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NCBI C++ ToolKit: src/app/grid/grid_cli/ns_cmds.cpp Source File

(!service_provided) {

.host.push_back(

);

(job_provided && service_provided) {

);

warning_handler = [&](

& m,

s) {

(!service_provided) {

);

printf(

, job_status.c_str());

printf(

,

(attr_name[0]) {

<< m_LineNumber << ", column " << attr_column

<< attr_name <<

);

<< attr_name <<

);

& job_key,

& server_host)

last_event_index = -1;

*

=

;

&job_status, &last_event_index))

=

;

(job_input_ostream.fail()) {

max_embedded_input_size,

numeric_limits<size_t>().

() :

max_embedded_input_size - max_embedded_input_size / 10);

remote_app_stdin.peek();

(!remote_app_stdin.eof())

request.

(job_input_ostream);

max_embedded_input_size,

&job_input_ostream)

remote_app_stdin, job_input_ostream);

max_embedded_input_size =

->GetMaxServerInputSize();

remote_app_stdin.write(job_input_record.

.data(),

remote_app_stdin, job_input_ostream);

job_input_ostream.write(job_input_record.

.data(),

(!job_input_record.

.empty())

(remaining_batch_size == 0) {

vector<CNetScheduleJob>& jobs =

(vector<CNetScheduleJob>, it, jobs)

, it->job_id.c_str());

batch_submitter.

();

remote_app_stdin.write(job_input_record.

.data(),

remote_app_stdin, job_input_ostream);

job_input_ostream.write(job_input_record.

.data(),

(!job_input_record.

.empty())

--remaining_batch_size;

vector<CNetScheduleJob>& jobs =

(vector<CNetScheduleJob>, it, jobs)

batch_submitter.

();

);

job_input_ostream(&job_input_writer, 0,

);

max_embedded_input_size =

->GetMaxServerInputSize();

job.

, server_host);

last_event_index = -1;

tie(job_status, last_event_index, ignore) =

);

printf(

, last_event_index,

fprintf(stderr,

,

fprintf(stderr,

,

std_stream.exceptions((ios::iostate) 0);

(!std_stream.eof()) {

(std_stream.fail() && !std_stream.eof())

bytes_read = (size_t) std_stream.gcount();

fwrite(

, bytes_read, 1, output_stream) != 1)

& data_or_blob_id)

unique_ptr<IReader> reader;

(fwrite(data_or_blob_id.data(), data_or_blob_id.length(), 1,

input_stream(reader.release(), 0, 0, kStreamFlags);

);

input_stream(reader.release(), 0, 0, kStreamFlags);

remote_app_result.

(input_stream);

:

,

:

);

fprintf(stderr,

,

);

(!reliable_second) {

reliable_first ?

:

);

rnj_result = job_reader.

(&job, &job_status);

rnj_result = job_reader.

(&job, &job_status, &timeout);

(rnj_result) {

);

fprintf(stderr,

,

server_address;

*

=

;

=

;

server_host.c_str(),

server_address.c_str());

);

fprintf(stderr,

);

TQueueRegister queue_register;

server_address = it->server.GetServerAddress();

(std::list<std::string>, queue, it->queues) {

queue_register[*queue].insert(server_address);

(TQueueRegister, it, queue_register) {

(it->second.size() != queues.size()) {

* sep =

;

(TServerSet, server, it->second) {

CJsonNode g_QueueClassInfoToJson(CNetScheduleAPI ns_api)

void g_ProcessJobInfo(CNetScheduleAPI ns_api, const string &job_key, IJobInfoProcessor *processor, bool verbose, CCompoundIDPool::TInstance id_pool)

void g_PrintJSON(FILE *output_stream, CJsonNode node, const char *indent)

CJsonNode g_QueueInfoToJson(CNetScheduleAPI ns_api, const string &queue_name)

ENextAttributeType NextAttribute(CTempString *attr_name, string *attr_value, size_t *attr_column)

void Reset(const char *position, const char *eol)

size_t GetLineNumber() const

CBatchSubmitAttrParser(istream *input_stream)

string m_JobAttributeValue

CAttrListParser m_AttrParser

EOption GetAttributeType() const

const string & GetAttributeValue() const

CCompoundID NewID(ECompoundIDClass new_id_class)

Create and return a new CCompoundID objects.

Base64-encoded ID string that contains extractable typed fields.

void AppendRandom(Uint4 random_number)

Append an eCIT_Random field at the end of this compound ID.

void AppendCurrentTime()

Get the current time and append it as an eCIT_Timestamp field at the end of this compound ID.

string ToString()

Pack the ID and return its string representation.

Grid Client (the submitter).

static bool OnWarning(bool worker_node_admin, const string &warn_msg, CNetServer server)

int DumpJobInputOutput(const string &data_or_blob_id)

CCompoundIDPool m_CompoundIDPool

bool IsOptionSet(int option) const

unique_ptr< CGridClient > m_GridClient

void SetUp_NetScheduleCmd(EAPIClass api_class, EAdminCmdSeverity cmd_severity=eReadOnlyAdminCmd, bool require_queue=true)

struct CGridCommandLineInterfaceApp::SOptions m_Opts

void PrepareRemoteAppJobInput(size_t max_embedded_input_size, const string &args, CNcbiIstream &remote_app_stdin, CNcbiOstream &job_input_ostream)

CNetScheduleSubmitter m_NetScheduleSubmitter

void JobInfo_PrintStatus(CNetScheduleAPI::EJobStatus status)

CNetScheduleAdmin m_NetScheduleAdmin

bool IsOptionAcceptedAndSetImplicitly(EOption option) const

CNetScheduleAPIExt m_NetScheduleAPI

void MarkOptionAsSet(int option)

@ eAdminCmdWithSideEffects

void PrintJobStatusNotification(CNetScheduleNotificationHandler &submit_job_handler, const string &job_key, const string &server_host)

enum CGridCommandLineInterfaceApp::EAPIClass m_APIClass

int PrintJobAttrsAndDumpInput(const CNetScheduleJob &job)

static void PrintLine(const string &line)

bool IsOptionExplicitlySet(int option) const

void x_LoadJobInput(size_t max_embedded_input_size, CNcbiOstream &job_input_ostream)

CNetScheduleExecutor m_NetScheduleExecutor

void CheckJobInputStream(CNcbiOstream &job_input_ostream)

CNetCacheAPI m_NetCacheAPI

Grid Job Batch Submitter.

CJsonNode GetRootNode() const

void DeleteQueue(const string &qname)

Delete queue Applicable only to queues, created through CreateQueue method.

void GetQueueList(TQueueList &result)

void CreateQueue(const string &qname, const string &qclass, const string &description=kEmptyStr)

Create an instance of the given queue class.

void DumpJob(CNcbiOstream &out, const string &job_key)

void CancelAllJobs(const string &job_statuses=kEmptyStr)

Cancel all jobs in the queue (optionally with particular statuses).

void DumpQueue(CNcbiOstream &output_stream, const string &start_after_job=kEmptyStr, size_t job_count=0, const string &job_statuses=kEmptyStr, const string &job_group=kEmptyStr)

void PrintQueueInfo(const string &queue_name, CNcbiOstream &output_stream)

list< SServerQueueList > TQueueList

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.

string SaveJobInput(const string &target_dir, CNetCacheAPI &nc_api)

CNetScheduleAPI::EJobStatus WaitForJobEvent(const string &job_key, CDeadline &deadline, CNetScheduleAPI ns_api, TJobStatusMask status_mask, int last_event_index=kMax_Int, int *new_event_index=NULL)

bool CheckJobStatusNotification(const string &job_id, CNetScheduleAPI::EJobStatus *job_status, int *last_event_index=NULL)

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

void CmdAppendTimeoutGroupAndClientInfo(string &cmd, const CDeadline *deadline, const string &job_group)

bool CheckRequestJobNotification(CNetScheduleExecutor::TInstance executor, CNetServer *server)

bool RequestJob(CNetScheduleExecutor::TInstance executor, CNetScheduleJob &job, const string &cmd)

TJobInfo RequestJobWatching(CNetScheduleAPI::TInstance ns_api, const string &job_id, const CDeadline &deadline)

void SubmitJob(CNetScheduleSubmitter::TInstance submitter, CNetScheduleJob &job, unsigned wait_time, CNetServer *server=NULL)

static string MkBaseGETCmd(CNetScheduleExecutor::EJobAffinityPreference affinity_preference, const string &affinity_list)

const string & GetMessage() const

CNetScheduleAPI::EJobStatus WaitForJobCompletion(CNetScheduleJob &job, CDeadline &deadline, CNetScheduleAPI ns_api, time_t *job_exptime=NULL)

void StickToServer(SSocketAddress address)

string GetServerAddress() const

void PrintCmdOutput(const string &cmd, CNcbiOstream &output_stream, ECmdOutputStyle output_style, CNetService::EIterationMode=CNetService::eSortByLoad)

void SetWarningHandler(TEventHandler warning_handler)

CNetServerPool GetServerPool()

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

@ fLeakExceptions

Exceptions leaked out.

@ fOwnReader

Own the underlying reader.

Remote Application Request (both client side and application executor side)

CNcbiIstream & GetStdInForRead()

Get the stdin stream of the remote application.

void SetMaxInlineSize(size_t max_inline_size)

void Send(CNcbiOstream &os)

Serialize a request to a given stream.

void Deserialize(CNcbiIstream &is)

CNcbiOstream & GetStdIn()

Get an output stream to write data to a remote application stdin.

void SetCmdLine(const string &cmdline)

Set the command line for the remote application.

Remote Application Result (both client side and application executor side)

CNcbiIstream & GetStdErr()

Get a remote application stderr.

CNcbiIstream & GetStdOut()

Get a remote application stdout.

void Receive(CNcbiIstream &is)

Deserialize a request from a given stream.

String or Blob Storage Reader.

String or Blob Storage Writer.

ERW_Result Write(const void *buf, size_t count, size_t *bytes_written=0) override

Write up to "count" bytes from the buffer pointed to by the "buf" argument onto the output device.

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

CTimeout – Timeout interval.

Writer-based output stream.

#define RAW_OUTPUT_FORMAT

#define QUEUEINFO_COMMAND

#define LOGIN_TOKEN_OPTION

#define ANY_AFFINITY_OPTION

#define CLIENT_SESSION_OPTION

#define NETSCHEDULE_OPTION

@ eUsePreferredAffinities

#define ALL_QUEUES_OPTION

#define WAIT_TIMEOUT_OPTION

#define CLAIM_NEW_AFFINITIES_OPTION

#define JOB_INPUT_DIR_OPTION

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Error(CExceptionArgs_Base &args)

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.

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

EJobStatus

Job status codes.

void ReadConfirm(const string &job_id, const string &auth_token)

Mark the specified job as successfully retrieved.

CNetScheduleSubmitter GetSubmitter()

Create an instance of CNetScheduleSubmitter.

void Submit(const string &job_group=kEmptyStr)

Submit a batch to the queue.

void SetJobMask(CNetScheduleAPI::TJobMask mask)

Set a job mask.

string output

Job result data.

void SetJobAffinity(const string &affinity)

Set a job affinity.

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

Get job details.

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

Get the current status of the specified job.

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

Create an instance of CNetScheduleJobReader.

void ReturnJob(const CNetScheduleJob &job)

Switch the job back to the "Pending" status so that it can be run again on a different worker node.

void ClearNode()

Unregister client-listener.

void PutResult(const CNetScheduleJob &job)

Put job result (job should be received by GetJob() or WaitJob())

CNetScheduleAPI::TJobMask mask

int ret_code

Job return code.

static string StatusToString(EJobStatus status)

Printable status type.

EReadNextJobResult ReadNextJob(CNetScheduleJob *job, CNetScheduleAPI::EJobStatus *job_status, const CTimeout *timeout=NULL)

Wait and return the next completed job.

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

Get full information about the specified job.

void SetJobGroup(const string &job_group)

Retrieve jobs from the specified group only.

CNetScheduleAPI::EJobStatus GetJobStatus(const string &job_key, time_t *job_exptime=NULL, ENetScheduleQueuePauseMode *pause_mode=NULL)

Get the current status of the specified job.

void JobDelayExpiration(const CNetScheduleJob &job, unsigned runtime_inc)

Increment job execution timeout.

EJobAffinityPreference

Affinity matching modes.

void CancelJobGroup(const string &job_group, const string &job_statuses=kEmptyStr)

Cancel job group.

void GetProgressMsg(CNetScheduleJob &job)

Update the progress_message field of the job structure.

void SetClientType(EClientType client_type)

void ReadRollback(const string &job_id, const string &auth_token)

Refuse from processing the results of the specified job.

void SetAffinityPreference(EJobAffinityPreference aff_pref)

Set preferred method of requesting jobs with affinities.

const SServerParams & GetServerParams()

EReadNextJobResult

Possible outcomes of ReadNextJob() calls.

void PutProgressMsg(const CNetScheduleJob &job)

Put job interim (progress) message.

bool GetJob(CNetScheduleJob &job, const string &affinity_list=kEmptyStr, CDeadline *dealine=NULL)

Get a pending job.

CNetScheduleExecutor GetExecutor()

Create an instance of CNetScheduleExecutor.

void ReadFail(const string &job_id, const string &auth_token, const string &error_message=kEmptyStr)

Refuse from processing the results of the specified job and increase its counter of failed job result...

CNetScheduleAdmin GetAdmin()

void PutFailure(const CNetScheduleJob &job, bool no_retries=false)

Submit job failure diagnostics.

string job_id

Output job key.

void CancelJob(const string &job_key)

Cancel job.

const vector< CNetScheduleJob > & GetBatch() const

CNcbiOstream & GetOStream()

Get a stream where a client can write an input data for the remote job.

@ eDone

Job is ready (computed successfully)

@ eConfirmed

Final state - read confirmed.

@ eReading

Job has its output been reading.

@ eRunning

Running on a worker node.

@ eJobNotFound

No such job.

@ ePending

Waiting for execution.

@ eReadFailed

Final state - read failed.

@ eExplicitAffinitiesOnly

@ eExclusiveJob

Exclusive job - the node executes only this job, even if there are processor resources.

@ eRNJ_NotReady

No matching jobs are ready for reading.

@ eRNJ_JobReady

A job is returned.

@ eRNJ_NoMoreJobs

No matching jobs.

@ eRNJ_Interrupt

ReadNextJob() has been interrupted.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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".

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Success

Everything is okay, I/O completed.

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

Get a printable version of the specified string.

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.

CTime GetFastLocalTime(void)

Quick and dirty getter of local time.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

const struct ncbi::grid::netcache::search::fields::KEY key

static const string s_NotificationTimestampFormat("Y/M/D h:m:s.l")

#define ATTR_CHECK_SET(name, type)

static bool s_DumpStdStream(CNcbiIstream &std_stream, FILE *output_stream)

Reader-writer based streams.

time_t extend_lifetime_by

EOutputFormat output_format

void ReSetClientSession(const string &)

void ReSetClientNode(const string &)

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

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

Meaningful information encoded in the NetSchedule key.

SBatchSubmitRecord(istream *input_stream)

CBatchSubmitAttrParser attr_parser

bool remote_app_args_defined

static SSocketAddress Parse(const string &address, SHost::EName name=SHost::EName::eResolved)

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