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NCBI C++ ToolKit: src/misc/biosample_util/biosample_util.cpp File Reference

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string  PrepareUrl (bool use_dev_server, const string &args)   CRef< CSeq_descr >  GetBiosampleData (const string &accession, bool use_dev_server, TBioSamples *cache)   EStatus  GetBioSampleStatusFromNode (const node &item)   TStatus  ProcessBiosampleStatusNode (node &item)   EStatus  GetBiosampleStatus (const string &accession, bool use_dev_server, TStatuses *cache)   void  ProcessBulkBioSample (TStatuses &status, string list, bool use_dev_server)   void  GetBiosampleStatus (TStatuses &status, bool use_dev_server)   string  GetBiosampleStatusName (EStatus status)   vector< string >  GetDBLinkIDs (const CUser_object &user, const string &field_name)   vector< string >  GetDBLinkIDs (const CSeqdesc &seqdesc, const string &field)   vector< string >  GetBiosampleIDs (CBioseq_Handle bh)   vector< string >  GetBioProjectIDs (CBioseq_Handle bh)   void  sPrintField (const string &value, size_t width, CNcbiOstream &ostr)   bool  s_CompareStructuredCommentFields (CRef< CStructuredCommentTableColumnBase > f1, CRef< CStructuredCommentTableColumnBase > f2)   TStructuredCommentTableColumnList  GetAvailableFields (vector< CConstRef< CUser_object > > src)   TBiosampleFieldDiffList  GetFieldDiffs (const string &sequence_id, const string &biosample_id, const CBioSource &src, const CBioSource &sample)   bool  s_ShouldIgnoreStructuredCommentFieldDiff (const string &label, const string &src_val, const string &sample_val)   TBiosampleFieldDiffList  GetFieldDiffs (const string &sequence_id, const string &biosample_id, const CUser_object &src, const CUser_object &sample)   TBiosampleFieldDiffList  GetFieldDiffs (const string &sequence_id, const string &biosample_id, CConstRef< CUser_object > src, CConstRef< CUser_object > sample)   bool  DoDiffsContainConflicts (const TBiosampleFieldDiffList &diffs, CNcbiOstream *log)   bool  s_IsReportableStructuredComment (const CSeqdesc &desc, const string &expected_prefix)   CRef< CSeqTable_column >  FindSeqTableColumnByName (CRef< CSeq_table > values_table, string column_name)   void  AddValueToColumn (CRef< CSeqTable_column > column, string value, size_t row)   void  AddValueToTable (CSeq_table &table, string column_name, string value, size_t row)   string  GetValueFromColumn (const CSeqTable_column &column, size_t row)   string  GetValueFromTable (const CSeq_table &table, string column_name, size_t row)   static bool  s_IsCitSub (const CSeqdesc &desc)   void  AddBioseqToTable (CBioseq_Handle bh, CSeq_table &table, bool with_id, bool include_comments, const string &expected_prefix)   void  HarmonizeAttributeName (string &attribute_name)   bool  AttributeNamesAreEquivalent (string name1, string name2)   bool  ResolveSuppliedBioSampleAccession (const string &biosample_accession, vector< string > &biosample_ids)   string  GetBestBioseqLabel (CBioseq_Handle bsh)   TBiosampleFieldDiffList  GetBioseqDiffs (CBioseq_Handle bh, const string &biosample_accession, size_t &num_processed, vector< string > &unprocessed_ids, bool use_dev_server, bool compare_structured_comments, const string &expected_prefix, TBioSamples *cache)   void  AddContact (node::iterator &organization, CConstRef< CAuth_list > auth_list)   void  s_AddSamplePair (node &sample_attrs, string attribute_name, string val)   void  AddBioSourceToAttributes (node &organism, node &sample_attrs, const CBioSource &src)   void  AddStructuredCommentToAttributes (node &sample_attrs, const CUser_object &usr)   string  OwnerFromAffil (const CAffil &affil)   void  PrintBioseqXML (CBioseq_Handle bh, const string &id_prefix, CNcbiOstream *report_stream, const string &bioproject_accession, const string &default_owner, const string &hup_date, const string &comment, bool first_seq_only, bool report_structured_comments, const string &expected_prefix)   void  GenerateDiffListFromBioSource (const CSeq_descr &bioSample, const CBioSource &bioSource, TBiosampleFieldDiffList &diffs)   void  SaveSerialObject (const string &filename, const CSerialObject &object)   bool  GenerateDiffListFromBioSource (const string &existingBiosampleAcc, const CBioSource &newBioSource, CBioSource &proposedNewBiosource, TBiosampleFieldDiffList &diffs)   bool  UpdateBiosourceFromBiosample (const CBioSource &existingBiosource, CBioSource &newBiosource)   CConstRef< CBiosampleFieldDiff >  sGetDiffByFieldName (const TBiosampleFieldDiffList &diffs, const string &fieldName)   bool  UpdateBiosourceFromBiosample (const TBiosampleFieldDiffList &diffs, const CBioSource &existingBiosource, CBioSource &newBiosource)   void  PrettyPrint (const TBiosampleFieldDiffList &diffList, CNcbiOstream &ostr, size_t keyWidth, size_t valueWidth)   ◆ AddBioseqToTable()

Definition at line 769 of file biosample_util.cpp.

References AddValueToTable(), CSeqdesc_Base::e_Pub, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_User, eUnknown, CPub_equiv_Base::Get(), CAffil_Base::C_Std::GetAffil(), GetBestBioseqLabel(), GetBioProjectIDs(), GetBiosampleIDs(), CAffil_Base::C_Std::GetDiv(), CBioSource::GetNameValPairs(), CPubdesc_Base::GetPub(), CSeqdesc_Base::GetPub(), CSeqdesc_Base::GetSource(), CAffil_Base::GetStd(), CAffil_Base::GetStr(), GetStructuredCommentFields(), CSeqdesc_Base::GetUser(), i, int, CAffil_Base::C_Std::IsSetAffil(), CAffil_Base::C_Std::IsSetDiv(), CAffil_Base::IsStd(), CAffil_Base::IsStr(), ITERATE, kAffilDept, kAffilInst, kBioProject, kSequenceID, label, msg(), NCBI_THROW, row, s_IsCitSub(), s_IsReportableStructuredComment(), table, and val.

Referenced by CBiosampleChkApp::ProcessBioseqHandle().

◆ AddBioSourceToAttributes()

Definition at line 1096 of file biosample_util.cpp.

References COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), CSubSource::GetSubtypeName(), COrgMod::GetSubtypeName(), COrg_ref_Base::GetTaxname(), xml::node::insert(), NStr::IsBlank(), CBioSource_Base::IsSetOrg(), COrg_ref::IsSetOrgMod(), CBioSource_Base::IsSetSubtype(), COrg_ref_Base::IsSetTaxname(), ITERATE, CSubSource::NeedsNoText(), s_AddSamplePair(), CBioSource::ShouldIgnoreConflict(), st(), and val.

Referenced by PrintBioseqXML().

◆ AddContact()

Definition at line 1020 of file biosample_util.cpp.

References first(), xml::node::get_attributes(), CAuth_list_Base::GetAffil(), CAffil_Base::C_Std::GetCity(), CAffil_Base::C_Std::GetCountry(), CAffil_Base::C_Std::GetEmail(), CName_std_Base::GetFirst(), CName_std_Base::GetLast(), CAuth_list_Base::GetNames(), CAuth_list_Base::C_Names::GetStd(), CAffil_Base::C_Std::GetStreet(), CAffil_Base::C_Std::GetSub(), xml::attributes::insert(), xml::node::insert(), NStr::IsBlank(), CAuth_list_Base::IsSetAffil(), CAffil_Base::C_Std::IsSetCity(), CAffil_Base::C_Std::IsSetCountry(), CAffil_Base::C_Std::IsSetEmail(), CName_std_Base::IsSetFirst(), CName_std_Base::IsSetLast(), CAuth_list_Base::IsSetNames(), CAffil_Base::C_Std::IsSetStreet(), CAffil_Base::C_Std::IsSetSub(), CAuth_list_Base::C_Names::IsStd(), last(), and NULL.

Referenced by PrintBioseqXML().

◆ AddStructuredCommentToAttributes()

Definition at line 1146 of file biosample_util.cpp.

References a, AttributeNamesAreEquivalent(), xml::node::begin(), xml::node::end(), NStr::Equal(), NStr::EqualNocase(), xml::node::get_attributes(), xml::attributes::attr::get_name(), xml::attributes::attr::get_value(), GetStructuredCommentFields(), xml::attributes::insert(), xml::node::insert(), ITERATE, kStructuredCommentPrefix, kStructuredCommentSuffix, label, and val.

Referenced by PrintBioseqXML().

◆ AddValueToColumn() ◆ AddValueToTable() ◆ AttributeNamesAreEquivalent() ◆ DoDiffsContainConflicts() ◆ FindSeqTableColumnByName() ◆ GenerateDiffListFromBioSource() [1/2] ◆ GenerateDiffListFromBioSource() [2/2] ◆ GetAvailableFields() ◆ GetBestBioseqLabel()

Definition at line 899 of file biosample_util.cpp.

References CSeq_id::BestRank(), FindBestChoice(), CBioseq_Handle::GetId(), CConstRef< C, Locker >::GetPointer(), CSeq_id_Base::IsGenbank(), ITERATE, label, and NULL.

Referenced by AddBioseqToTable(), GetBioseqDiffs(), PrintBioseqXML(), CBiosampleChkApp::ProcessBioseqForUpdate(), and CBiosampleChkApp::ProcessBioseqHandle().

◆ GetBioProjectIDs() ◆ GetBiosampleData()

Definition at line 93 of file biosample_util.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), NStr::IntToString(), NULL, PrepareUrl(), and CRef< C, Locker >::Reset().

Referenced by BOOST_AUTO_TEST_CASE(), GenerateDiffListFromBioSource(), GetBioseqDiffs(), LoadBioSampleFromAcc(), and CBiosampleChkApp::ProcessBioseqForUpdate().

◆ GetBiosampleIDs() ◆ GetBiosampleStatus() [1/2]

Definition at line 184 of file biosample_util.cpp.

References xml::node::begin(), map_checker< Container >::end(), xml::node::end(), NStr::Equal(), eStatus_Unknown, map_checker< Container >::find(), xml::node::get_name(), xml::document::get_root_node(), GetBioSampleStatusFromNode(), PrepareUrl(), and ProcessBiosampleStatusNode().

Referenced by CBiosampleStatusReport::AddSummary(), and CBiosampleChkApp::Run().

◆ GetBiosampleStatus() [2/2] void GetBiosampleStatus ( TStatuses &  status, bool  use_dev_server  ) ◆ GetBioSampleStatusFromNode()

Definition at line 134 of file biosample_util.cpp.

References xml::attributes::begin(), xml::attributes::end(), NStr::Equal(), NStr::EqualNocase(), eStatus_Hup, eStatus_Live, eStatus_Replaced, eStatus_Suppressed, eStatus_ToBeCurated, eStatus_Unknown, eStatus_Withdrawn, xml::node::get_attributes(), xml::attributes::attr::get_name(), xml::attributes::attr::get_value(), and val.

Referenced by GetBiosampleStatus(), and ProcessBiosampleStatusNode().

◆ GetBiosampleStatusName() ◆ GetBioseqDiffs()

Definition at line 925 of file biosample_util.cpp.

References CSeqdesc_Base::e_Source, CSeqdesc_Base::e_User, NStr::EqualNocase(), eUnknown, CSeq_descr_Base::Get(), GetBestBioseqLabel(), GetBiosampleData(), GetBiosampleIDs(), GetFieldDiffs(), CSeqdesc_Base::GetSource(), CComment_rule::GetStructuredCommentPrefix(), CSeqdesc_Base::GetUser(), ITERATE, msg(), NCBI_THROW, NULL, ResolveSuppliedBioSampleAccession(), and s_IsReportableStructuredComment().

Referenced by CBiosampleChkApp::GetBioseqDiffs(), and CCompareWithBiosample::x_LoadData().

◆ GetDBLinkIDs() [1/2] ◆ GetDBLinkIDs() [2/2]

Definition at line 293 of file biosample_util.cpp.

References NStr::EqualNocase(), CUser_field_Base::GetData(), CUser_object::GetField(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStrs(), CUser_object_Base::GetType(), CUser_field_Base::IsSetData(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStrs(), and ITERATE.

Referenced by GetBioProjectIDs(), and GetDBLinkIDs().

◆ GetFieldDiffs() [1/3] ◆ GetFieldDiffs() [2/3] ◆ GetFieldDiffs() [3/3] ◆ GetValueFromColumn() ◆ GetValueFromTable() ◆ HarmonizeAttributeName() void HarmonizeAttributeName ( string &  attribute_name ) ◆ OwnerFromAffil()

Definition at line 1186 of file biosample_util.cpp.

References NStr::EqualNocase(), CAffil_Base::C_Std::GetAffil(), CAffil_Base::C_Std::GetDiv(), CAffil_Base::GetStd(), CAffil_Base::GetStr(), CAffil_Base::C_Std::IsSetAffil(), CAffil_Base::C_Std::IsSetDiv(), CAffil_Base::IsStd(), CAffil_Base::IsStr(), and NStr::Join().

Referenced by PrintBioseqXML(), and CBiosampleChkApp::ProcessSeqSubmit().

◆ PrepareUrl() ◆ PrettyPrint() ◆ PrintBioseqXML()

Definition at line 1208 of file biosample_util.cpp.

References AddBioSourceToAttributes(), AddContact(), AddStructuredCommentToAttributes(), data, CSeqdesc_Base::e_Pub, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_User, CTime::eCurrent, NStr::EqualNocase(), eUnknown, CPub_equiv_Base::Get(), xml::node::get_attributes(), xml::document::get_root_node(), CAuth_list_Base::GetAffil(), GetBestBioseqLabel(), GetBioProjectIDs(), GetBiosampleIDs(), CPubdesc_Base::GetPub(), CSeqdesc_Base::GetPub(), CSeqdesc_Base::GetSource(), CSeqdesc_Base::GetUser(), xml::attributes::insert(), xml::node::insert(), NStr::IsBlank(), CAuth_list_Base::IsSetAffil(), CPubdesc_Base::IsSetPub(), ITERATE, msg(), NCBI_THROW, NULL, OwnerFromAffil(), NStr::ReplaceInPlace(), s_IsReportableStructuredComment(), xml::document::set_encoding(), and xml::document::set_is_standalone().

Referenced by CBiosampleChkApp::ProcessBioseqHandle().

◆ ProcessBiosampleStatusNode()

Definition at line 163 of file biosample_util.cpp.

References xml::attributes::begin(), xml::node::begin(), xml::attributes::end(), xml::node::end(), NStr::Equal(), xml::node::get_attributes(), xml::attributes::attr::get_name(), xml::node::get_name(), xml::attributes::attr::get_value(), GetBioSampleStatusFromNode(), and NStr::IsBlank().

Referenced by GetBiosampleStatus(), and ProcessBulkBioSample().

◆ ProcessBulkBioSample() ◆ ResolveSuppliedBioSampleAccession() bool ResolveSuppliedBioSampleAccession ( const string &  biosample_accession, vector< string > &  biosample_ids  ) ◆ s_AddSamplePair() ◆ s_CompareStructuredCommentFields() ◆ s_IsCitSub() ◆ s_IsReportableStructuredComment()

Definition at line 650 of file biosample_util.cpp.

References NStr::eNocase, NStr::Equal(), CObject_id_Base::GetStr(), CComment_rule::GetStructuredCommentPrefix(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), NStr::IsBlank(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CSeqdesc_Base::IsUser(), and NStr::StartsWith().

Referenced by AddBioseqToTable(), GetBioseqDiffs(), and PrintBioseqXML().

◆ s_ShouldIgnoreStructuredCommentFieldDiff() ◆ SaveSerialObject() ◆ sGetDiffByFieldName() ◆ sPrintField() ◆ UpdateBiosourceFromBiosample() [1/2]

Definition at line 1485 of file biosample_util.cpp.

References CSerialObject::Assign(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), COrg_ref::GetTaxId(), CBioSource::HasSubtype(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetSubtype(), CBioSource::IsSetTaxname(), CBioSource_Base::SetOrg(), CBioSource_Base::SetSubtype(), and ZERO_TAX_ID.

◆ UpdateBiosourceFromBiosample() [2/2]

Definition at line 1564 of file biosample_util.cpp.

References COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), CSubSource::GetSubtypeName(), COrgMod::GetSubtypeName(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetSubtype(), CBioSource_Base::SetOrg(), CBioSource_Base::SetSubtype(), sGetDiffByFieldName(), and ZERO_TAX_ID.

◆ kAffilDept const char* kAffilDept = "Department" static ◆ kAffilInst const char* kAffilInst = "Institution" static ◆ kBioProject const char* kBioProject = "BioProject" static ◆ kSequenceID const char* kSequenceID = "Sequence ID" static ◆ kStructuredCommentPrefix const char* kStructuredCommentPrefix = "StructuredCommentPrefix" static ◆ kStructuredCommentSuffix const char* kStructuredCommentSuffix = "StructuredCommentSuffix" static

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