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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/netschedule__api_8cpp_source.html below:

NCBI C++ ToolKit: src/connect/services/netschedule_api.cpp Source File

netschedule {

<<

(status));

*

,

remaining_seconds)

(remaining_seconds > 0) {

*

+=

;

* attr_values,

attr_count)

((attr_it = attr_parser.

(*attr_names)) !=

*attr_values = attr_it->value;

}

(--attr_count > 0);

*ns_node = parser(

);

reason = parser(

);

*ns_node = *next_server;

two_seconds = {2, 0};

(notif_type) {

& deadline,

* server_host)

(timeout.

== 0 && timeout.

== 0)

printf(

,

());

(

);

ns_conf ?

:

;

m_Registry(

), m_Sections(sections), m_NsConf(ns_conf), m_Mode(eImplicit)

param =

;

(name ==

)

;

(name ==

) {

(name ==

)

;

name.erase(0, prefix.size());

retry_guard =

->m_Service->CreateRetryGuard(retry_mode);

prefix =

?

:

;

(

& param : queue_params) {

name = param.first;

mem_registry->Set(section, name, param.second);

(mem_registry->

())

;

= &app->GetFullVersion();

name = app->GetProgramDisplayName();

package_name =

->GetPackageName();

(!package_name.empty()) {

auth +=

;

auth +=

;

auth +=

;

auth +=

;

auth +=

;

auth +=

;

auth +=

;

auth +=

->GetVersionInfo().Print();

auth +=

;

(!

.empty()) limits::Check<limits::SQueueName>(

);

(user.empty() ?

: user +

) +

affinities_initialized =

;

(!

.empty()) limits::Check<limits::SQueueName>(

);

(!affinities_initialized &&

.

(sections,

,

)) {

affinities_initialized =

;

}

(loader(

));

version_info(connection.

(

,

));

attr_name, attr_value;

ns_node, ns_session;

(attr_name ==

)

ns_node = attr_value;

(attr_name ==

)

ns_session = attr_value;

(attr_name ==

)

(!ns_node.empty() && !ns_session.empty()) {

(server_props->ns_node != ns_node ||

server_props->ns_session != ns_session) {

server_props->ns_node = ns_node;

server_props->ns_session = ns_session;

server_props->version =

;

server_props->affs_synced =

;

connection.

(

,

);

(err_msg ==

) {

& service_name,

& client_name,

& queue_name,

wn,

try_config) :

m_Mode(GetMode(wn, try_config)),

registry_builder, sections);

(registry_builder, sections);

m_Mode(parent->m_Mode),

m_SharedData(parent->m_SharedData),

m_RetryOnException(parent->m_RetryOnException),

m_Queue(parent->m_Queue),

m_ProgramVersion(parent->m_ProgramVersion),

m_ClientNode(parent->m_ClientNode),

m_ClientSession(parent->m_ClientSession),

m_AffinityPreference(parent->m_AffinityPreference),

m_UseEmbeddedStorage(parent->m_UseEmbeddedStorage)

& conf_section

) :

& conf_section) :

& client_name,

& queue_name) :

->m_ProgramVersion = pv;

->UpdateAuthString();

->m_ProgramVersion;

:

;

:

;

#warning_type ":")) { \

warn_msg.erase(0, sizeof("e" #warning_type ":") - 1); \

return eWarn##warning_type; \

(warning_type) {

;

& affinity)

->AllocNotificationThread();

->m_Service;

(job_exptime !=

)

& mode_str)

(pause_mode !=

)

+=

;

response =

->ExecOnJobServer(job,

);

job.

= parser(

);

job.

= parser(

);

(job_exptime !=

)

known_server = server_props_it->second;

(

+ queue);

(field->name[0] ==

) {

(field->name ==

) {

field_bits |= (1 << eMaxInputSize);

}

(field->name ==

) {

field_bits |= (1 << eMaxOutputSize);

(field_bits == (1 << eNumberOfSizeParams) - 1)

m_Impl->GetServerParams();

& queue_name,

& queue_params)

(

);

(!queue_name.empty()) {

limits::Check<limits::SQueueName>(queue_name);

}

(!

.empty()) {

queue_params[field->name] = field->value;

& queue_name,

& queue_params)

m_Impl->GetQueueParams(queue_name, queue_params);

(

);

queue_params[field->name] = field->value;

m_Impl->GetQueueParams(queue_params);

response = m_Impl->ExecOnJobServer(job,

);

(client_node.empty()) {

<< limits::SClientNode::Name() <<

);

limits::Check<limits::SClientNode>(client_node);

m_Impl->m_ClientNode = client_node;

m_Impl->UpdateAuthString();

(client_session.empty()) {

<< limits::SClientSession::Name() <<

);

limits::Check<limits::SClientSession>(client_session);

m_Impl->m_ClientSession = client_session;

m_Impl->UpdateAuthString();

m_Impl->m_ClientType = client_type;

m_Impl->UpdateAuthString();

& param_value)

(!param_value.empty()) {

auth_param(

+ param_name);

auth_param +=

;

claim_new_affinities =

.

(sections,

,

);

process_any_job =

.

(sections,

,

);

(affinity_ladder.empty()) {

(claim_new_affinities) {

}

(process_any_job) {

(affinity_list.empty())

;

limits::Check<limits::SAffinity>(affinity);

(claim_new_affinities) {

);

(!affinity_list.empty()) {

);

(!process_any_job) {

list<CTempString> affinities;

(affinities.empty())

;

affinity_step;

(

& affinity : affinities) {

limits::Check<limits::SAffinity>(affinity);

(!affinity_step.empty()) affinity_step +=

;

affinity_step += affinity;

patch_level = -1)

: m_DriverVersionInfo

m_DriverName(driver_name)

(!m_DriverName.empty());

(params && (driver.empty() || driver == m_DriverName) &&

info_list.push_back(

(m_DriverName, m_DriverVersionInfo));

& client_node(m_Impl->m_ClientNode);

client_node +=

;

client_node +=

;

m_Impl->UpdateAuthString();

m_Impl->UseOldStyleAuth();

limits::Check<limits::SClientNode>(client_node);

m_Impl->m_ClientNode = client_node;

m_Impl->UpdateAuthString();

limits::Check<limits::SClientSession>(client_session);

m_Impl->m_ClientSession = client_session;

m_Impl->UpdateAuthString();

& client_name)

& client_name,

& queue_name)

Pool of recycled CCompoundID objects.

static CNcbiApplication * Instance(void)

Singleton method.

IClassFactory< SNetScheduleAPIImpl > TParent

CVersionInfo m_DriverVersionInfo

virtual TInterface * CreateInstance(const string &driver=kEmptyStr, CVersionInfo version=NCBI_INTERFACE_VERSION(IFace), const TPluginManagerParamTree *params=0) const

Create instance of TDriver.

TParent::TDriverList TDriverList

SNetScheduleAPIImpl IFace

void GetDriverVersions(TDriverList &info_list) const

Versions of the interface exported by the factory.

TParent::SDriverInfo TDriverInfo

CNetScheduleAPICF(const string &driver_name=kNetScheduleAPIDriverName, int patch_level=-1)

Construction.

SNetScheduleAPIImpl TDriver

Client API for NCBI NetSchedule server.

CNetScheduleConfigLoader(CSynRegistry &registry, SRegSynonyms &sections, bool ns_conf=true)

bool Transform(const string &prefix, string &name) const

bool operator()(SNetScheduleAPIImpl *impl)

enum CNetScheduleConfigLoader::@1010 m_Mode

const SRegSynonyms & m_Sections

CSynRegistry & m_Registry

NetSchedule internal exception.

Smart pointer to a part of the NetSchedule API that does job retrieval and processing on the worker n...

Smart pointer to a part of the NetSchedule API that allows to retrieve completed jobs.

unsigned short GetPort() const

CNetScheduleNotificationHandler()

bool WaitForNotification(const CDeadline &deadline, string *server_host=NULL)

SNetScheduleNotificationReceiver m_Receiver

bool ReceiveNotification(string *server_host=NULL)

CRef< SNetScheduleSharedData > m_SharedData

void OnConnected(CNetServerConnection &connection) override

void OnErrorImpl(const string &err_msg, CNetServer &server) override

void OnWarningImpl(const string &warn_msg, CNetServer &server) override

CNetScheduleServerListener(bool non_wn, SNetScheduleSharedData *shared_data)

TPropCreator GetPropCreator() const override

void SetAuthString(const string &auth)

INetServerConnectionListener * Clone() override

Smart pointer to the job submission part of the NetSchedule API.

string Exec(const string &cmd, bool multiline_output=false, const STimeout *timeout=NULL)

Execute remote command 'cmd', wait for the reply, check that it starts with 'OK:',...

bool GetNextAttribute(string &attr_name, string &attr_value)

Return the next attribute.

CNetServer::SExecResult FindServerAndExec(const string &cmd, bool multiline_output=false)

bool IsLoadBalanced() const

CNetServiceIterator Iterate(EIterationMode mode=eSortByLoad)

void Add(const IRegistry &registry)

TR< TType >::T Get(const SRegSynonyms &sections, SRegSynonyms names, TType default_value)

bool Has(const SRegSynonyms &sections, SRegSynonyms names)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

definition of a Culling tree

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

parent_type::iterator iterator

static SQLCHAR output[256]

static const TDS_WORD limits[]

static CNcbiApplicationGuard InstanceGuard(void)

Singleton method.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

const string & GetHost(void) const

Get host name.

string GetStringUID(TUID uid=0) const

Return string representation of UID.

CDiagContext & GetDiagContext(void)

Get diag context instance.

static TPID GetPID(void)

Get cached PID (read real PID if not cached yet).

void SetDiagUserAndHost(TDiagUserAndHost flags=fDiag_AddUser|fDiag_AddHost)

Set username and hostname properties for the diag context.

#define ERR_POST(message)

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

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

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).

@ eInvalid

To be used ONLY as a return value; please, NEVER throw an exception with this code.

EJobStatus

Job status codes.

CNetScheduleSubmitter GetSubmitter()

Create an instance of CNetScheduleSubmitter.

string output

Job result data.

void GetQueueParams(const string &queue_name, TQueueParams &queue_params)

static const char * GetErrCodeDescription(CException::TErrCode err_code)

EJobStatus GetJobDetails(CNetScheduleJob &job, time_t *job_exptime=NULL, ENetScheduleQueuePauseMode *pause_mode=NULL)

Get job details.

void SetClientSession(const string &client_session)

static ENetScheduleWarningType ExtractWarningType(string &warn_msg)

CNetScheduleJobReader GetJobReader(const string &group=kEmptyStr, const string &affinity=kEmptyStr)

Create an instance of CNetScheduleJobReader.

CNetScheduleAPI::TJobMask mask

int ret_code

Job return code.

static string StatusToString(EJobStatus status)

Printable status type.

const string & GetProgramVersion() const

Get program version string.

CNetRef< SNetScheduleAPIImpl > m_Impl

const string & GetQueueName() const

Return Queue name.

static const char * WarningTypeToString(ENetScheduleWarningType warning_type)

void GetProgressMsg(CNetScheduleJob &job)

Update the progress_message field of the job structure.

EAppRegistry

Defines how this object must be initialized.

void SetClientType(EClientType client_type)

const SServerParams & GetServerParams()

void SetProgramVersion(const string &pv)

Set program version (like: MyProgram v.

CNetScheduleExecutor GetExecutor()

Create an instance of CNetScheduleExecutor.

static EJobStatus StringToStatus(const CTempString &status_str)

Parse status string into enumerator value.

CNetScheduleAdmin GetAdmin()

static CException::TErrCode GetCode(const string &name)

string job_id

Output job key.

void SetClientNode(const string &client_node)

@ eDeleted

The job has been wiped out of the database.

@ eDone

Job is ready (computed successfully)

@ eConfirmed

Final state - read confirmed.

@ eReading

Job has its output been reading.

@ eCanceled

Explicitly canceled.

@ eRunning

Running on a worker node.

@ eJobNotFound

No such job.

@ ePending

Waiting for execution.

@ eReadFailed

Final state - read failed.

@ eFailed

Failed to run (execution timeout)

@ eExplicitAffinitiesOnly

TObjectType & GetObject(void)

Get object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

ncbi::TDriverList TDriverList

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

#define NCBI_INTERFACE_VERSION(iface)

Macro to construct CVersionInfo class using interface name (relies on CInterfaceVersion class)

ncbi::SDriverInfo SDriverInfo

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

Get the parameter value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

EIO_Status Wait(const STimeout *timeout=kInfiniteTimeout)

EIO_Status Recv(void *buf, size_t buflen, size_t *msglen=0, string *sender_host=0, unsigned short *sender_port=0, size_t maxmsglen=0)

ESwitch SetDataLogging(ESwitch log=eOn)

EIO_Status SetTimeout(EIO_Event event, const STimeout *timeout)

Set timeout for I/O in the specified direction.

EIO_Status Send(const void *data, size_t datalen, const string &host=string(), unsigned short port=0)

EIO_Status Bind(unsigned short port, ESwitch ipv6=eDefault)

unsigned short GetLocalPort(ENH_ByteOrder byte_order=eNH_HostByteOrder, bool trueport=false) const

Get socket local port number.

static string PrintableString(const CTempString str, TPrintableMode mode=fNewLine_Quote|fNonAscii_Passthru)

Get a printable version of the specified string.

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 int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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 ParseEscapes(const CTempString str, EEscSeqRange mode=eEscSeqRange_Standard, char user_char='?')

Parse C-style escape sequences in the specified string.

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

Convert UInt to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static Uint8 StringToUInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Uint8.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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

Case-sensitive compare of a substring with another string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

bool Run(TRunMode flags=fRunDefault)

Run the thread.

static void SetCurrentThreadName(const CTempString &)

Set name for the current thread.

bool TryWait(unsigned int timeout_sec=0, unsigned int timeout_nsec=0)

Timed wait.

void Post(unsigned int count=1)

Increment the semaphore by "count".

void Join(void **exit_data=0)

Wait for the thread termination.

CNanoTimeout GetRemainingTime(void) const

Get time left to the expiration.

CTime GetFastLocalTime(void)

Quick and dirty getter of local time.

void Get(unsigned int *sec, unsigned int *microsec) const

Get timeout in seconds and microseconds.

TArgs::const_iterator const_iterator

const TArgs & GetArgs(void) const

Get the const list of arguments.

iterator FindFirst(const string &name)

Find the first argument with the given name.

unsigned int usec

microseconds (modulo 1,000,000)

const char * IO_StatusStr(EIO_Status status)

Get the text form of an enum status value.

@ eIO_Timeout

timeout expired before any I/O succeeded

@ eIO_Success

everything is fine, no error occurred

@ eNonCompatible

major, minor does not match

#define NCBI_XCONNECT_EXPORT

const string version

version string

void ThrowIllegalChar(const string &name, const string &value, char c)

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

static void s_SetJobExpTime(time_t *job_exptime, const string &time_str)

#define WARNING_TYPE_TO_STRING(warning_type)

#define EXTRACT_WARNING_TYPE(warning_type)

CTempString s_GetSection(bool ns_conf)

CUrlArgs s_CreateCUrlArgs(const string &output)

int g_ParseNSOutput(const string &attr_string, const char *const *attr_names, string *attr_values, size_t attr_count)

static void s_SetPauseMode(ENetScheduleQueuePauseMode *pause_mode, const string &mode_str)

void NCBI_EntryPoint_xnetscheduleapi(CPluginManager< SNetScheduleAPIImpl >::TDriverInfoList &info_list, CPluginManager< SNetScheduleAPIImpl >::EEntryPointRequest method)

#define COMPATIBLE_NETSCHEDULE_VERSION

const char *const kNetScheduleAPIDriverName

ENetScheduleQueuePauseMode

Defines whether the job queue is paused, and if so, defines the pause mode set by the administrator.

const unsigned int kNetScheduleMaxDBDataSize

void g_AppendClientIPSessionIDHitID(string &cmd)

Helper classes and templates to implement plugins.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

void ReSetClientSession(const string &)

void AddToClientNode(const string &data)

void ReSetClientNode(const string &)

CCompoundIDPool GetCompoundIDPool()

static TInstance CreateWnCompat(const string &, const string &)

static TInstance CreateNoCfgLoad(const string &, const string &, const string &)

CNetScheduleAPI GetServer(CNetServer::TInstance server)

Extract one of the servers comprising this service as a separate NetSchedule API object.

function< INetServerProperties *()> TPropCreator

void OnWarning(const string &warn_msg, CNetServer &server)

SCompoundIDObjectPool< SCompoundIDImpl, ECompoundIDClass > m_CompoundIDPool

const CNetScheduleAPI::SServerParams & operator()(CNetService &service, const string &queue)

constexpr static long kAskMaxCount

CNetScheduleAPI::SServerParams m_ServerParams

CNetScheduleExecutor::EJobAffinityPreference m_AffinityPreference

CRef< SNetScheduleSharedData > m_SharedData

CNetScheduleGetJob::TAffinityLadder m_AffinityLadder

CFastMutex m_NotificationThreadMutex

void StartNotificationThread()

void AllocNotificationThread()

bool GetServerByNode(const string &ns_node, CNetServer *server)

CNetScheduleAPI::EClientType m_ClientType

CNetScheduleServerListener * GetListener()

CAtomicCounter_WithAutoInit m_NotificationThreadStartStopCounter

void SetAuthParam(const string &param_name, const string &param_value)

bool m_UseEmbeddedStorage

void Init(CSynRegistry &registry, SRegSynonyms &sections)

string ExecOnJobServer(const TJob &job, const string &cmd, ESwitch roe=eDefault)

void InitAffinities(CSynRegistry &registry, const SRegSynonyms &sections)

SNetScheduleAPIImpl(CSynRegistryBuilder registry_builder, const string &section, const string &service_name=kEmptyStr, const string &client_name=kEmptyStr, const string &queue_name=kEmptyStr, bool wn=false, bool try_config=true)

CNetScheduleAPI::EJobStatus GetJobStatus(string cmd, const CNetScheduleJob &job, time_t *job_exptime, ENetScheduleQueuePauseMode *pause_mode)

list< string > m_AffinityList

CRef< SNetScheduleNotificationThread > m_NotificationThread

void GetQueueParams(const string &queue_name, TQueueParams &queue_params)

bool operator()(string *server_host)

SNetScheduleNotificationReceiver()

SServerNotifications m_GetNotifications

unsigned short GetPort() const

SNetScheduleAPIImpl * m_API

virtual void * Main()

Derived (user-created) class must provide a real thread function.

void CmdAppendPortAndTimeout(string *cmd, unsigned remaining_seconds)

SNetScheduleNotificationReceiver m_Receiver

ENotificationType CheckNotification(string *ns_node)

SServerNotifications m_ReadNotifications

SNetScheduleNotificationThread(SNetScheduleAPIImpl *ns_api)

const string & operator()(const string &param) const

SNetScheduleOutputParser(const string &output)

void WriteLine(const string &line)

CRef< SNetServerInPool > m_ServerInPool

CRef< TProperties > Get()

CNetServer::SExecResult ConnectAndExec(const string &cmd, bool multiline_output, bool retry_on_exception=false)

void ResetServerConnections()

CRef< SNetServerInPool > ReturnServer(SNetServerInPool *server_impl)

CNetServerPool m_ServerPool

static SNetServiceImpl * Create(const string &api_name, const string &service_name, const string &client_name, INetServerConnectionListener *listener, CSynRegistry &registry, SRegSynonyms &sections, const string &ns_client_name=kEmptyStr)

const string & GetClientName() const

void Insert(CTempString s)

void x_ClearInterruptFlag()

TReadyServers m_ReadyServers

bool GetNextNotification(string *ns_node)

void RegisterServer(const string &ns_node)

CSemaphore m_NotificationSemaphore

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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