/** Extract certain elements of a log to a separate log file. */
void ExtractLog() {
static const int kNoRange = -1;
std::vector<std::string> types;
Split(TrimQuotes(FLAGS_extract_types), ',', &types);
int frame_min = kNoRange, frame_max = kNoRange;
std::vector<int> frames;
Split(TrimQuotes(FLAGS_extract_frame_range), ',', &frames);
if (!frames.empty()) {
CHECK_EQ(2, frames.size()) << "extract_frame_range must be frame PAIR";
frame_min = frames[0];
frame_max = frames[1];
CHECK_LE(frame_min, frame_max)
<< "Minimum frame index must be <= than max frame index.";
}
hal::Reader reader(FLAGS_in);
if (FLAGS_extract_types.empty()) {
reader.EnableAll();
} else {
LOG(INFO) << "Extracting: ";
for (const std::string& type : types) {
LOG(INFO) << "\t" << type;
reader.Enable(MsgTypeForString(type));
}
}
int idx = 0;
std::unique_ptr<hal::Msg> msg;
while (frame_min != kNoRange && idx < frame_min) {
if ((msg = reader.ReadMessage()) && msg->has_camera()) {
++idx;
}
}
hal::Logger logger;
logger.LogToFile(FLAGS_out);
const uint32_t max_buffer_size = 5000; // This is the default in logger.
logger.SetMaxBufferSize(max_buffer_size);
while ((frame_max == kNoRange ||
idx <= frame_max) &&
(msg = reader.ReadMessage())) {
if (msg->has_camera()) {
++idx;
}
while (logger.buffer_size() == max_buffer_size) {
LOG(INFO) << "Hit max buffer size. Waiting 100ms.";
std::this_thread::sleep_for(std::chrono::milliseconds(100));
}
if (!logger.LogMessage(*msg)) {
break;
}
}
}
/**
IsValidE32Image: Checks whether the given file is E32 image
@internalComponent
@released
@param aFile - Input file name
*/
TBool Sis2Iby::IsValidE32Image(String aFile)
{
std::ifstream aIfs;
TInt8 aSig[5];
TUint32 e32SigOffset = 0x10, fileSize = 0;
TBool validE32 = EFalse;
TrimQuotes(aFile);
aIfs.open(aFile.c_str(), std::ios::in | std::ios::binary);
if( !aIfs.is_open() )
{
throw SisUtilsException(aFile.c_str(),"Cannot open file");
}
aIfs.seekg(0,std::ios::end);
fileSize = aIfs.tellg();
if(fileSize > 20)
{
aIfs.seekg(e32SigOffset,std::ios::beg);
aIfs.read((char*)aSig, 4);
aSig[4] = '\0';
if(!strcmp((char*)aSig, "EPOC"))
{
validE32 = ETrue;
}
}
aIfs.close();
return validE32;
}
int GetOptArgs (int argc, char* argv[], char* Username, char* Password, char* Logfile)
{
int args;
int i;
args = argc;
// Clear username and password
strcpy (Username, "");
strcpy (Password, "");
Pause = 0;
// Loop through all the arguments
for (i=1;i<argc;i++)
{
// copy pointer to the appropriate string, removing leading and trailing quotes
if (strncmp (argv[i], "/U=", 3) == 0 || strncmp (argv[i], "/u=", 3) == 0)
{
args--;
TrimQuotes (Username, argv[i] + 3, NW_MAX_USER_NAME_LEN);
}
if (strncmp (argv[i], "/P=", 3) == 0 || strncmp (argv[i], "/p=", 3) == 0)
{
args--;
TrimQuotes (Password, argv[i] + 3, 256);
}
if (strncmp (argv[i], "/LOG=", 5) == 0 || strncmp (argv[i], "/log=", 5) == 0)
{
args--;
TrimQuotes (Logfile, argv[i] + 5, 256);
}
if (strncmp (argv[i], "/PAUSE", 6) == 0 || strncmp (argv[i], "/pause", 6) == 0)
{
args--;
Pause = 1;
}
}
return args;
}
// TrimQuotedWhitespcExtd
// Removes leading/trailing quotes and then any leading/trailing whitespace and
// copies trimmed text back into original text buffer (pszText)
char *
CUtility::TrimQuotedWhitespcExtd(char *pszText)
{
if(pszText == NULL || pszText[0] == '\0')
return(pszText);
if(!TrimQuotes(pszText))
return(pszText);
return(TrimWhitespcExtd(pszText));
}
/**
AppendFileName: Appends file name to the given path
@internalComponent
@released
@param aPath - Source path
@param aFile - File name
*/
void Sis2Iby::AppendFileName(String& aPath, String aFile)
{
TUint pos = 0;
TrimQuotes(aPath);
TrimQuotes(aFile);
pos = aPath.rfind(PATHSEPARATOR);
if(pos == String::npos)
{
aPath.append(PATHSEPARATOR);
}
if(pos < (aPath.length()-1))
{
aPath.append(PATHSEPARATOR);
}
GetFileName(aFile, aPath);
return;
}
//! @brief Initializes the application.
//!
//! It will open the main window and connect default to server or open the connect window.
bool UpdaterApp::OnInit()
{
//this triggers the Cli Parser amongst other stuff
if (!wxApp::OnInit())
return false;
if ( m_paramcount == 5) {
WaitForExit(m_pid);
wxArrayString params;
if (!StartUpdate(TrimQuotes(m_source_dir), TrimQuotes(m_destination_dir), true)) { //update failed, try as admin
params.push_back(m_source_dir);
params.push_back(m_destination_dir);
RunProcess(m_updater_exe, params, false, true);
params.clear();
}
//start springlobby
return RunProcess(m_springlobby_exe, params, true);
} else if (m_paramcount != 2) {
return false;
}
return StartUpdate(TrimQuotes(m_source_dir), TrimQuotes(m_destination_dir), false);
}
/**
* Parses a config file with lines of the form
*
* flag = value
*
* and sets flags as appropriate.
*/
Status ParseConfigFile() {
Trace();
if (!g_configFile.wasSet()) {
Log(LL::Trace) << "No flag config file specified.";
return Status::ok();
}
const std::string &filename = g_configFile.get();
Log(LL::Trace) << "Begining parse of config file: " << filename;
std::ifstream ifile(filename.c_str());
if (!ifile.is_open()) {
Log(LL::Trace) << "Config file " << filename << " not found.";
return Status(Status::NOT_FOUND);
}
std::string line;
int lineno = 0;
while (std::getline(ifile, line)) {
if (line.empty()) {
lineno++;
continue;
}
std::vector< std::string > argstr =
Splitter().on('=').trimWhitespace().split(line, 2);
RET_SM(
argstr.size() == 2,
Status::BAD_INPUT,
"Error in config file \"" << filename << "\" "
<< "on line " << lineno
<< " is not a valid flag=value pair");
tFlagIter itr = GetGlobalFlags().find(argstr[0]);
RET_SM(
itr != GetGlobalFlags().end(),
Status::BAD_INPUT,
"Unknown flag: " << argstr[0] << " @ line " << lineno);
iFlagBase *pFlag = itr->second;
RET_SM(
pFlag->fromString(TrimQuotes(argstr[1])),
Status::BAD_INPUT,
"Invalid flag value for " << argstr[0] << " at line " << lineno
<< ". can't parse: " << argstr[1]);
lineno++;
}
return Status::ok();
}
/**
* Concatenate all the messages from the 'cat' log files into a
* single file.
*/
void CatLogs() {
std::vector<std::string> in;
Split(TrimQuotes(FLAGS_cat_logs), ',', &in);
hal::Logger logger;
logger.LogToFile(FLAGS_out);
for (const std::string& log : in) {
hal::Reader reader(log);
reader.EnableAll();
std::unique_ptr<hal::Msg> msg;
while ((msg = reader.ReadMessage())) {
while (!logger.LogMessage(*msg)) {}
}
}
}
/** Extracts single images out of a log file. */
void ExtractImages() {
static const int kNoRange = -1;
int frame_min = kNoRange, frame_max = kNoRange;
std::vector<int> frames;
Split(TrimQuotes(FLAGS_extract_frame_range), ',', &frames);
if (!frames.empty()) {
CHECK_EQ(2, frames.size()) << "extract_frame_range must be frame PAIR";
frame_min = frames[0];
frame_max = frames[1];
CHECK_LE(frame_min, frame_max)
<< "Minimum frame index must be <= than max frame index.";
}
hal::Reader reader(FLAGS_in);
reader.Enable(hal::Msg_Type_Camera);
int idx = 0;
std::unique_ptr<hal::Msg> msg;
while (frame_min != kNoRange && idx < frame_min) {
if ((msg = reader.ReadMessage()) && msg->has_camera()) {
++idx;
}
}
while ((frame_max == kNoRange ||
idx <= frame_max) &&
(msg = reader.ReadMessage())) {
if (msg->has_camera()) {
const hal::CameraMsg& cam_msg = msg->camera();
for (int ii = 0; ii < cam_msg.image_size(); ++ii) {
const hal::ImageMsg& img_msg = cam_msg.image(ii);
SaveImage(FLAGS_out, ii, idx, cam_msg.system_time(), img_msg);
}
++idx;
}
}
}
int wmain(int argc, wchar_t* argv[])
{
if (argc < 2)
{
PrintUsage();
return 1;
}
bool doTrace = false;
bool generateHash = false;
bool generateClientManifest = false;
std::wstring fileName;
std::wstring outputFileName;
std::wstring assemblyVersion;
std::wstring assemblyName;
std::wstring clientFileName;
bool batchMode = false;
std::wstring batchFileName;
bool directoryMode = false;
std::wstring directoryPath;
// Get the command line arguments
for (int i = 1; i < argc; ++i)
{
std::wstring arg = argv[i];
// Hopefully the filename doesn't start with -
if (arg[0] != L'-')
{
fileName = arg;
TrimQuotes(fileName);
}
else if (ToLower(arg.substr(1)) == L"trace")
{
doTrace = true;
}
else if (ToLower(arg.substr(1, 8)) == L"version")
{
assemblyVersion = arg.substr(10);
}
else if (ToLower(arg.substr(1, 4)) == L"name")
{
assemblyName = arg.substr(6);
TrimQuotes(assemblyName);
}
else if (ToLower(arg.substr(1, 4)) == L"hash")
{
generateHash = true;
}
else if (ToLower(arg.substr(1, 6)) == L"client")
{
generateClientManifest = true;
clientFileName = arg.substr(8) + L".manifest";
TrimQuotes(clientFileName);
}
else if (ToLower(arg.substr(1, 5)) == L"batch")
{
batchMode = true;
batchFileName = arg.substr(7);
}
else if (ToLower(arg.substr(1, 3)) == L"dir")
{
directoryMode = true;
directoryPath = arg.substr(5);
TrimQuotes(directoryPath);
}
else
{
std::wcout << L"Parameter: " << arg << L" was not recognised" << std::endl;;
}
}
// Processing and validation of command line arguments
if (fileName.empty() && !batchMode && !directoryMode)
{
std::wcout << L"No com_dll was given!" << std::endl;
return 1;
}
if (assemblyName.empty() && !batchMode && !directoryMode)
{
std::wstring localFile = fileName.substr(fileName.rfind(L'\\') + 1);
assemblyName = localFile.substr(0, localFile.rfind(L'.')) + L".sxs";
}
else if (assemblyName.empty() && directoryMode)
{
assemblyName = directoryPath.substr(directoryPath.rfind(L'\\') + 1);
}
else if (!assemblyName.empty() && directoryMode)
{
std::wcout << L"Directory mode: assemblyName cannot be used!" << std::endl;
return 1;
}
if (!assemblyName.empty() && batchMode)
{
std::wcout << L"Batch mode: assemblyName cannot be used!" << std::endl;
return 1;
}
std::wstring clientFileNamePath = clientFileName.substr(0, clientFileName.rfind(L'\\') + 1);
if (clientFileName.empty())
{
std::wstring fileNamePath = fileName.substr(0, fileName.rfind(L'\\') + 1);
outputFileName = fileNamePath + assemblyName + L".manifest";
}
else if (directoryMode)
{
outputFileName = assemblyName + L".manifest";
}
else
{
outputFileName = clientFileNamePath + assemblyName + L".manifest";
}
if (assemblyVersion.empty() && !batchMode)
{
assemblyVersion = L"1.0.0.0";
}
else if (!assemblyVersion.empty() && batchMode)
{
std::wcout << L"Batch mode: assemblyVersion cannot be used!" << std::endl;
return 1;
}
if (directoryMode && batchMode)
{
std::wcout << L"Batch mode and Directory mode cannot be used together!" << std::endl;
return 1;
}
// Generation of the manifest files
std::vector<DependencyInfo> depencencyList;
if (batchMode)
{
std::wifstream file(batchFileName.c_str());
std::wstring line;
while (std::getline(file, line))
{
std::wistringstream wis;
wis.str(line);
std::getline(wis, fileName, L'|');
TrimSpaces(fileName);
TrimQuotes(fileName);
bool isDirectory = IsDirectory(fileName);
if (!std::getline(wis, assemblyName, L'|') || isDirectory)
{
std::wstring localFile = fileName.substr(fileName.rfind(L'\\') + 1);
assemblyName = localFile.substr(0, localFile.rfind(L'.'));
if (!isDirectory)
{
assemblyName += + L".sxs";
}
}
if (!std::getline(wis, assemblyVersion, L'|'))
{
assemblyVersion = L"1.0.0.0";
}
outputFileName = clientFileNamePath + assemblyName + L".manifest";
if (isDirectory)
{
CreateManifestForDirectory(fileName, doTrace, assemblyName, assemblyVersion, generateHash, outputFileName);
}
else
{
CreateManifestForModule(fileName, doTrace, assemblyName, assemblyVersion, generateHash, outputFileName);
}
depencencyList.push_back(DependencyInfo(assemblyName, assemblyVersion));
}
}
else if (directoryMode)
{
CreateManifestForDirectory(directoryPath, doTrace, assemblyName, assemblyVersion, generateHash, outputFileName);
depencencyList.push_back(DependencyInfo(assemblyName, assemblyVersion));
}
else
{
CreateManifestForModule(fileName, doTrace, assemblyName, assemblyVersion, generateHash, outputFileName);
depencencyList.push_back(DependencyInfo(assemblyName, assemblyVersion));
}
if (generateClientManifest)
{
ManifestWriter::WriteClientManifest(clientFileName, depencencyList);
}
return 0;
}
int main (int argc, char* argv[])
{
NWDSCCODE res;
nstr8 UserName [NW_MAX_USER_NAME_LEN];
nstr8 Password [256];
nstr8 Object [MAX_DN_CHARS+1];
nstr8 FileName [256];
nstr8 Logfile [256];
nstr8 ServerName [50];
NWCONN_HANDLE ConnHandle;
FILE* BackupFile;
int NonOptArgs;
BYTE OldNameSpace;
// start off by auto destroying the screen
AutoDestroyScreen = 0xF;
// increment the thread counter
ThreadCount++;
// get the main thread group id
MainThreadGroupId = GetThreadGroupID ();
// set the signal handler, and disable CTRL-C
signal (SIGTERM, SigHandler);
SetCtrlCharCheckMode (FALSE);
// make sure we've got something to do - i know, this would be more appropriately done in the switch below
if (argc == 1)
{
Usage ();
return 1;
}
clrscr ();
gotoxy (28, 0);
printf ("NetWare Rights Utility\n");
gotoxy (28, 1);
printf ("(c) 2003 J. Gallimore\n");
printf ("\n\n");
// create a global context handle
if ((res = NWDSCreateContextHandle (&NDSContext)) != 0)
{
printf ("NWDSCreateContextHandle returned: %d\n", res);
return 1;
}
DoLogin = 0;
// attempt to retrieve the username and password from the command line
NonOptArgs = GetOptArgs (argc, argv, UserName, Password, Logfile);
// login if we need to
// ask for the username / password, if not specified on the command line
// if user input is required, don't automatically close the screen
if (!NWIsDSAuthenticated ())
{
printf ("Login to NDS\nUsername:"******"") == 0)
{
AutoDestroyScreen = 0x0;
AwaitingInput = TRUE;
gets (UserName);
AwaitingInput = FALSE;
}
else
printf ("%s\n", UserName);
// included if the nlm is unloaded whilst inputting details
if (NlmExiting)
{
Cleanup ();
return 1;
}
printf ("Password:"******"") == 0)
{
AutoDestroyScreen = 0x0;
AwaitingInput = TRUE;
GetPass (Password, 256);
AwaitingInput = FALSE;
}
else
printf ("*\n");
// included if the nlm is unloaded whilst inputting details
if (NlmExiting)
{
Cleanup ();
return 1;
}
if ((res = NWDSLogin (NDSContext, 0, UserName, Password, 0)) != 0)
{
printf ("NWDSLogin returned: %d\n", res);
Cleanup ();
return 1;
}
DoLogin = 1; // if we logged in, we must logout
}
// included if the nlm is unloaded whilst inputting details
if (NlmExiting)
{
Cleanup ();
return 1;
}
// open and authenticate a connection to the local box
GetFileServerName (0, ServerName);
if ((res = NWCCOpenConnByName (0, ServerName, NWCC_NAME_FORMAT_NDS, NWCC_OPEN_LICENSED, NWCC_RESERVED, &ConnHandle)) != 0)
{
printf ("NWDSOpenConnToNDSServer returned: %d\n", res);
Cleanup ();
return 1;
}
if ((res = NWDSAuthenticateConn (NDSContext, ConnHandle)) != 0)
{
printf ("NWDSAuthenticateConn returned: %d\n", res);
Cleanup ();
return 1;
}
// change to the [Root] context
if ((res = NWDSSetContext (NDSContext, DCK_NAME_CONTEXT, "[Root]")) != 0)
{
printf ("NWDSSetContext returned: %d\n", res);
Cleanup ();
return 1;
}
// process the command line arguments
switch (NonOptArgs)
{
case 0:
Usage ();
break;
case 1:
Usage ();
break;
case 2:
if (strncmp (argv [1], "/R=", 3) == 0 || strncmp (argv [1], "/r=", 3) == 0)
{
if (TrimQuotes (FileName, argv [1] + 3, 256) == 0)
{
// perform a restore
Restore (ConnHandle, FileName, Logfile);
}
}
else
{
// display trustee rights, don't auto close screen
AutoDestroyScreen = 0x0;
GetTrustees (ConnHandle, 0, argv [1], NW_NS_LONG, 1, NULL);
}
break;
case 3:
if (strncmp (argv [2], "/B=", 3) == 0 || strncmp (argv [2], "/b=", 3) == 0)
{
// backup the trustee rights to a file
if (TrimQuotes (FileName, argv[2] + 3, 256) == 0)
{
OldNameSpace = SetCurrentNameSpace (NW_NS_LONG);
if ((BackupFile = fopen (FileName, "w")) != NULL)
{
fprintf (BackupFile, "cx [Root]\n");
GetTrustees (ConnHandle, 0, argv [1], NW_NS_LONG, 1, BackupFile);
fclose (BackupFile);
}
}
}
break;
case 4:
// set trustee rights or IRF as appropriate
if (strncmp ("/F", argv [3], 2) == 0 || strncmp ("/f", argv [3], 2) == 0)
{
// inherited rights filter
InheritedRights (ConnHandle, 0, argv [1], NW_NS_LONG, argv [2]);
}
if (strncmp (argv[3], "/NAME=", 6) == 0 || strncmp (argv[3], "/name=", 6) == 0)
{
// get pointer to name, strip off leading and trailing "
if (TrimQuotes (Object, argv [3] + 6, MAX_DN_CHARS+1) == 0)
TrusteeRights (ConnHandle, 0, argv [1], NW_NS_LONG, Object, argv [2]);
}
break;
default:
Usage ();
break;
}
// close local connection and cleanup
if ((res = NWCCCloseConn (ConnHandle)) != 0)
printf ("NWCCCloseConn returned: %d\n", res);
Cleanup ();
return 0;
}
void Restore (NWCONN_HANDLE ConnHandle, char* FileName, char* Logfilename)
{
char Line [1024];
char* Next;
char Buffer [512];
FILE* BackupFile;
FILE* Logfile;
char FirstParam [512];
char Rights [12];
char Object [300];
int ArgNo;
char Op [8];
NWDSCCODE res;
BYTE OldNameSpace;
// save the default namespace
OldNameSpace = SetCurrentNameSpace (NW_NS_LONG);
// attempt to open the backup file
if ((BackupFile = fopen (FileName, "r")) == NULL)
printf ("Couldn\'t open file: %s\n", FileName);
else
{
if (Logfilename)
{
if ((Logfile = fopen (Logfilename, "w")) == NULL)
{
printf ("Couldn't open %s\n", Logfilename);
Logfile = NULL;
}
}
else
Logfile = NULL;
// read file line by line - also, check that the NLM hasn't been terminated
while ((!feof (BackupFile)) && (!NlmExiting))
{
fgets (Line, 1024, BackupFile);
if (!feof (BackupFile))
{
Next = Line;
ArgNo = 0;
// use GetParams to iteratively get the equivalent argvs
while (strcmp ((Next = GetParam (Next, Buffer, 512)), "") != 0 || strcmp (Buffer, "") != 0)
{
// copy string depending on the argument number
ArgNo++;
if (ArgNo == 1)
{
if (stricmp (Buffer, "RIGHTS") != 0 && stricmp (Buffer, "cx") != 0)
break;
else
strncpy (Op, Buffer, 8);
}
else if (ArgNo == 2)
strcpy (FirstParam, Buffer);
else if (ArgNo == 3)
{
strncpy (Rights, Buffer, 12);
Rights [11] = 0;
}
else if (ArgNo == 4)
{
if (strncmp (Buffer, "/NAME=", 6) == 0 || strncmp (Buffer, "/name=", 6) == 0)
TrimQuotes (Object, Buffer, MAX_DN_CHARS);
else if (stricmp (Buffer, "/F") == 0)
strcpy (Object, "/F");
else
strcpy (Object, "");
}
else
break;
}
// if the syntax is valid call the appropriate function to
// set trustee rights or IRFs
if (stricmp (Op, "RIGHTS") ==0 && ArgNo == 4)
{
if (strncmp (Object, "/F", 2) == 0 || strncmp (Object, "/f", 2) == 0)
{
// printf ("IRF: %s, %s\n", FirstParam, Rights);
// if (Clear != 0)
// InheritedRights (ConnHandle, 0, FirstParam, NW_NS_LONG, "RWCFEMA");
res = InheritedRights (ConnHandle, 0, FirstParam, NW_NS_LONG, Rights);
DisplayOutput (FirstParam, Rights, "/F", res, Logfile);
}
if (strncmp (Object, "/NAME=", 6) == 0 || strncmp (Object, "/name=", 6) == 0)
{
// printf ("Rights: %s, %s, %s\n", FirstParam, Rights, Object);
// if (Clear != 0)
// TrusteeRights (ConnHandle, 0, FirstParam, NW_NS_LONG, Object+6, "REM");
res = TrusteeRights (ConnHandle, 0, FirstParam, NW_NS_LONG, Object+6, Rights);
DisplayOutput (FirstParam, Rights, Object+6, res, Logfile);
}
}
// code to change context
if (stricmp (Op, "cx") == 0 && ArgNo == 2)
{
if ((res = NWDSSetContext (NDSContext, DCK_NAME_CONTEXT, FirstParam)) != 0)
printf ("NWDSSetContext returned: %d\n", res);
}
}
}
// close the file and restore the original name space
fclose (BackupFile);
if (Logfile)
fclose (Logfile);
SetTargetNameSpace (OldNameSpace);
}
}
void
LiveJobImpl::Set ( const char *_name, const char *_value )
{
if ( strcasecmp ( _name, ATTR_JOB_SUBMISSION ) == 0 )
{
std::string val = TrimQuotes( _value );
// TODO: grab the cluster from our key
PROC_ID id = getProcByString(m_job->GetKey());
if (m_job) {
m_job->SetSubmission ( val.c_str(), id.cluster );
}
}
// our status is changing...decrement for old one
if ( strcasecmp ( _name, ATTR_JOB_STATUS ) == 0 )
{
if ( m_job )
{
m_job->SetStatus(this->GetStatus());
m_job->DecrementSubmission ();
}
}
if ( strcasecmp ( _name, ATTR_OWNER ) == 0 )
{
// need to leave an owner for this job
// to be picked up soon
// if we are in here, we don't have m_submission
PROC_ID id = getProcByString(m_job->GetKey());
std::string val = TrimQuotes( _value );
g_ownerless_clusters[id.cluster] = val;
m_job->UpdateSubmission(id.cluster,val.c_str());
}
// parse the type
ExprTree *expr;
if ( ParseClassAdRvalExpr ( _value, expr ) )
{
dprintf ( D_ALWAYS,
"error: parsing %s[%s] = %s, skipping\n",
m_job->GetKey(), _name, _value );
return;
}
// add this value to the classad
classad::Value value;
expr->Evaluate(value);
switch ( value.GetType() )
{
case classad::Value::INTEGER_VALUE:
int i;
from_string<int> ( i, std::string ( _value ), std::dec );
m_full_ad->Assign ( _name, i );
break;
case classad::Value::REAL_VALUE:
float f;
from_string<float> ( f, std::string ( _value ), std::dec );
m_full_ad->Assign ( _name, f );
break;
case classad::Value::STRING_VALUE:
m_full_ad->Assign ( _name, _value );
break;
default:
m_full_ad->AssignExpr ( _name, _value );
break;
}
delete expr;
expr = NULL;
// our status has changed...increment for new one
if ( strcasecmp ( _name, ATTR_JOB_STATUS ) == 0 )
{
if ( m_job )
{
m_job->SetStatus(this->GetStatus());
m_job->IncrementSubmission ();
}
}
}
/** Extracts posys out of a log file. */
void ExtractPosys() {
static const int kNoRange = -1;
int frame_min = kNoRange, frame_max = kNoRange;
std::vector<int> frames;
Split(TrimQuotes(FLAGS_extract_frame_range), ',', &frames);
if (!frames.empty()) {
CHECK_EQ(2, frames.size()) << "extract_frame_range must be frame PAIR";
frame_min = frames[0];
frame_max = frames[1];
CHECK_LE(frame_min, frame_max)
<< "Minimum frame index must be <= than max frame index.";
}
hal::Reader reader(FLAGS_in);
reader.Enable(hal::Msg_Type_Posys);
int idx = 0;
std::unique_ptr<hal::Msg> msg;
while (frame_min != kNoRange && idx < frame_min) {
if ((msg = reader.ReadMessage()) && msg->has_camera()) {
++idx;
}
}
// A csv file is created per object with names object00.csv, object01.csv, etc
// Each csv file contains these columns (depending on data):
// 1. System timestamp
// 2. Device timestamp
// 3. Object id
// 4. Pose type
// 5. Size of pose data (this must be consistent with Pose type)
// 6. Pose data (as many columns as previous field says)
// 7. Size of covariance data (>= 0)
// 8. Covariance data (as many columns as previous field says)
// The redundancy in items 4 and 5 is due to the RAW pose type that can
// contain any number of elements.
// object id, csv file
std::map<int, std::shared_ptr<std::ofstream>> files;
while ((frame_max == kNoRange ||
idx <= frame_max) &&
(msg = reader.ReadMessage())) {
if (msg->has_pose()) {
const hal::PoseMsg& pose_msg = msg->pose();
std::shared_ptr<std::ofstream>& file = files[pose_msg.id()];
if (!file) {
std::stringstream filename;
filename << FLAGS_out << "/object" << std::setw(2) << std::setfill('0')
<< pose_msg.id() << ".csv";
file.reset(new std::ofstream(filename.str().c_str()));
}
*file << std::fixed << std::setprecision(9) << pose_msg.system_time()
<< ", " << std::setprecision(9) << pose_msg.device_time()
<< ", " << pose_msg.id() << ", " << pose_msg.type()
<< ", " << pose_msg.pose().data_size() << ",";
for (int i = 0; i < pose_msg.pose().data_size(); ++i)
*file << pose_msg.pose().data(i) << ",";
*file << " " << pose_msg.covariance().data_size();
if (pose_msg.covariance().data_size() > 0) {
for (int i = 0; i < pose_msg.covariance().data_size(); ++i)
*file << "," << pose_msg.covariance().data(i);
}
*file << std::endl;
}
++idx;
}
}
/** Extracts imu out of a log file. */
void ExtractImu() {
std::ofstream accel_file(FLAGS_out + "/accel.txt", std::ios_base::trunc);
std::ofstream gyro_file(FLAGS_out + "/gyro.txt", std::ios_base::trunc);
std::ofstream mag_file(FLAGS_out + "/mag.txt", std::ios_base::trunc);
std::ofstream timestamp_file(FLAGS_out + "/timestamp.txt",
std::ios_base::trunc);
static const int kNoRange = -1;
int frame_min = kNoRange, frame_max = kNoRange;
std::vector<int> frames;
Split(TrimQuotes(FLAGS_extract_frame_range), ',', &frames);
if (!frames.empty()) {
CHECK_EQ(2, frames.size()) << "extract_frame_range must be frame PAIR";
frame_min = frames[0];
frame_max = frames[1];
CHECK_LE(frame_min, frame_max)
<< "Minimum frame index must be <= than max frame index.";
}
hal::Reader reader(FLAGS_in);
reader.Enable(hal::Msg_Type_IMU);
int idx = 0;
std::unique_ptr<hal::Msg> msg;
while (frame_min != kNoRange && idx < frame_min) {
if ((msg = reader.ReadMessage()) && msg->has_camera()) {
++idx;
}
}
while ((frame_max == kNoRange ||
idx <= frame_max) &&
(msg = reader.ReadMessage())) {
if (msg->has_imu()) {
const hal::ImuMsg& imu_msg = msg->imu();
if (imu_msg.has_accel()) {
// Write the accel to the accel csv
accel_file << imu_msg.accel().data(0) << ", " <<
imu_msg.accel().data(1) << ", " <<
imu_msg.accel().data(2) << std::endl;
} else {
accel_file << "0, 0, 0" << std::endl;
}
if (imu_msg.has_gyro()) {
// Write the accel to the accel csv
gyro_file << imu_msg.gyro().data(0) << ", " <<
imu_msg.gyro().data(1) << ", " <<
imu_msg.gyro().data(2) << std::endl;
} else {
gyro_file << "0, 0, 0" << std::endl;
}
if (imu_msg.has_mag()) {
// Write the accel to the accel csv
mag_file << imu_msg.mag().data(0) << ", " <<
imu_msg.mag().data(1) << ", " <<
imu_msg.mag().data(2) << std::endl;
} else {
mag_file << "0, 0, 0" << std::endl;
}
timestamp_file << std::fixed << std::setprecision(9) << imu_msg.system_time() << ", "
<< std::setprecision(9) << imu_msg.device_time()
<< std::endl;
// WRITE THE IMU
++idx;
}
}
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int iMode;
char szOutputFile[_MAX_PATH];
char szInputFile[_MAX_PATH];
char szInSeqFile[_MAX_PATH];
char szInputBiobedFile[_MAX_PATH];
int iRegionsIn;
int iRegionsOut;
char szRegionsIn[128]; // regions to retain
char szRegionsOut[128]; // regions to exclude
int iRegLen;
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_int *ScreenLogLevel=arg_int0("S", "ScreenLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *Mode = arg_int0("m","procmode","<int>", "processing mode 0:default");
struct arg_int *RegLen = arg_int0("L","updnstream","<int>", "length of 5'up or 3'down stream regulatory region length (default = 2000) 0..1000000");
struct arg_file *InFile = arg_file1("i",NULL,"<file>", "input from loci csv file");
struct arg_file *OutFile = arg_file1("o",NULL,"<file>", "output to multifasta file");
struct arg_file *InSeqFile = arg_file1("a","assemb","<file>","get sequences fron this file");
struct arg_file *InBedFile = arg_file1("b","bed","<file>", "characterise regions from biobed file");
struct arg_str *RegionsOut = arg_str0("R","regionsout","<string>","Filter out random samples in any of these regions (space or comma delimit), 1: Intergenic, 2: US, 3: 5'UTR, 4: CDS, 5: Intron, 6: 3'UTR, 7: DS");
struct arg_str *RegionsIn = arg_str0("r","regionsin","<string>","Accept random samples in any of these exclusive regions (space or comma delimit), 1: Intergenic, 2: US, 3: 5'UTR, 4: CDS, 5: Intron, 6: 3'UTR, 7: DS");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,ScreenLogLevel,LogFile,
Mode,RegLen,InFile,OutFile,InSeqFile,InBedFile,RegionsIn,RegionsOut,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s ", gszProcName);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s: Version: %d.%2.2d\n",gszProcName,cProgVer/100,cProgVer%100);
exit(1);
}
if (!argerrors)
{
iScreenLogLevel = ScreenLogLevel->count ? ScreenLogLevel->ival[0] : eDLInfo;
if(iScreenLogLevel < eDLNone || iScreenLogLevel > eDLDebug)
{
printf("\nError: ScreenLogLevel '-S%d' specified outside of range %d..%d",iScreenLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
iMode = Mode->count ? Mode->ival[0] : eProcModeStandard;
if(iMode < eProcModeStandard || iMode > eProcModeStandard)
{
printf("\nError: Requested processing mode '-x%d' not supported",iMode);
exit(1);
}
if(RegionsIn->count)
{
strcpy(szRegionsIn,RegionsIn->sval[0]);
TrimQuotes(szRegionsIn);
if((iRegionsIn = ParseRegions(szRegionsIn)) < 0)
{
printf("Error: unable to parse '-r%s' into regions to retain",szRegionsIn);
exit(1);
}
}
else
{
szRegionsIn[0] = '\0';
iRegionsIn = (cFeatBitIG | cFeatBitUpstream | cFeatBit5UTR | cFeatBitCDS | cFeatBitIntrons | cFeatBit3UTR | cFeatBitDnstream);
}
if(RegionsOut->count)
{
strcpy(szRegionsOut,RegionsOut->sval[0]);
TrimQuotes(szRegionsOut);
if((iRegionsOut = ParseRegions(szRegionsOut)) < 0)
{
printf("Error: unable to parse '-R%s' into regions to remove",szRegionsOut);
exit(1);
}
}
else
{
szRegionsOut[0] = '\0';
iRegionsOut = 0;
}
iRegionsIn &= ~iRegionsOut;
if(!iRegionsIn)
{
printf("Error: no regions to retain");
exit(1);
}
iRegLen = RegLen->count ? RegLen->ival[0] : cDfltRegLen;
if(iRegLen < cMinRegLen)
{
printf("\nRegulatory region length '-L%d' less than minimum %d, assuming you meant to use '-L%d'",iRegLen,cMinRegLen,cMinRegLen);
iRegLen = cMinRegLen;
}
else
{
if(iRegLen > cMaxRegLen)
{
printf("\nRegulatory region length '-L%d' more than maximum %d, assuming you meant to use '-L%d'",iRegLen,cMaxRegLen,cMaxRegLen);
iRegLen = cMaxRegLen;
}
}
strcpy(szInputFile,InFile->filename[0]);
strcpy(szOutputFile,OutFile->filename[0]);
strcpy(szInputBiobedFile,InBedFile->filename[0]);
strcpy(szInSeqFile,InSeqFile->filename[0]);
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Loci file (.csv) file to process: '%s'",szInputFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"bio assembly (.seq) file to process: '%s'",szInSeqFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"where to write out fasta with random sequences: '%s'",szOutputFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"biobed file containing regional features: '%s'",szInputBiobedFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: %s",iMode == eProcModeStandard ? "standard" : iMode == eProcModeStandard ? "extended" : "summary");
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Accept random samples in any of these regions: '%s'",Regions2Txt(iRegionsIn));
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process(iMode,iRegionsIn,iRegLen,szInputFile,szInputBiobedFile,szInSeqFile,szOutputFile);
gStopWatch.Stop();
Rslt = Rslt < 0 ? 1 : 0;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit Code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nend of help\n");
exit(1);
}
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
int Idx;
int iProcMode;
char Strand; // process features on this strand
int MinLen;
int JoinLen;
int LenFileList;
int NumIncludeChroms;
char *pszIncludeChroms[cMaxIncludeChroms];
int NumExcludeChroms;
char *pszExcludeChroms[cMaxExcludeChroms];
etBEDRegion Region; // process for this functional region only
int NumInFiles; // number of control input files
char *pszInFileSpecs[cMaxNumBedFiles]; // input (wildcards allowed) BED files
char szOutFile[_MAX_PATH]; // write merged to this file
// command line args
struct arg_lit *help = arg_lit0("h","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *ProcMode = arg_int0("m","mode","<int>", "merge processing mode: 0 - Strand independent union, 1 - Strand dependent union");
struct arg_int *strand = arg_int0("s","strand","<int>", "filter for this strand: 0 - any, 1 - Watson '+', 2 - Crick '-' (default is any)");
struct arg_int *region = arg_int0("r","genomicregion","<int>", "Retain annotated regions 0:ALL,1:Intergenic,2:Exons,3:Introns,4:CDS,5:UTRs,6:5'UTR,7:3'UTR (default = ALL)");
struct arg_int *minlen = arg_int0("l","minlen","<int>", "generated merged features must be of at least this length (default is 20)");
struct arg_int *joinlen = arg_int0("j","joinlen","<int>", "merge features which are separated by at most this length, 0 if no merging (default is 1)");
struct arg_str *excludechroms = arg_strn("Z","chromexclude","<string>",0,cMaxExcludeChroms,"regular expressions defining chromosomes to always exclude");
struct arg_str *includechroms = arg_strn("z","chromeinclude","<string>",0,cMaxIncludeChroms,"regular expressions defining chromosomes to explicitly include if not already excluded");
struct arg_file *infiles = arg_filen("i","srcfiles","<file>",0, cMaxNumBedFiles,"merge features contained in these BED files (wildcards alllowed)");
struct arg_file *OutFile = arg_file1("o",NULL,"<file>", "output merged features to this BED file");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
ProcMode,strand,minlen,joinlen,region,excludechroms,includechroms,infiles,OutFile,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s BED Merge Blocks, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
iProcMode = ProcMode->count ? ProcMode->ival[0] : ePMDefault;
if(iProcMode < ePMDefault || iProcMode >= ePMplaceholder)
{
printf("Error: Processing mode '-p%d' is not in range 0..%d",iProcMode,ePMplaceholder-1);
exit(1);
}
MinLen = minlen->count ? minlen->ival[0] : cDfltMergeLen;
if(MinLen < cMinMergeLen || MinLen > cMaxMergeLen)
{
printf("Error: minimum length '-l%d' is not in range %d..%d",MinLen,cMinMergeLen,cMaxMergeLen);
exit(1);
}
JoinLen = joinlen->count ? joinlen->ival[0] : 1;
if(JoinLen < 0 || JoinLen > cMaxMergeLen)
{
printf("Error: Join length '-j%d' is not in range 0..%d",JoinLen,cMaxMergeLen);
exit(1);
}
Strand = strand->count ? strand->ival[0] : 0;
if(Strand < 0 || Strand > 2)
{
printf("\nError: Strand '-s%d' specified outside of range 0..2",Strand);
exit(1);
}
switch(Strand) {
case 1: Strand = (int)'+'; break;
case 2: Strand = (int)'-'; break;
case 0: Strand = (int)'*'; break;
}
Region = (etBEDRegion)(region->count ? region->ival[0] : eMEGRAny); // default as being any region
if(Region < eMEGRAny || Region > eMEG3UTR)
{
printf("\nSpecified region '-g%d' outside of range 0..%d",Region,eMEG3UTR);
exit(1);
}
NumIncludeChroms = includechroms->count;
for(Idx=0;Idx < includechroms->count; Idx++)
{
LenFileList = (int)strlen(includechroms->sval[Idx]);
pszIncludeChroms[Idx] = new char [LenFileList+1];
strcpy(pszIncludeChroms[Idx],includechroms->sval[Idx]);
TrimQuotes(pszIncludeChroms[Idx]);
}
NumExcludeChroms = excludechroms->count;
for(Idx=0;Idx < excludechroms->count; Idx++)
{
LenFileList = (int)strlen(excludechroms->sval[Idx]);
pszExcludeChroms[Idx] = new char [LenFileList+1];
strcpy(pszExcludeChroms[Idx],excludechroms->sval[Idx]);
TrimQuotes(pszExcludeChroms[Idx]);
}
if(!infiles->count)
{
printf("\nError: No input file(s) specified with with '-i<filespec>' option)");
exit(1);
}
for(NumInFiles=Idx=0;NumInFiles < cMaxNumBedFiles && Idx < infiles->count; Idx++)
{
pszInFileSpecs[Idx] = NULL;
if(pszInFileSpecs[NumInFiles] == NULL)
pszInFileSpecs[NumInFiles] = new char [_MAX_PATH];
strncpy(pszInFileSpecs[NumInFiles],infiles->filename[Idx],_MAX_PATH);
pszInFileSpecs[NumInFiles][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszInFileSpecs[NumInFiles]);
if(pszInFileSpecs[NumInFiles][0] != '\0')
NumInFiles++;
}
if(!NumInFiles)
{
printf("\nError: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)");
exit(1);
}
strncpy(szOutFile,OutFile->filename[0],_MAX_PATH);
szOutFile[_MAX_PATH-1] = '\0';
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
gDiagnostics.DiagOutMsgOnly(eDLInfo,"process for this strand only: '%c'",(char)Strand);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"generated merged features will be at least this length: %d",MinLen);
if(JoinLen == 0)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"keep separate features, no merging");
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"merge features separated by upto: %d",JoinLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Retain Region: %s",Region2Txt((etBEDRegion)Region));
for(Idx = 0; Idx < NumIncludeChroms; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to include: '%s'",pszIncludeChroms[Idx]);
for(Idx = 0; Idx < NumExcludeChroms; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to exclude: '%s'",pszExcludeChroms[Idx]);
for(Idx=0;Idx < NumInFiles; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"merge features from this input BED file (%d): '%s'",Idx+1,pszInFileSpecs[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output merged features into BED file: '%s'",szOutFile);
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process((etProcMode)iProcMode,Strand,MinLen,JoinLen,Region,
NumIncludeChroms, // number of chromosome regular expressions to include
pszIncludeChroms, // array of include chromosome regular expressions
NumExcludeChroms, // number of chromosome expressions to exclude
pszExcludeChroms, // array of exclude chromosome regular expressions
NumInFiles,pszInFileSpecs,szOutFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s BED Merge Blocks, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
bool FSubversionUpdateStatusWorker::Execute(FSubversionSourceControlCommand& InCommand)
{
// update using any special hints passed in via the operation
check(InCommand.Operation->GetName() == GetName());
TSharedRef<FUpdateStatus, ESPMode::ThreadSafe> Operation = StaticCastSharedRef<FUpdateStatus>(InCommand.Operation);
if(InCommand.Files.Num() > 0)
{
TArray<FXmlFile> ResultsXml;
TArray<FString> Parameters;
Parameters.Add(TEXT("--show-updates"));
Parameters.Add(TEXT("--verbose"));
TArray<FString> Files;
if(Operation->ShouldCheckAllFiles() && InCommand.Files.Num() > 1)
{
// Prime the resultant states here depending on whether the files are under the
// working copy or not.
// This works because these states will be processed first when they come to be updated on
// the main thread, before being updated with any later on in the array by any that were
// returned from the svn status command.
Files.Add(InCommand.WorkingCopyRoot);
for(auto Iter(InCommand.Files.CreateConstIterator()); Iter; ++Iter)
{
FSubversionSourceControlState State(*Iter);
if(State.GetFilename().StartsWith(InCommand.WorkingCopyRoot))
{
State.WorkingCopyState = EWorkingCopyState::NotControlled;
}
else
{
State.WorkingCopyState = EWorkingCopyState::NotAWorkingCopy;
}
OutStates.Add(State);
}
}
else
{
Files.Append(InCommand.Files);
}
InCommand.bCommandSuccessful = SubversionSourceControlUtils::RunCommand(TEXT("status"), Files, Parameters, ResultsXml, InCommand.ErrorMessages, InCommand.UserName);
SubversionSourceControlUtils::ParseStatusResults(ResultsXml, InCommand.ErrorMessages, InCommand.UserName, InCommand.WorkingCopyRoot, OutStates);
SubversionSourceControlUtils::RemoveRedundantErrors(InCommand, TEXT("' is not a working copy"));
}
else
{
InCommand.bCommandSuccessful = true;
}
if(Operation->ShouldUpdateHistory())
{
for(auto Iter(InCommand.Files.CreateConstIterator()); Iter; Iter++)
{
TArray<FXmlFile> ResultsXml;
TArray<FString> Parameters;
//limit to last 100 changes
Parameters.Add(TEXT("--limit 100"));
// output all properties
Parameters.Add(TEXT("--with-all-revprops"));
// we want all the output!
Parameters.Add(TEXT("--verbose"));
TArray<FString> Files;
Files.Add(*Iter);
InCommand.bCommandSuccessful &= SubversionSourceControlUtils::RunCommand(TEXT("log"), Files, Parameters, ResultsXml, InCommand.ErrorMessages, InCommand.UserName);
SubversionSourceControlUtils::ParseLogResults(Iter->TrimQuotes(), ResultsXml, InCommand.UserName, OutHistory);
}
}
if(Operation->ShouldGetOpenedOnly())
{
TArray<FXmlFile> ResultsXml;
TArray<FString> Parameters;
Parameters.Add(TEXT("--show-updates"));
Parameters.Add(TEXT("--verbose"));
TArray<FString> Files;
Files.Add(FPaths::RootDir());
InCommand.bCommandSuccessful &= SubversionSourceControlUtils::RunCommand(TEXT("status"), Files, Parameters, ResultsXml, InCommand.ErrorMessages, InCommand.UserName);
SubversionSourceControlUtils::ParseStatusResults(ResultsXml, InCommand.ErrorMessages, InCommand.UserName, InCommand.WorkingCopyRoot, OutStates);
}
// NOTE: we dont use the ShouldUpdateModifiedState() hint here as a normal svn status will tell us this information
return InCommand.bCommandSuccessful;
}