_Success)
    {
      throw OrthancException(code);
    }
  }


  void DatabaseWrapper::GetAllMetadata(std::map<MetadataType, std::string>& target,
                                       int64_t id)
  {
    target.clear();

    SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT type, value FROM Metadata WHERE id=?");
    s.BindInt64(0, id);

    while (s.Step())
    {
      MetadataType key = static_cast<MetadataType>(s.ColumnInt(0));
      target[key] = s.ColumnString(1);
    }
  }

}