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#include <cstdio>
#include <sstream>
#include "Alignment/Geners/interface/MultiFileArchive.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 {
MultiFileArchive::MultiFileArchive(const char *basename,
const char *mode,
const char *ann,
const unsigned typicalFileSizeInMB,
const unsigned dataFileBufferSize,
const unsigned catalogFileBufferSize)
: BinaryArchiveBase(basename, mode),
filebuf_(nullptr),
readbuf_(nullptr),
catabuf_(nullptr),
annotation_(ann ? std::string(ann) : std::string("")),
catalogFileName_(AbsArchive::name() + ".gsbmf"), // binary metafile
writeFileURI_("/ / / / / / /\\ \\ \\ \\"),
readFileURI_(writeFileURI_),
lastpos_(0),
jumppos_(0),
maxpos_(std::streamoff(1048576LL * typicalFileSizeInMB)),
writeFileNumber_(0),
catalogMergeLevel_(1),
annotationsMerged_(false),
streamFlushed_(true) {
if (!modeValid())
return;
try {
// Get a new buffer for the output stream
if (dataFileBufferSize)
filebuf_ = new char[dataFileBufferSize];
writeStream_.rdbuf()->pubsetbuf(filebuf_, dataFileBufferSize);
// Get a new buffer for the input stream
if (dataFileBufferSize)
readbuf_ = new char[dataFileBufferSize];
separateReadStream_.rdbuf()->pubsetbuf(readbuf_, dataFileBufferSize);
// 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::MultiFileArchive 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 {
catStream_.close();
catStream_.clear();
catStream_.open(catalogFileName_.c_str(), openmode() | std::ios_base::in);
if (!catStream_.is_open())
throw IOOpeningFailure("gs::MultiFileArchive constructor", catalogFileName_);
readCatalog<WriteOnlyCatalog>();
catStream_.seekp(0, std::ios_base::end);
}
}
// Open the write stream
if (openmode() & std::ios_base::out) {
setupWriteStream();
const std::streampos pos1 = writeStream_.tellp();
if (maxpos_ < pos1)
maxpos_ = pos1;
}
} catch (std::exception &e) {
setCatalog(nullptr);
releaseBuffers();
errorStream() << e.what();
}
}
void MultiFileArchive::releaseBuffers() {
if (writeStream_.is_open())
writeStream_.close();
if (separateReadStream_.is_open())
separateReadStream_.close();
if (catStream_.is_open())
catStream_.close();
catStream_.rdbuf()->pubsetbuf(nullptr, 0);
writeStream_.rdbuf()->pubsetbuf(nullptr, 0);
separateReadStream_.rdbuf()->pubsetbuf(nullptr, 0);
delete[] catabuf_;
catabuf_ = nullptr;
delete[] readbuf_;
readbuf_ = nullptr;
delete[] filebuf_;
filebuf_ = nullptr;
}
MultiFileArchive::~MultiFileArchive() {
flush();
releaseBuffers();
}
void MultiFileArchive::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 MultiFileArchive::writeCatalog: "
<< "failed to write catalog data to file " << catalogFileName_;
throw IOWriteFailure(os.str());
}
}
}
void MultiFileArchive::openWriteStream() {
assert(openmode() & std::ios_base::out);
assert(!writeStream_.is_open());
{
std::ostringstream os;
os << AbsArchive::name() << '.' << writeFileNumber_ << ".gsbd";
writeFileName_ = os.str();
}
writeFileURI_ = localFileURI(writeFileName_.c_str());
openDataFile(writeStream_, writeFileName_.c_str());
}
std::ostream &MultiFileArchive::plainOutputStream() {
if (isOpen()) {
assert(openmode() & std::ios_base::out);
if (writeStream_.is_open()) {
writeStream_.seekp(0, std::ios_base::end);
lastpos_ = writeStream_.tellp();
if (lastpos_ > maxpos_) {
writeStream_.close();
// Don't have to clear. "openDataFile" will do it.
// writeStream_.clear();
++writeFileNumber_;
} else if (injectMetadata()) {
jumppos_ = lastpos_;
std::streampos catpos(0);
write_pod(writeStream_, catpos);
lastpos_ = writeStream_.tellp();
}
}
if (!writeStream_.is_open()) {
openWriteStream();
writeStream_.seekp(0, std::ios_base::end);
if (injectMetadata()) {
jumppos_ = writeStream_.tellp();
std::streampos catpos(0);
write_pod(writeStream_, catpos);
}
lastpos_ = writeStream_.tellp();
}
streamFlushed_ = false;
}
return writeStream_;
}
void MultiFileArchive::flush() {
if (isOpen()) {
if (!streamFlushed_) {
writeStream_.flush();
streamFlushed_ = true;
}
if (openmode() & std::ios_base::out) {
if (dynamic_cast<WriteOnlyCatalog *>(catalog()) == nullptr)
writeCatalog();
catStream_.flush();
}
}
}
void MultiFileArchive::setupWriteStream() {
if (openmode() & std::ios_base::trunc) {
bool removed = true;
for (unsigned i = 0; removed; ++i) {
std::ostringstream os;
os << AbsArchive::name() << '.' << i << ".gsbd";
std::string fname = os.str();
removed = std::remove(fname.c_str()) == 0;
}
writeFileNumber_ = 0;
} else {
unsigned long firstNonExistent = 0;
for (;; ++firstNonExistent) {
std::ostringstream os;
os << AbsArchive::name() << '.' << firstNonExistent << ".gsbd";
std::string fname = os.str();
std::ifstream f(fname.c_str());
if (!f)
break;
}
writeFileNumber_ = firstNonExistent ? firstNonExistent - 1UL : 0UL;
}
openWriteStream();
}
std::istream &MultiFileArchive::plainInputStream(const unsigned long long id,
unsigned *compressionCode,
unsigned long long *length) {
std::fstream *readStream = &writeStream_;
if (isOpen()) {
assert(openmode() & std::ios_base::in);
if (!id)
throw gs::IOInvalidArgument("In gs::MultiFileArchive::plainInputStream: invalid item id");
// If we have a write stream, and if the archive
// has one file only, we should be able to retrieve
// stream position quickly
std::streampos pos(0);
if ((openmode() & std::ios_base::out) && writeFileNumber_ == 0UL) {
if (!catalog()->retrieveStreampos(id, compressionCode, length, &pos)) {
std::ostringstream os;
os << "In gs::MultiFileArchive::plainInputStream: "
<< "failed to locate item with id " << id << "in the catalog stored in file " << catalogFileName_;
throw gs::IOInvalidArgument(os.str());
}
} else {
// Here, we have to do a full catalog search
std::shared_ptr<const CatalogEntry> sptr = catalog()->retrieveEntry(id);
const CatalogEntry *pe = sptr.get();
if (!pe) {
std::ostringstream os;
os << "In gs::MultiFileArchive::plainInputStream: "
<< "failed to locate item with id " << id << "in the catalog stored in file " << catalogFileName_;
throw gs::IOInvalidArgument(os.str());
}
pos = pe->location().streamPosition();
if (pe->location().URI() != writeFileURI_) {
updateReadStream(pe->location().URI());
readStream = &separateReadStream_;
}
*compressionCode = pe->compressionCode();
*length = pe->itemLength();
}
// Flush the write stream if it will be used for reading
if (readStream == &writeStream_) {
assert(writeStream_.is_open());
if (!streamFlushed_) {
writeStream_.flush();
streamFlushed_ = true;
}
}
readStream->seekg(pos);
}
return *readStream;
}
void MultiFileArchive::updateReadStream(const std::string &uri) {
if (uri == readFileURI_)
return;
assert(openmode() & std::ios_base::in);
if (separateReadStream_.is_open()) {
separateReadStream_.close();
separateReadStream_.clear();
}
// We need to get the name of the local file from the URI.
// We will assume that it belongs to the archive we are
// working with right now.
readFileName_ = joinDir1WithName2(AbsArchive::name().c_str(), uri.c_str());
separateReadStream_.open(readFileName_.c_str(), std::ios_base::binary | std::ios_base::in);
if (!separateReadStream_.is_open())
throw IOOpeningFailure("gs::MultiFileArchive::updateReadStream", readFileName_);
readFileURI_ = uri;
}
unsigned long long MultiFileArchive::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_, writeFileURI_.c_str()));
if (id && injectMetadata()) {
const CatalogEntry *entry = catalog()->lastEntryMade();
assert(entry);
writeStream_.seekp(0, std::ios_base::end);
std::streampos now = writeStream_.tellp();
if (entry->write(writeStream_)) {
writeStream_.seekp(jumppos_);
write_pod(writeStream_, now);
writeStream_.seekp(0, std::ios_base::end);
} else
id = 0;
}
}
return id;
}
} // namespace gs
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