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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/exec__helpers_8cpp_source.html below:

NCBI C++ ToolKit: src/app/grid/remote_app/exec_helpers.cpp Source File

41 #if defined(NCBI_OS_UNIX) 48 #define PIPE_SIZE 64 * 1024 59 bool operator()

(

int

current,

int

max_attempts);

65 const bool

first_attempt = current == 1;

83 if

(current > max_attempts) {

104 bool operator()

(

int

current,

int

max_attempts)

const

;

110 if

(

path

.empty())

return

;

114 if

(dir.

Exists

())

return

;

121 if

(

path

.empty())

return true

;

123 const bool

first_attempt = current == 1;

128 if

(!first_attempt) {

138 if

(current > max_attempts) {

232

" second(s), stopping the child: "

<< pid);

271 string

app_ver(

out

.str(), 0, 1024);

307 ERR_POST

(

"Unknown parameter value: " 308 "parameter \"progress_message_on_timeout\", " 309 "value: \""

mode

"\". " 310 "Allowed values: smart, always, never"

);

351 if

(!(is >> skipws >> ch))

return

;

359 bool

interval =

false

;

364 if

(!(is >>

))

break

;

365 if

(!(is >> ch)) ch =

','

;

372

err <<

" is less or equal than previous number, " 373 "intervals must be sorted and not overlapping"

;

374 throw

invalid_argument(err.str());

385

}

else if

(ch ==

'-'

&& !interval) {

391

err <<

"Unexpected char '"

<< ch <<

"'"

;

392 throw

invalid_argument(err.str());

398

err <<

"Missing interval end"

;

399 throw

invalid_argument(err.str());

404

err <<

"Not a number near: "

<< is.rdbuf();

405 throw

invalid_argument(err.str());

414 return

(range -

m_Ranges

.begin()) % 2;

425 catch

(invalid_argument& ex) {

427 "Parameter '"

<< param <<

"' parsing error: "

<< ex.

what

());

447 int Get

(

const string

& param,

int

def)

const 452 bool Get

(

const string

& param,

bool

def)

const 462

m_NonZeroExitAction(eDoneOnNonZeroExit),

463

m_RemoveTempDir(

true

464

m_CacheStdOutErr(

true

)

471 if

(reg.

HasEntry

(sec_name,

"non_zero_exit_action"

) ) {

472 string val

= reg.

GetString

(sec_name,

"non_zero_exit_action"

""

);

480 ERR_POST

(

"Unknown parameter value: " 481 "section ["

<< sec_name <<

"], " 482 "parameter \"non_zero_exit_action\", " 483 "value: \""

val

"\". " 484 "Allowed values: fail, return, done"

);

486

}

else if

(sec.

Get

(

"fail_on_non_zero_exit"

false

))

490 s_ReadRanges

(reg, sec_name,

"fail_no_retries_if_exit_code"

));

494 if

(sec.

Get

(

"run_in_separate_dir"

false

)) {

495 if

(reg.

HasEntry

(sec_name,

"tmp_dir"

))

506 if

(reg.

HasEntry

(sec_name,

"remove_tmp_dir"

))

511 int

sleep = sec.

Get

(

"sleep_between_remove_tmp_attempts"

, 60);

512 int

max_attempts = sec.

Get

(

"max_remove_tmp_attempts"

, 60);

521 "Missing configuration parameter ["

<< sec_name <<

542

"\". The Monitor application will not run!"

);

561

list<string> added_env;

564 ITERATE

(list<string>, it, added_env) {

565 const string

& s = *it;

569 int

sleep = sec.

Get

(

"sleep_between_reap_attempts"

, 60);

570 int

max_attempts = sec.

Get

(

"max_reap_attempts_after_kill"

, 60);

574 const string

args = reg.

GetString

(sec_name,

"version_args"

"-version"

);

579 const string mode

= reg.

GetString

(sec_name,

"progress_message_on_timeout"

597 if

file

.GetMode(&user_mode))

620

CRemoteAppReaper::CScheduler& pm)

689 const string

& path,

const char

const

env

745

args.push_back(

"-pid"

);

747

args.push_back(

"-jid"

);

749

args.push_back(

"-jwdir"

);

757 out

, err, exit_value,

765 catch

(exception& ex) {

769

err <<

"Unknown error"

;

772 switch

(exit_value) {

776 if

(non_empty_output) {

782 x_Log

(

"exited with zero return code"

, err);

788 x_Log

(

"job is returned"

, err);

793 x_Log

(

"job failed"

, err);

798

errmsg =

"Monitor requested job termination"

;

799 throw

runtime_error(errmsg);

804 x_Log

(

"internal error"

, err);

837 if

(!tmp_dir.empty() && cache_std_out_err) {

846 ERR_POST

(

"Could not create a temporary file "

847 m_Name

" :"

<< ex.

what

() <<

" the data will be " 848 "written directly to the original stream"

);

853 #if defined(NCBI_OS_UNIX) 858

fcntl(fd, F_SETFD, fcntl(fd, F_GETFD, 0) | FD_CLOEXEC);

871 catch

(exception& ex) {

872 ERR_POST

(

"CTmpStreamGuard::~CTmpStreamGuard(): "

873 m_Name

" --> "

<< ex.what());

908 unsigned

app_run_timeout,

909 const char

const env

[])

const 912 if

(!tmp_path.empty()) {

914 bool

substitution_found =

false

;

916 while

((subst_pos = tmp_path.find(

'%'

)) != string::npos) {

917 if

(subst_pos + 1 >= tmp_path.length())

919 switch

(tmp_path[subst_pos + 1]) {

921

tmp_path.replace(subst_pos, 2, 1,

'%'

);

924

tmp_path.replace(subst_pos, 2, job_context.

GetQueueName

());

927

tmp_path.replace(subst_pos, 2, job_context.

GetJobKey

());

935

(

unsigned

)

.GetLocalTime().GetTimeT()));

938

tmp_path.erase(subst_pos, 2);

940

substitution_found =

true

;

942 if

(!substitution_found)

957 string

working_dir(tmp_path.empty() ?

CDir::GetCwd

() : tmp_path);

972

unique_ptr<CPipe::IProcessWatcher> watcher(monitor ?

981

tmp_path,

env

, watcher.get(),

985

std_err_guard.

();

986

std_out_guard.

();

996 if

context

.IsJobCommitted())

997 context

.CommitJobWithFailure(

"Job has been canceled"

);

1001 context

.CommitJobWithFailure(

1003 " - will not be rerun"

1010 context

.CommitJobWithFailure(

CScheduler & GetScheduler()

CInvalidParamException â.

CJobContextProcessWatcher(SParams &p)

virtual EAction OnStart(TProcessHandle pid)

This method is called when the process has just been started by the ExecWait() method.

CWorkerNodeJobContext & m_JobContext

virtual EAction Watch(TProcessHandle pid)

This method is getting called periodically during the process execution by the ExecWait() method.

CRemoteAppTimeoutReporter & m_TimeoutReporter

void x_Log(const string &what, CNcbiOstrstream &sstream)

CMonitoredProcessWatcher(SParams &p, const string &job_wdir, const string &path, const char *const *env, CTimeout run_period, CTimeout run_timeout)

const char *const * m_Env

virtual EAction Watch(TProcessHandle pid)

This method is getting called periodically during the process execution by the ExecWait() method.

EAction MonitorRun(TProcessHandle pid)

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

@ eShutdownImmediate

Urgent shutdown was requested.

Callback interface for ExecWait()

Extended exit information for waited process.

Note about the "buf_size" parameter for streams in this API.

Class representing (non overlapping) integer ranges.

bool Contain(int n) const

Checks whether provided number belongs to one of the ranges.

CRanges(istream &is)

Reads integer ranges from an input stream.

void Run(CWorkerNodeIdleTaskContext &)

Do the Idle task here.

list< string > m_IncludeEnv

static bool CanExec(const CFile &file)

unique_ptr< CRemoteAppTimeoutReporter > m_TimeoutReporter

unique_ptr< CRemoteAppVersion > m_Version

CRemoteAppLauncher(const string &sec_name, const IRegistry &)

unique_ptr< CRemoteAppRemover > m_Remover

void FinishJob(bool finished_ok, int ret, CWorkerNodeJobContext &context) const

bool ExecRemoteApp(const vector< string > &args, CNcbiIstream &in, CNcbiOstream &out, CNcbiOstream &err, int &exit_value, CWorkerNodeJobContext &job_context, unsigned app_run_timeout, const char *const env[]) const

string GetAppVersion(const string &) const

const string & GetAppPath() const

unique_ptr< CRanges > m_MustFailNoRetries

CTimeout m_MonitorRunTimeout

unique_ptr< CRemoteAppReaper > m_Reaper

CTimeout m_KeepAlivePeriod

ENonZeroExitAction m_NonZeroExitAction

list< string > m_ExcludeEnv

void Report(CWorkerNodeJobContext &job_context, unsigned seconds)

CRemoteAppTimeoutReporter(const string &mode)

static EMode Get(const string &mode)

string Get(CTimedProcessWatcher::SParams &p, const string &v) const

const vector< string > m_Args

CRemoteAppVersion(const string &app, const vector< string > &args)

virtual EAction Watch(TProcessHandle pid)

This method is getting called periodically during the process execution by the ExecWait() method.

const string m_ProcessType

CTimedProcessWatcher(SParams &p)

CRemoteAppReaper::CScheduler & m_ProcessManager

CTimeout â Timeout interval.

unsigned PresetSeconds() const

CTimer(const CTimeout &timeout)

CTmpStreamGuard(const string &tmp_dir, const string &name, CNcbiOstream &orig_stream, bool cache_std_out_err)

CNcbiOstream & GetOStream()

CNcbiOstream & m_OrigStream

unique_ptr< CFileReaderWriter > m_ReaderWriter

unique_ptr< CNcbiOstream > m_StreamGuard

Writer-based output stream.

Worker Node Idle Task Context.

std::ofstream out("events_result.xml")

main entry point for tests

CRanges * s_ReadRanges(const IRegistry &reg, const string &sec, string param)

CTimeout s_ToTimeout(unsigned sec)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const string & GetProgramDisplayName(void) const

Get the application's "display" name.

CDiagContext & GetDiagContext(void)

Get diag context instance.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static TExitCode System(const char *cmdline)

Execute the specified command.

static string NormalizePath(const string &path, EFollowLinks follow_links=eIgnoreLinks)

Normalize a path.

static bool IsAbsolutePath(const string &path)

Check if a "path" is absolute for the current OS.

unsigned int TMode

Bitwise OR of "EMode".

bool CreatePath(TCreateFlags flags=fCreate_Default) const

Create the directory path recursively possibly more than one at a time.

virtual bool Exists(void) const

Check if directory "dirname" exists.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

static string GetCwd(void)

Get the current working directory.

@ eCreate

Create a new file, or truncate an existing one.

@ fExecute

Execute / List(directory) permission.

@ eBegin

Absolute position from beginning of the file.

@ eRecursiveIgnoreMissing

Same as eRecursive, but do not report an error for disappeared entries (e.g.

const string & GetQueueName() const

Get a name of a queue where this node is connected to.

CNetScheduleAdmin::EShutdownLevel GetShutdownLevel()

Check if job processing must be aborted.

void PutProgressMessage(const string &msg, bool send_immediately=false, bool overwrite=true)

Put progress message.

void ReturnJob()

Schedule the job for return.

bool IsLogRequested() const

Check if logging was requested in config file.

const string & GetJobKey() const

Get a job key.

void JobDelayExpiration(unsigned runtime_inc)

Increment job execution timeout.

static EFinish ExecWait(const string &cmd, const vector< string > &args, CNcbiIstream &in, CNcbiOstream &out, CNcbiOstream &err, int &exit_code, const string &current_dir=kEmptyStr, const char *const envp[]=0, IProcessWatcher *watcher=0, const STimeout *kill_timeout=0, size_t pipe_size=0)

Execute a command with a vector of arguments, and wait for its completion.

virtual EAction OnStart(TProcessHandle)

This method is called when the process has just been started by the ExecWait() method.

EAction

An action which the ExecWait() method should take after the Watch() method has returned.

@ eDone

Process finished normally.

@ eContinue

Continue running.

@ eStop

Kill the child process and exit.

@ eExit

Exit without waiting for the child process.

uint64_t Uint8

8-byte (64-bit) unsigned integer

TProcessHandle GetHandle(void) const

Get stored process handle.

bool KillGroup(unsigned long timeout=kDefaultKillTimeout) const

Terminate a group of processes.

bool IsExited(void) const

TRUE if the process terminated normally.

int Wait(unsigned long timeout=kInfiniteTimeoutMs, CExitInfo *info=0) const

Wait until process terminates.

bool IsSignaled(void) const

TRUE if the process terminated by a signal (UNIX only).

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

virtual int GetInt(const string &section, const string &name, int default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get integer value of specified parameter name.

virtual bool HasEntry(const string &section, const string &name=kEmptyStr, TFlags flags=0) const

virtual void EnumerateEntries(const string &section, list< string > *entries, TFlags flags=fAllLayers) const

Enumerate parameter names for a specified section.

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

@ eReturn

Return default value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsOssEmpty(CNcbiOstrstream &oss)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

bool NcbiStreamCopy(CNcbiOstream &os, CNcbiIstream &is)

Copy the entire contents of stream "is" to stream "os".

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static string Sanitize(CTempString str, TSS_Flags flags=fSS_print)

Sanitize a string, allowing only specified classes of characters.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

bool IsExpired(void) const

Check if the deadline is expired.

double GetAsDouble(void) const

Get as number of seconds (fractional value).

bool IsFinite() const

Check if timeout holds a numeric value.

@ eInfinite

Infinite timeout.

unsigned int usec

microseconds (modulo 1,000,000)

where both of them are integers Note

Portable class to work with a spawned process via pipes.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Defines CRequestContext class for NCBI C++ diagnostic API.

Reader-writer based streams.

SParams(CWorkerNodeJobContext &jc, string pt, const CTimeout &rt, const CTimeout &kap, CRemoteAppTimeoutReporter &tr, CRemoteAppReaper::CScheduler &pm)

CWorkerNodeJobContext & job_context

const CTimeout & keep_alive_period

CRemoteAppTimeoutReporter & timeout_reporter

CRemoteAppReaperTask(TProcessHandle handle)

bool operator()(int current, int max_attempts)

CRemoteAppRemoverTask(string p)

bool operator()(int current, int max_attempts) const

CRemoteAppRemoverTask m_Task

SGuard(CRemoteAppRemover *remover, CRemoteAppRemoverTask task, bool remove_tmp_dir)

CRemoteAppRemover::CScheduler * m_Scheduler

CRemoteAppReaper::CScheduler & process_manager

const CTimeout & run_timeout

SParams(string pt, const CTimeout &rt, CRemoteAppReaper::CScheduler &pm)

SSection(const IRegistry &r, const string &n)

int Get(const string &param, int def) const

bool Get(const string &param, bool def) const

static CS_CONTEXT * context

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