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#include "streamFuns.h"
#include "ErrorWarning.h"
#include <fstream>
#include <sys/statvfs.h>
#include <sys/stat.h>
#include <stdio.h>
#define fstream_Chunk_Max 2147483647
#include <cstring>
void createDirectory(const string dirPathIn, const mode_t dirPerm, const string dirParameter, Parameters &P)
{
string dirPath = dirPathIn.substr(0,dirPathIn.find_last_of('/')+1);
if (mkdir(dirPath.c_str(), dirPerm) == -1) {
if ( errno == EEXIST ) {//directory exists
P.inOut->logMain << dirParameter << " directory exists and will be overwritten: " << dirPath <<std::endl;
} else {//other error
//will try to create parent directories
size_t i1=dirPath.find_first_of('/',1);
while (i1<dirPath.size()) {
string dirPath1=dirPath.substr(0,i1);
if (mkdir(dirPath1.c_str(), dirPerm) == -1) {
if ( !(errno == EEXIST) ) {//error
exitWithError("EXITING because of fatal OUTPUT FILE error: could not create output directory: " + dirPath1 +
" for " + dirParameter + " " + dirPathIn +
"\n ERROR: " + strerror(errno) +
"\nSOLUTION: check the path and permissions.\n",
std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
};
};
i1=dirPath.find_first_of('/',i1+1);
};
P.inOut->logMain << dirParameter << " directory and its parents created: " << dirPath <<std::endl;
};
} else {
P.inOut->logMain << dirParameter << " directory created: " << dirPath <<std::endl;
};
};
unsigned long long fstreamReadBig(std::ifstream &S, char* A, unsigned long long N) {
unsigned long long C=0;
for (unsigned long long ii=0; ii<N/fstream_Chunk_Max; ii++) {
S.read(A+C,fstream_Chunk_Max);
C+=S.gcount();
if (!S.good()) break;
};
S.read(A+C,N%fstream_Chunk_Max);
C+=S.gcount();
return C;
};
void fstreamWriteBig(std::ofstream &S, char* A, unsigned long long N, std::string fileName, std::string errorID, Parameters &P) {
struct statvfs statvfsBuf;
statvfs(fileName.c_str(), &statvfsBuf);
P.inOut->logMain << "Writing " << N << " bytes into " <<fileName << " ; empty space on disk = " << statvfsBuf.f_bavail * statvfsBuf.f_bsize <<" bytes ..." <<flush;
unsigned long long C=0;
unsigned long long iC;
for (iC=0; iC<N/fstream_Chunk_Max; iC++) {
S.write(A+C,fstream_Chunk_Max);
C+=fstream_Chunk_Max;
};
if (!S.fail()) S.write(A+C,N%fstream_Chunk_Max);
if (S.fail()) {//failed to write
struct statvfs statvfsBuf;
statvfs(fileName.c_str(), &statvfsBuf);
// system(( "ls -lL "+ P.pGe.gDir + " > "+ P.pGe.gDir +"/error.info 2>&1").c_str());
// ifstream error_info((P.pGe.gDir +"/error.info").c_str());
// P.inOut->logMain <<error_info.rdbuf();
struct stat statBuf;
stat(fileName.c_str(), &statBuf);
remove(fileName.c_str());
ostringstream errOut;
errOut << errorID<<": exiting because of *OUTPUT FILE* error: could not write the output file "<< fileName <<"\n";
errOut << "fail()=" <<S.fail() <<" ; bad()="<< S.bad()<<"\n";
errOut << "Error while trying to write chunk # " << iC << "; "<< C << " bytes\n";
errOut << "File size full = "<< N <<" bytes\n";
errOut << "File size on disk = " << statBuf.st_size<<" bytes\n";
errOut << "Solution: check that you have enough space on the disk\n";
errOut << "Empty space on disk = " << statvfsBuf.f_bavail * statvfsBuf.f_bsize <<" bytes\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_FILE_WRITE, P);
};
P.inOut->logMain << " done\n" <<flush;
};
std::ofstream &ofstrOpen (std::string fileName, std::string errorID, Parameters &P) {//open file 'fileName', generate error if cannot open
std::ofstream & ofStream = *new std::ofstream(fileName.c_str(), std::fstream::out | std::fstream::trunc);
if (ofStream.fail()) {//
ostringstream errOut;
errOut << errorID<<": exiting because of *OUTPUT FILE* error: could not create output file "<< fileName <<"\n";
errOut << "SOLUTION: check that the path exists and you have write permission for this file. Also check ""ulimit -n"" and increase it to allow more open files.\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_FILE_OPEN, P);
};
return ofStream;
};
std::fstream &fstrOpen (std::string fileName, std::string errorID, Parameters &P, bool flagDelete) {//open file 'fileName', generate error if cannot open
//std::fstream &fStream = *new std::fstream(fileName.c_str(), std::fstream::in | std::fstream::out );
//std::fstream &fStream = *new std::fstream(fileName.c_str(), std::fstream::in | std::fstream::out | std::fstream::trunc);
std::fstream *fStreamP;
if (flagDelete) {//truncate the file if it exists
fStreamP = new std::fstream(fileName.c_str(), std::fstream::in | std::fstream::out | std::fstream::trunc);
} else {//try to open exising file
fStreamP=new std::fstream(fileName.c_str(), std::fstream::in | std::fstream::out );
if (fStreamP->fail()) //did not work <= file does not exist => open with trunc (the above command does not work on new file)
fStreamP = new std::fstream(fileName.c_str(), std::fstream::in | std::fstream::out | std::fstream::trunc);
};
if (fStreamP->fail()) {//
ostringstream errOut;
errOut << errorID<<": exiting because of *OUTPUT FILE* error: could not create input/output file "<< fileName <<"\n";
errOut << "Solution: check that the path exists and you have write permission for this file\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_FILE_OPEN, P);
};
return *fStreamP;
};
std::ifstream & ifstrOpen (std::string fileName, std::string errorID, std::string solutionString, Parameters &P) {
//open file 'fileName', generate error if cannot open
std::ifstream & ifStream = *new std::ifstream(fileName.c_str());
if (ifStream.fail()) {//
ostringstream errOut;
errOut << errorID<<": exiting because of *INPUT FILE* error: could not open input file "<< fileName <<"\n";
errOut << "Solution: check that the file exists and you have read permission for this file\n";
if (solutionString.size()>0) {
errOut << " "<< solutionString <<"\n";
};
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_FILE_OPEN, P);
};
return ifStream;
};
ifstream & ifstrOpenGenomeFile (std::string fileName, std::string errorID, Parameters &P) {
//open one of the genome files
return ifstrOpen(P.pGe.gDir+"/"+fileName, errorID, "if this file is missing from the genome directory, you will need to *re-generate the genome*", P);
};
void copyFile(string fileIn, string fileOut)
{//copy fileIn into FileOut
std::ifstream src(fileIn, std::ios::binary);
std::ofstream dst(fileOut, std::ios::binary);
dst << src.rdbuf();
};
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