/** @file
 * $Author: kusanagi $
 * $Date: 2005/02/09 22:24:33 $
 * $Revision: 2.6 $
 * 
 * Implementation of the PamelaRun class.
 */
#include <iostream>
#include <iomanip>
#include <list>
#include <exception>
//#include <string>
#include <log4cxx/logger.h>

#include <TFile.h>  //Substituted by Maurizio 05 Feb 2004
#include <TTree.h>  //Substituted by Maurizio 05 Feb 2004
#include <TChain.h> //Substituted by Maurizio 05 Feb 2004
#include <TKey.h>   //Substituted by Maurizio 05 Feb 2004
#include <TList.h>  //Substituted by Maurizio 05 Feb 2004


#include "PamelaRun.h"
#include "EventHeader.h"
#include "Algorithm.h"
#include "AlgorithmInfo.h"
#include "Exception.h"
#include <sys/stat.h>

extern "C" {
#include <dirent.h>
#include "DirectoryStructure.h"
}

using namespace pamela;

static log4cxx::LoggerPtr logger = log4cxx::Logger::getLogger(_T("pamela.PamelaRun"));

/**
 * Get the run name according to a certain run number.
 * @param run Run number.
 * @return a string with the run name.
 */
std::string PamelaRun::GetRunName(int run) {
  std::stringstream temp;
  temp.str("");
  temp << std::setw( 4 ) << std::setfill( '0' ) << run;
  return "Run" + temp.str();
}

/**
 * Check if the run number is already assigned
 * @param int run - Number of the run to check
 * @return int
 */
/*int PamelaRun::RunExists(int run) throw (std::exception){
 int res;
 DIR *dirp;
 std::string pathDir((char*)getenv("YODA_DATA"));
 pathDir = pathDir + "/";
 pathDir = pathDir + GetRunName(run);
// Open the directory
if ((dirp = opendir(pathDir.c_str())) == NULL) {
res = 0;
} else {
closedir(dirp);
res = 1;
}
return res;
}*/


/**
 * Check if the run number is already assigned
 * @param int run - Number of the run to check
 * @return int
 */
 void PamelaRun::RunExists(std::string input) throw (std::exception){
 int res;
 DIR *dirp;
 std::string fileName;
 std::string pathDir((char*)getenv("YODA_DATA"));
 std::string tempName;
 std::string::size_type pos;
 
 pos = input.find_last_of("/");
 //if ((pos == std::string::npos) && !input.empty()) ;//throw Exception("Directories not allowed....");
 fileName = input.substr(pos+1);
 pos = fileName.find_last_of(".");
 fileName = fileName.substr(0,pos);
 pathDir = pathDir + "/";
 tempName = pathDir + fileName + "00";
 //oss << pathDir << fileName << std::setw( 2 ) << std::setfill( '0' );
 oss.str(tempName.c_str()); 
 int i = 0;
 while (res){
    //if ((dirp = opendir(tempName.c_str())) == NULL) {
    if ((dirp = opendir(oss.str().c_str())) == NULL) {
        res = 0;
    } else {
        closedir(dirp);
        oss.str(""); 
        oss << pathDir << fileName << std::setw( 2 ) << std::setfill( '0' ) << ++i;
        res = 1;
    }
 }
 oss.str(""); 
 oss << Path << "/" << fileName << std::setw( 2 ) << std::setfill( '0' ) << i;
 Path = oss.str();
 oss.str(""); 
 oss << fileName << std::setw( 2 ) << std::setfill( '0' ) << i;
 Run = oss.str();
//return (oss.str());
}

/**
 * Create a new Pamela run. 
 * @param run Run number
 * @param path Base path name to the data
 */
PamelaRun::PamelaRun(std::string fileName, std::string path):
  Path(path),
  Run(fileName),
  RunNumber(1){ //veirificare se è possibilie eliminare questa variabile
  logger->debug(_T("Constructor"));
  //Run = RunExists(fileName);
  RunExists(fileName);
  info = RunInfo(this);
}

/**
 * Get the directory name that contains the files of a certain event
 * type for this run.
 * @param type the packet type.
 * @return the complete path for this event type.
 */
std::string PamelaRun::GetDirName(PacketType const * type) const {
    //std::stringstream oss;
    //std::string name = type->GetName();
    //oss.str("");
    //oss << Path << "/" << Run << "/" << "pippo";
    //return oss.str();
    //return "pippo";
  //std::string EventType = type->GetName();
    return Path + "/" + Run + "/" + type->GetName();
}

/**
 * Get the file name for a certain event type.
 * @param type subpacket type.
 * @param name subpacket name.
 * @return the complete path and file name.
 */
std::string PamelaRun::GetFileName(const SubPacket* type, std::string name) {
  if (type->IsDetectorSpecific()) {
    return Path + "/" + type->GetPacketType()->GetName() + "/" 
      + Run + "." + type->GetPacketType()->GetName() + "."
      + type->GetSubDetector()->GetName() + "." 
      + name + ".root";
  } else {
    return Path + "/" + type->GetPacketType()->GetName() + "/" 
      + Run + "." + type->GetPacketType()->GetName() + "."
      + name + ".root";
   /*
    return Path + "/" + type->GetPacketType()->GetName() + "/" 
      + Run + "." + type->GetPacketType()->GetName() + "."
      + name + ".root"; */
  }
}

/**
 * Get the file name for a certain event type.
 * @param type subpacket type.
 * @return the complete path and file name.
 */
std::string PamelaRun::GetFileName(const SubPacket* type)  {
  //return GetFileName(type, type->GetSubPacketName());
    return GetFileName(type, "pippo");
}

/**
 * Get the branch name that corresponds to a certain
 * subpacket. Usually, this is the name of the subpacket.
 * @param type subpacket type.
 * @return the corresponding branch name.
 */
static std::string GetDefaultBranchName(const SubPacket* type) {
  return type->GetSubPacketName();
}

/**
 * Get the tree name for a certain subpacket. This is the name of the
 * subdetector for detector specific subpackets, and the packet name
 * ("Physics" etc.) for common packets.
 * @param type the packet type.
 * @return the corresponding tree name.
 */
static std::string GetTreeName(const SubPacket* type) {
  if (type->IsDetectorSpecific()) {
    return type->GetSubDetector()->GetName();
  } else {
    return type->GetPacketType()->GetName();
  }
}

/**
 * Get a list of all root files from a certain path.
 * @param path Path name to start the search.
 * @return A list of all file names.
 */
static std::list<std::string> GetRootFiles(std::string path) throw (std::exception) {
  std::list<std::string> files;
  DIR *dir = opendir(path.c_str());
  if (dir == 0) {
    logger->debug("Could not open " + path);
    //throw Exception("Could not open " + path);
  }
  
  for (struct dirent *d = readdir(dir); d != NULL; d = readdir(dir)) {
    if ((strcmp(".",d->d_name) == 0) || (strcmp("..",d->d_name) == 0))
      continue;
    std::string filename = path + "/" + d->d_name;
    struct stat buf;
    stat(filename.c_str(), &buf);
    if S_ISDIR(buf.st_mode) {
      std::list<std::string>toAdd = GetRootFiles(filename);
      files.insert(files.end(), toAdd.begin(), toAdd.end());
    } else if ((filename.substr(filename.size()-5, filename.size()) 
		== ".root")                                 // correct suffix
	       && (!isdigit(filename[filename.size()-6]))) {  // base file
      std::string nextfilename = filename;
      nextfilename.insert(filename.size()-5, "_1");
      if (stat(nextfilename.c_str(), &buf) == 0) {
	filename.insert(filename.size()-5, "*");
      }
      logger->debug("Using " + filename);
      files.push_back(filename);
    }
  }
  return files;
}

/**
 * Helper function to open the ROOT TTree of the header within the run 
 * framework.
 * @param type The packet type.
 * @return the ROOT TTree.
 */ 
TChain* PamelaRun::ReadHeaderTree(const PacketType *type) 
  throw (std::exception) {
  EventHeader header(type);
  std::string FileName = GetFileName(&header);
  std::string TreeName = GetTreeName(&header);
  TChain *tree = new TChain(TreeName.c_str());
  tree->Add(FileName.c_str());
  return tree;
}

/**
 * All add trees of a file as friend to a given tree. The tree name of
 * each tree found in the file is used as the name of the friend alias.
 * @param tree The base tree to add all other as friends.
 * @param FileName The name of the file with other trees.
 */
static void AddAllAsFriend(TChain* tree, std::string FileName) {
  std::string BaseFileName = FileName;
  bool HaveChain = false;
  if (BaseFileName[BaseFileName.size()-6] == '*') {
    BaseFileName.erase(BaseFileName.size()-6, 1);
    HaveChain = true;
  }
  TFile* File = new TFile(BaseFileName.c_str(), "read");
  if (!File->IsOpen()) {
    logger->error("Could not open file " + BaseFileName + " for reading.");
    return;
  }
  TList* list = File->GetListOfKeys();
  if (HaveChain) {
    for (TIter i(list); TKey* k = (TKey*)i();) {
      if (std::string(TTree::Class()->GetName()) == k->GetClassName()) {
	std::string TreeName = k->GetName();
	TChain* FriendChain = new TChain(TreeName.c_str());
	FriendChain->Add(FileName.c_str());
	tree->AddFriend(FriendChain, TreeName.c_str());	
        //logger->warn("Adding chain " + TreeName + " with " + FriendChain->GetEntries() + " entries as Friend");
      }
    }
    File->Close();
  } else {
    for (TIter i(list); TKey* k = (TKey*)i();) {
      if (std::string(TTree::Class()->GetName()) == k->GetClassName()) {
	std::string TreeName = k->GetName();
	TTree* FriendTree = (TTree *)File->Get(TreeName.c_str());
	tree->AddFriend(FriendTree, TreeName.c_str());	
        //logger->debug("Adding tree " + TreeName + " with " + FriendTree->GetEntries() + " entries as Friend");
      }
    }
  }
}

/**
 * Read all Root TTrees which belong to a certain event type and mount them
 * together as "friends".
 * @param type The packet type.
 * @return The root trees with the friends.
 */
TTree* PamelaRun::ReadTTree(const PacketType* type) {
  oss.str("");
  oss <<  "Getting root files of " << type->GetName();
  logger->debug(oss.str().c_str());
  RootTreeMap::iterator t = TTreeMap.find(type);
  if (t != TTreeMap.end()) {
    return t->second;
  } else {
    oss.str("");
    oss <<  "Reading root files of " << type->GetName();
    logger->debug(oss.str().c_str());
    EventHeader header(type);
    std::string HeaderFileName = GetFileName(&header);
    TChain* HeaderTree = ReadHeaderTree(type);
    std::list<std::string> rootfiles = GetRootFiles(GetDirName(type));
    for (std::list<std::string>::iterator i = rootfiles.begin(); 
	 i != rootfiles.end(); i++){
      if (*i == HeaderFileName) 
	continue; // dont add the header tree itself.
      AddAllAsFriend(HeaderTree, *i);
    }
    TTreeMap.insert(RootTreeMap::value_type(type, HeaderTree));
    return HeaderTree;
  }
}

/**
 * Register a certain SubPacket, identified by its name, to be read 
 * from the repository. This function is made for interactive work.
 * @param subpacket A pointer to the pointer of the packet.
 * @param name The name of the subpacket
 */
void PamelaRun::ReadSubPacket(void* subpacket, std::string name) {
  SubPacket *packet = *(SubPacket**)subpacket;

  // look into the map of subpackets if we already read it.
  std::string FullName = packet->GetPacketType()->GetName() + "." + name;
  SubPacketMap::iterator i = SubPacketAddresses.find(FullName);
  if (i != SubPacketAddresses.end()) { // it is in the map
    *(SubPacket**)subpacket = i->second;
    return;
  } else { // not found in the map of used subpackets
    TTree* tree = ReadTTree(packet->GetPacketType());
    TBranch* branch = tree->GetBranch(name.c_str());
    if (branch != 0) {
      branch->SetAddress(subpacket);
      SubPacketAddresses.insert(SubPacketMap::value_type(FullName, packet));
    } else {
        oss.str("");
        oss <<  "Could not find data for " << packet->GetPacketType()->GetName() << "/" << name ;
        logger->error(oss.str().c_str());
    }
  }
}

/**
 * Register a certain SubPacket, identified by its default name, to be
 * read from the repository. This function is made for
 * interactive work.
 * @param subpacket A pointer to the pointer of the packet. 
*/
void PamelaRun::ReadSubPacket(void* subpacket) {
  SubPacket *packet = *(SubPacket**)subpacket;
  ReadSubPacket(subpacket, GetDefaultBranchName(packet));
}

/**
 * Register a certain SubPacket with its default name, to be read from
 * the repository. This functions is for use from the algorithm.
 * @param algo Algorithm that needs this SubPacket.
 * @param subpacket A pointer to the pointer of the packet. 
 */
void PamelaRun::ReadSubPacket(const Algorithm* algo, void* subpacket) {
  //:TODO: store the request of the algorithm here.
  ReadSubPacket(subpacket);
}

/**
 * Register a certain SubPacket, with a custom name, to
 * be read from the repository. This functions is for use from 
 * the algorithm.
 * @param algo Algorithm that needs this SubPacket.
 * @param subpacket A pointer to the pointer of the packet.
 * @param name The name of the subpacket
 */
void PamelaRun::ReadSubPacket(const Algorithm* algo, void* subpacket, 
			      std::string name) {
  //:TODO: store the request of the algorithm here.
  ReadSubPacket(subpacket, name);
}

/**
 * Helper function to create a ROOT TTree within the run framework.
 * @param algo Algorithm that creates this SubPacket.
 * @param packet subpacket type
 * @param name the name of the subpacket
 * @return the ROOT TTree.
 */ 
TTree* PamelaRun::CreateTTree(Algorithm* algo, const SubPacket* packet, 
			      std::string name) 
  throw (std::exception) {
  std::string FileName = GetFileName(packet, name);
  std::string EventType = packet->GetPacketType()->GetName();
  CreateDirectoryStructure(FileName.c_str());
  TFile* File = new TFile(FileName.c_str(), "create");
  File->SetCompressionLevel(5);
  if (!File->IsOpen()) {
    logger->error("Could not open file " + FileName);
    //throw Exception("Could not open file " + FileName);
  }
  std::string TreeName = GetTreeName(packet);
  TTree *tree = new TTree(TreeName.c_str(), algo->GetAlgorithmName().c_str());
  WritingRootTrees[packet->GetPacketType()].push_back(tree);
  tree->GetCurrentFile()->cd();
  AlgorithmInfo ai(algo);
  ai.Write();
  info.Write();
  logger->debug("Creating file " + FileName + " with Tree " + TreeName);
  return tree;
}


/**
 * Register a certain SubPacket to be written to the repository. A
 * usual call sequence for this function ist
 * MyEvent *event = new MyEvent();
 * run->WriteSubPacket(this, &event, event->Class()
 * @param algo Algorithm that produces this SubPacket.
 * @param subpacket A pointer to the pointer of the subpacket.
 * @param c The class the subpacket belongs to.
 * @param name The name of the packet.
 */
void PamelaRun::WriteSubPacket(Algorithm *algo, void* subpacket, 
			       const TClass *c, std::string name) {
  SubPacket *packet = *(SubPacket **)subpacket;
  oss.str("");
  oss <<  "Register: " << name << " for " << algo->GetAlgorithmName() << " (writing)";
  logger->debug(oss.str().c_str());
  TTree* HeaderTree = ReadTTree(packet->GetPacketType());
  TTree* tree = CreateTTree(algo, packet, name);
  oss.str("");
  oss <<  "Branch: " << name << " Class: " << c->GetName();
  logger->debug(oss.str().c_str());
  tree->Branch(name.c_str(), c->GetName(),  subpacket);
  HeaderTree->AddFriend(tree, tree->GetName());

  std::string FullName = packet->GetPacketType()->GetName() + "." + name;
  SubPacketAddresses.insert(SubPacketMap::value_type(FullName, packet));
}

/**
 * Register a certain SubPacket with its default name to be written to 
 * the repository. A usual call sequence for this function ist
 * MyEvent *event = new MyEvent();
 * run->WriteSubPacket(this, &event, event->Class()
 * @param algo Algorithm that produces this SubPacket.
 * @param subpacket A pointer to the pointer of the subpacket.
 * @param c The class the subpacket belongs to.
 */
void PamelaRun::WriteSubPacket(Algorithm *algo, void* subpacket, 
			       const TClass *c) {
  SubPacket *packet = *(SubPacket **)subpacket;
  WriteSubPacket(algo, subpacket, c, GetDefaultBranchName(packet));
}

/**
 * Write the header packet of a specified packet type. This is mainly used
 * for the raw reader to create the base for the event structure.
 * @param algo Algorithm that produces this SubPacket.
 * @param subpacket A pointer to the pointer of the packet.
 * @param type The packet type.
 */
void PamelaRun::WriteHeader(Algorithm* algo, EventHeader** subpacket,
			    const PacketType* type) {
  EventHeader header(type);
  std::string FileName = GetFileName(&header, GetDefaultBranchName(&header));
  std::string EventType = (&header)->GetPacketType()->GetName();
  CreateDirectoryStructure(FileName.c_str());
  TFile* File = new TFile(FileName.c_str(), "create");
  if (!File->IsOpen()) {
    logger->error("Could not open file " + FileName);
    //throw Exception("Could not open file " + FileName);
  }
  //std::string TreeName = GetTreeName(packet);
  TTree *tree = new TTree("Pscu", algo->GetAlgorithmName().c_str());
  WritingRootTrees[(&header)->GetPacketType()].push_back(tree);
  tree->GetCurrentFile()->cd();
  AlgorithmInfo ai(algo);
  ai.Write();
  info.Write();
  std::stringstream temp;
  //temp.str("");
  //temp << "Created file" << FileName.c_str() << " with Tree Pscu" ;
  //logger->debug(temp.str());
  tree->Branch(GetDefaultBranchName(&header).c_str(), 
	       (*subpacket)->Class()->GetName(), subpacket);
  TTreeMap.insert(RootTreeMap::value_type(type, tree));
}


/**
 * Write the header packet to all ROOT files in the tree. Intended to
 * be used for raw data readers that create the initial event structure.
 * @param algo Algorithm that produces this SubPacket.
 * @param subpacket A pointer to the pointer of the header packet.
 */
void PamelaRun::WriteHeaders(Algorithm* algo, EventHeader** subpacket) {

    WriteHeader(algo, subpacket, PacketType::PhysEndRun);
    WriteHeader(algo, subpacket, PacketType::CalibCalPulse1);
    WriteHeader(algo, subpacket, PacketType::CalibCalPulse2);
    WriteHeader(algo, subpacket, PacketType::Physics);
    WriteHeader(algo, subpacket, PacketType::CalibTrkBoth);
    WriteHeader(algo, subpacket, PacketType::CalibTrk1);
    WriteHeader(algo, subpacket, PacketType::CalibTrk2);
    WriteHeader(algo, subpacket, PacketType::CalibTrd);
    WriteHeader(algo, subpacket, PacketType::CalibTof);
    WriteHeader(algo, subpacket, PacketType::CalibS4);
    WriteHeader(algo, subpacket, PacketType::CalibCalPed);
    WriteHeader(algo, subpacket, PacketType::Calib1_Ac1);
    WriteHeader(algo, subpacket, PacketType::Calib1_Ac2);
    WriteHeader(algo, subpacket, PacketType::Calib2_Ac1);
    WriteHeader(algo, subpacket, PacketType::Calib2_Ac2);
    WriteHeader(algo, subpacket, PacketType::RunHeader);
    WriteHeader(algo, subpacket, PacketType::RunTrailer);
    WriteHeader(algo, subpacket, PacketType::CalibHeader);
    WriteHeader(algo, subpacket, PacketType::CalibTrailer);
    WriteHeader(algo, subpacket, PacketType::InitHeader);
    WriteHeader(algo, subpacket, PacketType::InitTrailer);
    WriteHeader(algo, subpacket, PacketType::EventTrk);
    WriteHeader(algo, subpacket, PacketType::TestTrk);
    WriteHeader(algo, subpacket, PacketType::TestTof);
    WriteHeader(algo, subpacket, PacketType::Log);
    WriteHeader(algo, subpacket, PacketType::VarDump);
    WriteHeader(algo, subpacket, PacketType::ArrDump);
    WriteHeader(algo, subpacket, PacketType::TabDump);
    WriteHeader(algo, subpacket, PacketType::Tmtc);
    WriteHeader(algo, subpacket, PacketType::Mcmd);
    WriteHeader(algo, subpacket, PacketType::ForcedFECmd);
    WriteHeader(algo, subpacket, PacketType::Ac1Init);
    WriteHeader(algo, subpacket, PacketType::CalInit);
    WriteHeader(algo, subpacket, PacketType::TrkInit);
    WriteHeader(algo, subpacket, PacketType::TofInit);
    WriteHeader(algo, subpacket, PacketType::TrgInit);    
    WriteHeader(algo, subpacket, PacketType::NdInit);    
    WriteHeader(algo, subpacket, PacketType::S4Init);    
    WriteHeader(algo, subpacket, PacketType::Ac2Init);
    WriteHeader(algo, subpacket, PacketType::CalAlarm);    
    WriteHeader(algo, subpacket, PacketType::AcAlarm);    
    WriteHeader(algo, subpacket, PacketType::TrkAlarm);    
    WriteHeader(algo, subpacket, PacketType::TrgAlarm);    
    WriteHeader(algo, subpacket, PacketType::TofAlarm);
    WriteHeader(algo, subpacket, PacketType::S4Alarm);
    WriteHeader(algo, subpacket, PacketType::TsbT);
    WriteHeader(algo, subpacket, PacketType::TsbB);
}

/**
 * Write the ROOT files to disk.
 */
void PamelaRun::WriteFiles(void) {
  // Workaround: unlink all friend trees first top avoid to store
  // the links in the header tree file.
  for (RootTreeMap::iterator i = TTreeMap.begin(); i != TTreeMap.end(); i++) {
    if (i->second->GetListOfFriends() != 0) {
      i->second->GetListOfFriends()->Delete();
    }
  }

  for (TTreeListMap::iterator i = WritingRootTrees.begin();
       i != WritingRootTrees.end(); i++) {
    for (TTreeList::iterator j = i->second.begin();
         j != i->second.end(); j++) {
      (*j)->GetCurrentFile()->Write();
    }
  }
}

/**
 * Fill all ROOT trees of a certain type that were opened for writing.
 * @param type the package type of the trees to fill.
 */
void PamelaRun::FillTrees(const PacketType* type) {
  for (TTreeList::iterator j = WritingRootTrees[type].begin();
       j != WritingRootTrees[type].end(); j++) {
    (*j)->Fill();
    ;
  }
}