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NCBI C++ ToolKit: src/gui/objutils/macro_fn_pubfields.cpp Source File

it = find_if(pub_fncs.begin(), pub_fncs.end(),

[&fn_name](

& elem) { return NStr::EqualNocase(fn_name, elem); });

(it != pub_fncs.end());

* const_pubdesc =

*

(

.GetPointer());

(const_block) {

(res_oi.empty()) {

vector<string> statuses;

statuses.push_back(status);

(res_oi.empty()) {

(elem.

()) {

(const_block) {

(

&& it : res_oi) {

(elem.

()) {

objs_to.push_back(*it);

(pub.

()) {

(pub.

()) {

(pub.

()) {

(pub.

()) {

(pub.

()) {

field_name.assign(

);

field_name.assign(

);

field_name.assign(

);

(pub.

()) {

(pub.

()) {

(

(&res, oi,

) && res.size() == 1) {

(pub.

()) {

(

(&res, oi,

) && res.size() == 1) {

(

&& it: pdesc.

().

()) {

(pub.

()) {

(imp->IsSetPrepub()) {

var_name =

.GetCurrentChoiceVariant().GetVariantInfo()->GetId().GetName();

(

.GetCurrentChoiceVariantIndex()) {

(field_name.empty()) {

(

.GetCurrentChoiceVariantIndex() == 1) {

(elem.

()) {

}

(

.GetCurrentChoiceVariantIndex() == 3) {

(elem.

()) {

(elem.

()) {

(

(&res, sub_oi,

) && res.size() == 1) {

(

(&res, sub_oi,

) && res.size() == 1) {

& author_field =

[0]->GetString();

new_desc->

().

().Set().push_back(new_pub);

->AddCommand(*create_cmd);

<<

->GetBestDescr() <<

;

(; iter != sm_AuthorFixMap.end(); ++iter){

(iter->second == fix_type){

(iter != sm_AuthorFixMap.end()){

* const_pubdesc =

*

(

.GetPointer());

(const_pubdesc) {

(pub.

()) {

(const_block) {

(!

.IsStd())

vector<string>

;

(!first_name.empty()) {

vector<string>::iterator it =

.begin();

(it !=

.end()) {

((!first_name_initial.empty() &&

(*it, first_name_initial)) ||

it->length() <= 2) {

it =

.erase(it);

(

& it :

) {

(!first_name.empty()) {

(first_name.empty() ||

new_middle_init;

middle_init = original_init.substr(first_init.length());

(!middle_init.empty()) {

(!new_middle_init.empty()) {

middle_init = original_init.substr(first_init.length());

(!middle_init.empty()) {

new_initials = first_init + middle_init;

string::const_iterator p =

.begin();

(p !=

.end()) {

string::const_iterator q = p;

inits.append(

);

inits.append(

);

string::const_iterator p = first_name.begin();

(p != first_name.end()) {

(p != first_name.end() && (*p <=

|| *p ==

)) {

(p != first_name.end() &&

(*p)) {

inits.append(

);

(p != first_name.end() && *p >

&& *p !=

) {

(p != first_name.end() && *p ==

) {

inits.append(

);

modified =

;

middle_init = initials;

middle_init = middle_init.substr(first_init.length());

& lastname,

& suffix,

& name)

inits = macro::CMacroFunction_AuthorFix::s_GetFirstNameInitials(name.

());

inits.append(mid_initials);

inits.append(

);

(!const_pubdesc) {

(

&& it : pubdesc->

().Set()) {

&& it->GetArticle().IsSetFrom()

&& it->GetArticle().GetFrom().IsJournal()) {

=

;

+=

+ it.first +

+ it.second +

;

(

& it :

) {

(it.second.empty()) {

+=

+ it.first +

;

+=

+ it.first +

;

(

& title_it : it.second) {

+= title_it +

;

(!

.empty()) {

(titles.size() == 1) {

(old_title != titles[0]) {

(

& it : title.

()) {

(it->IsIso_jta()) {

it->SetIso_jta(titles[0]);

(find(titles.begin(), titles.end(), old_title) == titles.end()) {

.emplace(old_title, titles);

(

& title_it : title.

()) {

(title_it->IsJta() || title_it->IsName()) {

(titles.size() == 1) {

title_it->SetIso_jta(titles[0]);

.emplace(old_title, titles);

(title.

()) {

(

& title_it : title.

()) {

(title_it->IsIso_jta()) {

(title.

()) {

(

& title_it : title.

()) {

(title_it->IsIso_jta()) {

title_it->GetIso_jta();

vector<string> titles;

(

& isojta_updater =

->ISOJTAUpdater(); isojta_updater) {

isojta_updater->GetJournalAbbr(title, titles);

& isojta_map = pubdesc_iter->SetISOJTALookupMap();

(

it = isojta_map.find(title); it != isojta_map.end()) {

titles = it->second;

isojta_map[title] = titles;

(

.empty());

GenerateFirstName(

& author)

& std_name = author.

().SetName();

list<CRef<CAuthor>> standard_names;

GenerateFirstName(*new_auth);

standard_names.push_back(new_auth);

auth_list.

().SetStd().insert(auth_list.

().SetStd().begin(), standard_names.begin(), standard_names.end());

ConvertToStandardAuthors(

& auth_list)

FixMedLineList(auth_list);

((*it)->GetName().IsMl()) {

GenerateFirstName(*new_auth);

(*it)->Assign(*new_auth);

affil->Assign(auth_list.

().

().front()->GetAffil());

AdjustAuthors(

& pubdesc)

(

& pub_it : pubdesc.

().Set()) {

(pub_it->IsSetAuthors()) {

& auth_list = pub_it->SetAuthors();

(

& it : auth_list.

().SetStd()) {

GenerateFirstName(*it);

affil->Assign(auth_list.

().

().front()->GetAffil());

(!const_pubdesc) {

(

& remote_updater =

->RemoteUpdater(); remote_updater) {

orig_pubdesc.

(*pubdesc);

remote_updater->UpdatePubReferences(desc);

AdjustAuthors(*pubdesc);

(!pubdesc->

(orig_pubdesc)) {

(

&& it : pubdesc->

().Set()) {

(it !=

.

()) {

looked_up_pub = it->second;

(looked_up_pub) {

.emplace(pmid, looked_up_pub);

(looked_up_pub) {

pubdesc->

().Set().push_back(pmid_pub);

pubdesc->

().Set().push_back(looked_up_pub);

(

.empty());

vector<TEntrezId> uids;

uids.push_back(

);

ecli.

(

, uids, asnPubMedEntry,

);

(

<<

<<

<<

<< e.

());

(pubmed_entry->IsSetMedent() && pubmed_entry->GetMedent().IsSetCit()) {

edit::CEUtilsUpdater updater;

pub = updater.GetPub(

, &

);

ConvertToStandardAuthors(pub->

());

err_msg = oss.str();

(

<<

<<

<<

<< err_msg);

void CMacroFunction_DOILookup::TheFunction()

(!const_pubdesc) {

& new_doi = m_Args[0]->GetString();

(new_doi.empty())

modify =

;

(

& it : pubdesc->

().

()) {

& genref = it->GetGen();

(m_DataIter->IsHugeDataMode()) {

(

& doi_updater = m_DataIter->DOIUpdater(); doi_updater) {

pair<CRef<CPubdesc>,

> new_pubdesc_str = doi_updater->GetPub(new_doi);

(new_pubdesc_str.first) {

pubdesc->

(*new_pubdesc_str.first);

m_QualsChangedCount++;

<<

<< new_doi <<

<< new_pubdesc_str.second;

it =

.

(new_doi);

(it !=

.

()) {

looked_up_pubdesc = it->second;

looked_up_pubdesc = new_pubdesc_str.first;

(looked_up_pubdesc) {

.emplace(new_doi, looked_up_pubdesc);

<<

<< new_doi <<

<< new_pubdesc_str.second;

(looked_up_pubdesc) {

pubdesc->

(*looked_up_pubdesc);

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

CMacroFunction_DOILookup::x_ValidArguments()

(m_Args.size() == 1) && (m_Args[0]->IsString());

(

& it : pubdesc.

().

()) {

(it->IsGen() && it->GetGen().IsSetCit()) {

& citation = it->GetGen().GetCit();

(

& it : pubdesc.

().

()) {

(it->IsArticle() && it->GetArticle().IsSetIds()) {

(

&

: it->GetArticle().GetIds().Get()) {

doi =

->GetDoi();

m_getDoi = make_unique<CGetDOIFromCitGen>();

(!const_pubdesc) {

doi_name =

->GetDOI(*pubdesc);

(doi_name.empty())

(

& doi_updater =

->DOIUpdater(); doi_updater) {

pair<CRef<CPubdesc>,

> new_pubdesc_str = doi_updater->GetPub(doi_name);

(new_pubdesc_str.first) {

pubdesc->

(*new_pubdesc_str.first);

<<

<< doi_name <<

<< new_pubdesc_str.second;

it =

.

(doi_name);

(it !=

.

()) {

looked_up_pubdesc = it->second;

looked_up_pubdesc = new_pubdesc_str.first;

(looked_up_pubdesc) {

.emplace(doi_name, looked_up_pubdesc);

<<

<< doi_name <<

<< new_pubdesc_str.second;

(looked_up_pubdesc) {

pubdesc->

(*looked_up_pubdesc);

(

.empty());

m_getDoi = make_unique<CGetDOIFromCitArt>();

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

x_GetObjectsFromRef(res_oi, 0);

& newValue = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!newValue.empty()) {

(res_oi.empty()) {

(const_pubdesc) {

x_SetTitleInPubdesc(*pubdesc, newValue);

(const_block) {

x_SetTitleInSubmitBlock(*submit_block, newValue);

SetQualStringValue(obj, orig_value);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(remove_field) {

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

arg_nr =

.size();

(arg_nr > 5 || arg_nr < 3) {

(!

[index]->IsRef()) {

second_ok =

[index]->IsString() ||

[index]->IsInt() ||

[index]->IsDouble();

(!second_ok)

;

(!

[++index]->IsString())

;

(arg_nr > 3 && (!

[++index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 4 && !

[++index]->IsBool())

;

title->SetName(

);

(

& it : pubdesc.

().Set()) {

(it->Which())

it->SetGen().SetTitle(

);

it->SetSub().SetDescr(

);

it->SetArticle().SetTitle().Set().push_back(title);

it->SetBook().SetTitle().Set().push_back(title);

it->SetProc().SetBook().SetTitle().Set().push_back(title);

it->SetPatent().SetTitle(

);

it->SetMan().SetCit().SetTitle().Set().push_back(title);

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

& field = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!newValue.empty()) {

(const_pubdesc) {

(

& it : pubdesc->

().Set()) {

(it->IsSetAuthors()) {

x_SetAffilField(it->SetAuthors(), field, newValue, existing_text);

(const_block) {

(submit_block->

() && submit_block->

().IsSetAuthors()) {

x_SetAffilField(submit_block->

().SetAuthors(), field, newValue, existing_text);

(m_QualsChangedCount) {

<< m_DataIter->GetBestDescr() <<

;

(remove_field) {

(const_pubdesc) {

(

& it : pubdesc->

().Set()) {

(it->IsSetAuthors()) {

x_RemoveAffilField(it->SetAuthors(), field);

(m_QualsChangedCount) {

<< m_DataIter->GetBestDescr() <<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

;

(field ==

) {

<<

;

(field ==

) {

<<

;

(field ==

) {

x_LogFunction(

);

arg_nr =

.size();

(arg_nr < 3 || arg_nr > 5) {

(!

[index]->IsString())

;

(!

[index]->IsString() && !

[index]->IsInt()) {

(!

[++index]->IsString())

;

(arg_nr > 3 && (!

[++index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 4 && !

[++index]->IsBool())

;

field_name =

+ field;

orig_value = res_oi.front().field.GetPrimitiveValueString();

field_name =

+ field;

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

(m_Args[index]->AreObjects()) {

res_oi = m_Args[index]->GetObjects();

(m_Args[index]->IsRef()) {

x_GetObjectsFromRef(res_oi, index);

& field = m_Args[++index]->GetString();

& newValue = m_Args[++index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

(!newValue.empty()) {

(const_pubdesc) {

x_SetAuthorInPubdesc(*pubdesc, field, *m_Args[2], existing_text);

(const_block) {

x_SetNewAuthor(submit_block->

().SetAuthors(), field, *m_Args[2]);

(

&& it : res_oi) {

SetQualStringValue(obj, orig_value);

(field ==

) {

m_QualsChangedCount++;

(field ==

) {

m_QualsChangedCount++;

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(remove_field) {

(

&& it : res_oi) {

m_QualsChangedCount++;

(const_pubdesc) {

(

& it : pubdesc->

().Set()) {

& authors = auth_list.

().SetStd();

CAuth_list_Base::TNames::TStd::iterator auth_it = authors.begin();

(auth_it != authors.end()) {

((*auth_it)->IsSetName() &&

(*auth_it)->GetName().IsConsortium() &&

(*auth_it)->GetName().GetConsortium().empty()) {

auth_it = authors.erase(auth_it);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

arg_nr =

.size();

(arg_nr > 6 || arg_nr < 4) {

(!

[index]->IsRef() && !

[index]->AreObjects()) {

(

= 1;

< index; ++

) {

(!

[

]->IsString()) {

(arg_nr > 4 && (!

[index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 5 && !

[++index]->IsBool())

;

(

& it : pubdesc.

().Set()) {

(it->IsSetAuthors()) {

auth_list = &(it->SetAuthors());

auth_list = &(it->SetAuthors());

(field ==

) {

field_name =

+ field;

field_name =

+ field;

auth_list.

().SetStd().push_back(new_author);

void CMacroFunction_SetPubAuthorMI::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

(m_Args[0]->AreObjects()) {

res_oi = m_Args[0]->GetObjects();

(m_Args[0]->IsRef()) {

x_GetObjectsFromRef(res_oi, 0);

& newValue = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

<< m_DataIter->GetBestDescr();

(!newValue.empty()) {

(

&& it : res_oi) {

SetQualStringValue(obj, orig_value);

m_QualsChangedCount++;

(m_QualsChangedCount) {

(remove_field) {

(

&& it : res_oi) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

;

CMacroFunction_SetPubAuthorMI::x_ValidArguments()

arg_nr = m_Args.size();

(arg_nr > 5 || arg_nr < 3) {

(!m_Args[index]->IsRef() && !m_Args[index]->AreObjects()) {

(!m_Args[index]->IsString() || !m_Args[++index]->IsString())

(arg_nr > 3 && (!m_Args[++index]->IsString() && !m_Args[index]->IsBool()))

;

(arg_nr > 4 && !m_Args[++index]->IsBool())

;

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

(m_Args[0]->GetString().empty()) {

(const_pubdesc) {

x_AddAuthorInPubdesc(*pubdesc, existing_text);

(const_block) {

x_AddAuthor(submit_block->

().SetAuthors(), existing_text);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

& it :

) {

(!it->IsString()) {

(

& it : pubdesc.

().Set()) {

(it->IsSetAuthors()) {

auth_list = &(it->SetAuthors());

auth_list = &(it->SetAuthors());

middle_init =

[2]->GetString();

(!middle_init.empty()) {

initials.append(middle_init);

initials.append(

);

(!initials.empty()) {

(!

[3]->GetString().empty()) {

auth_list.

().SetStd().push_back(author);

auth_list.

().SetStd().push_back(author);

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

& newValue = m_Args[index]->GetString();

remove_field = (++index < m_Args.size()) ? m_Args[index]->GetBool() :

;

<< m_DataIter->GetBestDescr();

(!newValue.empty()) {

(const_pubdesc) {

x_AddAuthorListInPubdesc(*pubdesc);

(const_block) {

(m_QualsChangedCount) {

(remove_field) {

(const_pubdesc) {

(

& it : pubdesc->

().Set()) {

(it->IsSetAuthors()) {

auth_list.

().SetStr().push_back(

);

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(!

[index]->IsString())

(++index <

.size() && !

[index]->IsBool())

(

& it : pubdesc.

().Set()) {

(it->IsSetAuthors()) {

auth_list = &(it->SetAuthors());

auth_list = &(it->SetAuthors());

* const_pubdesc =

*

(

.GetPointer());

& newValue = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

<< m_DataIter->GetBestDescr();

(!newValue.empty()) {

x_SetJournalInPubdesc(*pubdesc, newValue, existing_text);

(m_QualsChangedCount) {

(remove_field) {

x_RemoveJournalInPubdesc(*pubdesc);

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

;

x_LogFunction(

);

arg_nr =

.size();

(arg_nr < 2 || arg_nr > 4) {

(!

[index]->IsString()) {

(!

[++index]->IsString())

;

(arg_nr > 2 && (!

[++index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 3 && !

[++index]->IsBool())

;

* title =

;

(

& it : pubdesc.

().Set()) {

(it->Which()) {

title = &it->SetGen().SetJournal();

title = &it->SetArticle().SetFrom().SetJournal().SetTitle();

title = &it->SetJournal().SetTitle();

(title->

()) {

(

& it : title->

()) {

orig_value = it->GetName();

it->SetName(orig_value);

(

& it : title->

()) {

it->SetName(newValue);

this_title->SetName(newValue);

title->

().push_back(this_title);

(

& it : pubdesc.

().Set()) {

(it->Which()) {

(it->GetGen().IsSetJournal()) {

it->SetGen().ResetJournal();

(it->GetArticle().IsSetFrom() &&

it->GetArticle().GetFrom().IsJournal() &&

it->GetArticle().GetFrom().GetJournal().IsSetTitle()) {

it->SetArticle().SetFrom().SetJournal().ResetTitle();

(it->GetJournal().IsSetTitle()) {

it->SetJournal().ResetTitle();

* const_pubdesc =

*

(

.GetPointer());

& newValue =

[index]->GetString();

& action_type =

[++index]->GetString();

remove_field =

;

(!newValue.empty()) {

(remove_field) {

<<

;

arg_nr =

.size();

(arg_nr < 2 || arg_nr > 4) {

(!

[index]->IsString()) {

(!

[++index]->IsString())

;

(arg_nr > 2 && (!

[++index]->IsString() && !

[index]->IsBool()))

;

(arg_nr > 3 && !

[++index]->IsBool())

;

(

& it : pubdesc.

().Set()) {

pub_oi(it.GetNCPointer(), it->GetThisTypeInfo());

(it->Which()) {

(field ==

) {

(it->GetArticle().IsSetFrom()) {

(it->GetArticle().GetFrom().Which()) {

(

& it : objs) {

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

date_field =

;

(const_pubdesc) {

(const_block) {

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

x_LogFunction(

);

arg_nr =

.size();

(arg_nr != 1 && arg_nr != 3)

;

(!

[0]->IsString())

(

& it :

) {

(objs.empty())

;

(

.size() == 3) {

it =

.begin();

((*it)->GetInt() > 0) {

orig_date =

[0]->GetString();

ambiguous =

, day_first =

;

month_ambiguous =

;

date_obj->

(date->GetStd());

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

(m_Args[index]->IsInt()) {

(m_Args[index]->IsString()) {

newValue = m_Args[index]->GetString();

(m_Args[0]->GetString() !=

&& !newValue.empty()) {

remove_field = (++index < m_Args.size()) ? m_Args[index]->GetBool() :

;

<< m_DataIter->GetBestDescr();

date_field =

;

(const_pubdesc) {

(!newValue.empty()) {

x_AddDateField(objs);

(m_QualsChangedCount) {

(remove_field) {

x_RemoveDateField(objs);

(m_QualsChangedCount) {

<<

;

(const_block) {

(!newValue.empty()) {

x_AddDateField(objs);

(m_QualsChangedCount) {

(remove_field) {

x_RemoveDateField(objs);

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

+ m_Args[0]->GetString();

x_LogFunction(

);

(!

[index]->IsString())

;

(!

[index]->IsString() && !

[index]->IsInt()) {

(++index <

.size() && !

[index]->IsBool())

;

(objs.empty())

;

(objs.empty())

;

void CMacroFunction_SetPubCitation::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

& newValue = m_Args[index]->GetString();

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

<< m_DataIter->GetBestDescr();

(!newValue.empty()) {

(

& it : pubdesc->

().Set()) {

pub_oi(it.GetNCPointer(), it->GetThisTypeInfo());

(it->Which()) {

(

& it : objs) {

(SetQualStringValue(obj, orig_value));

(m_QualsChangedCount) {

(remove_field) {

(

& it : pubdesc->

().Set()) {

pub_oi(it.GetNCPointer(), it->GetThisTypeInfo());

(it->Which()) {

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

;

CMacroFunction_SetPubCitation::x_ValidArguments()

arg_nr = m_Args.size();

(arg_nr < 2 || arg_nr > 4) {

(!m_Args[index]->IsString() || !m_Args[++index]->IsString()) {

(arg_nr > 2 && (!m_Args[++index]->IsString() && !m_Args[index]->IsBool()))

;

(arg_nr > 3 && !m_Args[++index]->IsBool())

;

void CMacroFunction_SetSerialNumber::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

(m_Args[index]->IsString()) {

newValue = m_Args[0]->GetString();

(m_Args[index]->IsInt()) {

& action_type = m_Args[++index]->GetString();

remove_field =

;

x_GetOptionalArgs(

, remove_field, index);

<< m_DataIter->GetBestDescr();

(!newValue.empty()) {

(

& it : pubdesc->

().Set()) {

pub_oi(it.GetNCPointer(), it->GetThisTypeInfo());

(it->Which()) {

(

& it : objs) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

(remove_field) {

(

& it : pubdesc->

().Set()) {

pub_oi(it.GetNCPointer(), it->GetThisTypeInfo());

(it->Which()) {

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_QualsChangedCount <<

;

CMacroFunction_SetSerialNumber::x_ValidArguments()

arg_nr = m_Args.size();

(arg_nr > 4 || arg_nr < 2) {

(!m_Args[index]->IsInt() && !m_Args[index]->IsString())

(!m_Args[++index]->IsString())

;

(arg_nr > 2 && (!m_Args[++index]->IsString() && !m_Args[index]->IsBool()))

;

(arg_nr > 3 && !m_Args[++index]->IsBool())

;

* const_pubdesc =

*

(

.GetPointer());

(const_pubdesc) {

(s_SetStatus(*pubdesc, m_Args[0]->GetString()))

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

x_LogFunction(

);

(

.size() == 1 &&

[0]->IsString());

(

&& it: pubdesc.

().Set()) {

(status == curr_status) {

new_imp->

(*old_imp);

(pub.

()) {

& cit_gen = tmp_pub.

();

(cit_gen.IsSetTitle()) {

new_title->SetName(cit_gen.GetTitle());

article.SetTitle().Set().push_back(new_title);

(cit_gen.IsSetAuthors()) {

article.SetAuthors().Assign(cit_gen.GetAuthors());

&

= article.SetFrom().SetJournal();

(cit_gen.IsSetJournal()) {

.SetTitle().Assign(cit_gen.GetJournal());

.SetTitle().Set().push_back(new_title);

(cit_gen.IsSetDate()) {

.SetImp().SetDate().Assign(cit_gen.GetDate());

.SetImp().SetDate().SetStd().SetYear(year);

(cit_gen.IsSetVolume()) {

.SetImp().SetVolume(cit_gen.GetVolume());

(cit_gen.IsSetIssue()) {

.SetImp().SetIssue(cit_gen.GetIssue());

(cit_gen.IsSetPages()) {

.SetImp().SetPages(cit_gen.GetPages());

void CMacroFunction_SetPubPMID::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc)

;

(m_Args[index]->IsString()) {

newStrValue = m_Args[index]->GetString();

(m_Args[index]->GetInt()) {

= m_Args[index]->GetInt();

remove_field = (++index < m_Args.size()) ? m_Args[index]->GetBool() :

;

<< m_DataIter->GetBestDescr();

(!newStrValue.empty()) {

has_pmid =

;

(

& it : pubdesc->

().Set()) {

(it->GetPmid().Get() != new_pmid) {

it->SetPmid().Set(new_pmid);

m_QualsChangedCount++;

(

& it : pubdesc->

().

()) {

new_pub->SetPmid().Set(new_pmid);

pubdesc->

().Set().push_back(new_pub);

m_QualsChangedCount++;

has_art_pmid =

;

(

& it : pubdesc->

().Set()) {

(it->IsArticle()) {

(it->SetArticle().IsSetIds()) {

((*id)->IsPubmed()) {

has_art_pmid =

;

((*id)->GetPubmed().Get() != new_pmid) {

(*id)->SetPubmed().Set(new_pmid);

m_QualsChangedCount++;

(!has_art_pmid) {

art_id->SetPubmed().Set(new_pmid);

it->SetArticle().SetIds().Set().push_back(art_id);

m_QualsChangedCount++;

(m_QualsChangedCount) {

<<

<< new_pmid;

(remove_field) {

CPub_equiv::Tdata::iterator pub_it = pubdesc->

().Set().begin();

(pub_it != pubdesc->

().Set().end()) {

& pub_elem = (*pub_it);

(pub_elem->IsPmid()) {

pub_it = pubdesc->

().Set().erase(pub_it);

m_QualsChangedCount++;

(pub_elem->IsArticle() && pub_elem->GetArticle().IsSetIds()) {

((*id)->IsPubmed()) {

m_QualsChangedCount++;

(pub_elem->GetArticle().GetIds().Get().empty()) {

pub_elem->SetArticle().ResetIds();

(m_QualsChangedCount) {

<<

;

(m_QualsChangedCount) {

m_DataIter->SetModified();

CMacroFunction_SetPubPMID::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 2) {

(!m_Args[0]->IsInt() && !m_Args[0]->IsString())

(m_Args.size() == 2 && !m_Args[1]->IsBool())

void CMacroFunction_SetPubDOI::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

& new_doi = m_Args[0]->GetString();

(new_doi.empty())

remove_field =

;

<< m_DataIter->GetBestDescr();

has_doi =

;

(

& it : pubdesc->

().Set()) {

(it->IsArticle()) {

(it->SetArticle().IsSetIds()) {

((*id)->IsDoi()) {

(*id)->SetDoi().Set(new_doi);

m_QualsChangedCount++;

art_id->SetDoi().Set(new_doi);

it->SetArticle().SetIds().Set().push_back(art_id);

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<<

<< new_doi;

CMacroFunction_SetPubDOI::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 1) {

(m_Args[0]->IsString());

void CMacroFunction_ApplyPmidToEntry::TheFunction()

(; b_iter; ++b_iter) {

multiple = (m_Args.size() == 2) ? m_Args[1]->GetBool() :

;

(

!= 1 && !multiple) {

<<

<< m_Args[0]->GetInt() <<

<<

<<

;

= m_Args[0]->GetInt();

(m_DataIter->IsHugeDataMode()) {

(

& remote_updater = m_DataIter->RemoteUpdater(); remote_updater) {

pubdesc.

().Set().emplace_back(&pmid_pub);

tmp_pubdesc.

(pubdesc);

remote_updater->UpdatePubReferences(desc);

AdjustAuthors(pubdesc);

(!pubdesc.

(tmp_pubdesc)) {

m_QualsChangedCount++;

new_pub.Reset(

);

(

& pub_it : pubdesc.

().

()) {

(!pub_it->IsPmid()) {

new_pub->Assign(*pub_it);

<< new_pmid <<

;

(orig_pmids.

(new_pmid) != orig_pmids.

()) {

m_DataIter->RunCommand(add_cmd, m_CmdComposite);

<<

<< new_pmid <<

<< best_id;

seq_nr = 0;

(orig_pmids.

(new_pmid) != orig_pmids.

()) {

pub->Assign(*new_pub);

m_DataIter->RunCommand(add_cmd, m_CmdComposite);

(m_DataIter->IsHugeDataMode()) {

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

<<

<< new_pmid <<

<< seq_nr <<

;

CMacroFunction_ApplyPmidToEntry::x_ValidArguments()

(m_Args.size() != 1 && m_Args.size() != 2)

(m_Args[0]->IsInt() && (m_Args.size() == 2) ? m_Args[1]->IsBool() :

);

(

& it : pub.

().

()) {

pmids.

(it->GetPmid().Get());

(it->IsArticle() && it->GetArticle().IsSetIds()) {

((*id)->IsPubmed()) {

pmids.

((*id)->GetPubmed().Get());

(it->IsMedline() && it->GetMedline().IsSetPmid()) {

pmids.

(it->GetMedline().GetPmid().Get());

new_pubdesc->SetPub().Set().push_back(pmid_pub);

new_pubdesc->SetPub().Set().push_back(new_pub);

new_desc->

(*new_pubdesc);

void CMacroFunction_ApplyDOIToEntry::TheFunction()

(; b_iter; ++b_iter) {

& new_doi = m_Args[0]->GetString();

multiple = (m_Args.size() == 2) ? m_Args[1]->GetBool() :

;

(

!= 1 && !multiple) {

<<

<< new_doi <<

<<

<<

;

pair<CRef<CPubdesc>,

> new_pubdesc_str;

(m_DataIter->IsHugeDataMode()) {

(

& doi_updater = m_DataIter->DOIUpdater(); doi_updater) {

new_pubdesc_str = doi_updater->GetPub(new_doi);

<<

<< new_doi <<

<< new_pubdesc_str.second;

(orig_dois.

(new_doi) != orig_dois.

()) {

new_desc->

(*new_pubdesc);

m_DataIter->RunCommand(add_cmd, m_CmdComposite);

<<

<< new_doi <<

<< best_id;

seq_nr = 0;

(orig_dois.

(new_doi) != orig_dois.

()) {

new_desc->

(*new_pubdesc);

m_DataIter->RunCommand(add_cmd, m_CmdComposite);

(m_DataIter->IsHugeDataMode()) {

report[new_doi +

] = seq_nr;

x_LogChangedQuals(fnc_log);

<<

<< new_doi <<

<< seq_nr <<

;

CMacroFunction_ApplyDOIToEntry::x_ValidArguments()

(m_Args.size() != 1 && m_Args.size() != 2)

(m_Args[0]->IsString() && (m_Args.size() == 2) ? m_Args[1]->IsBool() :

);

(

& it : pub.

().

()) {

(it->IsArticle() && it->GetArticle().IsSetIds()) {

((*id)->IsDoi()) {

dois.

((*id)->GetDoi());

void CMacroFunction_RemovePubAuthors::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

modified =

;

(const_pubdesc) {

(

& it : pubdesc->

().Set()) {

(it->IsSetAuthors()) {

auth_list.

().SetStr().push_back(

);

(const_block) {

(submit_block->

() && submit_block->

().IsSetAuthors()) {

submit_block->

().SetAuthors().ResetNames();

submit_block->

().SetAuthors().SetNames().SetStr().push_back(

);

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_RemovePubAuthors::x_ValidArguments()

m_Args.empty();

void CMacroFunction_RemovePubAuthorMI::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

(!const_pubdesc && !const_block)

(m_Args[0]->AreObjects()) {

res_oi = m_Args[0]->GetObjects();

(m_Args[0]->IsRef()) {

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

(

&& it : res_oi) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

;

CMacroFunction_RemovePubAuthorMI::x_ValidArguments()

(m_Args.size() != 1) {

(m_Args[0]->AreObjects() || m_Args[0]->IsRef());

(elem.

()) {

(pub.

()) {

it =

.begin();

(; mem.

() && it !=

.end(); ++mem, ++it) {

(pub.Which()) {

field_name(

);

field_name.append(

[0]->GetString());

vector<CMQueryNodeValue::EType> valid_types;

(

= 0;

<

.size(); ++

) {

(

== 3 && !

[

]->IsString()) {

(!

[

]->IsInt()) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Utility macros and typedefs for exploring NCBI objects from biblio.asn.

#define FOR_EACH_ARTICLEID_ON_CITART(Itr, Var)

#define EDIT_EACH_ARTICLEID_ON_CITART(Itr, Var)

#define ERASE_ARTICLEID_ON_CITART(Itr, Var)

@Affil.hpp User-defined methods of the data storage class.

@Auth_list.hpp User-defined methods of the data storage class.

size_t GetNameCount() const

static CRef< CAuthor > ConvertMlToStandard(const CAuthor &author, bool normalize_suffix=false)

void SetToTime(const CTime &time, EPrecision prec=ePrecision_second)

static pair< CRef< objects::CPubdesc >, string > GetPubFromCrossRef(const string &doi)

void Fetch(const string &db, const vector< objects::CSeq_id_Handle > &uids, CNcbiOstream &ostr, const string &retmode="xml")

void SetMaxReturn(int ret_max)

static void s_DoLookup(const string &old_title, vector< string > &titles)

Subclass of the IQueryParseUserObject which is held as the user-defined object in each CQueryParseNod...

CMacroBioData_PubdescIter - iterates over all publication descriptors and features in the seq-entry.

@Name_std.hpp User-defined methods of the data storage class.

static EPubFieldStatus GetStatusFromString(const string &str)

static bool SetImprint(objects::CPub &pub, const objects::CImprint &imp)

static string GetLabelForStatus(EPubFieldStatus status)

static CConstRef< objects::CImprint > GetImprint(const objects::CPub &pub)

@ ePubFieldStatus_InPress

@ ePubFieldStatus_Published

@ ePubFieldStatus_Unpublished

CAuth_list & SetAuthors(void)

bool IsSetAuthors(void) const

@Pubdesc.hpp User-defined methods of the data storage class.

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

static string FixDateFormat(const string &orig_date)

Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.

static CRef< CDate > DateFromCollectionDate(const string &str) THROWS((CException))

static void DetectDateFormat(const string &orig_date, bool &ambiguous, bool &day_first)

const string & GetTitle(C_E::E_Choice type=C_E::e_not_set) const

If the internal list contains a title (of the specified type, if given), returns the corresponding st...

static bool GetBestId(CSeq_id_Handle, CScope &, string &)

Base class for any user function that performs editing operations on ASN.1 data.

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

#define ENTREZ_ID_TO(T, entrez_id)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ENTREZ_ID_FROM(T, value)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

static void s_GetObjectsFromAuthListNames(const CObjectInfo &names, const string &field_name, CMQueryNodeValue::TObs &objs)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_GetObjectsForPubField_SerialNumber(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

void x_GetObjectsForPubField_Title(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

static string s_GetFirstNameInitials(const string &first_name)

void x_GetObjectsForPubField_VolIssuePage(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

bool ApplyMiddleInitial(objects::CName_std &std_name, const string &newValue, objects::edit::EExistingText existing_text)

static string s_InsertInitialPeriods(const string &orig)

bool SetQualStringValue(CObjectInfo &oi, const string &value)

Functions make the action and collect statistics.

void SetString(const string &data)

Set/get underlying data type.

unique_ptr< CGetDOI > m_getDoi

static const char * sm_PubIssue

void x_SetPubFieldInPub(CObjectInfo &pub_oi)

static bool s_FixInitials(objects::CName_std &name)

string m_ResField

used for resolving fields for authors, date, affiliation

string x_GetPubStatus(const CObjectInfo &pubdesc_oi)

void x_RemoveVolIssuePagesInPubdesc(objects::CPubdesc &pubdesc)

static bool s_SetStatus(objects::CPubdesc &pubdesc, const string &value)

ENestedFunc m_Nested

flag indicating whether the function is nested within another function

static const TAuthorFixPair s_AuthorFixString[]

static const char * sm_FunctionName

class CMacroFunction_SetPubField SetPub_Date(year, month, day, season, hour, minute,...

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual void TheFunction()

Function implementation.

static void s_GetObjectsFromTitle(const CObjectInfo &title, CMQueryNodeValue::TObs &objs)

CRef< CMacroCmdComposite > m_CmdComposite

static bool s_IsPubFieldFnc(const string &fn_name)

void x_LogChangedQuals(const CRef< IFunctionLog > &log)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static const char * sm_FunctionName

class CMacroFunction_ApplyPublication SetPub_Sub(author_field_name, author_field_value) Apply new pub...

void x_GetObjectsForPubField_Cit(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

static const char * sm_PubJournal

CStaticArrayMap< string, CMacroFunction_AuthorFix::EActionType > TAuthorFixTypeMap

CMQueryNodeValue::EType GetPrimitiveFromRef(CMQueryNodeValue &node)

virtual void TheFunction()

Function implementation.

void x_RemoveDateField(CMQueryNodeValue::TObs &objs)

static void s_GetObjectsFromImprint(const CObjectInfo &imp, const string &field_name, CMQueryNodeValue::TObs &objs)

DEFINE_STATIC_ARRAY_MAP(TAuthorFixTypeMap, sm_AuthorFixMap, s_AuthorFixString)

bool ResolveAndSetSimpleTypeValue(CObjectInfo &oi, const string &field_name, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)

Resolve dot qualified ASN.1 node_name using the object information instance provided as a parameter (...

bool RemoveFieldByName(CMQueryNodeValue::SResolvedField &res_field)

Remove the object information instance corresponding to field, using information about its parent nod...

list< SResolvedField > TObs

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

map< string, vector< string > > m_Hits

void x_GetObjectsForPubField_Date(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static void s_GetObjectsFromAffil(const CObjectInfo &affil, const string &field_name, CMQueryNodeValue::TObs &objs)

static const char * sm_PubSerialNumber

void AssignFromObjectInfo(const CObjectInfo &objinfo)

Assigns data from objinfo. It is used when storing evaluation result.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

objects::CPub::E_Choice m_PubType

static const char * sm_FuncVolume

class CMacroFunction_SetPubVolIssuePages SetPubVolume(newValue, existing_text, delimiter,...

void x_SetAuthorInPubdesc(objects::CPubdesc &pubdesc, const string &field, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text)

static const char * sm_PubAuthors

static void s_CopyResolvedObjs(const CMQueryNodeValue::TObs &objs_from, CMQueryNodeValue::TObs &objs_to)

bool SetSimpleTypeValue(CObjectInfo &oi, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)

Set single node data to the node specified by parameter of type CObjectInfo.

void x_GetPubFieldObjectFromPub(const CObjectInfo &pub_oi, CMQueryNodeValue::TObs &objs)

string GetStringValue(CRef< CMQueryNodeValue > &value)

converts ints and doubles into string, by changing the type of the value

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

unsigned ApplyAuthorNames(objects::CAuth_list &auth_list, const string &newValue)

void x_SetObjects_Date(objects::CPub &pub, CObjectInfo &pub_var)

void x_GetObjectsForPubField_Authors(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

void x_SetTitleInPubdesc(objects::CPubdesc &pubdesc, const string &value)

string GetDOI(const objects::CPubdesc &pubdesc) const override

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual void TheFunction()

Function implementation.

CMacroFunction_PubFields(EScopeEnum func_scope, objects::EPublication_field field)

CObjectInfo GetPrimitiveObjInfo(const CObjectInfo &info)

virtual void TheFunction()

Function implementation.

void x_LookupTitleInJournal(objects::CCit_jour &journal)

static const char * sm_FunctionName

static const string & GetDescription(EActionType fix_type)

vector< string > x_FindIsoJtaTitle(const string &title)

static void s_GetObjectsFromDate(const CObjectInfo &date, const string &field_name, CMQueryNodeValue::TObs &objs)

static set< string > s_GatherExistingDOIs(const CBioseq_Handle &bsh)

virtual void TheFunction()

Function implementation.

static bool s_ReverseAuthorNames(objects::CName_std &name)

bool x_HasIsoJtaTitle(const objects::CTitle &title) const

void x_GetOptionalArgs(string &delimiter, bool &remove_field, size_t &index)

void x_SetTitleInSubmitBlock(objects::CSubmit_block &submit_block, const string &value)

static string x_GetStatus(const objects::CPub &pub)

void x_GetObjectsForPubField_AffilField(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

void x_LogError(CNcbiOstrstream &logstr)

Int4 m_QualsChangedCount

Number of changed qualifiers during the function call.

bool GetFieldsByName(CMQueryNodeValue::TObs *results, const CObjectInfo &oi_i, const string &field_name)

Resolve existing dot qualified ASN.1 name (field_name) starting from the object information instance ...

static const char * sm_PubVolume

bool RemoveMiddleInitial(objects::CName_std &std_name)

void x_AddAuthorInPubdesc(objects::CPubdesc &pubdesc, objects::edit::EExistingText existing_text)

void SetRef(CRef< CMQueryNodeValue > node)

void x_SetAffilField(objects::CAuth_list &auth_list, const string &field, const string &value, objects::edit::EExistingText existing_text)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

objects::EPublication_field m_FieldType

void x_GetObjectsForPubField_DOI(objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

virtual void TheFunction()

Function implementation.

DEFINE_MACRO_FUNCNAME(CMacroFunction_MoveMiddleName, "MoveMiddleToFirstName")

class CMacroFunction_AuthorFix MoveMiddleToFirstName(); - moves middle name to first name and fixes t...

bool SetFieldsByName(CMQueryNodeValue::TObs *results, CObjectInfo &oi_i, const string &field_name)

Resolve not necessarily existing dot qualified ASN.1 name (field_name) starting from the object infor...

static const char * sm_FuncPages

void x_RemoveAffilField(objects::CAuth_list &auth_list, const string &field)

static const char * sm_PubStatus

void x_RemoveJournalInPubdesc(objects::CPubdesc &pubdesc)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

objects::edit::EExistingText ActionTypeToExistingTextOption(const string &action_type, const string &delimiter)

static const char * sm_PubTitle

class CMacroFunction_PubFields PUB_TITLE(), PUB_ISSUE(), PUB_AFFIL(subfield) - returns a list of CObj...

static const char * sm_PubDOI

static void s_BuildName(const string &firstname, const string &mid_initials, const string &lastname, const string &suffix, objects::CName_std &name)

void x_GetObjectsForPubField_PMID(objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

const string & x_GetIsoJtaTitle(const objects::CTitle &title) const

static bool s_TruncateMiddleInitials(objects::CName_std &name)

vector< pair< string, string > > m_TitlePairs

int x_MakeAuthorChanges(objects::CAuth_list &auth_list)

CRef< CMQueryNodeValue > m_Result

static bool s_IsUnpublished(const string &citation)

static Int4 s_RemoveFields(CIRef< IMacroBioDataIter > &dataiter, CMQueryNodeValue::TObs &objs)

static string s_GetFirstNameInitialsWithoutStops(const string &first_name)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_AddDate(CMQueryNodeValue::TObs &objs)

void x_SetNewAuthor(objects::CAuth_list &auth_list, const string &field, const CMQueryNodeValue &value)

void SetStrings(const vector< string > &data)

void x_GetPubFieldObjectFromSubmitBlock(const CObjectInfo &block_oi, CMQueryNodeValue::TObs &objs)

static const char * sm_PubPMID

static set< TEntrezId > s_GatherExistingPMIDs(const CBioseq_Handle &bsh)

static const char * sm_PubDate

static const char * sm_PubAffil

void x_AddDateField(CMQueryNodeValue::TObs &objs)

void x_AddAuthorListInPubdesc(objects::CPubdesc &pubdesc)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static const char * sm_PubCit

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_LogFunction(CNcbiOstrstream &logstr)

string GetDOI(const objects::CPubdesc &pubdesc) const override

static void s_GetObjectsFromPersonID(const CObjectInfo &names, const string &field_name, CMQueryNodeValue::TObs &objs)

bool ApplyFirstName(objects::CName_std &std_name, const string &newValue, objects::edit::EExistingText existing_text)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_SetJournalInPubdesc(objects::CPubdesc &pubdesc, const string &value, objects::edit::EExistingText existing_text)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_SetObjects_Affil(objects::CPub &pub, CObjectInfo &pub_var)

static CMQueryNodeValue::TObs s_GetPubVolIssuePagesDateObjects(CPubdesc &pubdesc, const string &field)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static string s_GetStatus(const objects::CPubdesc &pubdesc)

void SetObjects(const TObs &obs)

virtual void TheFunction()

Function implementation.

static const char * sm_PubPages

static CRef< objects::CPub > s_GetArticleFromEntrezById(TEntrezId pmid, bool asn_format=false)

static CRef< CSeqdesc > s_MakeNewPubdesc(CRef< CPub > &new_pub, TEntrezId pmid)

static EActionType GetActionType(const string &descr)

static const char * sm_FuncIssue

void x_GetObjectsForPubField_Journal(const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)

void x_AddAuthor(objects::CAuth_list &auth_list, objects::edit::EExistingText existing_text)

static bool s_MoveMiddleToFirst(objects::CName_std &name)

static CObjectInfo s_GetRelevantObjectInfoForPub(const CPub &pub, const CObjectInfo &pub_var)

CIRef< IMacroBioDataIter > m_DataIter

SStaticPair< const char *, CMacroFunction_AuthorFix::EActionType > TAuthorFixPair

static CPubFieldType::EPubFieldStatus s_GetStatusEnum(const objects::CPub &pub)

void x_SetVolIssuePagesInPubdesc(objects::CPubdesc &pubdesc, const string &value, objects::edit::EExistingText existing_text)

static const char * sm_PubClass

virtual void TheFunction()

Function implementation.

static bool x_SetStatus(objects::CPub &pub, CPubFieldType::EPubFieldStatus status)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

static const TObjectType * SafeCast(TTypeInfo type)

#define MSerial_AsnText

I/O stream manipulators –.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

@ ePrimitiveValueString

string|char*|const char*

@ ePrimitiveValueInteger

(signed|unsigned) (char|short|int|long)

bool Valid(void) const

Is iterator valid.

CElementIterator BeginElements(void) const

Create container elements iterator.

TMemberIndex GetMemberIndex(void) const

Get index of the member in the class.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

CObjectInfo GetPointedObject(void) const

Get data and type information of object to which this type refers.

CObjectInfo GetElement(void) const

Get element data and type information.

CMemberIterator BeginMembers(void) const

Create class member iterator.

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

CObjectInfo GetMember(void) const

Get class member data.

TMemberIndex GetCurrentChoiceVariantIndex(void) const

Get index of currently selected choice variant.

CChoiceVariant GetCurrentChoiceVariant(void) const

Get data and type information of selected choice variant.

int GetPrimitiveValueInt(void) const

Get data as int.

CObjectInfo GetVariant(void) const

Get variant data.

bool Valid(void) const

Is iterator valid.

ETypeFamily GetTypeFamily(void) const

Get data type family.

void GetPrimitiveValueString(string &value) const

Get string data.

CMemberIterator FindClassMember(const string &memberName) const

Find class member by its name.

const string & GetName(void) const

Get type name.

void SetPrimitiveValueInt(int value)

EPrimitiveValueType GetPrimitiveValueType(void) const

Get type of primitive value.

bool IsSet(void) const

Is member assigned a value.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

bool IsSetClass(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eTrunc_End

Truncate trailing whitespace only.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

CTime CurrentTime(CTime::ETimeZone tz=CTime::eLocal, CTime::ETimeZonePrecision tzp=CTime::eTZPrecisionDefault)

bool IsProc(void) const

Check if variant Proc is selected.

void SetBook(TBook &value)

Assign a value to Book data member.

const TBook & GetBook(void) const

Get the Book member data.

bool IsSetAuthors(void) const

Check if a value has been assigned to Authors data member.

bool IsSetAuthors(void) const

authors (ANSI requires) Check if a value has been assigned to Authors data member.

const TJournal & GetJournal(void) const

Get the variant data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

const TFrom & GetFrom(void) const

Get the From member data.

const TCit & GetCit(void) const

Get the Cit member data.

void ResetNames(void)

Reset Names data member.

void SetName(TName &value)

Assign a value to Name data member.

void SetAffil(TAffil &value)

Assign a value to Affil data member.

bool IsSetFrom(void) const

Check if a value has been assigned to From data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetAuthors(void) const

not necessarily authors of the paper Check if a value has been assigned to Authors data member.

const TName & GetName(void) const

Get the Name member data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void ResetPrepub(void)

Reset Prepub data member.

bool IsSetCit(void) const

anything, not parsable Check if a value has been assigned to Cit data member.

const TProc & GetProc(void) const

Get the variant data.

list< CRef< CAuthor > > TStd

void SetCit(TCit &value)

Assign a value to Cit data member.

void ResetCit(void)

Reset Cit data member.

bool IsSetNames(void) const

Check if a value has been assigned to Names data member.

void SetCit(const TCit &value)

Assign a value to Cit data member.

void SetNames(TNames &value)

Assign a value to Names data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

bool IsSetName(void) const

Author, Primary or Secondary Check if a value has been assigned to Name data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsBook(void) const

Check if variant Book is selected.

bool IsJournal(void) const

Check if variant Journal is selected.

const TNames & GetNames(void) const

Get the Names member data.

bool IsMl(void) const

Check if variant Ml is selected.

const TStd & GetStd(void) const

Get the variant data.

void SetPrepub(TPrepub value)

Assign a value to Prepub data member.

const TMl & GetMl(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

Tdata & Set(void)

Assign a value to data member.

bool IsStd(void) const

Check if variant Std is selected.

const TBook & GetBook(void) const

Get the variant data.

@ e_not_set

No variant selected.

@ ePrepub_in_press

accepted, not published

void SetYear(TYear value)

Assign a value to Year data member.

void ResetLast(void)

Reset Last data member.

void SetInitials(const TInitials &value)

Assign a value to Initials data member.

bool IsSetSuffix(void) const

Jr, Sr, III Check if a value has been assigned to Suffix data member.

void ResetInitials(void)

Reset Initials data member.

const TInitials & GetInitials(void) const

Get the Initials member data.

void ResetFirst(void)

Reset First data member.

bool IsName(void) const

Check if variant Name is selected.

void SetLast(const TLast &value)

Assign a value to Last data member.

void SetFirst(const TFirst &value)

Assign a value to First data member.

bool IsSetInitials(void) const

first + middle initials Check if a value has been assigned to Initials data member.

TConsortium & SetConsortium(void)

Select the variant.

bool IsSetLast(void) const

Check if a value has been assigned to Last data member.

void SetSuffix(const TSuffix &value)

Assign a value to Suffix data member.

TName & SetName(void)

Select the variant.

TYear GetYear(void) const

Get the Year member data.

const TFirst & GetFirst(void) const

Get the First member data.

const TLast & GetLast(void) const

Get the Last member data.

bool IsSetFirst(void) const

Check if a value has been assigned to First data member.

const TStd & GetStd(void) const

Get the variant data.

void ResetSuffix(void)

Reset Suffix data member.

EPublication_field

publication fields

@ ePublication_field_affiliation

@ ePublication_field_pages

@ ePublication_field_pmid

@ ePublication_field_pub_class

@ ePublication_field_issue

@ ePublication_field_date

@ ePublication_field_title

@ ePublication_field_serial_number

@ ePublication_field_authors

@ ePublication_field_volume

@ ePublication_field_journal

bool IsPmid(void) const

Check if variant Pmid is selected.

TProc & SetProc(void)

Select the variant.

TPmid & SetPmid(void)

Select the variant.

TBook & SetBook(void)

Select the variant.

const TArticle & GetArticle(void) const

Get the variant data.

bool IsSet(void) const

Check if a value has been assigned to data member.

const Tdata & Get(void) const

Get the member data.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

E_Choice Which(void) const

Which variant is currently selected.

TMan & SetMan(void)

Select the variant.

TSub & SetSub(void)

Select the variant.

bool IsSub(void) const

Check if variant Sub is selected.

virtual void Reset(void)

Reset the whole object.

TGen & SetGen(void)

Select the variant.

const TGen & GetGen(void) const

Get the variant data.

TPatent & SetPatent(void)

Select the variant.

bool IsArticle(void) const

Check if variant Article is selected.

TArticle & SetArticle(void)

Select the variant.

bool IsGen(void) const

Check if variant Gen is selected.

bool IsMan(void) const

Check if variant Man is selected.

@ e_Pat_id

identify a patent

@ e_Gen

general or generic unparsed

@ e_Proc

proceedings of a meeting

@ e_Equiv

to cite a variety of ways

@ e_Man

manuscript, thesis, or letter

@ eClass_nuc_prot

nuc acid and coded proteins

void SetPub(TPub &value)

Assign a value to Pub data member.

TPub & SetPub(void)

Select the variant.

virtual void Reset(void)

Reset the whole object.

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

const TPub & GetPub(void) const

Get the Pub member data.

@ e_Pub

a reference to the publication

@ eMol_na

just a nucleic acid

const TCit & GetCit(void) const

Get the Cit member data.

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

Functions that resolve field names described in asn format.

constexpr bool empty(list< Ts... >) noexcept

const GenericPointer< typename T::ValueType > T2 value

Utility macros and typedefs for exploring NCBI objects from pub.asn.

#define EDIT_EACH_PUB_ON_PUBEQUIV(Itr, Var)

string GetFirstInitial(string input, bool skip_rest)

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

static const char delimiter[]

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

@ eExistingText_append_none

@ eExistingText_prefix_none

@ eExistingText_replace_old

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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