ContiguousCatalog.cc

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

#include "Alignment/Geners/interface/CPP11_auto_ptr.hh"
#include "Alignment/Geners/interface/ContiguousCatalog.hh"
#include "Alignment/Geners/interface/IOException.hh"
#include "Alignment/Geners/interface/binaryIO.hh"

namespace gs {
  void ContiguousCatalog::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);
    } 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);
    }
  }

  unsigned long long ContiguousCatalog::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_.size() + firstId_;
    lastEntry_ = SPtr(new CatalogEntry(descriptor, nextId, compressionCode, itemLength, loc, offset));
    records_.push_back(lastEntry_);
    recordMap_[descriptor.category()].insert(std::make_pair(descriptor.name(), nextId));

    return nextId;
  }

  void ContiguousCatalog::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 ContiguousCatalog::isEqual(const AbsCatalog &other) const {
    if ((void *)this == (void *)(&other))
      return true;
    const ContiguousCatalog &r = static_cast<const ContiguousCatalog &>(other);
    if (firstId_ != r.firstId_)
      return false;
    if (recordMap_ != r.recordMap_)
      return false;
    const unsigned long nRecords = records_.size();
    if (nRecords != r.records_.size())
      return false;
    for (unsigned long i = 0; i < nRecords; ++i)
      if (*records_[i] != *r.records_[i])
        return false;
    return true;
  }

  // Version 1 write function
  // bool ContiguousCatalog::write(std::ostream& os) const
  // {
  //     bool status = ClassId::makeId<CatalogEntry>().write(os) &&
  //                   ClassId::makeId<ItemLocation>().write(os);
  //     const unsigned long long sz = records_.size();
  //     for (unsigned long long i=0; i<sz && status; ++i)
  //         status = records_[i]->write(os);
  //     return status;
  // }

  bool ContiguousCatalog::write(std::ostream &os) const {
    const unsigned long long sz = records_.size();
    long long nRecords = sz;
    write_pod(os, nRecords);
    bool status = !os.fail() && ClassId::makeId<CatalogEntry>().write(os) && ClassId::makeId<ItemLocation>().write(os);
    for (unsigned long long i = 0; i < sz && status; ++i)
      status = records_[i]->write(os);
    return status;
  }

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

    if (cid.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);

    CPP11_auto_ptr<ContiguousCatalog> catalog(new ContiguousCatalog());
    bool firstEntry = true;
    for (long long recnum = 0; recnum < nRecords; ++recnum) {
      CatalogEntry *rec = CatalogEntry::read(rId, locId, in);
      if (rec) {
        const unsigned long long id = rec->id();
        if (firstEntry) {
          catalog->firstId_ = id;
          firstEntry = false;
        } else {
          const unsigned long long nextId = catalog->records_.size() + catalog->firstId_;
          if (id != nextId) {
            delete rec;
            throw IOInvalidData(
                "In gs::ContiguousCatalog::read:"
                " unexpected item id. "
                "Catalog is corrupted.");
          }
        }
        catalog->records_.push_back(SPtr(rec));
        catalog->recordMap_[rec->category()].insert(std::make_pair(rec->name(), id));
      } else
        throw IOInvalidData(
            "In gs::ContiguousCatalog::read:"
            " failed to read catalog entry");
    }
    return catalog.release();
  }

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

    CPP11_auto_ptr<ContiguousCatalog> catalog(new ContiguousCatalog());
    bool firstEntry = true;
    for (in.peek(); !in.eof(); in.peek()) {
      CatalogEntry *rec = CatalogEntry::read(rId, locId, in);
      if (rec) {
        const unsigned long long id = rec->id();
        if (firstEntry) {
          catalog->firstId_ = id;
          firstEntry = false;
        } else {
          const unsigned long long nextId = catalog->records_.size() + catalog->firstId_;
          if (id != nextId) {
            delete rec;
            throw IOInvalidData(
                "In gs::ContiguousCatalog::read_v1:"
                " unexpected item id. "
                "Catalog is corrupted.");
          }
        }
        catalog->records_.push_back(SPtr(rec));
        catalog->recordMap_[rec->category()].insert(std::make_pair(rec->name(), id));
      } else
        throw IOInvalidData(
            "In gs::ContiguousCatalog::read_v1:"
            " failed to read catalog entry");
    }
    return catalog.release();
  }

  CPP11_shared_ptr<const CatalogEntry> ContiguousCatalog::retrieveEntry(const unsigned long long id) const {
    if (id >= firstId_ && id < records_.size() + firstId_)
      return records_[id - firstId_];
    else {
      CatalogEntry *ptr = nullptr;
      return CPP11_shared_ptr<const CatalogEntry>(ptr);
    }
  }

  bool ContiguousCatalog::retrieveStreampos(unsigned long long id,
                                            unsigned *compressionCode,
                                            unsigned long long *length,
                                            std::streampos *pos) const {
    assert(compressionCode);
    assert(length);
    assert(pos);

    if (id >= firstId_ && id < records_.size() + firstId_) {
      const CPP11_shared_ptr<const CatalogEntry> &rec(records_[id - firstId_]);
      *compressionCode = rec->compressionCode();
      *length = rec->itemLength();
      *pos = rec->location().streamPosition();
      return true;
    } else
      return false;
  }
}  // namespace gs