int DebuggerProxy::getStackDepth() {
TRACE(2, "DebuggerProxy::getStackDepth\n");
int depth = 0;
auto fp = vmfp();
if (!fp) return 0;
fp = fp->sfp();
while (fp) {
fp = fp->sfp();
depth++;
}
return depth;
}
void AbiCollab::_shutdownAsMaster()
{
UT_DEBUGMSG(("AbiCollab::_shutdownAsMaster()\n"));
UT_return_if_fail(m_pController == BuddyPtr());
UT_return_if_fail(!m_bProposedController);
AbiCollabSessionManager* pManager = AbiCollabSessionManager::getManager();
UT_return_if_fail(pManager);
// the session takeover is complete; inform everyone that all session data
// is flushed, and that everyone should talk to the new master from now on
SessionFlushedPacket sfp(m_sId, m_pDoc->getDocUUIDString());
for (std::map<BuddyPtr, std::string>::iterator it = m_vCollaborators.begin(); it != m_vCollaborators.end(); it++)
{
BuddyPtr pBuddy = (*it).first;
UT_continue_if_fail(pBuddy);
pBuddy->getHandler()->send(&sfp, pBuddy);
}
// session takeover is done as far as the leaving session contoller is concerned
pManager->endAsyncOperation(this);
}
int main(int argc, char *argv[])
{
int rv;
char *full;
if (argc != 3) {
fprintf(stderr,
"usage:\n"
" sbsnarf full-path-to-sb output-bytecode-file\n\n");
return -1;
}
full = realpath(argv[1], NULL);
printf("[+] full path to sb: \"%s\"\n", full);
void *h = dlopen("libsandbox.1.dylib", RTLD_FIRST | RTLD_LAZY | RTLD_LOCAL);
if (NULL == h) {
errx(-1, "dlopen failed: %s", dlerror());
}
void *(*scf)(char *, int, char **) = dlsym(h, "sandbox_compile_file");
if (NULL == scf) {
errx(-1, "dlsym failed: %s", dlerror());
}
void (*sfp)(void *) = dlsym(h, "sandbox_free_profile");
if (NULL == sfp) {
errx(-1, "dlsym failed: %s", dlerror());
}
char *error;
struct {
unsigned int type;
user_addr_t bytecode;
user_size_t bytecode_length;
} *sb = scf(full, 0, &error);
if (NULL == sb) {
dlclose(h);
errx(-1, "sandbox_compile_file failed: %s", error);
}
if (NULL != error) {
free(error);
}
FILE *f_out = fopen(argv[2], "wb");
if (NULL == f_out) {
sfp(sb);
dlclose(h);
err(-1, "fopen failed:");
}
rv = fwrite((void *) sb->bytecode, sb->bytecode_length, 1, f_out);
if (1 != rv) {
sfp(sb);
dlclose(h);
err(-1, "fwrite failed:");
}
fclose(f_out);
sfp(sb);
dlclose(h);
printf("[+] success!\n");
return 0;
}
PWIZ_API_DECL void initializeTiny(MSData& msd)
{
msd.id = "urn:lsid:psidev.info:mzML.instanceDocuments.tiny.pwiz";
// cvList
msd.cvs = defaultCVList();
// fileDescription
FileContent& fc = msd.fileDescription.fileContent;
fc.set(MS_MSn_spectrum);
fc.set(MS_centroid_spectrum);
SourceFilePtr sfp(new SourceFile);
sfp->id = "tiny1.yep";
sfp->name = "tiny1.yep";
sfp->location = "file://*****:*****@higglesworth.edu");
// paramGroupList
ParamGroupPtr pg1(new ParamGroup);
pg1->id = "CommonMS1SpectrumParams";
pg1->set(MS_MS1_spectrum);
pg1->set(MS_positive_scan);
msd.paramGroupPtrs.push_back(pg1);
ParamGroupPtr pg2(new ParamGroup);
pg2->id = "CommonMS2SpectrumParams";
pg2->set(MS_MSn_spectrum);
pg2->set(MS_negative_scan);
msd.paramGroupPtrs.push_back(pg2);
// sampleList
SamplePtr samplePtr(new Sample);
samplePtr->id = "20090101 - Sample 1";
samplePtr->name = "Sample 1";
msd.samplePtrs.push_back(samplePtr);
// instrumentConfigurationList
InstrumentConfigurationPtr instrumentConfigurationPtr(new InstrumentConfiguration("LCQ Deca"));
instrumentConfigurationPtr->set(MS_LCQ_Deca);
instrumentConfigurationPtr->set(MS_instrument_serial_number,"23433");
instrumentConfigurationPtr->componentList.push_back(Component(MS_nanoelectrospray, 1));
instrumentConfigurationPtr->componentList.push_back(Component(MS_quadrupole_ion_trap, 2));
instrumentConfigurationPtr->componentList.push_back(Component(MS_electron_multiplier, 3));
SoftwarePtr softwareCompassXtract(new Software);
softwareCompassXtract->id = "CompassXtract";
softwareCompassXtract->set(MS_CompassXtract);
softwareCompassXtract->version = "2.0.5";
instrumentConfigurationPtr->softwarePtr = softwareCompassXtract;
msd.instrumentConfigurationPtrs.push_back(instrumentConfigurationPtr);
// softwareList
SoftwarePtr softwareBioworks(new Software);
softwareBioworks->id = "Bioworks";
softwareBioworks->set(MS_Bioworks);
softwareBioworks->version = "3.3.1 sp1";
SoftwarePtr softwarepwiz(new Software);
softwarepwiz->id = "pwiz";
softwarepwiz->set(MS_pwiz);
softwarepwiz->version = "1.0";
msd.softwarePtrs.push_back(softwareBioworks);
msd.softwarePtrs.push_back(softwarepwiz);
msd.softwarePtrs.push_back(softwareCompassXtract);
// dataProcessingList
DataProcessingPtr dpCompassXtract(new DataProcessing);
dpCompassXtract->id = "CompassXtract processing";
ProcessingMethod procCXT;
procCXT.order = 1;
procCXT.softwarePtr = softwareCompassXtract;
procCXT.set(MS_deisotoping);
procCXT.set(MS_charge_deconvolution);
procCXT.set(MS_peak_picking);
dpCompassXtract->processingMethods.push_back(procCXT);
DataProcessingPtr dppwiz(new DataProcessing("pwiz_processing"));
ProcessingMethod procpwiz;
procpwiz.order = 2;
procpwiz.softwarePtr = softwarepwiz;
procpwiz.set(MS_Conversion_to_mzML);
dppwiz->processingMethods.push_back(procpwiz);
msd.dataProcessingPtrs.push_back(dpCompassXtract);
//msd.dataProcessingPtrs.push_back(dppwiz);
ScanSettingsPtr as1(new ScanSettings("tiny scan settings"));
as1->sourceFilePtrs.push_back(sfp_parameters);
Target t1;
t1.set(MS_selected_ion_m_z, 1000, MS_m_z);
Target t2;
t2.set(MS_selected_ion_m_z, 1200, MS_m_z);
as1->targets.push_back(t1);
as1->targets.push_back(t2);
msd.scanSettingsPtrs.push_back(as1);
// run
msd.run.id = "Experiment 1";
msd.run.defaultInstrumentConfigurationPtr = instrumentConfigurationPtr;
msd.run.samplePtr = samplePtr;
msd.run.startTimeStamp = "2007-06-27T15:23:45.00035";
msd.run.defaultSourceFilePtr = sfp;
shared_ptr<SpectrumListSimple> spectrumList(new SpectrumListSimple);
msd.run.spectrumListPtr = spectrumList;
spectrumList->dp = dppwiz;
spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
Spectrum& s19 = *spectrumList->spectra[0];
s19.id = "scan=19";
s19.index = 0;
s19.set(MS_ms_level, 1);
s19.set(MS_centroid_spectrum);
s19.set(MS_lowest_observed_m_z, 400.39, MS_m_z);
s19.set(MS_highest_observed_m_z, 1795.56, MS_m_z);
s19.set(MS_base_peak_m_z, 445.347, MS_m_z);
s19.set(MS_base_peak_intensity, 120053, MS_number_of_detector_counts);
s19.set(MS_total_ion_current, 1.66755e+007);
s19.paramGroupPtrs.push_back(pg1);
s19.scanList.scans.push_back(Scan());
s19.scanList.set(MS_no_combination);
Scan& s19scan = s19.scanList.scans.back();
s19scan.instrumentConfigurationPtr = instrumentConfigurationPtr;
s19scan.set(MS_scan_start_time, 5.890500, UO_minute);
s19scan.set(MS_filter_string, "+ c NSI Full ms [ 400.00-1800.00]");
s19scan.set(MS_preset_scan_configuration, 3);
s19scan.scanWindows.resize(1);
ScanWindow& window = s19.scanList.scans.back().scanWindows.front();
window.set(MS_scan_window_lower_limit, 400.000000, MS_m_z);
window.set(MS_scan_window_upper_limit, 1800.000000, MS_m_z);
BinaryDataArrayPtr s19_mz(new BinaryDataArray);
s19_mz->dataProcessingPtr = dpCompassXtract;
s19_mz->set(MS_m_z_array, "", MS_m_z);
s19_mz->data.resize(15);
for (int i=0; i<15; i++)
s19_mz->data[i] = i;
BinaryDataArrayPtr s19_intensity(new BinaryDataArray);
s19_intensity->dataProcessingPtr = dpCompassXtract;
s19_intensity->set(MS_intensity_array, "", MS_number_of_detector_counts);
s19_intensity->data.resize(15);
for (int i=0; i<15; i++)
s19_intensity->data[i] = 15-i;
s19.binaryDataArrayPtrs.push_back(s19_mz);
s19.binaryDataArrayPtrs.push_back(s19_intensity);
s19.defaultArrayLength = s19_mz->data.size();
Spectrum& s20 = *spectrumList->spectra[1];
s20.id = "scan=20";
s20.index = 1;
s20.paramGroupPtrs.push_back(pg2);
s20.set(MS_ms_level, 2);
s20.set(MS_profile_spectrum);
s20.set(MS_lowest_observed_m_z, 320.39, MS_m_z);
s20.set(MS_highest_observed_m_z, 1003.56, MS_m_z);
s20.set(MS_base_peak_m_z, 456.347, MS_m_z);
s20.set(MS_base_peak_intensity, 23433, MS_number_of_detector_counts);
s20.set(MS_total_ion_current, 1.66755e+007);
s20.precursors.resize(1);
Precursor& precursor = s20.precursors.front();
precursor.spectrumID= s19.id;
precursor.isolationWindow.set(MS_isolation_window_target_m_z, 445.3, MS_m_z);
precursor.isolationWindow.set(MS_isolation_window_lower_offset, .5, MS_m_z);
precursor.isolationWindow.set(MS_isolation_window_upper_offset, .5, MS_m_z);
precursor.selectedIons.resize(1);
precursor.selectedIons[0].set(MS_selected_ion_m_z, 445.34, MS_m_z);
precursor.selectedIons[0].set(MS_peak_intensity, 120053, MS_number_of_detector_counts);
precursor.selectedIons[0].set(MS_charge_state, 2);
precursor.activation.set(MS_collision_induced_dissociation);
precursor.activation.set(MS_collision_energy, 35.00, UO_electronvolt);
s20.scanList.scans.push_back(Scan());
s20.scanList.set(MS_no_combination);
Scan& s20scan = s20.scanList.scans.back();
s20scan.instrumentConfigurationPtr = instrumentConfigurationPtr;
s20scan.set(MS_scan_start_time, 5.990500, UO_minute);
s20scan.set(MS_filter_string, "+ c d Full ms2 [email protected] [ 110.00-905.00]");
s20scan.set(MS_preset_scan_configuration, 4);
s20scan.scanWindows.resize(1);
ScanWindow& window2 = s20scan.scanWindows.front();
window2.set(MS_scan_window_lower_limit, 110.000000, MS_m_z);
window2.set(MS_scan_window_upper_limit, 905.000000, MS_m_z);
BinaryDataArrayPtr s20_mz(new BinaryDataArray);
s20_mz->dataProcessingPtr = dpCompassXtract;
s20_mz->set(MS_m_z_array, "", MS_m_z);
s20_mz->data.resize(10);
for (int i=0; i<10; i++)
s20_mz->data[i] = i*2;
BinaryDataArrayPtr s20_intensity(new BinaryDataArray);
s20_intensity->dataProcessingPtr = dpCompassXtract;
s20_intensity->set(MS_intensity_array, "", MS_number_of_detector_counts);
s20_intensity->data.resize(10);
for (int i=0; i<10; i++)
s20_intensity->data[i] = (10-i)*2;
s20.binaryDataArrayPtrs.push_back(s20_mz);
s20.binaryDataArrayPtrs.push_back(s20_intensity);
s20.defaultArrayLength = s20_mz->data.size();
// spectrum with no data
Spectrum& s21 = *spectrumList->spectra[2];
s21.id = "scan=21";
s21.index = 2;
s21.paramGroupPtrs.push_back(pg1);
s21.set(MS_ms_level, 1);
s21.set(MS_centroid_spectrum);
s21.userParams.push_back(UserParam("example", "spectrum with no data"));
s21.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_detector_counts);
s21.scanList.scans.push_back(Scan());
s21.scanList.scans.back().instrumentConfigurationPtr = instrumentConfigurationPtr;
s21.scanList.set(MS_no_combination);
// Cover ETD, ETD+SA, and ECD precursor activation mode usage
Spectrum& s22 = *spectrumList->spectra[3];
s22.id = "scan=22";
s22.index = 3;
s22.paramGroupPtrs.push_back(pg2);
s22.set(MS_ms_level, 2);
s22.set(MS_profile_spectrum);
s22.set(MS_lowest_observed_m_z, 320.39, MS_m_z);
s22.set(MS_highest_observed_m_z, 1003.56, MS_m_z);
s22.set(MS_base_peak_m_z, 456.347, MS_m_z);
s22.set(MS_base_peak_intensity, 23433, MS_number_of_detector_counts);
s22.set(MS_total_ion_current, 1.66755e+007);
s22.precursors.resize(1);
Precursor& precursor22 = s22.precursors.front();
precursor22.spectrumID= s19.id;
precursor22.isolationWindow.set(MS_isolation_window_target_m_z, 545.3, MS_m_z);
precursor22.isolationWindow.set(MS_isolation_window_lower_offset, .5, MS_m_z);
precursor22.isolationWindow.set(MS_isolation_window_upper_offset, .5, MS_m_z);
precursor22.selectedIons.resize(1);
precursor22.selectedIons[0].set(MS_selected_ion_m_z, 545.34, MS_m_z);
precursor22.selectedIons[0].set(MS_peak_intensity, 120053, MS_number_of_detector_counts);
precursor22.selectedIons[0].set(MS_charge_state, 2);
precursor22.activation.set(MS_ETD);
precursor22.activation.set(MS_CID);
precursor22.activation.set(MS_collision_energy, 60.00, UO_electronvolt);
s22.scanList.scans.push_back(Scan());
s22.scanList.set(MS_no_combination);
Scan& s22scan = s22.scanList.scans.back();
s22scan.instrumentConfigurationPtr = instrumentConfigurationPtr;
s22scan.set(MS_scan_start_time, 6.5, UO_minute);
s22scan.set(MS_filter_string, "+ c d Full ms2 [email protected] [ 110.00-905.00]");
s22scan.set(MS_preset_scan_configuration, 4);
s22scan.scanWindows.resize(1);
window2 = s22scan.scanWindows.front();
window2.set(MS_scan_window_lower_limit, 110.000000, MS_m_z);
window2.set(MS_scan_window_upper_limit, 905.000000, MS_m_z);
BinaryDataArrayPtr s22_mz(new BinaryDataArray);
s22_mz->dataProcessingPtr = dpCompassXtract;
s22_mz->set(MS_m_z_array, "", MS_m_z);
s22_mz->data.resize(10);
for (int i=0; i<10; i++)
s22_mz->data[i] = i*2;
BinaryDataArrayPtr s22_intensity(new BinaryDataArray);
s22_intensity->dataProcessingPtr = dpCompassXtract;
s22_intensity->set(MS_intensity_array, "", MS_number_of_detector_counts);
s22_intensity->data.resize(10);
for (int i=0; i<10; i++)
s22_intensity->data[i] = (10-i)*2;
s22.binaryDataArrayPtrs.push_back(s22_mz);
s22.binaryDataArrayPtrs.push_back(s22_intensity);
s22.defaultArrayLength = s22_mz->data.size();
// spectrum with MALDI spot information
Spectrum& s23 = *spectrumList->spectra[4];
s23.id = "sample=1 period=1 cycle=23 experiment=1";
s23.index = 4;
s23.spotID = "A1,42x42,4242x4242";
s23.sourceFilePtr = sfp2;
s23.set(MS_ms_level, 1);
s23.set(MS_centroid_spectrum);
s23.set(MS_lowest_observed_m_z, 142.39, MS_m_z);
s23.set(MS_highest_observed_m_z, 942.56, MS_m_z);
s23.set(MS_base_peak_m_z, 422.42, MS_m_z);
s23.set(MS_base_peak_intensity, 42, MS_number_of_detector_counts);
s23.set(MS_total_ion_current, 4200);
s23.userParams.push_back(UserParam("alternate source file", "to test a different nativeID format"));
s23.paramGroupPtrs.push_back(pg1);
s23.scanList.scans.push_back(Scan());
s23.scanList.set(MS_no_combination);
Scan& s23scan = s23.scanList.scans.back();
s23scan.instrumentConfigurationPtr = instrumentConfigurationPtr;
s23scan.set(MS_scan_start_time, 42.0500, UO_second);
s23scan.set(MS_filter_string, "+ c MALDI Full ms [100.00-1000.00]");
s23scan.scanWindows.resize(1);
ScanWindow& window3 = s23scan.scanWindows.front();
window3.set(MS_scan_window_lower_limit, 100.000000, MS_m_z);
window3.set(MS_scan_window_upper_limit, 1000.000000, MS_m_z);
s23.binaryDataArrayPtrs.push_back(s19_mz);
s23.binaryDataArrayPtrs.push_back(s19_intensity);
s23.defaultArrayLength = s19_mz->data.size();
// chromatograms
shared_ptr<ChromatogramListSimple> chromatogramList(new ChromatogramListSimple);
msd.run.chromatogramListPtr = chromatogramList;
chromatogramList->dp = dppwiz;
chromatogramList->chromatograms.push_back(ChromatogramPtr(new Chromatogram));
chromatogramList->chromatograms.push_back(ChromatogramPtr(new Chromatogram));
Chromatogram& tic = *chromatogramList->chromatograms[0];
tic.id = "tic";
tic.index = 0;
tic.defaultArrayLength = 15;
tic.dataProcessingPtr = dpCompassXtract;
tic.set(MS_total_ion_current_chromatogram);
BinaryDataArrayPtr tic_time(new BinaryDataArray);
tic_time->dataProcessingPtr = dppwiz;
tic_time->set(MS_time_array, "", UO_second);
tic_time->data.resize(15);
for (int i=0; i<15; i++)
tic_time->data[i] = i;
BinaryDataArrayPtr tic_intensity(new BinaryDataArray);
tic_intensity->dataProcessingPtr = dppwiz;
tic_intensity->set(MS_intensity_array, "", MS_number_of_detector_counts);
tic_intensity->data.resize(15);
for (int i=0; i<15; i++)
tic_intensity->data[i] = 15-i;
tic.binaryDataArrayPtrs.push_back(tic_time);
tic.binaryDataArrayPtrs.push_back(tic_intensity);
Chromatogram& sic = *chromatogramList->chromatograms[1];
sic.id = "sic";
sic.index = 1;
sic.defaultArrayLength = 10;
sic.dataProcessingPtr = dppwiz;
sic.set(MS_selected_ion_current_chromatogram);
sic.precursor.isolationWindow.set(MS_isolation_window_target_m_z, 456.7, MS_m_z);
sic.precursor.activation.set(MS_CID);
sic.product.isolationWindow.set(MS_isolation_window_target_m_z, 678.9, MS_m_z);
BinaryDataArrayPtr sic_time(new BinaryDataArray);
sic_time->dataProcessingPtr = dppwiz;
sic_time->set(MS_time_array, "", UO_second);
sic_time->data.resize(10);
for (int i=0; i<10; i++)
sic_time->data[i] = i;
BinaryDataArrayPtr sic_intensity(new BinaryDataArray);
sic_intensity->dataProcessingPtr = dppwiz;
sic_intensity->set(MS_intensity_array, "", MS_number_of_detector_counts);
sic_intensity->data.resize(10);
for (int i=0; i<10; i++)
sic_intensity->data[i] = 10-i;
sic.binaryDataArrayPtrs.push_back(sic_time);
sic.binaryDataArrayPtrs.push_back(sic_intensity);
} // initializeTiny()
PRIVATE inline
L4_msg_tag
Thread_object::sys_vcpu_resume(L4_msg_tag const &tag, Utcb *utcb)
{
if (this != current() || !(state() & Thread_vcpu_enabled))
return commit_result(-L4_err::EInval);
Space *s = space();
Vcpu_state *vcpu = vcpu_state().access(true);
L4_obj_ref user_task = vcpu->user_task;
if (user_task.valid())
{
L4_fpage::Rights task_rights = L4_fpage::Rights(0);
Task *task = Kobject::dcast<Task*>(s->lookup_local(user_task.cap(),
&task_rights));
if (EXPECT_FALSE(task && !(task_rights & L4_fpage::Rights::W())))
return commit_result(-L4_err::EPerm);
if (task != vcpu_user_space())
vcpu_set_user_space(task);
vcpu->user_task = L4_obj_ref();
}
else if (user_task.op() == L4_obj_ref::Ipc_reply)
vcpu_set_user_space(0);
L4_snd_item_iter snd_items(utcb, tag.words());
int items = tag.items();
if (vcpu_user_space())
for (; items && snd_items.more(); --items)
{
if (EXPECT_FALSE(!snd_items.next()))
break;
Lock_guard<Lock> guard;
if (!guard.check_and_lock(&static_cast<Task *>(vcpu_user_space())->existence_lock))
return commit_result(-L4_err::ENoent);
cpu_lock.clear();
L4_snd_item_iter::Item const *const item = snd_items.get();
L4_fpage sfp(item->d);
Reap_list rl;
L4_error err = fpage_map(space(), sfp,
vcpu_user_space(), L4_fpage::all_spaces(),
item->b, &rl);
rl.del();
cpu_lock.lock();
if (EXPECT_FALSE(!err.ok()))
return commit_error(utcb, err);
}
if ((vcpu->_saved_state & Vcpu_state::F_irqs)
&& (vcpu->sticky_flags & Vcpu_state::Sf_irq_pending))
{
assert_kdb(cpu_lock.test());
do_ipc(L4_msg_tag(), 0, 0, true, 0,
L4_timeout_pair(L4_timeout::Zero, L4_timeout::Zero),
&vcpu->_ipc_regs, L4_fpage::Rights::FULL());
vcpu = vcpu_state().access(true);
if (EXPECT_TRUE(!vcpu->_ipc_regs.tag().has_error()
|| this->utcb().access(true)->error.error() == L4_error::R_timeout))
{
vcpu->_ts.set_ipc_upcall();
Address sp;
// tried to resume to user mode, so an IRQ enters from user mode
if (vcpu->_saved_state & Vcpu_state::F_user_mode)
sp = vcpu->_entry_sp;
else
sp = vcpu->_ts.sp();
arch_load_vcpu_kern_state(vcpu, true);
LOG_TRACE("VCPU events", "vcpu", this, Vcpu_log,
l->type = 4;
l->state = vcpu->state;
l->ip = vcpu->_entry_ip;
l->sp = sp;
l->space = static_cast<Task*>(_space.vcpu_aware())->dbg_id();
);