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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/project__storage_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/uudutil/project_storage.cpp Source File

*

=

;

m_CmprsFmt(eNC_Uncompressed),

m_ServiceName(nc_service),

m_HasNetStorage(

),

ns_service =

;

(sec > 0 &&

) {

num_sec = (

)floor(sec);

num_msec = (

)((sec - num_sec) * 1000000.0f);

time_to_live,

nc_key =

;

(time_to_live > 0)

time_to_live,

nc_key =

;

(time_to_live > 0)

time_to_live,

nc_key =

;

unique_ptr<CNcbiOstream> ostr =

(nc_key, time_to_live, default_flags, nso);

(time_to_live > 0)

time_to_live,

nc_key =

;

unique_ptr<CNcbiOstream> ostr =

(nc_key, time_to_live, default_flags, nso);

(time_to_live > 0)

time_to_live,

time_to_live,

time_to_live,

(time_to_live > 0)

time_to_live,

new_key =

;

(time_to_live > 0)

(time_to_live > 0)

new_key = nso_clone.

();

*obj_istr >> *real_project;

(

<<

(; annot_iter; ++annot_iter) {

(; annot_iter; ++annot_iter) {

*obj_istr >> *real_project;

(

<<

(

<<

unique_ptr<CNcbiIstream> strm;

valid_header =

;

valid_header =

;

p->GetDecompressor()->SetWindowBits(

);

p->GetDecompressor()->SetMemoryLevel(

);

eUnsupportedCompression,

);

strm.reset(zip_str.release());

( !valid_header ) {

=

;

=

;

<<

}

(exception& e) {

<<

);

unique_ptr<CNcbiOstream> ostr;

unique_ptr<CCompressionStreamProcessor> compressor;

p->GetCompressor()->SetMemoryLevel(

);

unique_ptr<CNcbiOstream> zip_ostr(

(no_throw)

;

=

;

+=

;

(no_throw)

;

=

;

(no_throw)

;

=

;

+=

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CBZip2StreamCompressor – bzip2 based compression stream processor.

CBZip2StreamDecompressor – bzip2 based decompression stream processor.

In-memory stream (a la strstream or stringstream)

CLZOStreamCompressor – lzo based compression stream processor.

CLZOStreamDecompressor – lzo based decompression stream processor.

Client API for NetCache server.

NetCache internal exception.

Basic network-based data object I/O.

Network BLOB storage API.

CProjectStorage(const string &client, const string &nc_service="", const string &password="", TNetStorageFlags default_flags=0)

Constructor.

CIRef< objects::IGBProject > GetProject(const string &key)

Retrieve a NC blob as a GB project.

bool Exists(const string &key)

Check existence of a NetCache blob.

void GetString(const string &key, string &str)

Download the data as a string from NetCache with a key.

string SaveString(const string &str, const string &key="", TCompressionFormat compression_fmt=eNC_ZlibCompressed, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Save a string to NetCache.

string Clone(const string &key, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Duplicate an existing data Blob.

bool x_ValidateSerialFormat(TDataFormat fmt, bool no_throw=false) const

Check if the object format is valid.

CRef< CSerialObject > GetObject(const string &key)

Construct and return a serializable ASN object.

string m_Password

For password-protected Blobs.

string SaveObject(const CSerialObject &obj, const string &key="", TCompressionFormat compression_fmt=eNC_ZlibCompressed, TDataFormat data_fmt=eSerial_AsnBinary, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Save a serializable ASN object to NetCache.

bool x_ValidateCompressionFormat(TCompressionFormat fmt, bool no_throw=false) const

Check if the compression is valid.

void GetVector(const string &key, vector< char > &vec)

Download the data as a blob from NetCache with a key.

Uint2 m_Version

Version number for stored data blob.

list< CRef< objects::CSeq_annot > > TAnnots

string SaveRawData(const void *buf, size_t size, const string &key="", unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Save any raw data to NetCache.

AutoPtr< CNetCacheAPI > m_NC

bool x_ValidateAsnSerialFormat(TDataFormat fmt, bool no_throw=false) const

Check if the object format is valid ASN format.

CObjectOStream * x_GetObjectOStream(TDataFormat data_fmt, CNetStorageObject &nso, string &key, TCompressionFormat compression_fmt=eNC_ZlibCompressed, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Get a object ostream to allow save data to NetCache.

string SaveProject(const objects::IGBProject &project, const string &key="", TCompressionFormat compression_fmt=eNC_ZlibCompressed, TDataFormat data_fmt=eSerial_AsnBinary, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Save a GB project to NetCache.

unique_ptr< CNcbiIstream > GetIstream(const string &key, bool raw=false)

Create an input stream using the key.

CObjectOStream * AsObjectOStream(TDataFormat data_fmt, string &key, TCompressionFormat compression_fmt=eNC_ZlibCompressed, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Get a object ostream to allow save data to NetCache.

TDataFormat m_DataFmt

Data serialization format (one of ESerialDataFormat).

string SaveStream(CNcbiIstream &istream, const string &key, TCompressionFormat compression_fmt=eNC_ZlibCompressed, unsigned int time_to_live=0, TNetStorageFlags default_flags=0)

Save data from an incoming stream to NetCache.

unique_ptr< CNcbiOstream > x_GetOutputStream(string &key, unsigned int time_to_live, TNetStorageFlags default_flags, CNetStorageObject &nso)

Create an output stream.

TAnnots GetAnnots(const string &key)

Return a NC blob as a list of seq-annots.

void Delete(const string &key)

Delete an existing Blob from NetCache.

unique_ptr< CObjectIStream > GetObjectIstream(const string &key)

Create a CObjectIStream.

TCompressionFormat m_CmprsFmt

Data compression format.

void SetCommTimeout(float sec)

Set netservice communication time out.

Uint2 m_Magic

Data/application related magic number.

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

Base class for all serializable objects.

Reallocable memory buffer (no memory copy overhead) Mimics vector<>, without the overhead of explicit...

const value_type * data() const

CTimeout – Timeout interval.

Template class for iteration on objects of class C.

Writer-based output stream.

CZipStreamCompressor – zlib based compression stream processor.

CZipStreamDecompressor – zlib based decompression stream processor.

IGBProject - abstract interface for a project used by CGBProjectHandle.

static const char * str(char *buf, int n)

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

@ eTakeOwnership

An object can take ownership of another.

ELevel

Compression level.

void ToVector(vector< char > *)

fill in the data, NULL is not accepted

void ToString(string *)

The CConnMemoryStream::To* methods allow to obtain unread portion of the stream into a single contain...

#define ERR_POST(message)

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

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.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

#define nc_blob_password

Blob password.

#define nc_blob_ttl

Blob life span in seconds.

CNcbiOstream * CreateOStream(string &key, const CNamedParameterList *optional=NULL)

Create a stream object for sending data to a blob.

void Remove(const string &blob_id, const CNamedParameterList *optional=NULL)

Remove BLOB by key.

string PutData(const void *buf, size_t size, const CNamedParameterList *optional=NULL)

Put BLOB to server.

bool HasBlob(const string &blob_id, const CNamedParameterList *optional=NULL)

Check if the BLOB identified by the key "key" exists.

void SetCommunicationTimeout(const STimeout &to)

CNcbiIstream * GetIStream(const string &key, size_t *blob_size=NULL, const CNamedParameterList *optional=NULL)

Create an istream object for reading blob data.

IReader * GetData(const string &key, size_t *blob_size=NULL, const CNamedParameterList *optional=NULL)

Retrieve BLOB from server by key.

EReadResult

Status of GetData() call.

@ eNotFound

BLOB not found or error.

@ eAccessDenied

Blob could not be read completely.

IReader & GetReader()

Get a reference to the IReader interface for reading the data stream of this object.

bool Exists(const string &object_loc)

Check if the object addressed by 'object_loc' exists.

string GetLoc(void) const

Return object locator.

unsigned TNetStorageFlags

Bitwise OR of ENetStorageFlags.

CNetStorageObject Create(TNetStorageFlags flags=0)

Create new NetStorage object.

CNcbiIostream * GetRWStream()

Get an iostream instance for reading the data stream of this NetStorage object as well as storing dat...

void Write(const void *buffer, size_t buf_size)

Write data to the object (starting at the current position)

void SetExpiration(const CTimeout &ttl)

Updates expiration on the object.

void Close(void)

Finalize and close the current object stream.

void SetAttribute(const string &attr_name, const string &attr_value)

Set the new value for the specified attribute.

CNetStorageObject Open(const string &object_loc)

Open an existing NetStorage object for reading.

IEmbeddedStreamWriter & GetWriter()

Get a reference to the IWriter interface for storing data into this object.

ENetStorageRemoveResult Remove(const string &object_loc)

Remove the object addressed by 'object_loc'.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

uint16_t Uint2

2-byte (16-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void NcbiStreamCopyThrow(CNcbiOstream &os, CNcbiIstream &is)

Same as NcbiStreamCopy() but throws an CCoreException when copy fails.

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 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 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.

const string & GetName(void) const

Get name of this type.

const string & GetValue(const string &name, bool *is_found=0) const

Get value for the given name.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

@ eVoid

To create a void (uninitialized) instance of a component.

static const char * kKeyError

static const Uint2 kNC_StringMagic

string magic number This is used only when explicitly calling SaveString().

static const CCompression::ELevel kCompressionLevel

static const streamsize kBufSize

static const int kWindowBits

static const Uint2 kNC_CurrentVersion

version number

static const Uint2 kNC_ProjectMagic

Predefined constants.

static const int kMemLevel

Reader-writer based streams.

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

static CNamedPipeClient * client

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