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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
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