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// The following program merges contents of several object catalogs
// stored in "geners" binary metafiles
#include <fstream>
#include <iostream>
#include <vector>
#include <memory>
#include "Alignment/Geners/interface/CatalogIO.hh"
#include "Alignment/Geners/interface/ContiguousCatalog.hh"
#include "Alignment/Geners/interface/uriUtils.hh"
#include "CmdLine.hh"
using namespace gs;
using namespace std;
static void print_usage(const char *progname) {
cout << "\nUsage: " << progname << " -o output_file input_file0 input_file1 ...\n\n"
<< "This program merges the contents of several object catalogs stored "
"in \"geners\"\n"
<< "binary metafiles. The output metafile can be used as a single "
"\"geners\" archive\n"
<< "which includes all items from the merged catalogs.\n"
<< endl;
}
static const char *update_uri(const char *inputfile, const std::string &originalUri) {
static std::string result, old_inputfile, old_URI;
if (old_inputfile != inputfile || old_URI != originalUri) {
old_inputfile = inputfile;
old_URI = originalUri;
result = joinDir1WithName2(inputfile, originalUri.c_str());
}
return result.c_str();
}
static ItemLocation update_location(const char *inputfile, const ItemLocation &original) {
ItemLocation loc(original);
loc.setURI(update_uri(inputfile, original.URI()));
return loc;
}
int main(int argc, char const *argv[]) {
CmdLine cmdline(argc, argv);
if (argc == 1) {
print_usage(cmdline.progname());
return 0;
}
std::string outputfile;
std::vector<std::string> inputfiles;
try {
cmdline.require("-o") >> outputfile;
cmdline.optend();
while (cmdline) {
std::string s;
cmdline >> s;
inputfiles.push_back(s);
}
if (inputfiles.empty())
throw CmdLineError("must specify at least one input file");
} catch (CmdLineError &e) {
cerr << "Error in " << cmdline.progname() << ": " << e.str() << endl;
print_usage(cmdline.progname());
return 1;
}
// Before we perform any significant data processing,
// make sure that we can open all input files
const unsigned nfiles = inputfiles.size();
for (unsigned ifile = 0; ifile < nfiles; ++ifile) {
const std::string &inputfile(inputfiles[ifile]);
ifstream in(inputfile.c_str(), ios_base::binary);
if (!in.is_open()) {
cerr << "Error: failed to open file \"" << inputfile << "\"" << endl;
return 1;
}
}
// Variables which summarize the combined catalog
unsigned totalMergeLevel = 0, lastCompressionCode = 0;
bool compressionCodeMixed = false;
std::vector<std::string> allAnnotations;
ContiguousCatalog merged;
// Now, do the real cycle over the input files
for (unsigned ifile = 0; ifile < nfiles; ++ifile) {
const std::string &inputfile(inputfiles[ifile]);
const unsigned long long fileOffset = merged.size();
ifstream in(inputfile.c_str(), ios_base::binary);
if (!in.is_open()) {
cerr << "Error: failed to open file \"" << inputfile << "\"" << endl;
return 1;
}
unsigned compressionCode = 0, mergeLevel = 0;
std::vector<std::string> annotations;
std::unique_ptr<ContiguousCatalog> cat;
try {
cat = std::unique_ptr<ContiguousCatalog>(
readBinaryCatalog<ContiguousCatalog>(in, &compressionCode, &mergeLevel, &annotations, true));
} catch (std::exception &e) {
cerr << "Failed to read catalog from file \"" << inputfile << "\". " << e.what() << endl;
return 1;
}
// Update compression code info
if (ifile)
if (compressionCode != lastCompressionCode)
compressionCodeMixed = true;
lastCompressionCode = compressionCode;
// Update merge level
if (mergeLevel == 0)
++mergeLevel;
totalMergeLevel += mergeLevel;
// Update annotations
std::copy(annotations.begin(), annotations.end(), std::back_inserter(allAnnotations));
const unsigned long long last = cat->largestId();
for (unsigned long long id = cat->smallestId(); id <= last; ++id) {
if (!cat->itemExists(id))
continue;
std::shared_ptr<const CatalogEntry> e = cat->retrieveEntry(id);
const unsigned long long newid = merged.makeEntry(*e,
e->compressionCode(),
e->itemLength(),
update_location(inputfile.c_str(), e->location()),
e->offset() + fileOffset);
assert(newid);
}
}
ofstream of(outputfile.c_str(), ios_base::binary);
if (!of.is_open()) {
cerr << "Error: failed to open file \"" << outputfile << "\"" << endl;
return 1;
}
const unsigned compress = compressionCodeMixed ? 1 : lastCompressionCode;
if (!writeBinaryCatalog(of, compress, totalMergeLevel, allAnnotations, merged)) {
cerr << "Error: failed to write merged catalog to file \"" << outputfile << "\"" << endl;
return 1;
}
of.close();
return 0;
}
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