NCBI C++ Toolkit Cross Reference

  C++/src/gui/objects/GBProjectHandle.cpp


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/* $Id: GBProjectHandle.cpp 38284 2017-04-21 20:31:04Z katargir $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: ....... * * File Description: * ....... * * Remark: * This code was originally generated by application DATATOOL * using the following specifications: * 'gui_project.asn'. */ // standard includes #include <ncbi_pch.hpp> #include <serial/objistr.hpp> #include <serial/serial.hpp> #include <connect/ncbi_conn_stream.hpp> #include <gui/objutils/label.hpp> #include <gui/objutils/registry.hpp> #include <gui/utils/id_generator.hpp> #include <corelib/rwstream.hpp> #include <serial/pack_string.hpp> #include <serial/objostr.hpp> #include <serial/iterator.hpp> #include <objects/general/Dbtag.hpp> #include <objects/general/Object_id.hpp> #include <objects/seqfeat/Imp_feat.hpp> #include <objects/seqfeat/Gb_qual.hpp> #include <util/format_guess.hpp> #include <corelib/ncbifile.hpp> // generated includes #include <gui/objects/GBProjectHandle.hpp> #include <gui/objects/PluginMessage.hpp> #include <objects/gbproj/LoaderDescriptor.hpp> // generated classes BEGIN_NCBI_SCOPE BEGIN_objects_SCOPE // namespace ncbi::objects:: /// This class is intended to skip over plugin messages in /// gbench projects that do not meet the current spec for a plugin message class CReadHook_SkipError : public CReadObjectHook { public: CReadHook_SkipError(const string& msg, bool discard = true) : m_Message(msg) , m_Discard(discard) { } virtual void ReadObject(CObjectIStream& in, const CObjectInfo& info) { CStreamDelayBufferGuard guard(in); in.SkipAnyContentObject(); CRef<CByteSource> bytes = guard.EndDelayBuffer(); try { auto_ptr<CObjectIStream> tmp (CObjectIStream::Create(in.GetDataFormat(), *bytes)); tmp->ReadObject(info); } catch (CException& e) { LOG_POST(Error << "Failed to read " << m_Message << ": " << e.what()); if (m_Discard) { in.SetDiscardCurrObject(); } } } private: string m_Message; bool m_Discard; }; typedef pair<CFormatGuess::EFormat, ESerialDataFormat> TSerialTypePair; static const TSerialTypePair sc_DataTypes[] = { TSerialTypePair(CFormatGuess::eBinaryASN, eSerial_AsnBinary), TSerialTypePair(CFormatGuess::eTextASN, eSerial_AsnText), TSerialTypePair(CFormatGuess::eXml, eSerial_Xml) }; template <class ProjectType> CRef<ProjectType> ReadProject(CNcbiIstream& istr, const char* typeName, ICanceled* canceledCallback) { CGuiRegistry& reg = CGuiRegistry::GetInstance(); /// do we use memory pooling on deserialization? /// we have a compile-time constant as well as a config file override bool use_mempool = #ifdef _DEBUG false; #else true; #endif use_mempool = reg.GetBool("GBENCH.Application.IO.UseMempool", use_mempool); /// should we pack strings? bool pack_strings = reg.GetBool("GBENCH.Application.IO.PackStrings", true); /// we try, in order, ASN.1 binary, ASN.1 text, and XML /// this is a different order from workspaces, and this /// is intentional. For the release mode builds, binary ASN.1 projects /// will be written, so we try these first. Debug mode will write /// ASN.1 text. CFormatGuess fg(istr); for (size_t i = 0; i < sizeof(sc_DataTypes) / sizeof(TSerialTypePair); ++i) { if (!fg.TestFormat(sc_DataTypes[i].first)) continue; string errMsg = "ReadProject<"; errMsg += typeName; errMsg += ">() : failed to read "; errMsg += CFormatGuess::GetFormatName(sc_DataTypes[i].first); try { CRef<ProjectType> project(new ProjectType()); istr.clear(); istr.seekg(0); auto_ptr<CObjectIStream> obj_istr (CObjectIStream::Open(sc_DataTypes[i].second, istr)); if (canceledCallback) obj_istr->SetCanceledCallback(canceledCallback); /// memory profile optimization: /// we should use pooled strings to reduce the memory burden /// (from Eugene Vasilchenko) if (pack_strings) { CObjectTypeInfo info; info = CObjectTypeInfo(CType<CObject_id>()); info.FindVariant("str") .SetLocalReadHook(*obj_istr, new CPackStringChoiceHook); info = CObjectTypeInfo(CType<CImp_feat>()); info.FindMember("key") .SetLocalReadHook(*obj_istr, new CPackStringClassHook(32, 128)); info = CObjectTypeInfo(CType<CDbtag>()); info.FindMember("db") .SetLocalReadHook(*obj_istr, new CPackStringClassHook); info = CType<CGb_qual>(); info.FindMember("qual") .SetLocalReadHook(*obj_istr, new CPackStringClassHook); } if (use_mempool) { obj_istr->UseMemoryPool(); } /// add a read hook to track the reading of a plugin message /// we will permit a plugin message to be ill-formed /// in the case of an ill-formed object, we will ignore it CObjectTypeInfo msg_hook = CType<CPluginMessage>(); CRef<CReadHook_SkipError> msg_hook_monitor (new CReadHook_SkipError("PluginMessage")); msg_hook.SetLocalReadHook(*obj_istr, msg_hook_monitor); /** CObjectTypeInfo item_hook = CType<CProjectItem>(); CRef<CReadHook_SkipError> item_hook_monitor (new CReadHook_SkipError("ProjectItem")); item_hook.SetLocalReadHook(*obj_istr, item_hook_monitor); **/ *obj_istr >> *project; return project; } NCBI_CATCH(errMsg); } return CRef<ProjectType>(); } /////////////////////////////////////////////////////////// // label handler for genome workbench projects class CGBDocumentLabelHandler : public ILabelHandler { public: void GetLabel(const CObject& obj, string* str, CLabel::ELabelType type, CScope* scope) const { const CGBProjectHandle* project = dynamic_cast<const CGBProjectHandle*>(&obj); if (project) { switch (type) { case CLabel::eUserType: case CLabel::eUserSubtype: *str += "CGBDocument - must not be shown"; break; case CLabel::eType: *str += "Project"; break; case CLabel::eDescriptionBrief: case CLabel::eDescription: case CLabel::eContent: if (project->IsLoaded()) { string title; if (project->GetDescr().IsSetTitle()) { title = project->GetDescr().GetTitle(); } else { /// /// poke around in the internals /// const IGBProject& proj = project->GetProject(); const CGBProject* ver1 = dynamic_cast<const CGBProject*>(&proj); const CGBProject_ver2* ver2 = dynamic_cast<const CGBProject_ver2*>(&proj); if (ver1) { CLabel::GetLabel(*ver1, &title, type, scope); } else if (ver2) { CLabel::GetLabel(*ver2, &title, type, scope); } } if ( !title.empty() ) { *str += title; } } else { /// unloaded - just report the file name const string& fname = project->GetFilename(); if ( ! fname.empty() ) { *str += fname; } else { *str += "(empty project)"; } } break; case CLabel::eUserTypeAndContent: default: {{ string type_str; GetLabel(obj, &type_str, CLabel::eType, scope); string content_str; GetLabel(obj, &content_str, CLabel::eContent, scope); *str += type_str; if ( !type_str.empty() && !content_str.empty() ) { *str += ": "; } if ( !content_str.empty() ) { *str += content_str; } }} break; } } } }; ////////////////////////////////////////////////////////////////////////////////////// /// CGBProjectHandle CAtomicCounter CGBProjectHandle::sm_Counter; CGBProjectHandle::TId CGBProjectHandle::sm_NullId = 0; CGBProjectHandle::CGBProjectHandle(void) : m_Dirty(false) , m_Loaded(false) { //m_Id = GetNextId(); if ( !CLabel::HasHandler(*CGBProjectHandle::GetTypeInfo()) ) { CLabel::RegisterLabelHandler(*CGBProjectHandle::GetTypeInfo(), *new CGBDocumentLabelHandler()); } SetFilename(""); } CGBProjectHandle::CGBProjectHandle(CGBProject_ver2& proj_impl) : m_Dirty(false) , m_Loaded(true) { m_Project = &proj_impl; //m_Id = GetNextId(); if ( !CLabel::HasHandler(*CGBProjectHandle::GetTypeInfo()) ) { CLabel::RegisterLabelHandler(*CGBProjectHandle::GetTypeInfo(), *new CGBDocumentLabelHandler()); } SetFilename(""); x_LinkChildFolders(SetData()); } CGBProjectHandle::~CGBProjectHandle(void) { } const IGBProject& CGBProjectHandle::GetProject() const { _ASSERT(m_Project); return m_Project.GetObject(); } IGBProject& CGBProjectHandle::SetProject() { // this function shall not create projects "on first use"; // projects must be created explicitly! _ASSERT(m_Project); return m_Project.GetObject(); } void CGBProjectHandle::SetScope(CScope* scope) { _ASSERT(m_Scope.GetPointer() == NULL); _ASSERT(m_Project); m_Scope.Reset(scope); } CScope* CGBProjectHandle::GetScope() const { return const_cast<CScope*>(m_Scope.GetPointer()); } CGBProjectHandle::TId CGBProjectHandle::GetId() const { return m_Id; } CGBProjectHandle::TId CGBProjectHandle::GetNextId() { TId id = sm_Counter.Add(1); LOG_POST(Info << "CGBProjectHandle::GetNextId() " << id); return id; } bool CGBProjectHandle::IsLoaded() const { return (m_Loaded.Get() != 0); } void CGBProjectHandle::SetLoaded(bool loaded) { m_Loaded.Set(1); } bool CGBProjectHandle::IsDirty() const { if (m_Loaded.Get() == 0) return false; return m_Project && m_Dirty; } void CGBProjectHandle::SetDirty(bool dirty) { // SetFileName can be called on not loaded project // _ASSERT(m_Project); if(m_Project) { m_Dirty = dirty; if (dirty) { CTime time(CTime::eCurrent); m_Project->SetModifiedDate(time); } } } /// retrieve our project's descriptor set const CProjectDescr& CGBProjectHandle::GetDescr() const { return GetProject().GetDescr(); } CProjectDescr& CGBProjectHandle::SetDescr() { return SetProject().SetDescr(); } // Get a description of our contents. // This is suitable for display in a GUI component such as a list view. const string& CGBProjectHandle::GetTitle(void) const { m_Title.erase(); const CObject* obj = dynamic_cast<const CObject*>(m_Project.GetPointer()); if (obj) { CLabel::GetLabel(*obj, &m_Title, CLabel::eDefault, GetScope()); } return m_Title; } const string& CGBProjectHandle::GetShortTitle(void) const { m_ShortTitle.erase(); const CObject* obj = dynamic_cast<const CObject*>(m_Project.GetPointer()); CLabel::GetLabel(*obj, &m_ShortTitle, CLabel::eDefault, GetScope()); return m_ShortTitle; } bool CGBProjectHandle::Load(CNcbiIstream& istr, ICanceled* canceledCallback) { /// try to read version 2 first {{ CRef<CGBProject_ver2> ver2 = ReadProject<CGBProject_ver2>(istr, "CGBProject_ver2", canceledCallback); if (ver2) { m_Project.Reset(ver2.GetPointer()); SetDirty(false); x_LinkChildFolders(SetData()); x_FixIdGenerator(*ver2); return true; } }} /// now try to read version 1 {{ CRef<CGBProject> ver1 = ReadProject<CGBProject>(istr, "CGBProject", canceledCallback); if (ver1) { /// convert to version-2 CRef<CGBProject_ver2> ver2(new CGBProject_ver2); ver2->SetCounter(ver1->GetCounter()); ver2->SetDescr(ver1->SetDescr()); ver2->SetData().SetItems() .push_back(CRef<CProjectItem>(&ver1->SetCore())); if (ver1->IsSetExtra()) { if (ver1->GetExtra().IsSetFolders()) { NON_CONST_ITERATE (CProjectFolder::TFolders, iter, ver1->SetExtra().SetFolders()) { ver2->SetData().SetFolders().push_back(*iter); } } if (ver1->GetExtra().IsSetItems()) { NON_CONST_ITERATE (CProjectFolder::TItems, iter, ver1->SetExtra().SetItems()) { ver2->SetData().SetItems().push_back(*iter); } } } if (ver1->IsSetOrig_message()) { // Orig_message is ingored intentionally after removal of // 'orig-message PluginMessage' from GBProject-ver2. //ver2->SetOrig_message(ver1->SetOrig_message()); } if (ver1->IsSetHistory()) { ver2->SetHistory().swap(ver1->SetHistory()); } if (ver1->IsSetData_plugin()) { ver2->SetData_plugin(ver1->SetData_plugin()); } if (ver1->IsSetPlugin_param()) { ver2->SetPlugin_param(ver1->SetPlugin_param()); } if (ver1->IsSetAnnot()) { ver2->SetAnnot().swap(ver1->SetAnnot()); } /// save the project m_Project.Reset(ver2.GetPointer()); SetDirty(false); x_LinkChildFolders(SetData()); return true; } }} return false; } void CGBProjectHandle::Save(CNcbiOstream& ostr, ESerialDataFormat fmt) const { auto_ptr<CObjectOStream> os(CObjectOStream::Open(fmt, ostr)); const IGBProject& project = GetProject(); switch (project.GetVersion()) { case IGBProject::eVersion1: *os << dynamic_cast<const CGBProject&>(project); break; case IGBProject::eVersion2: *os << dynamic_cast<const CGBProject_ver2&>(project); break; default: _ASSERT(false); NCBI_THROW(CException, eUnknown, "Unknown project version"); break; } /// shut 'er down cleanly /// if we rely on destructors, we never see the exception os->Close(); ostr.flush(); if ( ! ostr) { NCBI_THROW(CException, eUnknown, "stream write failure"); } else { CGBProjectHandle* nc_this = const_cast<CGBProjectHandle*>(this); nc_this->SetDirty(false); } } void CGBProjectHandle::Clear(void) { m_Loaded.Set(0); m_Project.Reset(); m_Scope.Reset(); } bool CGBProjectHandle::IsProjectItemLabelUnique(const string& label) const { const CProjectFolder& data = GetData(); // TODO - iterator for ( CTypeConstIterator<CProjectItem> it(data); it; ++it) { const string& s = it->GetLabel(); if(s == label) return false; } return true; } string CGBProjectHandle::MakeUniqueItemLabel(const string& label) const { CUniqueLabelGenerator generator; const CProjectFolder& data = GetData(); // TODO - iterator for ( CTypeConstIterator<CProjectItem> it(data); it; ++it) { const string& s = it->GetLabel(); generator.AddExistingLabel(s); } return generator.MakeUniqueLabel(label); } // folder labels is not stored in m_LabelsSet and should be unique in the scope // of its parent folder string CGBProjectHandle::MakeUniqueFolderLabel(const string& label, CProjectFolder& parent_folder) const { CUniqueLabelGenerator generator; if(parent_folder.CanGetFolders()) { ITERATE(CProjectFolder::TFolders, it, parent_folder.GetFolders()) { const string& s = (*it)->GetInfo().GetTitle(); generator.AddExistingLabel(s); } } return generator.MakeUniqueLabel(label); } string CGBProjectHandle::MakeUniqueDataLoaderLabel(const string& label) const { CUniqueLabelGenerator generator; if (m_Project->IsSetDataLoaders()) { ITERATE (IGBProject::TDataLoaders, iter, m_Project->GetDataLoaders()) { const string& s = (*iter)->GetLabel(); generator.AddExistingLabel(s); } } return generator.MakeUniqueLabel(label); } /// retrieve this project's version /// this is fixed per subclass IGBProject::EProjectVersion CGBProjectHandle::GetVersion() const { return GetProject().GetVersion(); } void CGBProjectHandle::AddDataLoader(CLoaderDescriptor& loader) { m_Project->SetDataLoaders().push_back(CRef<CLoaderDescriptor>(&loader)); } const CGBProjectHandle::TDataLoaders& CGBProjectHandle::GetDataLoaders() const { return m_Project->GetDataLoaders(); } CGBProjectHandle::TDataLoaders& CGBProjectHandle::GetDataLoaders() { return m_Project->SetDataLoaders(); } CRef<CLoaderDescriptor> CGBProjectHandle::FindDataLoaderByLabel(const string& label) { CRef<CLoaderDescriptor> loader; if (m_Project->IsSetDataLoaders()) { NON_CONST_ITERATE (IGBProject::TDataLoaders, iter, m_Project->SetDataLoaders()) { if ((*iter)->GetLabel() == label) { loader = *iter; break; } } } return loader; } CProjectFolder* CGBProjectHandle::FindProjectFolderById(CProjectFolder::TId id) { CProjectFolder& data_folder = SetData(); if (data_folder.GetId() == id) return &data_folder; return data_folder.FindChildFolderById(id); } CProjectItem* CGBProjectHandle::FindProjectItemById(CProjectItem::TId id) { return SetData().FindProjectItemById(id); } string CGBProjectHandle::GetViewSettings(const string& view_type, const string& view_ins_id) const { string settings; if (m_Project->IsSetViewSettings()) { ITERATE (IGBProject::TViewSettings, iter, m_Project->GetViewSettings()) { if ((*iter)->GetType().IsStr() && (*iter)->GetType().GetStr() == view_type) { CConstRef<CUser_field> field = (*iter)->GetFieldRef(view_ins_id); if (field) { settings = field->GetData().GetStr(); } break; } } } return settings; } void CGBProjectHandle::SaveViewSettings(const string& view_type, const string& view_ins_id, const string& settings) { CRef<CUser_object> obj; if (m_Project->IsSetViewSettings()) { // first check if there is settings for this view type NON_CONST_ITERATE (IGBProject::TViewSettings, iter, m_Project->SetViewSettings()) { if ((*iter)->GetType().IsStr() && (*iter)->GetType().GetStr() == view_type) { obj = *iter; break; } } } if ( !obj ) { obj.Reset(new CUser_object); obj->SetType().SetStr(view_type); m_Project->SetViewSettings().push_back(obj); } CUser_field& field = obj->SetField(view_ins_id); field.SetData().SetStr(settings); } void CGBProjectHandle::AddItem(CProjectItem& item, CProjectFolder& folder) { m_Project->AddItem(item, folder); } /// retrieve our project's data, in the form of a project folder /// this may be a contrived entity, and it is up to a project to determine /// what parts belong where const CProjectFolder& CGBProjectHandle::GetData() const { return GetProject().GetData(); } CProjectFolder& CGBProjectHandle::SetData() { return SetProject().SetData(); } /// retrieve a set of annotations for this project bool CGBProjectHandle::IsSetAnnot() const { return GetProject().IsSetAnnot(); } const IGBProject::TAnnot& CGBProjectHandle::GetAnnot() const { return GetProject().GetAnnot(); } IGBProject::TAnnot& CGBProjectHandle::SetAnnot() { return SetProject().SetAnnot(); } void CGBProjectHandle::SetCreateDate(const CDate& date) { SetProject().SetCreateDate(date); } void CGBProjectHandle::SetModifiedDate(const CDate& date) { SetProject().SetModifiedDate(date); } // updates links to Parent Folder in Project Folders and Items void CGBProjectHandle::x_LinkChildFolders(CProjectFolder& folder) { if(folder.CanGetItems()) { CProjectFolder::TItems& items = folder.SetItems(); NON_CONST_ITERATE(CProjectFolder::TItems, it, items) { CProjectItem& item = **it; if( ! item.CanGetLabel()) { CLabel::SetLabelByData(item); } } } if(folder.CanGetFolders()) { CProjectFolder::TFolders& folders = folder.SetFolders(); NON_CONST_ITERATE(CProjectFolder::TFolders, it, folders) { CProjectFolder& sub_folder = **it; x_LinkChildFolders(sub_folder); } } } void CGBProjectHandle::x_FixIdGenerator(CGBProject_ver2& project) { int counter = 0; CTypeConstIterator<CProjectItem> item_iter(project.GetData()); for (; item_iter; ++item_iter) { const CProjectItem& item = *item_iter; counter = max(counter, item.GetId()); } ++counter; if (!project.IsSetCounter() || project.GetCounter() < counter) { project.SetCounter(counter); } } END_objects_SCOPE // namespace ncbi::objects:: END_NCBI_SCOPE /* Original file checksum: lines: 57, chars: 1754, CRC32: 1289f084 */

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