Search Toolkit Book for CSplitCacheApp
#include "split_cache.hpp"
(Private to src/app/split_cache.)
Definition at line 194 of file split_cache.hpp.
◆ TContentMap ◆ TProcessedBlobs ◆ TProcessedIds ◆ CSplitCacheApp() ◆ ~CSplitCacheApp() ◆ GetBioseqHandle() ◆ GetBlob_id() ◆ GetCache() ICache& CSplitCacheApp::GetCache ( void ) inline ◆ GetFileName() ◆ GetIdCache() ICache& CSplitCacheApp::GetIdCache ( void ) inline ◆ GetParams() ◆ Info() ◆ Init() void CSplitCacheApp::Init ( void ) virtualInitialize the application.
The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.
Reimplemented from CNcbiApplicationAPI.
Definition at line 194 of file split_cache.cpp.
References CArgDescriptions::eDouble, CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eIntId, CArgDescriptions::eString, CArgDescriptions::fBinary, CNcbiApplicationAPI::GetArguments(), NStr::IntToString(), SSplitterParams::kDefaultChunkSize, SSplitterParams::kDefaultMinChunkCount, SSplitterParams::kDefaultSplitNonFeatureSeqTables, and CNcbiApplicationAPI::SetupArgDescriptions().
◆ PrintVersion() void CSplitCacheApp::PrintVersion ( int version ) ◆ Process() void CSplitCacheApp::Process ( void )Definition at line 530 of file split_cache.cpp.
References SSplitterParams::eCompression_nlm_zip, ERR_FATAL, CNcbiApplicationAPI::GetArgs(), in(), ncbi::grid::netcache::search::fields::key, SSplitterParams::m_Compression, SSplitterParams::m_DisableSplitAnnotations, SSplitterParams::m_DisableSplitAssembly, SSplitterParams::m_DisableSplitDescriptions, SSplitterParams::m_DisableSplitSequence, m_DumpAsnBinary, m_DumpAsnText, SSplitterParams::m_JoinSmallChunks, SSplitterParams::m_MinChunkCount, m_Recurse, m_Resplit, SSplitterParams::m_SplitNonFeatureSeqTables, m_SplitterParams, SSplitterParams::m_Verbose, MSerial_AsnText, NcbiGetline(), NPOS, ProcessBlob(), ProcessEntry(), ProcessGi(), ProcessSeqId(), SSplitterParams::SetChunkSize(), CBlob_id::SetSat(), CBlob_id::SetSatKey(), CBlob_id::SetSubSat(), NStr::Split(), and NStr::StringToInt().
Referenced by Run().
◆ ProcessBlob() [1/3]Definition at line 783 of file split_cache.cpp.
References CSeq_id_Handle::AsString(), ERR_POST, GetBioseqHandle(), CDataLoader::GetBlobId(), CSeq_entry_Handle::GetBlobId(), CGBDataLoader::GetRealBlobId(), CBioseq_Handle::GetTopLevelEntry(), set< Key, Compare >::insert(), LINE, m_Loader, m_ProcessedBlobs, and WAIT_LINE.
Referenced by Process(), ProcessBlob(), and ProcessSeqId().
◆ ProcessBlob() [2/3] ◆ ProcessBlob() [3/3]Definition at line 854 of file split_cache.cpp.
References _ASSERT, CollectDescriptors(), data, Dump(), DumpData(), CWriter::eBlobWriter, CID2_Reply_Data_Base::eData_type_id2s_chunk, CID2_Reply_Data_Base::eData_type_id2s_split_info, CID2_Reply_Data_Base::eData_type_seq_entry, eSerial_AsnBinary, eSerial_AsnText, CProcessor::eType_ID2, CProcessor::eType_ID2AndSkel, AutoPtr< X, Del >::get(), CBlobSplitter::GetBlob(), SCacheInfo::GetBlobKey(), CSeq_entry_Handle::GetBlobVersion(), CID2S_Split_Info_Base::GetChunks(), CSplitBlob::GetChunks(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSplitDataMaker::GetData(), CSplitBlob::GetMainBlob(), GetParams(), CReadDispatcher::GetProcessor(), ICache::GetSize(), CSplitBlob::GetSplitInfo(), CReadDispatcher::GetWriter(), CSplitContentIndex::IndexChunkContent(), NStr::IntToString(), ITERATE, ncbi::grid::netcache::search::fields::key, kMain_ChunkId, kSplitVersion, LINE, m_Cache, m_ContentMap, m_DumpAsnBinary, m_DumpAsnText, m_Loader, m_RecursionLevel, m_Resplit, m_SplitterParams, PrintVersion(), proc, ICache::Remove(), CRef< C, Locker >::Reset(), result, CProcessor_ID2AndSkel::SaveDataAndSkel(), CSplitContentIndex::SetSeqDescCount(), CSplitContentIndex::SetSetDescCount(), CBlobSplitter::Split(), dtl::version, WAIT_LINE, x_GetDispatcher(), x_GetSubkey0(), x_GetSubkey1(), and x_InitBlob().
◆ ProcessEntry() [1/2] ◆ ProcessEntry() [2/2]Definition at line 1029 of file split_cache.cpp.
References _ASSERT, CScope::AddTopLevelSeqEntry(), CollectDescriptors(), data, Dump(), DumpData(), CWriter::eBlobWriter, CID2_Reply_Data_Base::eData_type_id2s_chunk, CID2_Reply_Data_Base::eData_type_id2s_split_info, CID2_Reply_Data_Base::eData_type_seq_entry, eSerial_AsnBinary, eSerial_AsnText, CProcessor::eType_ID2, CProcessor::eType_ID2AndSkel, AutoPtr< X, Del >::get(), CBlobSplitter::GetBlob(), CID2S_Split_Info_Base::GetChunks(), CSplitBlob::GetChunks(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSplitDataMaker::GetData(), CSplitBlob::GetMainBlob(), GetParams(), CReadDispatcher::GetProcessor(), ICache::GetSize(), CSplitBlob::GetSplitInfo(), CReadDispatcher::GetWriter(), CSplitContentIndex::IndexChunkContent(), NStr::IntToString(), ITERATE, ncbi::grid::netcache::search::fields::key, kMain_ChunkId, kSplitVersion, LINE, m_Cache, m_ContentMap, m_DumpAsnBinary, m_DumpAsnText, m_Loader, m_RecursionLevel, m_Resplit, m_Scope, m_SplitterParams, PrintVersion(), proc, ICache::Remove(), CRef< C, Locker >::Reset(), result, CProcessor_ID2AndSkel::SaveDataAndSkel(), CSplitContentIndex::SetSeqDescCount(), CSplitContentIndex::SetSetDescCount(), CBlobSplitter::Split(), dtl::version, WAIT_LINE, x_GetDispatcher(), x_GetSubkey0(), x_GetSubkey1(), and x_InitBlob().
◆ ProcessGi() void CSplitCacheApp::ProcessGi ( TIntId gi ) ◆ ProcessSeqId() void CSplitCacheApp::ProcessSeqId ( const CSeq_id & seq_id )Definition at line 654 of file split_cache.cpp.
References CSeq_id_Handle::AsString(), CSeqMap::fFindRef, GetBioseqHandle(), CSeq_id_Handle::GetHandle(), CBioseq_Handle::GetSeqMap(), set< Key, Compare >::insert(), ITERATE, LINE, m_ProcessedIds, m_Recurse, m_RecursionLevel, m_Scope, ProcessBlob(), and CScope::ResetHistory().
Referenced by Process(), and ProcessGi().
◆ Run() int CSplitCacheApp::Run ( void ) virtual ◆ SetupCache() void CSplitCacheApp::SetupCache ( void )Definition at line 318 of file split_cache.cpp.
References CScope::AddDefaults(), CDir::Create(), CWriter::eBlobWriter, CTime::eCurrent, IRegistry::eErrPost, ICache::eKeepAll, eNoOwnership, ERR_FATAL, CBDB_Cache::eWriteNoSync, CDir::Exists(), ICache::fCheckExpirationAlways, ICache::fExpireLeastFrequentlyUsed, flags, ICache::fPurgeOnStartup, ICache::fTimeStampOnCreate, ICache::fTimeStampOnRead, ICache::fTrackSubKey, CNcbiApplicationAPI::GetArgs(), CCacheHolder::GetBlobCache(), CNcbiApplicationAPI::GetConfig(), CCacheHolder::GetIdCache(), CObjectManager::GetInstance(), IRegistry::GetInt(), CNcbiApplicationAPI::GetRWConfig(), IRegistry::GetString(), CTime::GetTimeT(), CReadDispatcher::GetWriter(), kDefaultCacheBlobAge, kDefaultCacheIdAge, LINE, m_Cache, m_IdCache, m_Loader, m_ObjMgr, m_Scope, CBDB_Cache::Open(), CBDB_Cache::Purge(), CGBDataLoader::RegisterInObjectManager(), AutoPtr< X, Del >::reset(), CRef< C, Locker >::Reset(), result, IRWRegistry::Set(), CBDB_Cache::SetReadUpdateLimit(), CBDB_Cache::SetTimeStampPolicy(), CBDB_Cache::SetVersionRetention(), CBDB_Cache::SetWriteSync(), WAIT_LINE, and x_GetDispatcher().
Referenced by Run().
◆ TestSplit() void CSplitCacheApp::TestSplit ( void )Definition at line 1232 of file split_cache.cpp.
References CScope::AddDefaults(), CDataLoader::GetName(), ITERATE, m_Cache, m_ContentMap, m_IdCache, m_Loader, m_ObjMgr, m_Scope, CGBDataLoader::RegisterInObjectManager(), AutoPtr< X, Del >::reset(), CRef< C, Locker >::Reset(), CObjectManager::RevokeDataLoader(), and TestSplitBlob().
Referenced by Run().
◆ TestSplitBioseq() ◆ TestSplitBlob()Definition at line 1252 of file split_cache.cpp.
References _ASSERT, CollectDescriptors(), CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSplitContentIndex::fDesc, CSplitContentIndex::fDescHigh, CSplitContentIndex::fDescLow, CSplitContentIndex::fDescOther, CSplitContentIndex::fSetDesc, CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSplitContentIndex::GetContentIndex(), CSplitContentIndex::GetDescCount(), CSeq_inst_Base::GetHist(), CBioseq_Base::GetInst(), CSeq_entry_Handle::GetSeq_entryCore(), CSplitContentIndex::GetSeqDescCount(), CSplitContentIndex::GetSetDescCount(), CSplitContentIndex::GetSplitContent(), CBioseq_Handle::GetTopLevelEntry(), CSplitContentIndex::HaveSplitAssembly(), CSplitContentIndex::HaveSplitBioseq(), CSeq_hist_Base::IsSetAssembly(), ITERATE, m_Scope, NcbiCout, NcbiEndl, and TestSplitBioseq().
Referenced by TestSplit().
◆ m_Cache ◆ m_ContentMap ◆ m_DumpAsnBinary bool CSplitCacheApp::m_DumpAsnBinary private ◆ m_DumpAsnText bool CSplitCacheApp::m_DumpAsnText private ◆ m_IdCache ◆ m_Loader ◆ m_ObjMgr ◆ m_ProcessedBlobs ◆ m_ProcessedIds ◆ m_Recurse bool CSplitCacheApp::m_Recurse private ◆ m_RecursionLevel size_t CSplitCacheApp::m_RecursionLevel private ◆ m_Resplit bool CSplitCacheApp::m_Resplit private ◆ m_Scope ◆ m_SplitterParamsThe documentation for this class was generated from the following files:
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