CGencollService Class Reference

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Inheritance diagram for CGencollService:

Collaboration diagram for CGencollService:

Public Member Functions
	CGencollService (const string &cgi_url, bool nocache)
	CGencollService (bool nocache)
	CGencollService (const CArgs &args)
Public Member Functions inherited from CGenomicCollectionsService
	CGenomicCollectionsService (const string &cache_file="")
	CGenomicCollectionsService (const CArgs &args)
	~CGenomicCollectionsService ()
CRef< CGC_Assembly >	GetAssembly (const string &acc, const string &mode)
CRef< CGC_Assembly >	GetAssembly (int releaseId, const string &mode)
string	ValidateChrType (const string &chrType, const string &chrLoc)
CRef< CGCClient_AssemblyInfo >	FindOneAssemblyBySequences (const string &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default)
	Find assembly by sequence accession. More...
CRef< CGCClient_AssemblySequenceInfo >	FindOneAssemblyBySequences (const list< string > &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default, bool with_roles=false)
	Find assembly by sequence accessions. More...
CRef< CGCClient_AssembliesForSequences >	FindAssembliesBySequences (const string &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default, bool with_roles=false)
	Find assemblies by sequence accession. More...
CRef< CGCClient_AssembliesForSequences >	FindAssembliesBySequences (const list< string > &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default, bool with_roles=false)
	Find assemblies by sequence accessions. More...
CRef< CGCClient_EquivalentAssemblies >	GetEquivalentAssemblies (const string &acc, int equivalency)
Public Member Functions inherited from CGenomicCollectionsService_Base
	CGenomicCollectionsService_Base (void)
virtual	~CGenomicCollectionsService_Base (void)
virtual void	Ask (const TRequest &request, TReply &reply)
virtual void	Ask (const TRequest &request, TReply &reply, TReplyChoice::E_Choice wanted)
virtual string	AskGet_chrtype_valid (const CGCClient_ValidateChrTypeLocRequest &req, TReply *reply=0)
virtual CRef< CGCClient_EquivalentAssemblies >	AskGet_equivalent_assemblies (const CGCClient_GetEquivalentAssembliesRequest &req, TReply *reply=0)
virtual vector< char >	AskGet_assembly_blob (const CGCClient_GetAssemblyBlobRequest &req, TReply *reply=0)
virtual CRef< CGCClient_AssembliesForSequences >	AskGet_assembly_by_sequence (const CGCClient_GetAssemblyBySequenceRequest &req, TReply *reply=0)
Public Member Functions inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
	CRPCClient (const string &service=kEmptyStr)
	CRPCClient (const string &service, ESerialDataFormat format)
	CRPCClient (const string &service, ESerialDataFormat format, unsigned int try_limit)
virtual	~CRPCClient (void)
virtual void	WriteRequest (CObjectOStream &out, const CGCClientRequest &request)
virtual void	ReadReply (CObjectIStream &in, CGCClientResponse &reply)
EIO_Status	SetTimeout (const STimeout *timeout, EIO_Event direction=eIO_ReadWrite)
const STimeout *	GetTimeout (EIO_Event direction=eIO_Read) const
EIO_Status	AsyncConnect (void *handle_buf, size_t handle_size)
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const
Public Member Functions inherited from CRPCClient_Base
	CRPCClient_Base (const string &service, ESerialDataFormat format)
	CRPCClient_Base (const string &service, ESerialDataFormat format, unsigned int try_limit)
virtual	~CRPCClient_Base (void)
void	Connect (void)
void	Disconnect (void)
void	Reset (void)
void	SetArgs (const string &args)
	Set additional connection arguments. More...
void	SetArgs (const CUrlArgs &args)
const string &	GetArgs (void) const
	Get additional connection arguments. More...
const string &	GetService (void) const
void	SetService (const string &service)
ESerialDataFormat	GetFormat (void) const
void	SetFormat (ESerialDataFormat fmt)
unsigned int	GetTryLimit (void) const
	Get number of request attempts. More...
void	SetTryLimit (unsigned int n)
unsigned int	GetRetryLimit (void) const
void	SetRetryLimit (unsigned int n)
const CTimeSpan	GetRetryDelay (void) const
	Get retry delay. More...
void	SetRetryDelay (const CTimeSpan &ts)
void	SetCanceledCallback (const ICanceled *canceled)
	Set request canceler. More...
bool	IsCanceled (void) const

Private Member Functions
virtual string	x_GetURL ()
virtual void	x_Connect ()
	These run with m_Mutex already acquired. More...

Private Attributes
const string	cgiUrl

Additional Inherited Members
Public Types inherited from CGenomicCollectionsService_Base
typedef CGCClientRequest	TRequest
typedef CGCClientResponse	TReply
typedef TRequest	TRequestChoice
typedef TReply	TReplyChoice
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...
Static Public Member Functions inherited from CGenomicCollectionsService
static void	AddArguments (CArgDescriptions &arg_desc)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...
Protected Member Functions inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
virtual string	GetAffinity (const CGCClientRequest &) const
virtual void	x_WriteRequest (CObjectOStream &out, const CSerialObject &request) override
virtual void	x_ReadReply (CObjectIStream &in, CSerialObject &reply) override
virtual string	x_GetAffinity (const CSerialObject &request) const override
void	x_ConnectURL (const string &url)
	Connect to a URL. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...
Protected Member Functions inherited from CRPCClient_Base
void	SetAffinity (const string &affinity)
virtual void	x_Disconnect (void)
	Disconnect as cleanly as possible. More...
void	x_SetStream (CNcbiIostream *stream)
void	x_Ask (const CSerialObject &request, CSerialObject &reply)
virtual bool	x_ShouldRetry (unsigned int tries)
CTimeSpan	x_GetRetryDelay (double max_delay) const
Protected Member Functions inherited from CConnIniter
	CConnIniter (void)
Static Protected Member Functions inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
static EHTTP_HeaderParse	sx_ParseHeader (const char *http_header, void *user_data, int server_error)
static bool	sx_IsSpecial (const STimeout *timeout)
Static Protected Member Functions inherited from CRPCClient_Base
static const char *	GetContentTypeHeader (ESerialDataFormat format)
Protected Attributes inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
const STimeout *	m_Timeout
	Cloned if not special. More...
Protected Attributes inherited from CRPCClient_Base
string	m_Service
	Used by default Connect(). More...
string	m_Args
unique_ptr< CNcbiIostream >	m_Stream
unique_ptr< CObjectIStream >	m_In
unique_ptr< CObjectOStream >	m_Out
string	m_Affinity
unsigned int	m_TryLimit
CHttpRetryContext	m_RetryCtx
CConstIRef< ICanceled >	m_Canceler

Detailed Description

Definition at line 65 of file gc_cli.cpp.

Constructor & Destructor Documentation

CGencollService() [1/3]

CGencollService::CGencollService ( const string &  cgi_url, bool  nocache  )

inline

Definition at line 68 of file gc_cli.cpp.

CGencollService() [2/3]

CGencollService::CGencollService ( bool  nocache )

inline

Definition at line 73 of file gc_cli.cpp.

References CNcbiApplication::Instance(), and NStr::ToUpper().

CGencollService() [3/3]

CGencollService::CGencollService ( const CArgs &  args )

inline

Definition at line 82 of file gc_cli.cpp.

Member Function Documentation

x_Connect()

virtual void CGencollService::x_Connect ( void  )

inlineprivatevirtual

These run with m_Mutex already acquired.

Reimplemented from CRPCClient< CGCClientRequest, CGCClientResponse >.

Definition at line 89 of file gc_cli.cpp.

References ctll::empty(), CUrlArgs::GetValue(), Info(), CUrlArgs::IsSetValue(), LOG_POST, and CRPCClient< CGCClientRequest, CGCClientResponse >::x_Connect().

x_GetURL()

virtual string CGencollService::x_GetURL ( )

inlineprivatevirtual

Definition at line 87 of file gc_cli.cpp.

Member Data Documentation

cgiUrl

const string CGencollService::cgiUrl

private

Definition at line 104 of file gc_cli.cpp.

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The documentation for this class was generated from the following file:

• src/objects/genomecoll/gc_cli/gc_cli.cpp