BinaryFileArchive.cc

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#include <sstream>
 
#include "Alignment/Geners/interface/BinaryFileArchive.hh"
 
#include "Alignment/Geners/interface/ContiguousCatalog.hh"
#include "Alignment/Geners/interface/IOException.hh"
#include "Alignment/Geners/interface/WriteOnlyCatalog.hh"
#include "Alignment/Geners/interface/streamposIO.hh"
#include "Alignment/Geners/interface/uriUtils.hh"
 
namespace gs {
  BinaryFileArchive::BinaryFileArchive(const char *basename,
                                       const char *mode,
                                       const char *ann,
                                       const unsigned dataFileBufferSize,
                                       const unsigned catalogFileBufferSize)
      : BinaryArchiveBase(basename, mode),
        filebuf_(nullptr),
        catabuf_(nullptr),
        annotation_(ann ? std::string(ann) : std::string("")),
        dataFileName_(AbsArchive::name() + ".0.gsbd"),    // binary data
        catalogFileName_(AbsArchive::name() + ".gsbmf"),  // binary metafile
        dataFileURI_(localFileURI(dataFileName_.c_str())),
        lastpos_(0),
        jumppos_(0),
        catalogMergeLevel_(1),
        annotationsMerged_(false),
        streamFlushed_(true) {
    if (!modeValid())
      return;
 
    try {
      // Get a new buffer for the data and open the data stream
      if (dataFileBufferSize)
        filebuf_ = new char[dataFileBufferSize];
      dataStream_.rdbuf()->pubsetbuf(filebuf_, dataFileBufferSize);
      openDataFile(dataStream_, dataFileName_.c_str());
      dataStream_.seekp(0, std::ios_base::end);
 
      // Get a new buffer for the catalog and open the catalog stream.
      // We may have to rewrite the complete catalog, so remove the flag
      // std::ios_base::app from the opening mode.
      if (catalogFileBufferSize)
        catabuf_ = new char[catalogFileBufferSize];
      catStream_.rdbuf()->pubsetbuf(catabuf_, catalogFileBufferSize);
      catStream_.open(catalogFileName_.c_str(), openmode() & ~std::ios_base::app);
      if (!catStream_.is_open())
        throw IOOpeningFailure("gs::BinaryFileArchive constructor", catalogFileName_);
 
      // Can we use a write-only catalog?
      if (openmode() & std::ios_base::in) {
        // Reading is allowed. Have to use in-memory catalog.
        // If the file data already exists, get the catalog in.
        if (isEmptyFile(catStream_))
          setCatalog(new ContiguousCatalog());
        else
          readCatalog<ContiguousCatalog>();
      } else {
        // Yes, we can use a write-only catalog.
        // Is the catalog file empty? If so, write out
        // the stuff needed at the beginning of the file.
        // If not, assume that the necessary stuff is
        // already there. Note that in this case we will
        // not be able to add the annotation.
        if (isEmptyFile(catStream_)) {
          setCatalog(new WriteOnlyCatalog(catStream_));
          writeCatalog();
        } else {
          // Have to read in the catalog contents
          catStream_.close();
          catStream_.clear();
          catStream_.open(catalogFileName_.c_str(), openmode() | std::ios_base::in);
          if (!catStream_.is_open())
            throw IOOpeningFailure("gs::BinaryFileArchive constructor", catalogFileName_);
          readCatalog<WriteOnlyCatalog>();
          catStream_.seekp(0, std::ios_base::end);
        }
      }
    } catch (std::exception &e) {
      setCatalog(nullptr);
      releaseBuffers();
      errorStream() << e.what();
    }
  }
 
  void BinaryFileArchive::releaseBuffers() {
    if (dataStream_.is_open())
      dataStream_.close();
    if (catStream_.is_open())
      catStream_.close();
    catStream_.rdbuf()->pubsetbuf(nullptr, 0);
    dataStream_.rdbuf()->pubsetbuf(nullptr, 0);
    delete[] catabuf_;
    catabuf_ = nullptr;
    delete[] filebuf_;
    filebuf_ = nullptr;
  }
 
  BinaryFileArchive::~BinaryFileArchive() {
    flush();
    releaseBuffers();
  }
 
  void BinaryFileArchive::writeCatalog() {
    if (isOpen()) {
      if (!annotationsMerged_) {
        if (!annotation_.empty())
          catalogAnnotations_.push_back(annotation_);
        annotationsMerged_ = true;
      }
      const unsigned compress = static_cast<unsigned>(compressionMode());
      if (!writeBinaryCatalog(catStream_, compress, catalogMergeLevel_, catalogAnnotations_, *catalog())) {
        std::ostringstream os;
        os << "In BinaryFileArchive::writeCatalog: "
           << "failed to write catalog data to file " << catalogFileName_;
        throw IOWriteFailure(os.str());
      }
    }
  }
 
  std::istream &BinaryFileArchive::plainInputStream(const unsigned long long id,
                                                    unsigned *compressionCode,
                                                    unsigned long long *length) {
    if (isOpen()) {
      assert(openmode() & std::ios_base::in);
      if (!id)
        throw gs::IOInvalidArgument("In gs::BinaryFileArchive::plainInputStream: invalid item id");
      std::streampos pos;
      if (!catalog()->retrieveStreampos(id, compressionCode, length, &pos)) {
        std::ostringstream os;
        os << "In gs::BinaryFileArchive::plainInputStream: "
           << "failed to locate item with id " << id << "in the catalog stored in file " << catalogFileName_;
        throw gs::IOInvalidArgument(os.str());
      }
      if (!streamFlushed_) {
        dataStream_.flush();
        streamFlushed_ = true;
      }
      dataStream_.seekg(pos);
    }
    return dataStream_;
  }
 
  unsigned long long BinaryFileArchive::addToCatalog(const AbsRecord &record,
                                                     const unsigned compressionCode,
                                                     const unsigned long long itemLength) {
    unsigned long long id = 0;
    if (isOpen()) {
      id = catalog()->makeEntry(record, compressionCode, itemLength, ItemLocation(lastpos_, dataFileURI_.c_str()));
      if (id && injectMetadata()) {
        const CatalogEntry *entry = catalog()->lastEntryMade();
        assert(entry);
        dataStream_.seekp(0, std::ios_base::end);
        std::streampos now = dataStream_.tellp();
        if (entry->write(dataStream_)) {
          dataStream_.seekp(jumppos_);
          write_pod(dataStream_, now);
          dataStream_.seekp(0, std::ios_base::end);
        } else
          id = 0;
      }
    }
    return id;
  }
 
  std::ostream &BinaryFileArchive::plainOutputStream() {
    if (isOpen()) {
      assert(openmode() & std::ios_base::out);
      dataStream_.seekp(0, std::ios_base::end);
      if (injectMetadata()) {
        jumppos_ = dataStream_.tellp();
        std::streampos catpos(0);
        write_pod(dataStream_, catpos);
      }
      lastpos_ = dataStream_.tellp();
      streamFlushed_ = false;
    }
    return dataStream_;
  }
 
  void BinaryFileArchive::flush() {
    if (isOpen()) {
      if (!streamFlushed_) {
        dataStream_.flush();
        streamFlushed_ = true;
      }
 
      if (openmode() & std::ios_base::out) {
        if (dynamic_cast<WriteOnlyCatalog *>(catalog()) == nullptr)
          writeCatalog();
        catStream_.flush();
      }
    }
  }
}  // namespace gs