biosource_tests.cpp File Reference

#include <ncbi_pch.hpp>
#include <sstream>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/general/Dbtag.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objects/macro/Source_qual.hpp>
#include <objects/taxon3/taxon3.hpp>
#include <util/xregexp/regexp.hpp>
#include "discrepancy_core.hpp"

Include dependency graph for biosource_tests.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
class	CCompareValues< T, R >

Macros
#define	SARS_TAX_ID   2697049

Typedefs
typedef list< string >	TInconsistecyDescriptionList

Functions
	USING_SCOPE (objects)
bool	HasCultureCollectionForATCCStrain (const COrgName::TMod &mods, const string &strain)
bool	HasStrainForATCCCultureCollection (const COrgName::TMod &mods, const string &culture_collection)
static bool	SetCultureCollectionFromStrain (CBioSource &src)
static bool	MatchExceptSpaceColon (const string &a, const string &b)
bool	HasAmplifiedWithSpeciesSpecificPrimerNote (const CBioSource &src)
static bool	IsMissingRequiredClone (const CBioSource &biosource)
static bool	IsSameSubtype (const CBioSource::TSubtype &first, const CBioSource::TSubtype &second)
static bool	IsSameDb (const COrg_ref::TDb &first, const COrg_ref::TDb &second)
static void	GetOrgnameDifferences (const COrgName &first, const COrgName &second, TInconsistecyDescriptionList &diffs)
static void	GetOrgrefDifferences (const COrg_ref &first_org, const COrg_ref &second_org, TInconsistecyDescriptionList &diffs)
static void	GetBiosourceDifferences (const CBioSource &first_biosrc, const CBioSource &second_biosrc, TInconsistecyDescriptionList &diffs)
static const CDbtag *	GetTaxonTag (const COrg_ref &org)
static bool	OrgDiffers (const COrg_ref &first, const COrg_ref &second)
static CRef< CTaxon3_reply >	GetOrgRefs (vector< CRef< COrg_ref >> &orgs)
static bool	RemoveCountryColon (CBioSource &src)
static bool	ChangeCountryColonToComma (CBioSource &src)
static bool	FixHumanHost (CBioSource &src)
static string	GetSrcQual (const CBioSource &bs, int qual)
static bool	SetEnvSampleFixAmplifiedPrimers (CBioSource &src)
static bool	EqualPrimerSets (const CPCRPrimerSet::Tdata &a, const CPCRPrimerSet::Tdata &b)
static bool	FindDuplicatePrimers (const CPCRReaction &a, const CPCRReaction &b)
static string	GetOrgModName (const COrgMod &qual)
static string	GetSubtypeName (const CSubSource &qual)

Variables
static constexpr CDiscrepancyCaseProps	s_testcase_props_MAP_CHROMOSOME_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: MAP_CHROMOSOME_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: MAP_CHROMOSOME_CONFLICT , "MAP_CHROMOSOME_CONFLICT" , "Eukaryotic sequences with a map source qualifier should also have a chromosome source qualifier" , eDisc | eOncaller | eSmart | eFatal , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_INFLUENZA_DATE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_DATE_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_DATE_MISMATCH , "INFLUENZA_DATE_MISMATCH" , "Influenza Strain/Collection Date Mismatch" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_INFLUENZA_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_QUALS , "INFLUENZA_QUALS" , "Influenza must have strain, host, isolation_source, country, collection_date" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_INFLUENZA_SEROTYPE = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE , "INFLUENZA_SEROTYPE" , "Influenza A virus must have serotype" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_INFLUENZA_SEROTYPE_FORMAT = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE_FORMAT >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE_FORMAT , "INFLUENZA_SEROTYPE_FORMAT" , "Influenza A virus serotype must match /^H[1-9]\\d*$|^N[1-9]\\d*$|^H[1-9]\\d*N[1-9]\\d*$|^mixed$/" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_UNCULTURED_NOTES = { CDiscrepancyVisitorImpl<eTestNames:: UNCULTURED_NOTES >::Create, eTestTypes:: BIOSRC , eTestNames:: UNCULTURED_NOTES , "UNCULTURED_NOTES" , "Uncultured Notes" , eOncaller | eFatal , nullptr }
const string	kMissingViralQualsTop = "[n] virus organism[s] [is] missing required qualifiers"
static constexpr CDiscrepancyCaseProps	s_testcase_props_MISSING_VIRAL_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_VIRAL_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_VIRAL_QUALS , "MISSING_VIRAL_QUALS" , "Viruses should specify collection-date, country, and specific-host" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_ATCC_CULTURE_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: ATCC_CULTURE_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: ATCC_CULTURE_CONFLICT , "ATCC_CULTURE_CONFLICT" , "ATCC strain should also appear in culture collection" , eDisc | eOncaller , nullptr }
const string	kAmplifiedWithSpeciesSpecificPrimers = "amplified with species-specific primers"
static constexpr CDiscrepancyCaseProps	s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE , "BACTERIA_SHOULD_NOT_HAVE_ISOLATE" , "Bacterial sources should not have isolate" , eDisc | eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_MAG_SHOULD_NOT_HAVE_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN , "MAG_SHOULD_NOT_HAVE_STRAIN" , "Organism assembled from metagenome reads should not have strain" , eDisc | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_MAG_MISSING_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: MAG_MISSING_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_MISSING_ISOLATE , "MAG_MISSING_ISOLATE" , "Organism assembled from metagenome reads should have isolate" , eDisc | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_MULTISRC = { CDiscrepancyVisitorImpl<eTestNames:: MULTISRC >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTISRC , "MULTISRC" , "Comma or semicolon appears in strain or isolate" , eDisc | eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_MULTIPLE_CULTURE_COLLECTION = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CULTURE_COLLECTION >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTIPLE_CULTURE_COLLECTION , "MULTIPLE_CULTURE_COLLECTION" , "Multiple culture-collection quals" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_REQUIRED_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_STRAIN , "REQUIRED_STRAIN" , "Bacteria should have strain" , eDisc | eSubmitter | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_STRAIN_CULTURE_COLLECTION_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH , "STRAIN_CULTURE_COLLECTION_MISMATCH" , "Strain and culture-collection values conflict" , eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_SP_NOT_UNCULTURED = { CDiscrepancyVisitorImpl<eTestNames:: SP_NOT_UNCULTURED >::Create, eTestTypes:: BIOSRC , eTestNames:: SP_NOT_UNCULTURED , "SP_NOT_UNCULTURED" , "Organism ending in sp. needs tax consult" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_FIND_STRAND_TRNAS = { CDiscrepancyVisitorImpl<eTestNames:: FIND_STRAND_TRNAS >::Create, eTestTypes:: SEQUENCE , eTestNames:: FIND_STRAND_TRNAS , "FIND_STRAND_TRNAS" , "Find tRNAs on the same strand" , eDisc , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_REQUIRED_CLONE = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_CLONE >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_CLONE , "REQUIRED_CLONE" , "Uncultured or environmental sources should have clone" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_STRAIN_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_TAXNAME_MISMATCH , "STRAIN_TAXNAME_MISMATCH" , "BioSources with the same strain should have the same taxname" , eDisc | eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_SPECVOUCHER_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH , "SPECVOUCHER_TAXNAME_MISMATCH" , "BioSources with the same specimen voucher should have the same taxname" , eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_CULTURE_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: CULTURE_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: CULTURE_TAXNAME_MISMATCH , "CULTURE_TAXNAME_MISMATCH" , "Test BioSources with the same culture collection but different taxname" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_BIOMATERIAL_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH , "BIOMATERIAL_TAXNAME_MISMATCH" , "Test BioSources with the same biomaterial but different taxname" , eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_ORGANELLE_ITS = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: ORGANELLE_ITS , "ORGANELLE_ITS" , "Test Bioseqs for suspect rRNA / ITS on organelle" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_INCONSISTENT_BIOSOURCE = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_BIOSOURCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_BIOSOURCE , "INCONSISTENT_BIOSOURCE" , "Inconsistent BioSource" , eDisc | eSubmitter | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_TAX_LOOKUP_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISMATCH , "TAX_LOOKUP_MISMATCH" , "Find Tax Lookup Mismatches" , eDisc , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_TAX_LOOKUP_MISSING = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISSING >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISSING , "TAX_LOOKUP_MISSING" , "Find Missing Tax Lookup" , eDisc , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_UNNECESSARY_ENVIRONMENTAL = { CDiscrepancyVisitorImpl<eTestNames:: UNNECESSARY_ENVIRONMENTAL >::Create, eTestTypes:: BIOSRC , eTestNames:: UNNECESSARY_ENVIRONMENTAL , "UNNECESSARY_ENVIRONMENTAL" , "Unnecessary environmental qualifier present" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_END_COLON_IN_COUNTRY = { CDiscrepancyVisitorImpl<eTestNames:: END_COLON_IN_COUNTRY >::Create, eTestTypes:: BIOSRC , eTestNames:: END_COLON_IN_COUNTRY , "END_COLON_IN_COUNTRY" , "Country name end with colon" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_COUNTRY_COLON = { CDiscrepancyVisitorImpl<eTestNames:: COUNTRY_COLON >::Create, eTestTypes:: BIOSRC , eTestNames:: COUNTRY_COLON , "COUNTRY_COLON" , "Country description should only have 1 colon" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_HUMAN_HOST = { CDiscrepancyVisitorImpl<eTestNames:: HUMAN_HOST >::Create, eTestTypes:: BIOSRC , eTestNames:: HUMAN_HOST , "HUMAN_HOST" , "\'Human\' in host should be \'Homo sapiens\'" , eDisc | eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_CHECK_AUTHORITY = { CDiscrepancyVisitorImpl<eTestNames:: CHECK_AUTHORITY >::Create, eTestTypes:: BIOSRC , eTestNames:: CHECK_AUTHORITY , "CHECK_AUTHORITY" , "Authority and Taxname should match first two words" , eDisc | eOncaller , nullptr }
static const pair< int, string >	srcqual_keywords []
static const size_t	srcqual_keywords_sz = ArraySize(srcqual_keywords)
static constexpr CDiscrepancyCaseProps	s_testcase_props_TRINOMIAL_SHOULD_HAVE_QUALIFIER = { CDiscrepancyVisitorImpl<eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER >::Create, eTestTypes:: BIOSRC , eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER , "TRINOMIAL_SHOULD_HAVE_QUALIFIER" , "Trinomial sources should have corresponding qualifier" , eDisc | eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE = { CDiscrepancyVisitorImpl<eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE >::Create, eTestTypes:: BIOSRC , eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE , "AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE" , "Species-specific primers, no environmental sample" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_MISSING_PRIMER = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PRIMER >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_PRIMER , "MISSING_PRIMER" , "Missing values in primer set" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_DUPLICATE_PRIMER_SET = { CDiscrepancyVisitorImpl<eTestNames:: DUPLICATE_PRIMER_SET >::Create, eTestTypes:: BIOSRC , eTestNames:: DUPLICATE_PRIMER_SET , "DUPLICATE_PRIMER_SET" , "Duplicate PCR primer pair" , eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_METAGENOMIC = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOMIC >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOMIC , "METAGENOMIC" , "Source has metagenomic qualifier" , eDisc | eOncaller | eSmart , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_METAGENOME_SOURCE = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOME_SOURCE >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOME_SOURCE , "METAGENOME_SOURCE" , "Source has metagenome_source qualifier" , eDisc | eOncaller | eSmart , nullptr }
static const char *	kDupSrc = "[n] source[s] [has] two or more qualifiers with the same value"
static constexpr std::initializer_list< const char * >	g_aliases_DUP_SRC_QUAL = { "DUP_SRC_QUAL_DATA" }
static constexpr CDiscrepancyCaseProps	s_testcase_props_DUP_SRC_QUAL = { CDiscrepancyVisitorImpl<eTestNames:: DUP_SRC_QUAL >::Create, eTestTypes:: BIOSRC , eTestNames:: DUP_SRC_QUAL , "DUP_SRC_QUAL" , "Each qualifier on a source should have different value" , eDisc | eOncaller | eSmart , &g_aliases_DUP_SRC_QUAL }
static constexpr CDiscrepancyCaseProps	s_testcase_props_UNUSUAL_ITS = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_ITS , "UNUSUAL_ITS" , "Test Bioseqs for unusual rRNA / ITS" , eDisc | eOncaller , nullptr }
static constexpr CDiscrepancyCaseProps	s_testcase_props_SARS_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: SARS_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: SARS_QUALS , "SARS_QUALS" , "SARS-CoV-2 isolate must have correct format" , eOncaller , nullptr }

Macro Definition Documentation

SARS_TAX_ID

#define SARS_TAX_ID   2697049

Definition at line 2119 of file biosource_tests.cpp.

Typedef Documentation

TInconsistecyDescriptionList

typedef list<string> TInconsistecyDescriptionList

Definition at line 1048 of file biosource_tests.cpp.

Function Documentation

ChangeCountryColonToComma()

static bool ChangeCountryColonToComma ( CBioSource &  src )

static

Definition at line 1578 of file biosource_tests.cpp.

References count, CSubSource_Base::eSubtype_country, CBioSource_Base::GetSubtype(), i, CBioSource_Base::IsSetSubtype(), and CSubSource_Base::SetName().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

EqualPrimerSets()

static bool EqualPrimerSets ( const CPCRPrimerSet::Tdata &  a, const CPCRPrimerSet::Tdata &  b  )

static

Definition at line 1887 of file biosource_tests.cpp.

References a, and b.

Referenced by FindDuplicatePrimers().

FindDuplicatePrimers()

static bool FindDuplicatePrimers ( const CPCRReaction &  a, const CPCRReaction &  b  )

inlinestatic

Definition at line 1911 of file biosource_tests.cpp.

References a, b, and EqualPrimerSets().

FixHumanHost()

static bool FixHumanHost ( CBioSource &  src )

static

Definition at line 1640 of file biosource_tests.cpp.

References COrgMod_Base::eSubtype_nat_host, NStr::FindNoCase(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::IsSetOrg(), NPOS, om, and NStr::ReplaceInPlace().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

GetBiosourceDifferences()

static void GetBiosourceDifferences ( const CBioSource &  first_biosrc, const CBioSource &  second_biosrc, TInconsistecyDescriptionList &  diffs  )

static

Definition at line 1231 of file biosource_tests.cpp.

References CBioSource_Base::eGenome_unknown, CBioSource_Base::eOrigin_unknown, CBioSource_Base::GetGenome(), CBioSource_Base::GetOrg(), GetOrgrefDifferences(), CBioSource_Base::GetOrigin(), CBioSource_Base::GetSubtype(), IsSameSubtype(), CBioSource_Base::IsSetGenome(), CBioSource_Base::IsSetIs_focus(), CBioSource_Base::IsSetOrg(), CBioSource_Base::IsSetOrigin(), and CBioSource_Base::IsSetSubtype().

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

GetOrgModName()

static string GetOrgModName ( const COrgMod &  qual )

static

Definition at line 1976 of file biosource_tests.cpp.

References COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_other, COrgMod::eVocabulary_raw, COrgMod_Base::GetSubtype(), and COrgMod::GetSubtypeName().

GetOrgnameDifferences()

static void GetOrgnameDifferences ( const COrgName &  first, const COrgName &  second, TInconsistecyDescriptionList &  diffs  )

static

Definition at line 1118 of file biosource_tests.cpp.

References ENUM_METHOD_NAME, first(), COrgMod_Base::GetAttrib(), COrgName_Base::GetAttrib(), COrgName_Base::GetDiv(), COrgName_Base::GetGcode(), COrgName_Base::GetLineage(), COrgName_Base::GetMgcode(), COrgName_Base::GetMod(), COrgName_Base::GetName(), COrgMod_Base::GetSubname(), COrgMod_Base::GetSubtype(), COrgMod_Base::IsSetAttrib(), COrgName_Base::IsSetAttrib(), COrgName_Base::IsSetDiv(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMgcode(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetName(), COrgMod_Base::IsSetSubname(), COrgMod_Base::IsSetSubtype(), and COrgName_Base::C_Name::Which().

Referenced by GetOrgrefDifferences().

GetOrgrefDifferences()

static void GetOrgrefDifferences ( const COrg_ref &  first_org, const COrg_ref &  second_org, TInconsistecyDescriptionList &  diffs  )

static

Definition at line 1198 of file biosource_tests.cpp.

References COrg_ref_Base::GetCommon(), COrg_ref_Base::GetDb(), COrg_ref_Base::GetOrgname(), GetOrgnameDifferences(), COrg_ref_Base::GetSyn(), COrg_ref_Base::GetTaxname(), IsSameDb(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), COrg_ref_Base::IsSetOrgname(), COrg_ref_Base::IsSetSyn(), and COrg_ref_Base::IsSetTaxname().

Referenced by GetBiosourceDifferences().

GetOrgRefs()

static CRef<CTaxon3_reply> GetOrgRefs ( vector< CRef< COrg_ref >> &  orgs )

static

Definition at line 1363 of file biosource_tests.cpp.

References CTaxon3::SendOrgRefList(), and CTaxon3::yes.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

GetSrcQual()

static string GetSrcQual ( const CBioSource &  bs, int  qual  )

static

Definition at line 1732 of file biosource_tests.cpp.

References COrgName_Base::CanGetMod(), COrg_ref_Base::CanGetOrgname(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), and kEmptyStr.

GetSubtypeName()

static string GetSubtypeName ( const CSubSource &  qual )

static

Definition at line 1983 of file biosource_tests.cpp.

References CSubSource_Base::eSubtype_other, CSubSource::eVocabulary_raw, CSubSource_Base::GetSubtype(), and CSubSource::GetSubtypeName().

Referenced by CExportTableDlg::AddBioSource(), CSrcTableSubSourceColumn::GetLabel(), CSrcTableOrgModColumn::GetLabel(), CSrcStructuredVoucherPartColumn::GetLabel(), SrcEditDialog::GetLabelForTitle(), SrcEditDialog::GetQualChoices(), CSrcModPanel::s_GetModifierList(), and COrgAdvancedPanel::TransferDataToWindow().

GetTaxonTag()

static const CDbtag* GetTaxonTag ( const COrg_ref &  org )

static

Definition at line 1335 of file biosource_tests.cpp.

References NStr::EqualNocase(), COrg_ref_Base::GetDb(), and COrg_ref_Base::IsSetDb().

Referenced by OrgDiffers().

HasAmplifiedWithSpeciesSpecificPrimerNote()

bool HasAmplifiedWithSpeciesSpecificPrimerNote

(

const CBioSource &

src

)

Definition at line 767 of file biosource_tests.cpp.

References NStr::Equal(), CSubSource_Base::eSubtype_other, COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetSubtype(), and kAmplifiedWithSpeciesSpecificPrimers.

Referenced by IsMissingRequiredClone().

HasCultureCollectionForATCCStrain()

bool HasCultureCollectionForATCCStrain	(	const COrgName::TMod &	mods,
		const string &	strain
	)

Definition at line 327 of file biosource_tests.cpp.

References NStr::Equal(), COrgMod_Base::eSubtype_culture_collection, NStr::Find(), NStr::IsBlank(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().

Referenced by SetCultureCollectionFromStrain().

HasStrainForATCCCultureCollection()

bool HasStrainForATCCCultureCollection	(	const COrgName::TMod &	mods,
		const string &	culture_collection
	)

Definition at line 351 of file biosource_tests.cpp.

References NStr::Equal(), COrgMod_Base::eSubtype_strain, NStr::Find(), NStr::IsBlank(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().

IsMissingRequiredClone()

static bool IsMissingRequiredClone ( const CBioSource &  biosource )

static

Definition at line 788 of file biosource_tests.cpp.

References NStr::eNocase, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_environmental_sample, COrgMod_Base::eSubtype_isolate, NStr::FindNoCase(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), COrg_ref_Base::GetTaxname(), HasAmplifiedWithSpeciesSpecificPrimerNote(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetSubtype(), COrg_ref_Base::IsSetTaxname(), NPOS, and NStr::StartsWith().

IsSameDb()

static bool IsSameDb ( const COrg_ref::TDb &  first, const COrg_ref::TDb &  second  )

static

Definition at line 1100 of file biosource_tests.cpp.

References first().

Referenced by GetOrgrefDifferences().

IsSameSubtype()

static bool IsSameSubtype ( const CBioSource::TSubtype &  first, const CBioSource::TSubtype &  second  )

static

Definition at line 1074 of file biosource_tests.cpp.

References first(), CSubSource_Base::GetAttrib(), CSubSource_Base::GetName(), CSubSource_Base::GetSubtype(), CSubSource_Base::IsSetAttrib(), CSubSource_Base::IsSetName(), and CSubSource_Base::IsSetSubtype().

Referenced by GetBiosourceDifferences().

MatchExceptSpaceColon()

static bool MatchExceptSpaceColon ( const string &  a, const string &  b  )

static

Definition at line 668 of file biosource_tests.cpp.

References a, b, and i.

OrgDiffers()

static bool OrgDiffers ( const COrg_ref &  first, const COrg_ref &  second  )

static

Definition at line 1348 of file biosource_tests.cpp.

References CSerialObject::Equals(), first(), COrg_ref_Base::GetTaxname(), GetTaxonTag(), and COrg_ref_Base::IsSetTaxname().

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

RemoveCountryColon()

static bool RemoveCountryColon ( CBioSource &  src )

static

Definition at line 1512 of file biosource_tests.cpp.

References CSubSource_Base::eSubtype_country, CBioSource_Base::GetSubtype(), CBioSource_Base::IsSetSubtype(), and CSubSource_Base::SetName().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

SetCultureCollectionFromStrain()

static bool SetCultureCollectionFromStrain ( CBioSource &  src )

static

Definition at line 400 of file biosource_tests.cpp.

References COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_strain, COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), HasCultureCollectionForATCCStrain(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref::IsSetOrgMod(), CBioSource_Base::SetOrg(), and NStr::StartsWith().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

SetEnvSampleFixAmplifiedPrimers()

static bool SetEnvSampleFixAmplifiedPrimers ( CBioSource &  src )

static

Definition at line 1804 of file biosource_tests.cpp.

References NStr::Equal(), CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_other, CBioSource::HasSubtype(), orig, NStr::ReplaceInPlace(), and CBioSource_Base::SetSubtype().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix().

USING_SCOPE()

USING_SCOPE

(

objects

)

References CSerialObject::Assign(), CSeq_feat_Base::GetData(), CScope::GetSeq_featHandle(), CSeqFeatData_Base::IsBiosrc(), CSeq_feat_Base::IsSetData(), CSeqdesc_Base::IsSource(), n, CSeq_feat_EditHandle::Replace(), CSeq_feat_Base::SetData(), and CSeqdesc_Base::SetSource().

Variable Documentation

g_aliases_DUP_SRC_QUAL

constexpr std::initializer_list<const char*> g_aliases_DUP_SRC_QUAL = { "DUP_SRC_QUAL_DATA" }

staticconstexpr

Definition at line 1994 of file biosource_tests.cpp.

kAmplifiedWithSpeciesSpecificPrimers

const string kAmplifiedWithSpeciesSpecificPrimers = "amplified with species-specific primers"

Definition at line 447 of file biosource_tests.cpp.

Referenced by HasAmplifiedWithSpeciesSpecificPrimerNote().

kDupSrc

const char* kDupSrc = "[n] source[s] [has] two or more qualifiers with the same value"

static

Definition at line 1990 of file biosource_tests.cpp.

kMissingViralQualsTop

const string kMissingViralQualsTop = "[n] virus organism[s] [is] missing required qualifiers"

Definition at line 277 of file biosource_tests.cpp.

s_testcase_props_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE

constexpr CDiscrepancyCaseProps s_testcase_props_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE = { CDiscrepancyVisitorImpl<eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE >::Create, eTestTypes:: BIOSRC , eTestNames:: AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE , "AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE" , "Species-specific primers, no environmental sample" , eOncaller , nullptr }

staticconstexpr

Definition at line 1775 of file biosource_tests.cpp.

s_testcase_props_ATCC_CULTURE_CONFLICT

constexpr CDiscrepancyCaseProps s_testcase_props_ATCC_CULTURE_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: ATCC_CULTURE_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: ATCC_CULTURE_CONFLICT , "ATCC_CULTURE_CONFLICT" , "ATCC strain should also appear in culture collection" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 375 of file biosource_tests.cpp.

s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_ISOLATE

constexpr CDiscrepancyCaseProps s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: BACTERIA_SHOULD_NOT_HAVE_ISOLATE , "BACTERIA_SHOULD_NOT_HAVE_ISOLATE" , "Bacterial sources should not have isolate" , eDisc | eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 449 of file biosource_tests.cpp.

s_testcase_props_BIOMATERIAL_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_BIOMATERIAL_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: BIOMATERIAL_TAXNAME_MISMATCH , "BIOMATERIAL_TAXNAME_MISMATCH" , "Test BioSources with the same biomaterial but different taxname" , eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 953 of file biosource_tests.cpp.

s_testcase_props_CHECK_AUTHORITY

constexpr CDiscrepancyCaseProps s_testcase_props_CHECK_AUTHORITY = { CDiscrepancyVisitorImpl<eTestNames:: CHECK_AUTHORITY >::Create, eTestTypes:: BIOSRC , eTestNames:: CHECK_AUTHORITY , "CHECK_AUTHORITY" , "Authority and Taxname should match first two words" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 1679 of file biosource_tests.cpp.

s_testcase_props_COUNTRY_COLON

constexpr CDiscrepancyCaseProps s_testcase_props_COUNTRY_COLON = { CDiscrepancyVisitorImpl<eTestNames:: COUNTRY_COLON >::Create, eTestTypes:: BIOSRC , eTestNames:: COUNTRY_COLON , "COUNTRY_COLON" , "Country description should only have 1 colon" , eOncaller , nullptr }

staticconstexpr

Definition at line 1554 of file biosource_tests.cpp.

s_testcase_props_CULTURE_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_CULTURE_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: CULTURE_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: CULTURE_TAXNAME_MISMATCH , "CULTURE_TAXNAME_MISMATCH" , "Test BioSources with the same culture collection but different taxname" , eOncaller , nullptr }

staticconstexpr

Definition at line 916 of file biosource_tests.cpp.

s_testcase_props_DUP_SRC_QUAL

constexpr CDiscrepancyCaseProps s_testcase_props_DUP_SRC_QUAL = { CDiscrepancyVisitorImpl<eTestNames:: DUP_SRC_QUAL >::Create, eTestTypes:: BIOSRC , eTestNames:: DUP_SRC_QUAL , "DUP_SRC_QUAL" , "Each qualifier on a source should have different value" , eDisc | eOncaller | eSmart , &g_aliases_DUP_SRC_QUAL }

staticconstexpr

Definition at line 1994 of file biosource_tests.cpp.

s_testcase_props_DUPLICATE_PRIMER_SET

constexpr CDiscrepancyCaseProps s_testcase_props_DUPLICATE_PRIMER_SET = { CDiscrepancyVisitorImpl<eTestNames:: DUPLICATE_PRIMER_SET >::Create, eTestTypes:: BIOSRC , eTestNames:: DUPLICATE_PRIMER_SET , "DUPLICATE_PRIMER_SET" , "Duplicate PCR primer pair" , eOncaller , nullptr }

staticconstexpr

Definition at line 1919 of file biosource_tests.cpp.

s_testcase_props_END_COLON_IN_COUNTRY

constexpr CDiscrepancyCaseProps s_testcase_props_END_COLON_IN_COUNTRY = { CDiscrepancyVisitorImpl<eTestNames:: END_COLON_IN_COUNTRY >::Create, eTestTypes:: BIOSRC , eTestNames:: END_COLON_IN_COUNTRY , "END_COLON_IN_COUNTRY" , "Country name end with colon" , eOncaller , nullptr }

staticconstexpr

Definition at line 1495 of file biosource_tests.cpp.

s_testcase_props_FIND_STRAND_TRNAS

constexpr CDiscrepancyCaseProps s_testcase_props_FIND_STRAND_TRNAS = { CDiscrepancyVisitorImpl<eTestNames:: FIND_STRAND_TRNAS >::Create, eTestTypes:: SEQUENCE , eTestNames:: FIND_STRAND_TRNAS , "FIND_STRAND_TRNAS" , "Find tRNAs on the same strand" , eDisc , nullptr }

staticconstexpr

Definition at line 741 of file biosource_tests.cpp.

s_testcase_props_HUMAN_HOST

constexpr CDiscrepancyCaseProps s_testcase_props_HUMAN_HOST = { CDiscrepancyVisitorImpl<eTestNames:: HUMAN_HOST >::Create, eTestTypes:: BIOSRC , eTestNames:: HUMAN_HOST , "HUMAN_HOST" , "\'Human\' in host should be \'Homo sapiens\'" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 1626 of file biosource_tests.cpp.

s_testcase_props_INCONSISTENT_BIOSOURCE

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_BIOSOURCE = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_BIOSOURCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_BIOSOURCE , "INCONSISTENT_BIOSOURCE" , "Inconsistent BioSource" , eDisc | eSubmitter | eSmart , nullptr }

staticconstexpr

Definition at line 1265 of file biosource_tests.cpp.

s_testcase_props_INFLUENZA_DATE_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_DATE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_DATE_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_DATE_MISMATCH , "INFLUENZA_DATE_MISMATCH" , "Influenza Strain/Collection Date Mismatch" , eOncaller , nullptr }

staticconstexpr

Definition at line 113 of file biosource_tests.cpp.

s_testcase_props_INFLUENZA_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_QUALS , "INFLUENZA_QUALS" , "Influenza must have strain, host, isolation_source, country, collection_date" , eOncaller , nullptr }

staticconstexpr

Definition at line 165 of file biosource_tests.cpp.

s_testcase_props_INFLUENZA_SEROTYPE

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_SEROTYPE = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE , "INFLUENZA_SEROTYPE" , "Influenza A virus must have serotype" , eOncaller , nullptr }

staticconstexpr

Definition at line 220 of file biosource_tests.cpp.

s_testcase_props_INFLUENZA_SEROTYPE_FORMAT

constexpr CDiscrepancyCaseProps s_testcase_props_INFLUENZA_SEROTYPE_FORMAT = { CDiscrepancyVisitorImpl<eTestNames:: INFLUENZA_SEROTYPE_FORMAT >::Create, eTestTypes:: BIOSRC , eTestNames:: INFLUENZA_SEROTYPE_FORMAT , "INFLUENZA_SEROTYPE_FORMAT" , "Influenza A virus serotype must match /^H[1-9]\\d*$|^N[1-9]\\d*$|^H[1-9]\\d*N[1-9]\\d*$|^mixed$/" , eOncaller , nullptr }

staticconstexpr

Definition at line 241 of file biosource_tests.cpp.

s_testcase_props_MAG_MISSING_ISOLATE

constexpr CDiscrepancyCaseProps s_testcase_props_MAG_MISSING_ISOLATE = { CDiscrepancyVisitorImpl<eTestNames:: MAG_MISSING_ISOLATE >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_MISSING_ISOLATE , "MAG_MISSING_ISOLATE" , "Organism assembled from metagenome reads should have isolate" , eDisc | eSmart , nullptr }

staticconstexpr

Definition at line 537 of file biosource_tests.cpp.

s_testcase_props_MAG_SHOULD_NOT_HAVE_STRAIN

constexpr CDiscrepancyCaseProps s_testcase_props_MAG_SHOULD_NOT_HAVE_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: MAG_SHOULD_NOT_HAVE_STRAIN , "MAG_SHOULD_NOT_HAVE_STRAIN" , "Organism assembled from metagenome reads should not have strain" , eDisc | eSmart , nullptr }

staticconstexpr

Definition at line 503 of file biosource_tests.cpp.

s_testcase_props_MAP_CHROMOSOME_CONFLICT

constexpr CDiscrepancyCaseProps s_testcase_props_MAP_CHROMOSOME_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: MAP_CHROMOSOME_CONFLICT >::Create, eTestTypes:: BIOSRC , eTestNames:: MAP_CHROMOSOME_CONFLICT , "MAP_CHROMOSOME_CONFLICT" , "Eukaryotic sequences with a map source qualifier should also have a chromosome source qualifier" , eDisc | eOncaller | eSmart | eFatal , nullptr }

staticconstexpr

Definition at line 86 of file biosource_tests.cpp.

s_testcase_props_METAGENOME_SOURCE

constexpr CDiscrepancyCaseProps s_testcase_props_METAGENOME_SOURCE = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOME_SOURCE >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOME_SOURCE , "METAGENOME_SOURCE" , "Source has metagenome_source qualifier" , eDisc | eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 1959 of file biosource_tests.cpp.

s_testcase_props_METAGENOMIC

constexpr CDiscrepancyCaseProps s_testcase_props_METAGENOMIC = { CDiscrepancyVisitorImpl<eTestNames:: METAGENOMIC >::Create, eTestTypes:: BIOSRC , eTestNames:: METAGENOMIC , "METAGENOMIC" , "Source has metagenomic qualifier" , eDisc | eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 1942 of file biosource_tests.cpp.

s_testcase_props_MISSING_PRIMER

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PRIMER = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PRIMER >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_PRIMER , "MISSING_PRIMER" , "Missing values in primer set" , eOncaller , nullptr }

staticconstexpr

Definition at line 1849 of file biosource_tests.cpp.

s_testcase_props_MISSING_VIRAL_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_VIRAL_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_VIRAL_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: MISSING_VIRAL_QUALS , "MISSING_VIRAL_QUALS" , "Viruses should specify collection-date, country, and specific-host" , eOncaller , nullptr }

staticconstexpr

Definition at line 279 of file biosource_tests.cpp.

s_testcase_props_MULTIPLE_CULTURE_COLLECTION

constexpr CDiscrepancyCaseProps s_testcase_props_MULTIPLE_CULTURE_COLLECTION = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CULTURE_COLLECTION >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTIPLE_CULTURE_COLLECTION , "MULTIPLE_CULTURE_COLLECTION" , "Multiple culture-collection quals" , eOncaller , nullptr }

staticconstexpr

Definition at line 599 of file biosource_tests.cpp.

s_testcase_props_MULTISRC

constexpr CDiscrepancyCaseProps s_testcase_props_MULTISRC = { CDiscrepancyVisitorImpl<eTestNames:: MULTISRC >::Create, eTestTypes:: BIOSRC , eTestNames:: MULTISRC , "MULTISRC" , "Comma or semicolon appears in strain or isolate" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 578 of file biosource_tests.cpp.

s_testcase_props_ORGANELLE_ITS

constexpr CDiscrepancyCaseProps s_testcase_props_ORGANELLE_ITS = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: ORGANELLE_ITS , "ORGANELLE_ITS" , "Test Bioseqs for suspect rRNA / ITS on organelle" , eOncaller , nullptr }

staticconstexpr

Definition at line 992 of file biosource_tests.cpp.

s_testcase_props_REQUIRED_CLONE

constexpr CDiscrepancyCaseProps s_testcase_props_REQUIRED_CLONE = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_CLONE >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_CLONE , "REQUIRED_CLONE" , "Uncultured or environmental sources should have clone" , eOncaller , nullptr }

staticconstexpr

Definition at line 829 of file biosource_tests.cpp.

s_testcase_props_REQUIRED_STRAIN

constexpr CDiscrepancyCaseProps s_testcase_props_REQUIRED_STRAIN = { CDiscrepancyVisitorImpl<eTestNames:: REQUIRED_STRAIN >::Create, eTestTypes:: BIOSRC , eTestNames:: REQUIRED_STRAIN , "REQUIRED_STRAIN" , "Bacteria should have strain" , eDisc | eSubmitter | eSmart , nullptr }

staticconstexpr

Definition at line 620 of file biosource_tests.cpp.

s_testcase_props_SARS_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_SARS_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: SARS_QUALS >::Create, eTestTypes:: BIOSRC , eTestNames:: SARS_QUALS , "SARS_QUALS" , "SARS-CoV-2 isolate must have correct format" , eOncaller , nullptr }

staticconstexpr

Definition at line 2121 of file biosource_tests.cpp.

s_testcase_props_SP_NOT_UNCULTURED

constexpr CDiscrepancyCaseProps s_testcase_props_SP_NOT_UNCULTURED = { CDiscrepancyVisitorImpl<eTestNames:: SP_NOT_UNCULTURED >::Create, eTestTypes:: BIOSRC , eTestNames:: SP_NOT_UNCULTURED , "SP_NOT_UNCULTURED" , "Organism ending in sp. needs tax consult" , eOncaller , nullptr }

staticconstexpr

Definition at line 726 of file biosource_tests.cpp.

s_testcase_props_SPECVOUCHER_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_SPECVOUCHER_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: SPECVOUCHER_TAXNAME_MISMATCH , "SPECVOUCHER_TAXNAME_MISMATCH" , "BioSources with the same specimen voucher should have the same taxname" , eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 879 of file biosource_tests.cpp.

s_testcase_props_STRAIN_CULTURE_COLLECTION_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_STRAIN_CULTURE_COLLECTION_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_CULTURE_COLLECTION_MISMATCH , "STRAIN_CULTURE_COLLECTION_MISMATCH" , "Strain and culture-collection values conflict" , eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 688 of file biosource_tests.cpp.

s_testcase_props_STRAIN_TAXNAME_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_STRAIN_TAXNAME_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: STRAIN_TAXNAME_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: STRAIN_TAXNAME_MISMATCH , "STRAIN_TAXNAME_MISMATCH" , "BioSources with the same strain should have the same taxname" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 841 of file biosource_tests.cpp.

s_testcase_props_TAX_LOOKUP_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_TAX_LOOKUP_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISMATCH >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISMATCH , "TAX_LOOKUP_MISMATCH" , "Find Tax Lookup Mismatches" , eDisc , nullptr }

staticconstexpr

Definition at line 1323 of file biosource_tests.cpp.

s_testcase_props_TAX_LOOKUP_MISSING

constexpr CDiscrepancyCaseProps s_testcase_props_TAX_LOOKUP_MISSING = { CDiscrepancyVisitorImpl<eTestNames:: TAX_LOOKUP_MISSING >::Create, eTestTypes:: BIOSRC , eTestNames:: TAX_LOOKUP_MISSING , "TAX_LOOKUP_MISSING" , "Find Missing Tax Lookup" , eDisc , nullptr }

staticconstexpr

Definition at line 1403 of file biosource_tests.cpp.

s_testcase_props_TRINOMIAL_SHOULD_HAVE_QUALIFIER

constexpr CDiscrepancyCaseProps s_testcase_props_TRINOMIAL_SHOULD_HAVE_QUALIFIER = { CDiscrepancyVisitorImpl<eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER >::Create, eTestTypes:: BIOSRC , eTestNames:: TRINOMIAL_SHOULD_HAVE_QUALIFIER , "TRINOMIAL_SHOULD_HAVE_QUALIFIER" , "Trinomial sources should have corresponding qualifier" , eDisc | eOncaller | eSmart , nullptr }

staticconstexpr

Definition at line 1745 of file biosource_tests.cpp.

s_testcase_props_UNCULTURED_NOTES

constexpr CDiscrepancyCaseProps s_testcase_props_UNCULTURED_NOTES = { CDiscrepancyVisitorImpl<eTestNames:: UNCULTURED_NOTES >::Create, eTestTypes:: BIOSRC , eTestNames:: UNCULTURED_NOTES , "UNCULTURED_NOTES" , "Uncultured Notes" , eOncaller | eFatal , nullptr }

staticconstexpr

Definition at line 260 of file biosource_tests.cpp.

s_testcase_props_UNNECESSARY_ENVIRONMENTAL

constexpr CDiscrepancyCaseProps s_testcase_props_UNNECESSARY_ENVIRONMENTAL = { CDiscrepancyVisitorImpl<eTestNames:: UNNECESSARY_ENVIRONMENTAL >::Create, eTestTypes:: BIOSRC , eTestNames:: UNNECESSARY_ENVIRONMENTAL , "UNNECESSARY_ENVIRONMENTAL" , "Unnecessary environmental qualifier present" , eOncaller , nullptr }

staticconstexpr

Definition at line 1444 of file biosource_tests.cpp.

s_testcase_props_UNUSUAL_ITS

constexpr CDiscrepancyCaseProps s_testcase_props_UNUSUAL_ITS = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_ITS >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_ITS , "UNUSUAL_ITS" , "Test Bioseqs for unusual rRNA / ITS" , eDisc | eOncaller , nullptr }

staticconstexpr

Definition at line 2094 of file biosource_tests.cpp.

srcqual_keywords

const pair<int, string> srcqual_keywords[]

static

Initial value:

= {
    { COrgMod::eSubtype_forma_specialis, " f. sp." } ,
    { COrgMod::eSubtype_forma, " f." } ,
    { COrgMod::eSubtype_sub_species, " subsp." } ,
    { COrgMod::eSubtype_variety, " var." } ,
    { COrgMod::eSubtype_pathovar, " pv." }
}

Definition at line 1722 of file biosource_tests.cpp.

srcqual_keywords_sz

const size_t srcqual_keywords_sz = ArraySize(srcqual_keywords)

static

Definition at line 1730 of file biosource_tests.cpp.