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NCBI C++ ToolKit: src/misc/discrepancy/biosource_tests.cpp File Reference
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) 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 }
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