GeneralCatalog.cc

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#include <algorithm>
#include <cassert>
#include <utility>

#include "Alignment/Geners/interface/CPP11_shared_ptr.hh"
#include "Alignment/Geners/interface/GeneralCatalog.hh"
#include "Alignment/Geners/interface/IOException.hh"
#include "Alignment/Geners/interface/binaryIO.hh"

namespace gs {
  GeneralCatalog::GeneralCatalog() : smallestId_(1ULL), largestId_(0) {}

  void GeneralCatalog::findByName(const NameMap &m,
                                  const SearchSpecifier &namePattern,
                                  std::vector<unsigned long long> *found) const {
    typedef NameMap::const_iterator Nameiter;

    if (namePattern.useRegex()) {
      const Nameiter itend = m.end();
      for (Nameiter it = m.begin(); it != itend; ++it)
        if (namePattern.matches(it->first))
          found->push_back(it->second->id());
    } else {
      const std::pair<Nameiter, Nameiter> limits = m.equal_range(namePattern.pattern());
      for (Nameiter it = limits.first; it != limits.second; ++it)
        found->push_back(it->second->id());
    }
  }

  bool GeneralCatalog::addEntry(const SPtr inptr) {
    assert(inptr.get());

    const bool first = records_.empty();
    const unsigned long long id = inptr->id();
    if (id && records_.insert(std::make_pair(id, inptr)).second) {
      recordMap_[inptr->category()].insert(std::make_pair(inptr->name(), inptr));
      if (first) {
        smallestId_ = id;
        largestId_ = id;
      } else {
        if (id < smallestId_)
          smallestId_ = id;
        if (id > largestId_)
          largestId_ = id;
      }
      return true;
    } else
      return false;
  }

  bool GeneralCatalog::removeEntry(const unsigned long long id) {
    typedef RecordMap::iterator Mapiter;
    typedef NameMap::iterator Nameiter;

    IdMap::iterator rit = records_.find(id);
    if (rit == records_.end())
      return false;

    const SPtr item = rit->second;
    records_.erase(rit);

    bool found = false;
    const Mapiter mit = recordMap_.find(item->category());
    assert(mit != recordMap_.end());
    const std::pair<Nameiter, Nameiter> limits = mit->second.equal_range(item->name());
    for (Nameiter nit = limits.first; nit != limits.second; ++nit)
      if (nit->second->id() == id) {
        mit->second.erase(nit);
        found = true;
        break;
      }
    assert(found);
    if (mit->second.empty())
      recordMap_.erase(mit);

    if (records_.empty()) {
      recordMap_.clear();
      smallestId_ = 0;
      largestId_ = 0;
    } else if (id == smallestId_ || id == largestId_) {
      IdMap::const_iterator it = records_.begin();
      smallestId_ = it->first;
      largestId_ = it->first;
      const IdMap::const_iterator itend = records_.end();
      for (++it; it != itend; ++it)
        if (it->first < smallestId_)
          smallestId_ = it->first;
        else if (it->first > largestId_)
          largestId_ = it->first;
    }
    return true;
  }

  unsigned long long GeneralCatalog::makeEntry(const ItemDescriptor &descriptor,
                                               const unsigned compressionCode,
                                               const unsigned long long itemLength,
                                               const ItemLocation &loc,
                                               const unsigned long long offset) {
    const unsigned long long nextId = records_.empty() ? 1ULL : largestId_ + 1;
    lastEntry_ = SPtr(new CatalogEntry(descriptor, nextId, compressionCode, itemLength, loc, offset));
    assert(addEntry(lastEntry_));
    return nextId;
  }

  void GeneralCatalog::search(const SearchSpecifier &namePattern,
                              const SearchSpecifier &categoryPattern,
                              std::vector<unsigned long long> *found) const {
    typedef RecordMap::const_iterator Mapiter;

    assert(found);
    found->clear();

    const Mapiter endMap = recordMap_.end();
    if (categoryPattern.useRegex()) {
      for (Mapiter it = recordMap_.begin(); it != endMap; ++it)
        if (categoryPattern.matches(it->first))
          findByName(it->second, namePattern, found);
    } else {
      Mapiter it = recordMap_.find(categoryPattern.pattern());
      if (it != endMap)
        findByName(it->second, namePattern, found);
    }
    std::sort(found->begin(), found->end());
  }

  bool GeneralCatalog::isEqual(const AbsCatalog &other) const {
    if ((void *)this == (void *)(&other))
      return true;
    const GeneralCatalog &r = static_cast<const GeneralCatalog &>(other);
    if (smallestId_ != r.smallestId_)
      return false;
    if (largestId_ != r.largestId_)
      return false;
    if (records_.size() != r.records_.size())
      return false;
    IdMap::const_iterator itend = records_.end();
    IdMap::const_iterator itend2 = r.records_.end();
    for (IdMap::const_iterator it = records_.begin(); it != itend; ++it) {
      IdMap::const_iterator it2 = r.records_.find(it->first);
      if (it2 == itend2)
        return false;
      if (!(*it->second == *it2->second))
        return false;
    }
    return true;
  }

  // Version 1 write function
  // bool GeneralCatalog::write(std::ostream& os) const
  // {
  //     if (!ClassId::makeId<CatalogEntry>().write(os))
  //         return false;
  //     if (!ClassId::makeId<ItemLocation>().write(os))
  //         return false;

  //     // Sort item ids in the increasing order first
  //     std::vector<unsigned long long> idlist;
  //     const unsigned long sz = records_.size();
  //     idlist.reserve(sz);
  //     const IdMap::const_iterator itend = records_.end();
  //     for (IdMap::const_iterator it = records_.begin(); it != itend; ++it)
  //         idlist.push_back(it->first);
  //     std::sort(idlist.begin(), idlist.end());

  //     // Now, write the catalog records in the order of increasing ids
  //     for (unsigned long i=0; i<sz; ++i)
  //     {
  //         IdMap::const_iterator it = records_.find(idlist[i]);
  //         if (!it->second->write(os))
  //             return false;
  //     }

  //     return true;
  // }

  bool GeneralCatalog::write(std::ostream &os) const {
    const unsigned long sz = records_.size();
    long long ltmp = sz;
    write_pod(os, ltmp);
    if (os.fail())
      return false;
    if (!ClassId::makeId<CatalogEntry>().write(os))
      return false;
    if (!ClassId::makeId<ItemLocation>().write(os))
      return false;

    // Sort item ids in the increasing order first
    std::vector<unsigned long long> idlist;
    idlist.reserve(sz);
    const IdMap::const_iterator itend = records_.end();
    for (IdMap::const_iterator it = records_.begin(); it != itend; ++it)
      idlist.push_back(it->first);
    std::sort(idlist.begin(), idlist.end());

    // Now, write the catalog records in the order of increasing ids
    for (unsigned long i = 0; i < sz; ++i) {
      IdMap::const_iterator it = records_.find(idlist[i]);
      if (!it->second->write(os))
        return false;
    }

    return true;
  }

  GeneralCatalog *GeneralCatalog::read(const ClassId &id, std::istream &in) {
    static const ClassId current(ClassId::makeId<GeneralCatalog>());
    id.ensureSameName(current);
    id.ensureVersionInRange(1, version());

    if (id.version() == 1)
      return read_v1(in);

    long long nRecords;
    read_pod(in, &nRecords);
    if (nRecords < 0)
      return read_v1(in);

    ClassId rId(in, 1);
    ClassId locId(in, 1);

    GeneralCatalog *catalog = new GeneralCatalog();
    bool ok = true;
    for (long long recnum = 0; ok && recnum < nRecords; ++recnum) {
      CatalogEntry *rec = CatalogEntry::read(rId, locId, in);
      if (rec) {
        if (!catalog->addEntry(CPP11_shared_ptr<const CatalogEntry>(rec)))
          ok = false;
      } else
        ok = false;
    }

    if (!ok) {
      delete catalog;
      throw IOInvalidData(
          "In gs::GeneralCatalog::read: "
          "duplicate item id. "
          "Catalog is corrupted.");
    }
    return catalog;
  }

  GeneralCatalog *GeneralCatalog::read_v1(std::istream &in) {
    ClassId rId(in, 1);
    ClassId locId(in, 1);

    GeneralCatalog *catalog = new GeneralCatalog();
    bool ok = true;
    for (in.peek(); ok && !in.eof(); in.peek()) {
      CatalogEntry *rec = CatalogEntry::read(rId, locId, in);
      if (rec) {
        if (!catalog->addEntry(CPP11_shared_ptr<const CatalogEntry>(rec)))
          ok = false;
      } else
        ok = false;
    }

    if (!ok) {
      delete catalog;
      throw IOInvalidData(
          "In gs::GeneralCatalog::read_v1: "
          "duplicate item id. "
          "Catalog is corrupted.");
    }
    return catalog;
  }

  CPP11_shared_ptr<const CatalogEntry> GeneralCatalog::retrieveEntry(const unsigned long long id) const {
    IdMap::const_iterator it = records_.find(id);
    if (it == records_.end()) {
      CatalogEntry *ptr = nullptr;
      return CPP11_shared_ptr<const CatalogEntry>(ptr);
    } else
      return it->second;
  }

  bool GeneralCatalog::retrieveStreampos(unsigned long long id,
                                         unsigned *compressionCode,
                                         unsigned long long *length,
                                         std::streampos *pos) const {
    IdMap::const_iterator it = records_.find(id);
    if (it == records_.end())
      return false;

    assert(compressionCode);
    assert(length);
    assert(pos);

    *compressionCode = it->second->compressionCode();
    *length = it->second->itemLength();
    *pos = it->second->location().streamPosition();

    return true;
  }
}  // namespace gs