diff --git a/libIRDB/include/utils.hpp b/libIRDB/include/utils.hpp
index 224f26a3d06de28cc0af03bed8ce9993ed7389d9..6f4a9046e6a03b03bbdc2eb0d320ae03434ba2e2 100644
--- a/libIRDB/include/utils.hpp
+++ b/libIRDB/include/utils.hpp
@@ -120,6 +120,9 @@ inline Funct for_randomOrder_each(const IterType &b, const IterType & e, const F
return callback;
}
+int command_to_stream(const std::string& command, std::ostream& stream);
+
+
#endif
diff --git a/libIRDB/src/core/address.cpp b/libIRDB/src/core/address.cpp
index ea1cfe71e464c4dc51314cc29bb7ead62d6798d8..f06a0783a0aff1a79f45fa3386bf907a1171a6f2 100644
--- a/libIRDB/src/core/address.cpp
+++ b/libIRDB/src/core/address.cpp
@@ -22,6 +22,7 @@
#include <all.hpp>
#include <utils.hpp>
#include <stdlib.h>
+
using namespace libIRDB;
using namespace std;
diff --git a/libIRDB/src/core/file.cpp b/libIRDB/src/core/file.cpp
index b7560f892ea421811aeafb8bbfb2b78c37b0f98b..7aa10476f6a13748430cde33781069b76d51e6f4 100644
--- a/libIRDB/src/core/file.cpp
+++ b/libIRDB/src/core/file.cpp
@@ -26,12 +26,11 @@
#include <fstream>
#include <iostream>
+#include <utils.hpp>
+
using namespace libIRDB;
using namespace std;
-static void ignore_result(int /* res */) { }
-
-
File_t::File_t(const db_id_t &myfile_id, const db_id_t &my_orig_fid, const std::string &myurl,
const std::string &myhash, const std::string &myarch, const int &myoid,
@@ -82,7 +81,8 @@ void File_t::CreateTables()
ehcss_table_name+" "+
tmpfile;
- ignore_result(system(command.c_str()));
+ // ignore_result(system(command.c_str()));
+ command_to_stream(command,cout);
std::ifstream t(tmpfile.c_str());
diff --git a/libIRDB/src/core/fileir.cpp b/libIRDB/src/core/fileir.cpp
index 1eef33f0b9288e351001fcd05f7e96ea15fef63f..59ec13bcf49ea7734f7ec3b913527b09373e90a2 100644
--- a/libIRDB/src/core/fileir.cpp
+++ b/libIRDB/src/core/fileir.cpp
@@ -28,9 +28,6 @@
#include <stdlib.h>
#include <sys/wait.h>
#include <iomanip>
-//#include <bea_deprecated.hpp>
-
-
using namespace libIRDB;
using namespace std;
@@ -42,6 +39,29 @@ using namespace std;
#undef EIP
+int command_to_stream(const string& command, ostream& stream)
+{
+ auto redirect_command=command+" 2>&1 ";
+ auto buffer=array<char,128>();
+
+ std::cout << "Issuing subcommand: "<< command << std::endl;
+ auto pipe = popen(redirect_command.c_str(), "r");
+ if (!pipe)
+ {
+ stream << "Couldn't start command:"<< strerror(errno) << endl;
+ return 1;
+ }
+ while (fgets(buffer.data(), 128, pipe) != NULL)
+ {
+ stream<<buffer.data();
+ }
+ auto returnCode = pclose(pipe);
+ if(returnCode==-1)
+ stream << "Could not close pipe: "<< strerror(errno) << endl;
+
+ std::cout << "Return code = "<<returnCode << std::endl;
+ return returnCode;
+}
static void UpdateEntryPoints(
const std::map<db_id_t,Instruction_t*> &insnMap,
@@ -192,14 +212,8 @@ void FileIR_t::AssembleRegistry()
string binaryOutputFile = "tmp.bin";
string command = "rm -f " + assemblyFile + " " + binaryOutputFile;
- int rt = system(command.c_str());
+ auto actual_exit = command_to_stream(command, cout); // system(command.c_str());
- int actual_exit = -1;
- //int actual_signal = -1;
-
- if (WIFEXITED(rt)) actual_exit = WEXITSTATUS(rt);
- //else actual_signal = WTERMSIG(rt);
-
assert(actual_exit == 0);
ofstream asmFile;
@@ -219,14 +233,7 @@ void FileIR_t::AssembleRegistry()
asmFile.close();
command = string("nasm ") + assemblyFile + string(" -o ") + binaryOutputFile;
- rt = system(command.c_str());
-
- actual_exit = -1;
- //actual_signal = -1;
-
- if (WIFEXITED(rt)) actual_exit = WEXITSTATUS(rt);
- //else actual_signal = WTERMSIG(rt);
-
+ actual_exit = command_to_stream(command,cout); // system(command.c_str());
assert(actual_exit == 0);
diff --git a/libIRDB/src/core/instruction.cpp b/libIRDB/src/core/instruction.cpp
index 27a990218f4f83a65ef03faa8d418a325497700c..7a876821660082bf3116ac9b57082fdf200c7ade 100644
--- a/libIRDB/src/core/instruction.cpp
+++ b/libIRDB/src/core/instruction.cpp
@@ -24,15 +24,13 @@
#include <fstream>
#include <sstream>
#include <iomanip>
+#include <utils.hpp>
#undef EIP
using namespace libIRDB;
using namespace std;
-static void ignore_result(int /* res */) { }
-
-
Instruction_t::Instruction_t() :
BaseObj_t(NULL),
my_address(NULL),
@@ -115,9 +113,9 @@ bool Instruction_t::Assemble(string assembly)
//remove any preexisting assembly or nasm generated files
string command = "rm -f " + assemblyFile;
- ignore_result(system(command.c_str()));
+ command_to_stream(command,cout);
command = "rm -f "+assemblyFile+".bin";
- ignore_result(system(command.c_str()));
+ command_to_stream(command,cout);
ofstream asmFile;
asmFile.open(assemblyFile.c_str());
@@ -132,7 +130,7 @@ bool Instruction_t::Assemble(string assembly)
asmFile.close();
command = "nasm " + assemblyFile + " -o "+ binaryOutputFile;
- ignore_result(system(command.c_str()));
+ command_to_stream(command,cout);
ifstream binreader;
unsigned int filesize;
diff --git a/plugins_install/p1transform.sh b/plugins_install/p1transform.sh
deleted file mode 100755
index c288c305cf6b7d1998a8d8de75101233b00a9225..0000000000000000000000000000000000000000
--- a/plugins_install/p1transform.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-PN_TIMEOUT_VALUE=21600
-
-varid=$1
-shift
-
-$PEASOUP_HOME/tools/do_p1transform.sh $varid a.ncexe a.ncexe.annot $PEASOUP_HOME/tools/bed.sh $PN_TIMEOUT_VALUE $*
-
diff --git a/tools/thanos/thanos.cpp b/tools/thanos/thanos.cpp
index 18766be55dc4ba9a848d97ff36e7c45200ee0901..b17231b568274eb75dddb2d40966322542bb0152 100644
--- a/tools/thanos/thanos.cpp
+++ b/tools/thanos/thanos.cpp
@@ -9,6 +9,8 @@
#include <fcntl.h>
#include <fstream>
#include <ctime>
+#include <ext/stdio_filebuf.h>
+
using namespace std;
@@ -18,7 +20,8 @@ using namespace Transform_SDK;
#define ALLOF(a) begin(a),end(a)
// global to be used like cout/cerr for writing to the logs
-ofstream thanos_log;
+int thanos_log_fd=-1;
+ostream *thanos_log;
ostream *real_cout;
ostream *real_cerr;
string thanos_path;
@@ -69,22 +72,32 @@ PluginList_t getPlugins(const int argc, char const *const argv[]);
int main(int argc, char* argv[])
{
thanos_path=argv[0];
- ostream my_real_cerr(cerr.rdbuf());
- ostream my_real_cout(cout.rdbuf());
- real_cerr=&my_real_cerr;
- real_cout=&my_real_cout;
- thanos_log.open("logs/thanos.log", ofstream::out|ofstream::app);
+ auto new_stdout_fd=dup(STDOUT_FILENO);
+ auto new_stderr_fd=dup(STDERR_FILENO);
+
+ __gnu_cxx::stdio_filebuf<char> stdout_filebuf(new_stdout_fd, ios::out);
+ __gnu_cxx::stdio_filebuf<char> stderr_filebuf(new_stderr_fd, ios::out);
+
+ ostream my_real_cout(&stderr_filebuf);
+ ostream my_real_cerr(&stdout_filebuf);
+ real_cout=&my_real_cout;
+ real_cerr=&my_real_cerr;
- if(!thanos_log)
+ auto thanos_log_fileptr=fopen("logs/thanos.log", "a+");
+ if(!thanos_log_fileptr)
{
- cerr<<"Cannot open logs/thanos.log"<<endl;
+ *real_cerr<<"Cannot open logs/thanos.log"<<endl;
exit(1);
}
- // catch any misc stuff to the thanos log
- cout.rdbuf(thanos_log.rdbuf());
- cerr.rdbuf(thanos_log.rdbuf());
+ thanos_log_fd=fileno(thanos_log_fileptr);
+ __gnu_cxx::stdio_filebuf<char> thanos_log_filebuf(thanos_log_fd, ios::out);
+ ostream thanos_log_stream(&thanos_log_filebuf);
+ thanos_log=&thanos_log_stream;
+ // make sure stuff goes to the log unless otherwise indicated by using real_cout
+ dup2(thanos_log_fd, STDOUT_FILENO);
+ dup2(thanos_log_fd, STDERR_FILENO);
// get plugins
auto argv_iter=1;
@@ -110,8 +123,8 @@ int main(int argc, char* argv[])
// for now, usage is pretty strict to enable simple
// parsing, because this program is only used by an
// automated script
- thanos_log << "Syntax error in arguments." << endl;
- thanos_log << "USAGE: <thanos opts> (\"<step name> [-optional] [--step-args [ARGS]]\")+" << endl;
+ *thanos_log << "Syntax error in arguments." << endl;
+ *thanos_log << "USAGE: <thanos opts> (\"<step name> [-optional] [--step-args [ARGS]]\")+" << endl;
return 1;
}
@@ -123,8 +136,8 @@ int main(int argc, char* argv[])
// if that returns failure AND the step is not optional
if(result != 0 && !plugin->isOptional())
{
- thanos_log << "A critical step failed: " << plugin->getStepName() << endl;
- thanos_log << "If DEBUG_STEPS is not on, this failure could "
+ *thanos_log << "A critical step failed: " << plugin->getStepName() << endl;
+ *thanos_log << "If DEBUG_STEPS is not on, this failure could "
<< "be due to an earlier critical step." << endl;
return 1; // critical step failed, abort
}
@@ -133,9 +146,9 @@ int main(int argc, char* argv[])
const int result = ThanosPlugin_t::saveChanges();
if(result != 0)
{
- thanos_log << "A critical step failed: " << (thanos_plugins.back())->getStepName()
+ *thanos_log << "A critical step failed: " << (thanos_plugins.back())->getStepName()
<< endl;
- thanos_log << "If DEBUG_STEPS is not on, this failure could "
+ *thanos_log << "If DEBUG_STEPS is not on, this failure could "
<< "be due to an earlier critical step." << endl;
return 1; // critical step failed, abort
}
@@ -211,7 +224,7 @@ int ThanosPlugin_t::runPlugin()
static const char *const base_path = getenv("SECURITY_TRANSFORMS_HOME");
if(base_path == NULL)
{
- thanos_log << "Environment variables not set." << endl;
+ *thanos_log << "Environment variables not set." << endl;
return -1;
}
static const auto plugin_path (string(base_path).append("/plugins_install/"));
@@ -220,7 +233,7 @@ int ThanosPlugin_t::runPlugin()
if(dlhdl == NULL)
{
const auto err=dlerror();
- thanos_log<<"Cannot open "<<step_name<<": "<<err<<endl;
+ *thanos_log<<"Cannot open "<<step_name<<": "<<err<<endl;
return -1;
}
@@ -228,7 +241,7 @@ int ThanosPlugin_t::runPlugin()
if(sym == NULL)
{
const auto err=dlerror();
- thanos_log<<"Cannot find GetTransformStep in "<<step_name<<": "<<err<<endl;
+ *thanos_log<<"Cannot find GetTransformStep in "<<step_name<<": "<<err<<endl;
return -1;
}
@@ -239,17 +252,14 @@ int ThanosPlugin_t::runPlugin()
static const char *const are_debugging = getenv("DEBUG_STEPS");
-
- auto saved_cerrbuf = cerr.rdbuf();
- auto saved_coutbuf = cout.rdbuf();
- ofstream logfile;
+ auto logfile=(FILE*)nullptr;
auto are_logging = !((bool) are_debugging);
if(are_logging)
{
// setup logging
auto logfile_path = "./logs/"+step_name+".log";
- logfile.open(logfile_path,ofstream::out);
+ logfile=fopen(logfile_path.c_str(), "a+");
if(!logfile)
{
*real_cout<<"Cannot open log file "<<logfile_path<<endl;
@@ -257,8 +267,8 @@ int ThanosPlugin_t::runPlugin()
}
if(redirect_opt)
{
- cout.rdbuf(logfile.rdbuf());
- cerr.rdbuf(logfile.rdbuf());
+ dup2(fileno(logfile), STDOUT_FILENO);
+ dup2(fileno(logfile), STDERR_FILENO);
}
}
@@ -283,8 +293,10 @@ int ThanosPlugin_t::runPlugin()
cout<< "#ATTRIBUTE step_exitcode="<<dec<<step_result<<endl;
- cerr.rdbuf(saved_cerrbuf);
- cout.rdbuf(saved_coutbuf);
+ dup2(thanos_log_fd, STDOUT_FILENO);
+ dup2(thanos_log_fd, STDERR_FILENO);
+ if(logfile)
+ fclose(logfile);
the_step.reset(); // explicitly get rid of the handle to the library so we can close it.
dlclose(dlhdl);
@@ -315,7 +327,7 @@ int ThanosPlugin_t::executeStep(TransformStep_t& the_step, const bool are_debugg
pqxxDB_t* pqxx_interface = shared_objects->getDBInterface();
if(step_optional)
{
- const int error = shared_objects->writeBackAll(&thanos_log);
+ const int error = shared_objects->writeBackAll(thanos_log);
if(error)
{
return 1; // the failure must be from a critical step, abort
@@ -355,7 +367,7 @@ int ThanosPlugin_t::executeStep(TransformStep_t& the_step, const bool are_debugg
if(step_optional)
{
// write changes to DB to see if it succeeds
- const int error = shared_objects->writeBackAll(&thanos_log);
+ const int error = shared_objects->writeBackAll(thanos_log);
if(error)
{
// abort changes by resetting DB interface
@@ -371,7 +383,7 @@ int ThanosPlugin_t::executeStep(TransformStep_t& the_step, const bool are_debugg
else if(are_debugging)
{
// write changes to DB in case next step fails
- const int error = shared_objects->writeBackAll(&thanos_log);
+ const int error = shared_objects->writeBackAll(thanos_log);
if(error)
{
return 1; // critical step failed, abort
@@ -391,7 +403,7 @@ int ThanosPlugin_t::executeStep(TransformStep_t& the_step, const bool are_debugg
int ThanosPlugin_t::saveChanges()
{
pqxxDB_t* pqxx_interface = shared_objects->getDBInterface();
- const int error = shared_objects->writeBackAll(&thanos_log);
+ const int error = shared_objects->writeBackAll(thanos_log);
if(error)
{
return 1; // critical step failed, abort