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NCBI C++ ToolKit: src/app/grid/cgi2rcgi/cgi2rcgi.cpp Source File

(

& name,

&

,

is_requested =

);

<void(

&)>

;

<<

<<

);

(((found ==

.end()) || !found->Check(

)) && is_requested) {

(

& job_id : rv) {

(!

.empty()) {

(!

.version) {

message =

->

(

,

,

);

message.empty() ? what : message;

(

include_entries =

)

;

&

)

;

m_InputValidator(input_validator),

m_CustomHTTPHeader(custom_http_header),

m_NeedRenderPage(

)

kNoMetaRefreshHeader =

;

(!include_entries) {

& name = it->first;

&

= it->second;

(!name.empty() && !

.empty()) {

& entry_name)

&

)

v = eit->second;

&

)

v = eit->second;

& entry_name,

&

,

pulling)

&

)

(

.empty()) {

(

+ eit->first, eit->second, encode_mode);

(

+ view_name +

));

();

ifd,

ofd,

);

(

& job_ids_value,

& timeout_value);

grid_cgi_section(

);

.Set(

,

,

);

(!

.HasEntry(

,

)) {

.Set(

,

,

);

.GetBool(grid_cgi_section,

,

.GetBool(grid_cgi_section,

,

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

arg_desc->AddOptionalKey(

,

cgi2rcgi_section(

);

,

);

);

=

.GetString(cgi2rcgi_section,

,

);

vector<string> affinity_methods;

,

),

, affinity_methods,

(vector<string>::const_iterator it = affinity_methods.begin();

it != affinity_methods.end(); ++it) {

(*it ==

)

<< *it <<

);

, 0);

(

.GetBool(cgi2rcgi_section,

,

,

);

,

);

ifd,

ofd,

)

content_length = 0;

, ifd, ofd,

| (content_length > 0 &&

& test_pattern);

& test_pattern)

stringstream node_stream;

regexp.

(node_stream.str());

(callback_pos ==

)

* callback_end = strchr(query_string->c_str() +

(callback_end !=

)

query_string->erase(callback_pos,

callback_end - query_string->data() - callback_pos + 1);

(callback_pos == 0)

query_string->clear();

(query_string->at(callback_pos - 1) ==

)

query_string->erase(callback_pos - 1);

->AddTagMap(

, stat_view);

(exception& e) {

(

<<

<<

<< e.what());

(jquery_callback_it !=

.end()) {

.erase(jquery_callback_it);

query_string_param(

query_string =

.Get(query_string_param);

(!query_string.empty()) {

.Set(query_string_param, query_string);

(!listen_jobs.empty()) {

(exception& ex) {

(

<< ex.what());

(exception& e) {

<< e.what());

(job_status) {

: unordered_map<string, SJob>

(job_ids.empty())

;

(

& job_id : job_ids) {

jobs.emplace(job_id, job_id);

wait_notifications =

;

(

&& j : jobs) {

& job_id = j.first;

& job = j.second;

wait_notifications = wait_notifications && !deadline.IsExpired();

(wait_notifications) {

tie(job.status, ignore, job.progress_msg) =

(wait_notifications) {

(

.WaitForNotification(deadline)) {

it = jobs.find(parser(

));

(it != jobs.end()) {

& job = it->second;

job.progress_msg = parser(

);

job.progress_msg_truncated = !parser(

).empty();

(

&& j : jobs) {

& job = j.second;

job.progress_msg_truncated =

;

job.progress_msg.clear();

(exception& e) {

(

<<

<< e.what());

<<

;

(

& j : jobs) {

& job_id = j.first;

& job = j.second;

<<

<<

<< job_id <<

<< status <<

;

(!job.progress_msg.empty()) {

<<

<< message;

(job.progress_msg_truncated)

<<

;

<<

<< endl;

(

()[

] ||

(!affinity.empty()) {

.AddChars(affinity.data(), affinity.length());

(!saved_content.empty())

os.write(saved_content.data(), saved_content.length());

(exception& ex) {

hidden_fields;

hidden_fields +=

+ it->first

->AddTagMap(

,

->AddTagMap(

,

(!since_time.empty()) {

grid_ctx.

(

, since_time);

->AddTagMap(

,

->AddTagMap(

,

(

));

->AddTagMap(

,

progress_message;

progress_message =

->GetProgressMessage();

(

<<

vector<string>::const_iterator it;

->LoadTemplateLibFile(lib, &page_filter);

stringstream header_stream;

} status_line_status = eNoStatusLine;

(header_stream.good()) {

getline(header_stream, header_line);

(header_line.empty())

(status_line_status == eReadingStatusLine) {

(

(header_line[0])) {

status_line += header_line;

status_line_status = eGotStatusLine;

status_line_status = eReadingStatusLine;

status_line = header_line;

<< header_line <<

;

(status_line_status != eNoStatusLine) {

status_line.data() + (

(

) - 1),

status_line.size() - (

(

) - 1));

status_code, reason,

(exception& e) {

<< e.what());

& url,

idelay)

);

->AddTagMap(

, redirect);

->AddTagMap(

, delay);

);

(

<<

+ e.

()));

kFormat =

;

parser.

(event);

}

(name != kTimestamp);

=

;

kEvent1 =

;

(

.ReadLine(line)) {

no_jquery =

.GetJqueryCallback().empty();

.NeedRenderPage(

);

(getline(is, header_line)) {

(header_line.empty())

<< header_line <<

;

<<

;

<< header_line <<

;

<<

.GetJqueryCallback() <<

;

.NeedRenderPage(

);

(exception& ex) {

err_msg = ex.

();

(

<< err_msg);

}

(!

) {

(

<<

<< err_msg);

.NeedRenderPage(

);

(

<< err_msg);

.SelectView(

);

* str_page;

str_page =

;

.GetHTMLPage().SetTemplateString(str_page);

.SelectView(

);

.GetHTMLPage().AddTagMap(

,

(

argc,

* argv[])

app.

(argc, argv);

static const string kSinceTime

Checksum and hash calculation classes.

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

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

CCgiRequestException –.

CChecksum – Checksum calculator.

Pool of recycled CCompoundID objects.

Grid CGI Context Context in which a request is processed.

void SetJobProgressMessage(const string &msg)

void DefinePersistentEntry(const string &entry_name, const string &value)

void PullUpPersistentEntry(const string &entry_name)

CHTMLPage & GetHTMLPage()

bool NeedRenderPage() const

const string & GetJobProgressMessage() const

Grid Client (the submitter).

Client API for NetCache server.

Client API for NCBI NetSchedule server.

void GetQueueInfo(CNetServer server, const string &queue_name, TQueueInfo &queue_info)

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

NetSchedule internal exception.

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)

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

CNetServer GetServer(unsigned host, unsigned short port)

CNetServiceIterator ExcludeServer(CNetServer::TInstance server)

Start iteration excluding 'server' (return the next server after 'server' or NULL).

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

CTimeout – Timeout interval.

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

container_type::iterator iterator

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

The NCBI C++ standard methods for dealing with std::string.

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

main entry point for tests

static void get_results(DBPROCESS *dbproc, int start)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static SQLCHAR output[256]

static const char * column

#define GRID_APP_CHECK_VERSION_ARGS()

NetSchedule Framework specs.

CNcbiEnvironment & SetEnvironment(void)

Get a non-const copy of the application's cached environment.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CNcbiRegistry & GetRWConfig(void)

Get the application's cached configuration parameters, accessible for read-write for an application's...

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eString

An arbitrary string.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CCgiRequest & GetRequest(void) const

void SetRequestFlags(int flags)

Set cgi parsing flag.

void Init(void) override

This method is called on the CGI application initialization – before starting to process a HTTP reque...

void RegisterDiagFactory(const string &key, CDiagFactory *fact)

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments extended with CGI parameters.

void SetRequestId(const string &rid, bool is_done)

virtual CCgiContext * CreateContextWithFlags(CNcbiArguments *args, CNcbiEnvironment *env, CNcbiIstream *inp, CNcbiOstream *out, int ifd, int ofd, int flags)

The same as CreateContext(), but allows for a custom set of flags to be specified in the CCgiRequest ...

const string & GetSelfURL(ESelfUrlPort) const

Using HTTP environment variables, compose the CGI's own URL as: SCHEME://SERVER_NAME[:SERVER_PORT]/SC...

#define NCBI_CGI_THROW_WITH_STATUS(exception, err_code, message, status)

const TCgiEntries & GetEntries(void) const

Get a set of entries(decoded) received from the client.

static SIZE_TYPE ParseEntries(const string &str, TCgiEntries &entries)

Decode the URL-encoded(FORM or ISINDEX) string "str" into a set of entries <"name",...

void SetHeaderValue(const string &name, const string &value)

void Serialize(CNcbiOstream &os) const

Serialize/Deserialize a request to/from a stream.

CNcbiOstream & out(void) const

Get output stream. Throw exception if GetOutput() is NULL.

void SetStatus(unsigned int code, const string &reason=kEmptyStr)

void RequireWriteHeader(bool require)

Define if WriteHeader() must be called or can be skipped.

const string & GetProperty(ECgiProp prop) const

Get value of a "standard" property (return empty string if not defined)

const string & GetContent(void) const

Get request content.

void SetContentType(const string &type)

Set content type (text/html by default if not provided)

const string & GetRandomProperty(const string &key, bool http=true) const

Get value of a random client property; if "http" is TRUE then add prefix "HTTP_" to the property name...

CNcbiOstream & WriteHeader(void) const

Write HTTP response header to the output stream.

int TFlags

Startup initialization.

static const string GetPropertyName(ECgiProp prop)

Get name (not value!) of a "standard" property.

@ fSaveRequestContent

Save request content (available through GetContent())

@ fDoNotParseContent

do not automatically parse the request's content body (from "istr")

@ fCaseInsensitiveArgs

use case insensitive CGI arguments

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define ERR_POST(message)

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

static void SetOldPostFormat(bool value)

Set old/new format flag.

#define LOG_POST(message)

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

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.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

#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).

#define FORMAT(message)

Format message using iostreams library.

virtual CNCBINode * MapTag(const string &name)

Resolve <@XXX> tag.

class CHTMLPage::CTemplateLibFilter TTemplateLibFilter

Interface for a filter, which must be passed to one the LoadTemplateLib methods to select relevant pa...

virtual void AddTagMap(const string &name, BaseTagMapper *mapper)

Tag mappers.

virtual CNcbiOstream & Print(CNcbiOstream &out, TMode mode=eHTML)

@ eJSONEncode

Encode for JSON output.

@ eNoEncode

Do not encode prior to printing.

@ eHTMLEncode

Encode for HTML output.

vector< SEntry > m_Entries

static vector< string > GetListenJobs(const string &value)

CCgiContext & m_CgiContext

bool m_InterceptJQueryCallback

unique_ptr< CHTMLPage > m_Page

CNcbiRegistry * m_Registry

EJobStatus

Job status codes.

bool CheckIfJobDone(CGridCgiContext &, CNetScheduleAPI::EJobStatus)

TCgiEntries m_ParsedQueryString

unique_ptr< CHTMLPage > m_CustomHTTPHeader

void SetJobProgressMessage(const string &msg)

CNetScheduleSubmitter GetSubmitter()

Create an instance of CNetScheduleSubmitter.

SExceptionMessage m_ExceptionMessage

void SubmitJob(CCgiRequest &request, CGridCgiContext &grid_ctx)

CHTMLPlainText::EEncodeMode m_TargetEncodeMode

string m_ElapsedTimeFormat

void DefinePersistentEntry(const string &entry_name, const string &value)

void PullUpPersistentEntry(const string &entry_name)

Save this entry as a cookie add it to serf url.

void Clear()

Remove all persisted entries from cookie and self url.

void DefineRefreshTags(CGridCgiContext &grid_ctx, const string &url, int delay)

CRegexpTemplateFilter(CHTMLPage *page)

CHTMLPage & GetHTMLPage(void)

Get an HTML page.

CNetScheduleAPI::EJobStatus GetStatus(CGridCgiContext &)

CHTMLPage & m_CustomHTTPHeader

void NeedRenderPage(bool value)

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

Get job details.

static void s_RemoveCallbackParameter(string *query_string)

const TPersistentEntries & GetPersistentEntries() const

function< void(const string &)> m_Func

CNetScheduleAPI::EJobStatus GetStatusAndCtgTime(CGridCgiContext &grid_ctx)

void GetQueryStringEntryValue(const string &entry_name, string &value) const

bool s_IsPendingOrRunning(CNetScheduleAPI::EJobStatus job_status)

void SelectView(const string &view_name)

SExceptionMessage(CNcbiRegistry *registry=nullptr)

string operator()(const string &what)

map< string, string > TPersistentEntries

CNetCacheAPI m_NetCacheAPI

static void CheckGetResults(const string &value)

void CheckEntry(const string &name, const string &value, bool is_requested=true)

TPersistentEntries m_PersistentEntries

string GetSelfURL(void) const

Get Self URL.

CNetScheduleAPI::EJobStatus status

virtual bool TestAttribute(const string &attr_name, const string &test_pattern)

static const string kPlainTextView

static string StatusToString(EJobStatus status)

Printable status type.

bool NeedMetaRefresh() const

bool NeedRenderPage() const

void ReadJob(istream &, CGridCgiContext &)

void s_GetCtgTime(CGridCgiContext &grid_ctx, string event)

SInputValidator m_InputValidator

static const string kGridCgiForm

void LoadQueryStringTags(CHTMLPlainText::EEncodeMode encode_mode)

const string & GetJobKey(void) const

Get Current job key.

virtual CCgiContext * CreateContextWithFlags(CNcbiArguments *args, CNcbiEnvironment *env, CNcbiIstream *inp, CNcbiOstream *out, int ifd, int ofd, int flags)

The same as CreateContext(), but allows for a custom set of flags to be specified in the CCgiRequest ...

virtual int ProcessRequest(CCgiContext &ctx)

This is the method you should override.

static CDeadline GetDeadline(const string &value)

SInputValidator & m_InputValidator

static void CheckCancel(const string &value)

void PopulatePage(CGridCgiContext &grid_ctx)

virtual void Init()

This method is called on the CGI application initialization – before starting to process a HTTP reque...

CCgiResponse * m_Response

int main(int argc, const char *argv[])

void AddAffinityEntry(string name)

const string & GetPersistentEntryValue(const string &entry_name) const

void GetRequestEntryValue(const string &entry_name, string &value) const

void OnJobFailed(const string &msg, CGridCgiContext &ctx)

void OnJobDone(CGridCgiContext &)

void CheckJob(CGridCgiContext &grid_ctx)

void ListenJobs(const string &job_ids_value, const string &timeout_value)

static void CheckCtgTime(const string &value)

CNetScheduleAPIExt m_NetScheduleAPI

static void CheckJobKey(const string &value)

unique_ptr< CGridClient > m_GridClient

bool Check(const string &value)

static EJobStatus StringToStatus(const CTempString &status_str)

Parse status string into enumerator value.

CNetScheduleAdmin GetAdmin()

friend CNcbiOstream & operator<<(CNcbiOstream &out, SJobs jobs)

bool progress_msg_truncated

string job_id

Output job key.

string & GetJqueryCallback()

static void CheckAffinity(const string &value)

CGridCgiContext(CHTMLPage &page, CCgiContext &ctx)

vector< string > m_HtmlIncs

void AddTagMap(const string &n, const string &v, CHTMLPlainText::EEncodeMode m=CHTMLPlainText::eHTMLEncode)

@ eDone

Job is ready (computed successfully)

@ eCanceled

Explicitly canceled.

@ eRunning

Running on a worker node.

@ eJobNotFound

No such job.

@ ePending

Waiting for execution.

@ eFailed

Failed to run (execution timeout)

uint64_t Uint8

8-byte (64-bit) unsigned integer

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

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.

static const char * kHeader_Url

static const char * kHeader_Delay

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 bool StringToBool(const CTempString str)

Convert string to bool.

NCBI_NS_STD::string::size_type SIZE_TYPE

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 bool MatchesMask(CTempString str, CTempString mask, ECase use_case=eCase)

Match "str" against the "mask".

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static string HtmlEncode(const CTempString str, THtmlEncode flags=fHtmlEnc_EncodeAll)

Encode a string for HTML.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the 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 unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

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

Sanitize a string, allowing only specified classes of characters.

static string JsonEncode(const CTempString str, EJsonEncode encoding=eJsonEnc_UTF8)

Encode a string for JSON.

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 string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ eJsonEnc_Quoted

Quote resulting string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ eUrlEnc_URIPath

Encode path part of an URI.

@ eTrunc_End

Truncate trailing whitespace only.

@ eNocase

Case insensitive compare.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

string AsString(const CTimeFormat &fmt=kEmptyStr) const

Transform time span to string.

void Set(EType type)

Set special value.

CTime GetFastLocalTime(void)

Quick and dirty getter of local time.

CTime & SetTimeT(const time_t t)

Set time using time_t time value.

@ eZero

Zero timeout, equal to CTimeout(0,0).

where both of them are integers Note

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

const GenericPointer< typename T::ValueType > T2 value

Miscellaneous common-use basic types and functionality.

static const string kStatus

static const char delimiter[]

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

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

void AddToClientNode(const string &data)

CCompoundIDPool GetCompoundIDPool()

Meaningful information encoded in the NetSchedule key.

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

static wxAcceleratorEntry entries[3]

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