OrgMod.cpp

Go to the documentation of this file.

Go to the SVN repository for this file.

/* $Id: OrgMod.cpp 99337 2023-03-13 16:05:25Z foleyjp $
 * ===========================================================================
 *
 *                            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:
 *   'seqfeat.asn'.
 */
 
// standard includes
#include <ncbi_pch.hpp>
#include <util/static_map.hpp>
#include <util/util_misc.hpp>
#include <util/line_reader.hpp>
#include <util/compile_time.hpp>
#include <serial/enumvalues.hpp>
 
#include <objects/general/general_macros.hpp>
 
// generated includes
#include <objects/seqfeat/OrgMod.hpp>
 
// generated classes
 
BEGIN_NCBI_SCOPE
 
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
// destructor
COrgMod::~COrgMod(void)
{
}
 
 
COrgMod::TSubtype COrgMod::GetSubtypeValue(const string& str,
                                           EVocabulary vocabulary)
{
    string name = NStr::TruncateSpaces(str);
    NStr::ToLower(name);
    replace(name.begin(), name.end(), '_', '-');
    replace(name.begin(), name.end(), ' ', '-');
    
    if (name == "note" ||
        NStr::EqualNocase(name, "orgmod-note") ||
        NStr::EqualNocase(name, "note-orgmod")) {
        return eSubtype_other;
    } else if (vocabulary == eVocabulary_insdc) {
        if (name == "host" || name == "specific-host") {
            return eSubtype_nat_host;
        } else if (name == "sub-strain") {
            return eSubtype_substrain;
        }
    }
 
    return ENUM_METHOD_NAME(ESubtype)()->FindValue(name);
}
 
 
bool COrgMod::IsValidSubtypeName(const string& str, 
                                 EVocabulary vocabulary)
{
    string name = NStr::TruncateSpaces(str);
    NStr::ToLower(name);
    replace(name.begin(), name.end(), '_', '-');
    replace(name.begin(), name.end(), ' ', '-');
 
    if (name == "note" ||
        name == "orgmod-note" ||
        name == "note-orgmod") {
        return true;
    } else if (vocabulary == eVocabulary_insdc) {
        if (name == "host" || name == "sub-strain") {
            return true;
        }
    }
 
    return ENUM_METHOD_NAME(ESubtype)()->IsValidName(name);
}
 
 
string COrgMod::GetSubtypeName(COrgMod::TSubtype stype, EVocabulary vocabulary)
{
    if (stype == eSubtype_other) {
        return "note";
    } else if (vocabulary == eVocabulary_insdc) {
        switch (stype) {
        case eSubtype_substrain: return "sub_strain";
        case eSubtype_nat_host:  return "host";
        default:
            return NStr::Replace
                (ENUM_METHOD_NAME(ESubtype)()->FindName(stype, true),
                 "-", "_");
        }
    } else {
        return ENUM_METHOD_NAME(ESubtype)()->FindName(stype, true);
    }
}
 
 
bool COrgMod::IsMultipleValuesAllowed(TSubtype subtype)
{
    switch( subtype ) { // per TM-863
    case eSubtype_strain: // (2) ,
    case eSubtype_substrain: // (3) ,
    case eSubtype_variety: // (6) ,
    case eSubtype_serotype: // (7) ,        
    case eSubtype_serogroup: // (8) ,
    case eSubtype_serovar: // (9) ,
    case eSubtype_cultivar: // (10) ,
    case eSubtype_pathovar: // (11) ,
    case eSubtype_chemovar: // (12) ,
    case eSubtype_biovar: // (13) ,
    case eSubtype_biotype: // (14) ,
    case eSubtype_nat_host: // (21) ,        -- natural host of this specimen
    case eSubtype_sub_species: // (22) ,
    case eSubtype_forma: // (25) ,
    case eSubtype_forma_specialis: // (26) ,
    case eSubtype_ecotype: // (27) ,
    case eSubtype_breed: // (31) ,
    case eSubtype_gb_acronym: // (32) ,       -- used by taxonomy database
    case eSubtype_gb_anamorph: // (33) ,      -- used by taxonomy database
    case eSubtype_gb_synonym: // (34) ,       -- used by taxonomy database
    case eSubtype_metagenome_source: // (37) ,
    case eSubtype_nomenclature: // (39) ,
    case eSubtype_old_name: // (254) ,
        return false;
    default: return true;
    }
}
 
 
bool COrgMod::IsDiscouraged(const TSubtype subtype, bool indexer)
{
    if (subtype == eSubtype_dosage
        || subtype == eSubtype_gb_acronym
        || subtype == eSubtype_gb_anamorph
        || subtype == eSubtype_gb_synonym
        || subtype == eSubtype_old_lineage
        || subtype == eSubtype_old_name
        || (subtype == eSubtype_metagenome_source && !indexer)) {
        return true;
    } else {
        return false;
    }
}
 
 
bool COrgMod::HoldsInstitutionCode(const TSubtype stype)
{
    switch(stype) {
    case eSubtype_specimen_voucher:
    case eSubtype_culture_collection:
    case eSubtype_bio_material:
        return true;
    default:
        return false;
    }
}
 
 
bool COrgMod::ParseStructuredVoucher(const string& str, string& inst, string& coll, string& id)
{
    if (NStr::IsBlank(str)) {
        return false;
    }
    inst = kEmptyStr;
    coll = kEmptyStr;
    id = kEmptyStr;
    size_t pos = NStr::Find(str, ":");
    if (pos == string::npos) {
        id = str;
        return true;
    }
    inst = str.substr(0, pos);
    id = str.substr(pos + 1);
    pos = NStr::Find(id, ":");
    if (pos != string::npos) {
        coll = id.substr(0, pos);
        id = id.substr(pos + 1);
    }
    return true;
}
 
 
// ===== biomaterial, and culture-collection BioSource subsource modifiers     ================
 
static COrgMod::TInstitutionCodeMap s_BiomaterialInstitutionCodeMap;
static COrgMod::TInstitutionCodeMap s_SpecimenVoucherInstitutionCodeMap;
static COrgMod::TInstitutionCodeMap s_CultureCollectionInstitutionCodeMap;
 
// holds all the data in the specific ones above
static COrgMod::TInstitutionCodeMap s_CompleteInstitutionCodeMap;
static COrgMod::TInstitutionCodeMap s_CompleteInstitutionFullNameMap;
static COrgMod::TInstitutionCodeMap s_InstitutionCodeTypeMap;
static COrgMod::TInstitutionCodeMap s_InstitutionCodeSynonymsMap;
static bool                s_InstitutionCollectionCodeMapInitialized = false;
 
DEFINE_STATIC_FAST_MUTEX(s_InstitutionCollectionCodeMutex);
 
#include "institution_codes.inc"
 
static void s_ProcessInstitutionCollectionCodeLine(const CTempString& line)
{
    if (NStr::StartsWith(line, "#")) {
        // ignore line, this is a comment
        return;
    }
    vector<string> tokens;
    NStr::Split(line, "\t", tokens);
    if (tokens.size() < 3) {
//        ERR_POST_X(1, Warning << "Bad format in institution_codes.txt entry " << line
//                   << "; disregarding");
    } else {
        NStr::TruncateSpacesInPlace( tokens[0] );
        NStr::TruncateSpacesInPlace( tokens[1] );
        NStr::TruncateSpacesInPlace( tokens[2] );
        string& vouch_types = tokens[1];
        for (size_t i = 0; i < vouch_types.size(); i++) {
            switch (vouch_types[i]) {
                case 'b':
                    s_BiomaterialInstitutionCodeMap[tokens[0]] = tokens[2];
                    break;
                case 'c':
                    s_CultureCollectionInstitutionCodeMap[tokens[0]] = tokens[2];
                    break;
                case 's':
                    s_SpecimenVoucherInstitutionCodeMap[tokens[0]] = tokens[2];
                    break;
                default:
//                  ERR_POST_X(1, Warning << "Bad format in institution_codes.txt entry " << line
//                             << "; unrecognized subtype (" << tokens[1] << "); disregarding");
                    break;
            }
        }
        s_CompleteInstitutionCodeMap[tokens[0]] = tokens[2];
        s_CompleteInstitutionFullNameMap[tokens[2]] = tokens[0];
        s_InstitutionCodeTypeMap[tokens[0]] = tokens[1];
        if (tokens.size() > 3 && !NStr::IsBlank(tokens[3])) {
            NStr::TruncateSpacesInPlace(tokens[3]);
            vector<string> synonyms;
            NStr::Split(tokens[3], ",", synonyms);
            NON_CONST_ITERATE(vector<string>, s, synonyms) {
                NStr::TruncateSpacesInPlace(*s);
                s_InstitutionCodeSynonymsMap[*s] = tokens[0];
            }
        }
    }
}
 
 
static void s_InitializeInstitutionCollectionCodeMaps(void)
{
    CFastMutexGuard GUARD(s_InstitutionCollectionCodeMutex);
    if (s_InstitutionCollectionCodeMapInitialized) {
        return;
    }
    string file = g_FindDataFile("institution_codes.txt");
    CTime builtin_timestamp
        (static_cast<time_t>(kInstitutionCollectionCodeList_Timestamp));
    CRef<ILineReader> lr;
    if ( !file.empty() && !g_IsDataFileOld(file, builtin_timestamp) ) {
        try {
            lr = ILineReader::New(file);
        } NCBI_CATCH("s_InitializeInstitutionCollectionCodeMaps")
    }
 
    if (lr.Empty()) {
        if (getenv("NCBI_DEBUG")) {
            LOG_POST("Falling back on built-in data for institution code list.");
        }
        size_t num_codes = sizeof (kInstitutionCollectionCodeList) / sizeof (char *);
        for (size_t i = 0; i < num_codes; i++) {
            const char *p = kInstitutionCollectionCodeList[i];
            s_ProcessInstitutionCollectionCodeLine(p);
        }
    } else {
        if (getenv("NCBI_DEBUG")) {
            LOG_POST("Reading from " + file + " for instition code list.");
        }
        do {
            s_ProcessInstitutionCollectionCodeLine(*++*lr);
        } while ( !lr->AtEOF() );
    }
 
    s_InstitutionCollectionCodeMapInitialized = true;
}
 
 
COrgMod::TInstitutionCodeMap::iterator COrgMod::FindInstitutionCode(const string& inst_coll, TInstitutionCodeMap& code_map,
    bool& is_miscapitalized, string& correct_cap, bool& needs_country, bool& erroneous_country)
{
    TInstitutionCodeMap::iterator it = code_map.find(inst_coll);
    if (it != code_map.end()) {
        if (NStr::EqualCase(it->first, inst_coll)) {
        } else if (NStr::EqualNocase(it->first, inst_coll)) {
            is_miscapitalized = true;
        }
        correct_cap = it->first;
        return it;
    } else {
        size_t pos = NStr::Find(inst_coll, "<");
        if (pos == string::npos) {
            string check = inst_coll + "<";
            it = code_map.begin();
            while (it != code_map.end()) {
                if (NStr::StartsWith(it->first, check, NStr::eNocase)) {
                    needs_country = true;
                    if (!NStr::StartsWith(it->first, check, NStr::eCase)) {
                        is_miscapitalized = true;
                    }
                    correct_cap = it->first.substr(0, inst_coll.length());
                    return it;
                }
                ++it;
            }
        } else {
            string inst_sub = inst_coll.substr(0, pos);
            it = code_map.find(inst_sub);
            if (it != code_map.end()) {
                erroneous_country = true;
                return it;
            }
        }
    }
    return code_map.end();
}
 
 
bool COrgMod::IsInstitutionCodeValid(const string& inst_coll, string &voucher_type, bool& is_miscapitalized, string& correct_cap, bool& needs_country, bool& erroneous_country)
{
    is_miscapitalized = false;
    needs_country = false;
    erroneous_country = false;
    correct_cap.clear();
 
    s_InitializeInstitutionCollectionCodeMaps();
    
    TInstitutionCodeMap::iterator ic = FindInstitutionCode(inst_coll, s_InstitutionCodeTypeMap, is_miscapitalized, correct_cap, needs_country, erroneous_country);
    if (ic != s_InstitutionCodeTypeMap.end()) {
        if (needs_country) {
            // check to see if non-country-requiring code is in synonyms
            bool syn_is_miscapitalized = false;
            string syn_correct_cap = "";
            bool syn_needs_country = false;
            bool syn_erroneous_country = false;
            TInstitutionCodeMap::iterator it = FindInstitutionCode(inst_coll, 
                s_InstitutionCodeSynonymsMap, syn_is_miscapitalized, syn_correct_cap, 
                syn_needs_country, syn_erroneous_country);
            if (it != s_InstitutionCodeSynonymsMap.end() && !syn_needs_country) {
                TInstitutionCodeMap::iterator is = s_InstitutionCodeTypeMap.find(it->second);
                if (is != s_InstitutionCodeTypeMap.end()) {
                    is_miscapitalized = syn_is_miscapitalized;
                    correct_cap = syn_correct_cap;
                    needs_country = syn_needs_country;
                    erroneous_country = syn_erroneous_country;
                    voucher_type = is->second;
                    return true;
                }
            }
        } else if (erroneous_country) {
            // check to see if country-requiring code is in synonyms
            bool syn_is_miscapitalized = false;
            string syn_correct_cap = "";
            bool syn_needs_country = false;
            bool syn_erroneous_country = false;
            TInstitutionCodeMap::iterator it = FindInstitutionCode(inst_coll,
                s_InstitutionCodeSynonymsMap, syn_is_miscapitalized, syn_correct_cap,
                syn_needs_country, syn_erroneous_country);
            if (it != s_InstitutionCodeSynonymsMap.end() && !syn_needs_country) {
                TInstitutionCodeMap::iterator is = s_InstitutionCodeTypeMap.find(it->second);
                if (is != s_InstitutionCodeTypeMap.end()) {
                    is_miscapitalized = syn_is_miscapitalized;
                    correct_cap = syn_correct_cap;
                    needs_country = syn_needs_country;
                    erroneous_country = syn_erroneous_country;
                    voucher_type = is->second;
                    return true;
                }
            }
        }
        voucher_type = ic->second;
        return true;
    }
    ic = FindInstitutionCode(inst_coll, s_InstitutionCodeSynonymsMap, is_miscapitalized, correct_cap, needs_country, erroneous_country);
    if (ic != s_InstitutionCodeSynonymsMap.end()) {
        TInstitutionCodeMap::iterator it = s_InstitutionCodeTypeMap.find(ic->second);
        if (it != s_InstitutionCodeTypeMap.end()) {
            voucher_type = it->second;
        }
        return true;
    }
    return false;
}
 
 
string 
COrgMod::IsCultureCollectionValid(const string& culture_collection)
{
    if (NStr::Find(culture_collection, ":") == string::npos) {
        return "Culture_collection should be structured, but is not";
    } else {
        return IsStructuredVoucherValid(culture_collection, "c");
    }
}
 
 
string 
COrgMod::IsSpecimenVoucherValid(const string& specimen_voucher)
{
    if (NStr::Find(specimen_voucher, ":") == string::npos) {
        return kEmptyStr;
    } else {
        return IsStructuredVoucherValid(specimen_voucher, "s");
    }
}
 
 
string 
COrgMod::IsBiomaterialValid(const string& biomaterial)
{
    if (NStr::Find(biomaterial, ":") == string::npos) {
        return kEmptyStr;
    } else {
        return IsStructuredVoucherValid(biomaterial, "b");
    }
}
 
 
const string kMissingInst = "Voucher is missing institution code";
const string kMissingId = "Voucher is missing specific identifier";
 
string 
COrgMod::IsStructuredVoucherValid(const string& val, const string& v_type)
{
    string inst_code;
    string coll_code;
    string inst_coll;
    string id;
 
    ParseStructuredVoucher(val, inst_code, coll_code, id);
    string rval = kEmptyStr;
    if (NStr::IsBlank(inst_code)) {
        rval = kMissingInst;
    }
    if (NStr::IsBlank(id)) {
        rval = NStr::IsBlank(rval) ? kMissingId : rval + "\n" + kMissingId;
    }
    if (!NStr::IsBlank(rval)) {
        return rval;
    }
 
    if (NStr::IsBlank (coll_code)) {
        inst_coll = inst_code;
    } else {
        inst_coll = inst_code + ":" + coll_code;
    }    
 
    // first, check combination of institution and collection (if collection found)
    string voucher_type;
    bool is_miscapitalized;
    bool needs_country;
    bool erroneous_country;
    string correct_cap;
    if (COrgMod::IsInstitutionCodeValid(inst_coll, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country)) {
        if (needs_country) {
            return "Institution code " + inst_coll + " needs to be qualified with a <COUNTRY> designation";
        } else if (erroneous_country) {
            return "Institution code " + inst_coll + " should not be qualified with a <COUNTRY> designation";
        } else if (is_miscapitalized) {
            return "Institution code " + inst_coll + " exists, but correct capitalization is " + correct_cap;
        } else {   
            if (NStr::FindNoCase(voucher_type, v_type) == string::npos) {
                if (NStr::FindNoCase (voucher_type, "b") != string::npos) {
                    return "Institution code " + inst_coll + " should be bio_material";
                } else if (NStr::FindNoCase (voucher_type, "c") != string::npos) {
                    return "Institution code " + inst_coll + " should be culture_collection";
                } else if (NStr::FindNoCase (voucher_type, "s") != string::npos) {
                    return "Institution code " + inst_coll + " should be specimen_voucher";
                }
            }
            return kEmptyStr;
        } 
    } else if (NStr::StartsWith(inst_coll, "personal", NStr::eNocase)) {
        if (NStr::EqualNocase (inst_code, "personal") && NStr::IsBlank (coll_code)) {
            return "Personal collection does not have name of collector";
        }
        return kEmptyStr;
    } else if (NStr::IsBlank(coll_code)) {
        return "Institution code " + inst_coll + " is not in list";
    } else if (IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country)) {
        if (needs_country) {
            return "Institution code in " + inst_coll + " needs to be qualified with a <COUNTRY> designation";
        } else if (erroneous_country) {
            return "Institution code " + inst_code + " should not be qualified with a <COUNTRY> designation";
        } else if (is_miscapitalized) {
            return "Institution code " + inst_code + " exists, but correct capitalization is " + correct_cap;
        } else if (NStr::Equal (coll_code, "DNA")) {
            // DNA is a valid collection for any institution (using bio_material)
            if (!NStr::Equal(v_type, "b")) {
                return "DNA should be bio_material";
            }
        } else {
            return "Institution code " + inst_code + " exists, but collection "
                        + inst_coll + " is not in list";
        }
    } else {
        return "Institution code " + inst_coll + " is not in list";
    }
    return kEmptyStr;
}
 
 
string COrgMod::MakeStructuredVoucher(const string& inst, const string& coll, const string& id)
{
    string rval;
    if (NStr::IsBlank(inst) && NStr::IsBlank(coll) && NStr::IsBlank(id)) {
        rval = kEmptyStr;
    } else if (NStr::IsBlank(inst) && NStr::IsBlank(coll)) {
        rval = id;
    } else if (NStr::IsBlank(coll)) {
        rval = inst + ":" + id;
    } else {
        rval = inst + ":" + coll + ":" + id;
    }
    return rval;
}
 
 
// As described in SQD-1655, we can only rescue an unstructured
// structured voucher if it consists of a series of three or
// more letters followed by a series of digits, optionally separated
// by space, and if the series of letters looks up as a valid
// institution code.
bool FindInstCodeAndSpecID(COrgMod::TInstitutionCodeMap& code_map, string& val)
{
    // nothing to do if value is blank
    if (NStr::IsBlank(val)) {
        return false;
    }
    
    // find first non-letter position
    size_t len = 0;
    string::iterator sit = val.begin();
    while (sit != val.end() && isalpha(*sit)) {
        len++;
        sit++;
    }
    if (len < 3 || len == val.length()) {
        // institution code too short or no second token
        return false;
    }
    string inst_code = val.substr(0, len);
    string remainder = val.substr(len);
    NStr::TruncateSpacesInPlace(remainder); 
    if (NStr::IsBlank(remainder)) {
        // no second token
        return false;
    }
    // remainder must be all digits
    sit = remainder.begin();
    while (sit != remainder.end()) {
        if (!isdigit(*sit)) {
            return false;
        }
        sit++;
    }
 
    bool rval = false;
    COrgMod::TInstitutionCodeMap::iterator it = code_map.find(inst_code);
    if (it != code_map.end()) {
        val = inst_code + ":" + remainder;
        rval = true;
    }
 
    return rval;
}
 
 
bool COrgMod::AddStructureToVoucher(string& val, const string& v_type)
{
    // nothing to do if value is blank
    if (NStr::IsBlank(val)) {
        return false;
    }    
 
    s_InitializeInstitutionCollectionCodeMaps();
    if (NStr::Find(v_type, "b") != string::npos && FindInstCodeAndSpecID(s_BiomaterialInstitutionCodeMap, val)) {
        return true;
    } else if (NStr::Find(v_type, "c") != string::npos && FindInstCodeAndSpecID(s_CultureCollectionInstitutionCodeMap, val)) {
        return true;
    } else if (NStr::Find(v_type, "s") != string::npos && FindInstCodeAndSpecID(s_SpecimenVoucherInstitutionCodeMap, val)) {
        return true;
    } else {
        return false;
    }            
}
 
 
bool COrgMod::RescueInstFromParentheses(string& val, const string& voucher_type)
{
    bool rval = false;
 
    if (!NStr::EndsWith(val, ")")) {
        return false;
    } 
    size_t colon_pos = NStr::Find(val, ":");
    if (colon_pos != 0 && colon_pos != string::npos) {
        return false;
    }
    size_t pos = NStr::Find(val, "(", NStr::eNocase, NStr::eReverseSearch);
    if (pos == string::npos) {
        return false;
    }
    string inst = val.substr(pos + 1, val.length() - pos - 2);
    bool miscap = false, needs_country = false, wrong_country = false;
    string capfix;
 
    string v_type = voucher_type;
    if (IsInstitutionCodeValid(inst, v_type, miscap, capfix, needs_country, wrong_country)) {
        if (colon_pos == 0) {
            val = inst + val.substr(0, pos);
        } else {
            val = inst + ":" + val.substr(0, pos);
        }
        NStr::TruncateSpacesInPlace(val);
        rval = true;
    }
    
 
    return rval;
}
 
 
bool 
COrgMod::FixStructuredVoucher(string& val, const string& v_type)
{
    string inst_code;
    string coll_code;
    string id;
 
    ParseStructuredVoucher(val, inst_code, coll_code, id);
    if (NStr::IsBlank(inst_code)) {
        if (AddStructureToVoucher(val, v_type)) {
            return true;
        } else {
            return RescueInstFromParentheses(val, v_type);
        }
    }
    bool rval = false;
    bool found = false;
    s_InitializeInstitutionCollectionCodeMaps();
 
    TInstitutionCodeMap::iterator it = s_InstitutionCodeTypeMap.begin();
 
    string new_inst_code = inst_code;
    while ((!found) && (it != s_InstitutionCodeTypeMap.end())) {
        if (NStr::Find(it->second, v_type) != string::npos) {
            if (NStr::EqualNocase (it->first, inst_code)) {
                if (!NStr::Equal (it->first, inst_code)) {
                    new_inst_code = it->first;
                    rval = true;
                }
                found = true;
            } else if (NStr::StartsWith(inst_code, it->first)
                       && inst_code.c_str()[it->first.length()] == '<') {
                /*
                new_inst_code = it->first;
                rval = true;
                */
            }
        }
        ++it;
    }
 
 
    if (rval) {
        val = MakeStructuredVoucher(new_inst_code, coll_code, id);
    }
    return rval;
}
 
 
const string &
COrgMod::GetInstitutionFullName( const string &short_name )
{
    s_InitializeInstitutionCollectionCodeMaps();
    TInstitutionCodeMap::const_iterator iter = s_CompleteInstitutionCodeMap.find( short_name );
    if( iter != s_CompleteInstitutionCodeMap.end() ) {
        return iter->second;
    } else {
        return kEmptyStr;
    }
}
 
const string &
COrgMod::GetInstitutionShortName( const string &full_name )
{
    s_InitializeInstitutionCollectionCodeMaps();
    TInstitutionCodeMap::const_iterator iter = s_CompleteInstitutionFullNameMap.find( full_name );
    if( iter != s_CompleteInstitutionFullNameMap.end() ) {
        return iter->second;
    } else {
        return kEmptyStr;
    }
}
 
 
// look for multiple source vouchers
string COrgMod::CheckMultipleVouchers(const vector<string>& vouchers)
{
    ITERATE(vector<string>, it, vouchers) {
        string inst1, coll1, id1;
        COrgMod::ParseStructuredVoucher(*it, inst1, coll1, id1);
        if (NStr::IsBlank(inst1)) continue;
        if (NStr::EqualNocase(inst1, "personal") || NStr::EqualCase(coll1, "DNA")) continue;
 
        vector<string>::const_iterator it_next = it;
        for (++it_next; it_next != vouchers.end(); ++it_next) {
            string inst2, coll2, id2;
            COrgMod::ParseStructuredVoucher(*it_next, inst2, coll2, id2);
            if (NStr::IsBlank(inst2)) continue;
            if (NStr::EqualNocase(inst2, "personal") || NStr::EqualCase(coll2, "DNA")) continue;
            if (!NStr::EqualNocase (inst1, inst2) || NStr::IsBlank(inst1)) continue;
            return NStr::EqualNocase(coll1, coll2) && !NStr::IsBlank(coll1) ? "Multiple vouchers with same institution:collection" : "Multiple vouchers with same institution";
        }
    }
    return kEmptyStr;
}
 
 
bool s_IsAllDigits(string str)
{
    return (str.find_first_not_of("0123456789") == NPOS);
}
 
 
bool s_FixStrainForPrefix(const string& prefix, string& strain)
{
    bool rval = false;
 
    if (NStr::StartsWith(strain, prefix, NStr::eNocase)) {
        string tmp = strain.substr(prefix.length());
        NStr::TruncateSpacesInPlace(tmp);
        if (NStr::StartsWith(tmp, ":") || NStr::StartsWith(tmp, "/")) {
            tmp = tmp.substr(1);
        }
        NStr::TruncateSpacesInPlace(tmp);
        if (!NStr::IsBlank(tmp) && s_IsAllDigits(tmp)) {
            strain = prefix + " " + tmp;
            rval = true;
        }
    }
    return rval;
}
 
 
string s_FixOneStrain( const string& strain)
{
    string new_val = strain;
    if (s_FixStrainForPrefix("ATCC", new_val)) {
        // fixed for ATCC
    } else if (s_FixStrainForPrefix("DSM", new_val)) {
        // fixed for DSM
    } else {
        // no fix
        new_val = kEmptyStr;
    }
    return new_val;
}
 
 
string COrgMod::FixStrain( const string& strain)
{
    string new_val = strain;
    vector<string> words;
    vector<string> results;
    NStr::Split(strain, ";", words);
    FOR_EACH_STRING_IN_VECTOR(itr, words) {
        string str = *itr;
        NStr::TruncateSpacesInPlace(str);
        string fixed = s_FixOneStrain(str);
        if (fixed.empty()) {
            results.push_back (str);
        } else {
            results.push_back (fixed);
        }
    }
    return NStr::Join(results,"; ");
}
 
 
const char* sm_BadStrainValues[] = {
    "yes",
    "no",
    "-",
    "microbial"
};
 
bool COrgMod::IsStrainValid(const string& strain)
{
    size_t max = sizeof(sm_BadStrainValues) / sizeof(const char*);
    for (size_t i = 0; i < max; i++) {
        if (NStr::EqualNocase(strain, sm_BadStrainValues[i])) {
            return false;
        }
    }
    return true;
}
 
 
const char* sm_KnownHostWords[] = {
  "alfalfa",
  "almond",
  "apple",
  "asparagus",
  "badger",
  "bean",
  "bitter melon",
  "blackberry",
  "blossoms",
  "blueberry",
  "bovine",
  "brinjal",
  "broad bean",
  "cabbage",
  "canine",
  "cantaloupe",
  "caprine",
  "carrot",
  "cassava",
  "cat",
  "catfish",
  "cattle",
  "cauliflower",
  "Channel catfish",
  "chestnut",
  "chicken",
  "chimpanzee",
  "clover",
  "corn",
  "cotton",
  "cow",
  "cowpea",
  "crab",
  "cucumber",
  "curd",
  "dairy cow",
  "dog",
  "duck",
  "equine",
  "feline",
  "fish",
  "fox",
  "goat",
  "goldfish",
  "goose",
  "guanabana",
  "honeydew",
  "horse",
  "ice cream",
  "juniper",
  "larva",
  "laurel",
  "leek",
  "lentil",
  "lilac",
  "lily",
  "maize",
  "mamey",
  "mamey sapote",
  "mango",
  "mangrove",
  "mangroves",
  "marigold",
  "marine sponge",
  "melon",
  "mosquito",
  "mulberry",
  "mungbean",
  "nematode",
  "oat",
  "ornamental pear",
  "ovine",
  "papaya",
  "pea",
  "peach",
  "peacock",
  "pear",
  "pepper",
  "pig",
  "pomegranate",
  "porcine",
  "potato",
  "raccoon dog",
  "red fox",
  "rhizospheric soil",
  "rice",
  "salmon",
  "seagrass",
  "sesame",
  "sheep",
  "shrimp",
  "sorghum",
  "sour cherry",
  "sourdough",
  "soybean",
  "sponge",
  "squash",
  "strawberry",
  "sugar beet",
  "sunflower",
  "sweet cherry",
  "swine",
  "tobacco",
  "tomato",
  "turf",
  "turfgrass",
  "turkey",
  "turtle",
  "watermelon",
  "wheat",
  "white clover",
  "willow",
  "wolf",
  "yak",
};
 
 
string COrgMod::FixHostCapitalization(const string& value)
{
    string fix = value;
 
    size_t max = sizeof(sm_KnownHostWords) / sizeof(const char*);
    for (size_t i = 0; i < max; i++) {
        if (NStr::EqualNocase(fix, sm_KnownHostWords[i])) {
            fix = sm_KnownHostWords[i];
            break;
        }
    }
    return fix;
}
 
 
static constexpr auto s_hostFixupMap =
ct::const_map<ct::tagStrNocase, const char*>::construct({
    { "-", "missing" },
    { "no", "missing" },
    { "none", "missing" },
    { "NA", "not available" },
    { "N/A", "not available" },
    { "n/a", "not available" },
    { "free-living", "natural / free-living" },
    { "natural", "natural / free-living" },
    { "not available", "not available" },
    { "not collected", "not collected" },
    { "not applicable", "not applicable" },
    { "NR", "not applicable" },
    { "not known", "unknown" },
    { "other", "missing" },
    { "misc", "missing" },
    { "not determined", "unknown" },
    { "unknown", "unknown" },
    { "not available: to be reported later", "not available" },
    { "obscured", "obscured" },
    { "human", "Homo sapiens" },
    { "homo sapiens", "Homo sapiens" }
});
 
 
 
 
string COrgMod::FixHost(const string& value)
{
    string fix = value;
 
    auto possible_fix = s_hostFixupMap.find(value);
    if (possible_fix != s_hostFixupMap.end()) {
        fix = possible_fix->second;
    }
 
    return fix;
}
 
 
string COrgMod::FixCapitalization(TSubtype subtype, const string& value)
{
    string new_val = value;
    switch (subtype) {
        case COrgMod::eSubtype_nat_host:
            new_val = FixHostCapitalization(value);
            break;
        default:
            new_val = value;
            break;
    }
    return new_val;
}
 
 
void COrgMod::FixCapitalization()
{
    if (!IsSetSubtype() || !IsSetSubname()) {
        return;
    }
 
    string new_val = FixCapitalization(GetSubtype(), GetSubname());
 
    if (!NStr::IsBlank(new_val)) {
        SetSubname(new_val);
    }
 
}
 
 
string COrgMod::AutoFix(TSubtype subtype, const string& value)
{
    string new_val;
    switch (subtype) {
        case COrgMod::eSubtype_strain:
            new_val = FixStrain(value);
            break;
        case COrgMod::eSubtype_nat_host:
            new_val = FixHost(value);
            break;
        default:
            break;
    }
    return new_val;
}
 
 
void COrgMod::AutoFix()
{
    if (!IsSetSubtype() || !IsSetSubname()) {
        return;
    }
 
    string new_val = AutoFix(GetSubtype(), GetSubname());
 
    if (!NStr::IsBlank(new_val)) {
        SetSubname(new_val);
    }
 
}
 
 
void s_HarmonizeString(string& s) 
{
    NStr::ReplaceInPlace (s, " ", "");
    NStr::ReplaceInPlace (s, "_", "");
    NStr::ReplaceInPlace (s, "-", "");
    NStr::ReplaceInPlace (s, ":", "");
    NStr::ReplaceInPlace (s, "/", "");
}
 
 
bool COrgMod::FuzzyStrainMatch( const string& strain1, const string& strain2 )
{
    string s1 = strain1;
    string s2 = strain2;
 
    s_HarmonizeString(s1);
    s_HarmonizeString(s2);
    return NStr::EqualNocase(s1, s2);    
}
 
 
bool COrgMod::RemoveAbbreviation()
{
    bool any_change = false;
 
    if (IsSetSubtype() && IsSetSubname()) {
        string& val = SetSubname();
        switch (GetSubtype()) {
            case eSubtype_serovar:
                if (NStr::StartsWith(val, "serovar ")) {
                    val = val.substr(8);
                    any_change = true;
                }
                break;
            case eSubtype_sub_species:
                if (NStr::StartsWith(val, "subsp. ")) {
                    val = val.substr(7);
                    any_change = true;
                }
                break;
            default:
                break;
        }
    }
    return any_change;
}
 
 
static const COrgMod::TSubtype sUnexpectedViralOrgModQualifiers[] = {
    COrgMod::eSubtype_breed,
    COrgMod::eSubtype_cultivar,
    COrgMod::eSubtype_specimen_voucher
};
 
static const size_t sNumUnexpectedViralOrgModQualifiers = sizeof(sUnexpectedViralOrgModQualifiers) / sizeof(COrgMod::TSubtype);
 
bool COrgMod::IsUnexpectedViralOrgModQualifier(COrgMod::TSubtype subtype)
{
    bool rval = false;
 
    for (size_t i = 0; i < sNumUnexpectedViralOrgModQualifiers && !rval; i++) {
        if (subtype == sUnexpectedViralOrgModQualifiers[i]) {
            rval = true;
        }
    }
    return rval;
}
 
 
bool COrgMod::IsUnexpectedViralOrgModQualifier() const
{
    if (IsSetSubtype() && IsUnexpectedViralOrgModQualifier(GetSubtype())) {
        return true;
    } else {
        return false;
    }
}
 
 
static const string sValidTypeMaterialPrefixes[] = {
    "type material",
    "type strain",
    "reference material",
    "reference strain",
    "neotype strain",
    "paralectotype",
    "hapantotype",
    "allotype",
    "culture from reference material",
    "culture from type material",
    "ex-type",
    "culture from hapantotype",
    "pathotype strain"
};
 
static const int sNumValidTypeMaterialPrefixes = sizeof(sValidTypeMaterialPrefixes) / sizeof(string);
 
static const string sValidCultureTypeMaterialPrefixes[] = {
    "epitype",
    "hapantotype",
    "holotype",
    "isoepitype",
    "isoepitype",
    "isolectotype",
    "isoneotype",
    "isoparatype",
    "isosyntype",
    "isotype",
    "lectotype",
    "neotype",
    "paratype",
    "reference",
    "syntype",
    "type material"
};
 
static const int sNumValidCultureTypeMaterialPrefixes = sizeof(sValidCultureTypeMaterialPrefixes) / sizeof(string);
 
bool COrgMod::IsValidTypeMaterial(const string& type_material)
{
    for (int i = 0; i < sNumValidTypeMaterialPrefixes; i++) {
        if (NStr::StartsWith(type_material, sValidTypeMaterialPrefixes[i])) {
            return true;
        }
    }
 
    for (int i = 0; i < sNumValidCultureTypeMaterialPrefixes; i++) {
        if (NStr::StartsWith(type_material, sValidCultureTypeMaterialPrefixes[i])) {
            return true;
        } else if (NStr::StartsWith(type_material, "culture from " + sValidCultureTypeMaterialPrefixes[i])) {
            return true;
        } else if (NStr::StartsWith(type_material, "ex-" + sValidCultureTypeMaterialPrefixes[i])) {
            return true;
        }
    }
    return false;
}
 
 
// note that the INSDC method now calls IsValidTypeMaterial
bool COrgMod::IsINSDCValidTypeMaterial(const string& type_material)
{
    if (NStr::IsBlank(type_material)) {
        return false;
    }
 
    return IsValidTypeMaterial(type_material);
}
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
/* Original file checksum: lines: 65, chars: 1882, CRC32: efba64e1 */