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fix(macOS): spawn readFilesCommand via shell (posix_spawnp) so gzipped input works #2693

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fix(macOS): spawn readFilesCommand via shell (posix_spawnp) so gzipped input works #2693

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47 changes: 30 additions & 17 deletions source/Parameters_openReadsFiles.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,14 @@
#include "ErrorWarning.h"
#include <fstream>
#include <sys/stat.h>
void Parameters::openReadsFiles()
#include <spawn.h>
#include <unistd.h>

// environ is declared in <unistd.h> on glibc but not on macOS; declare it
// explicitly so posix_spawnp can pass the current environment on every platform.
extern char **environ;

void Parameters::openReadsFiles()
{
if (readFilesCommandString=="") {//read from file
for (uint ii=0;ii<readFilesIn.size();ii++) {//open readIn files
Expand Down Expand Up @@ -79,24 +86,30 @@ void Parameters::openReadsFiles()

readFilesCommandPID[imate]=0;

// Run the generated readsCommand script through a shell using
// posix_spawnp. Invoking it explicitly as "<shell> <script>" means
// the script does not need a #! shebang line (none is written by
// default, i.e. when --sysShell is "-") and we do not rely on
// execvp's ENOEXEC -> /bin/sh fallback, which posix_spawn does not
// provide. This fixes "Failed spawning readFilesCommand" on macOS
// (issue #2663). posix_spawnp also avoids the undefined behavior of
// the previous vfork()+exit(0): calling exit() in a vfork child
// flushes the parent's stdio buffers and runs atexit handlers in the
// shared address space, and reported success even when exec failed.
ostringstream errOut;
pid_t PID=vfork();
switch (PID) {
case -1:
errOut << "EXITING: because of fatal EXECUTION error: Failed vforking readFilesCommand\n";
errOut << errno << ": " << strerror(errno) << "\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
break;

case 0:
//this is the child
execlp(readsCommandFileName.at(imate).c_str(), readsCommandFileName.at(imate).c_str(), (char*) NULL);
exit(0);

default:
//this is the father, record PID of the children
readFilesCommandPID[imate]=PID;
string readsCommandShell = (sysShell!="-" ? sysShell : "/bin/sh");
char* spawnArgv[] = { const_cast<char*>(readsCommandShell.c_str()),
const_cast<char*>(readsCommandFileName.at(imate).c_str()),
(char*) NULL };
pid_t PID=0;
int spawnErr = posix_spawnp(&PID, readsCommandShell.c_str(), NULL, NULL, spawnArgv, environ);
if (spawnErr != 0) {
errOut << "EXITING: because of fatal EXECUTION error: Failed spawning readFilesCommand: "
<< readsCommandShell << " " << readsCommandFileName.at(imate) << "\n";
errOut << spawnErr << ": " << strerror(spawnErr) << "\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
readFilesCommandPID[imate]=PID; //record PID of the child

inOut->readIn[imate].open(readFilesInTmp.at(imate).c_str());
};
Expand Down