CitationManager Class Reference

Citation manager class. More...

#include <src/cite.h>

Classes
struct	Private

Public Member Functions
void	insert (const DString &label)
	Insert a citation identified by label into the database.
const CiteInfo *	find (const DString &label) const
	Return the citation info for a given label.
void	generatePage ()
	Generate the citations page.
void	clear ()
	clears the database
bool	empty () const
	return true if there are no citations.
DString	latexBibFiles ()
	lists the bibtex cite files in a comma separated list
DString	fileName () const
DString	anchorPrefix () const

Static Public Member Functions
static CitationManager &	instance ()

Private Member Functions
	CitationManager ()
	Create the database, with an expected maximum of size entries.
	~CitationManager ()=default
void	insertCrossReferencesForBibFile (const DString &bibFile)
DString	getFormulas (const DString &s)
DString	replaceFormulas (const DString &s)

Private Attributes
std::unique_ptr< Private >	p

Detailed Description

Citation manager class.

This class provides access do the database of bibliographic references through the bibtex backend.

Definition at line 84 of file cite.h.

Constructor & Destructor Documentation

CitationManager()

CitationManager::CitationManager ( )

private

Create the database, with an expected maximum of size entries.

Definition at line 92 of file cite.cpp.

                                 : p(new Private)
{
}

References p.

Referenced by instance(), and ~CitationManager().

~CitationManager()

CitationManager::~CitationManager ( )

privatedefault

References CitationManager(), getFormulas(), insertCrossReferencesForBibFile(), NON_COPYABLE, and replaceFormulas().

Member Function Documentation

anchorPrefix()

DString CitationManager::anchorPrefix

(

)

const

Definition at line 127 of file cite.cpp.

{
  return "CITEREF_";
}

Referenced by DocAnchor::DocAnchor(), DocCite::DocCite(), LatexDocVisitor::operator()(), and TextDocVisitor::operator()().

clear()

void CitationManager::clear

(

)

clears the database

Definition at line 111 of file cite.cpp.

{
  p->entries.clear();
}

References p.

Referenced by clearAll().

empty()

bool CitationManager::empty

(

)

const

return true if there are no citations.

Definition at line 116 of file cite.cpp.

{
  size_t numFiles = Config_getList(CITE_BIB_FILES).size();
  return (numFiles==0 || p->entries.empty());
}

References Config_getList, and p.

Referenced by generatePage(), substituteLatexKeywords(), writeLatexMakefile(), and writeMakeBat().

fileName()

DString CitationManager::fileName

(

)

const

Definition at line 122 of file cite.cpp.

{
  return "citelist";
}

Referenced by DocAnchor::DocAnchor(), DocCite::DocCite(), and generatePage().

find()

const CiteInfo * CitationManager::find

(

const DString &

label

)

const

Return the citation info for a given label.

Ownership of the info stays with the manager.

Definition at line 102 of file cite.cpp.

{
  if (auto it = p->entries.find(label.lower().str()); it != p->entries.end())
  {
    return it->second.get();
  }
  return nullptr;
}

References DString::lower(), p, and DString::str().

Referenced by DocAnchor::DocAnchor(), DocCite::DocCite(), DocCite::getText(), and insertCrossReferencesForBibFile().

generatePage()

void CitationManager::generatePage

(

)

Generate the citations page.

Definition at line 332 of file cite.cpp.

{
  //printf("** CitationManager::generatePage() count=%d\n",m_ordering.count());
 
  // do not generate an empty citations page
  if (empty()) return; // nothing to cite
 
  bool citeDebug = Debug::isFlagSet(Debug::Cite);
 
  // 0. add cross references from the bib files to the cite dictionary
  StringVector citeDataList = Config_getList(CITE_BIB_FILES);
  for (const auto &bibdata : citeDataList)
  {
    DString bibFile = getBibFile(bibdata);
    insertCrossReferencesForBibFile(bibFile);
  }
 
  // 1. generate file with markers and citations to OUTPUT_DIRECTORY
  DString outputDir = Config_getString(OUTPUT_DIRECTORY);
  DString citeListFile = outputDir+"/citelist.doc";
  {
    std::ofstream t = Portable::openOutputStream(citeListFile);
    if (!t.is_open())
    {
      err("could not open file {} for writing\n",citeListFile);
    }
    t << "<!-- BEGIN CITATIONS -->\n";
    t << "<!--\n";
    for (const auto &it : p->entries)
    {
      t << "\\citation{" << it.second->label() << "}\n";
    }
    t << "-->\n";
    t << "<!-- END CITATIONS -->\n";
    t << "<!-- BEGIN BIBLIOGRAPHY -->\n";
    t << "<!-- END BIBLIOGRAPHY -->\n";
    t.close();
  }
 
  // 2. generate bib2xhtml
  DString bib2xhtmlFile  = outputDir+"/bib2xhtml.pl";
  ResourceMgr::instance().copyResource("bib2xhtml.pl",outputDir);
 
  // 3. generate doxygen.bst
  DString doxygenBstFile = outputDir+"/doxygen.bst";
  ResourceMgr::instance().copyResource("doxygen.bst",outputDir);
 
  // 4. for all formats we just copy the bib files to as special output directory
  //    so bibtex can find them without path (bibtex doesn't support paths or
  //    filenames with spaces!)
  //    Strictly not required when only latex is generated
  DString bibOutputDir = outputDir+"/"+bibTmpDir;
  DString bibOutputFiles = "";
  Dir thisDir;
  if (!thisDir.exists(bibOutputDir.str()) && !thisDir.mkdir(bibOutputDir.str()))
  {
    err("Failed to create temporary output directory '{}', skipping citations\n",bibOutputDir);
    return;
  }
  size_t i = 0;
  for (const auto &bibdata : citeDataList)
  {
    DString bibFile = getBibFile(bibdata);
    FileInfo fi(bibFile.str());
    if (fi.exists())
    {
      if (!bibFile.empty())
      {
        ++i;
        std::ifstream f_org = Portable::openInputStream(bibFile);
        if (!f_org.is_open())
        {
          err("could not open file {} for reading\n",bibFile);
        }
        std::ofstream f_out = Portable::openOutputStream(bibOutputDir + bibTmpFile + DString().setNum(i) + ".bib");
        if (!f_out.is_open())
        {
          err("could not open file {}{}{:d}{} for reading\n",bibOutputDir,bibTmpFile,i,".bib");
        }
        DString docs;
        std::string lineStr;
        while (getline(f_org,lineStr))
        {
          docs += lineStr + "\n";
        }
        docs = getFormulas(docs);
        f_out << docs;
        if (f_org.is_open()) f_org.close();
        if (f_out.is_open()) f_out.close();
        bibOutputFiles = bibOutputFiles + " " + bibTmpDir + bibTmpFile + DString().setNum(i) + ".bib";
      }
    }
  }
 
  std::string oldDir = Dir::currentDirPath();
  Dir::setCurrent(outputDir.str());
 
  // 5. run bib2xhtml perl script on the generated file which will insert the
  //    bibliography in citelist.doc
  DString perlArgs = "\""+bib2xhtmlFile+"\" "+bibOutputFiles+" \""+ citeListFile+"\"";
  if (citeDebug) perlArgs+=" -d";
  int exitCode = Portable::system("perl",perlArgs);
  if (exitCode!=0)
  {
    err("Problems running bibtex. Verify that the command 'perl --version' works from the command line. Exit code: {}\n",
        exitCode);
  }
 
  Dir::setCurrent(oldDir);
 
  // 6. read back the file
  DString doc;
  {
    std::ifstream f = Portable::openInputStream(citeListFile);
    if (!f.is_open())
    {
      err("could not open file {} for reading\n",citeListFile);
    }
 
    bool insideBib=false;
    //printf("input=[%s]\n",qPrint(input));
    std::string lineStr;
    while (getline(f,lineStr))
    {
      DString line(lineStr);
      //printf("pos=%d s=%d line=[%s]\n",pos,s,qPrint(line));
 
      if      (line.find("<!-- BEGIN BIBLIOGRAPHY")!=DString::npos) insideBib=true;
      else if (line.find("<!-- END BIBLIOGRAPH")!=DString::npos)    insideBib=false;
      // determine text to use at the location of the @cite command
      if (insideBib && ((i=line.find("name=\"CITEREF_"))!=DString::npos || (i=line.find("name=\"#CITEREF_"))!=DString::npos))
      {
        size_t j=line.find("\">[");
        size_t j1=line.find("<!--[");
        size_t k=line.find("]<!--");
        size_t k1=line.find("]-->");
        if (j!=DString::npos && k!=DString::npos)
        {
          DString label       = line.mid(i+14,j-i-14);
          StringVector optList = split(line.mid(j1+5,k1-j1-5).str(),",");
          DString number      = optList[0];
          DString shortAuthor = optList[1];
          DString year;
          if (optList.size() == 3)
          {
            year = optList[2];
          }
          line = line.left(i+14) + label + line.mid(j);
          auto it = p->entries.find(label.lower().str());
          //printf("label='%s' number='%s' => %p\n",qPrint(label),qPrint(number),it->second.get());
          if (it!=p->entries.end())
          {
            it->second->setText(number);
            it->second->setShortAuthor(shortAuthor);
            it->second->setYear(year.stripWhiteSpace());
          }
        }
      }
      if (insideBib) doc+=line+"\n";
    }
    //printf("doc=[%s]\n",qPrint(doc));
  }
 
  // 7. place formulas back and run the conversion of \f$ ... \f$ to the internal required format
  {
    doc = replaceFormulas(doc);
    Entry            current;
    bool             needsEntry = false;
    CommentScanner   commentScanner;
    int              lineNr = 0;
    int              pos = 0;
    GuardedSectionStack guards;
    Protection       prot = Protection::Public;
    commentScanner.parseCommentBlock(
        nullptr,
        &current,
        doc,          // text
        fileName(),   // file
        lineNr,       // line of block start
        false,        // isBrief
        false,        // isJavaDocStyle
        false,        // isInBody
        prot,         // protection
        pos,          // position,
        needsEntry,
        false,
        &guards
        );
    doc = current.doc;
  }
 
  // 8. add it as a page
  addRelatedPage(fileName(),theTranslator->trCiteReferences(),doc,fileName(),1,1);
 
  // 9. for latex we just copy the bib files to the output and let
  //    latex do this work.
  if (Config_getBool(GENERATE_LATEX))
  {
    // copy bib files to the latex output dir
    DString latexOutputDir = Config_getString(LATEX_OUTPUT)+"/";
    i = 0;
    for (const auto &bibdata : citeDataList)
    {
      DString bibFile = getBibFile(bibdata);
      FileInfo fi(bibFile.str());
      if (fi.exists())
      {
        if (!bibFile.empty())
        {
          // bug_700510, multiple times the same name were overwriting; creating new names
          // also for names with spaces
          ++i;
          copyFile(bibFile,latexOutputDir + bibTmpFile + DString().setNum(i) + ".bib");
        }
      }
      else
      {
        err("bib file {} not found!\n",bibFile);
      }
    }
  }
 
  // 10. Remove temporary files
  if (!citeDebug)
  {
    thisDir.remove(citeListFile.str());
    thisDir.remove(doxygenBstFile.str());
    thisDir.remove(bib2xhtmlFile.str());
    // we might try to remove too many files as empty files didn't get a corresponding new file
    // but the remove function does not emit an error for it and we don't catch the error return
    // so no problem.
    for (size_t j = 1; j <= citeDataList.size(); j++)
    {
      DString bibFile = bibOutputDir + bibTmpFile + DString().setNum(static_cast<int>(j)) + ".bib";
      thisDir.remove(bibFile.str());
    }
    thisDir.rmdir(bibOutputDir.str());
  }
}

References addRelatedPage(), bibTmpDir, bibTmpFile, Debug::Cite, Config_getBool, Config_getList, Config_getString, copyFile(), ResourceMgr::copyResource(), Dir::currentDirPath(), Entry::doc, DString::DString(), empty(), DString::empty(), err, Dir::exists(), FileInfo::exists(), fileName(), DString::find(), getBibFile(), getFormulas(), insertCrossReferencesForBibFile(), ResourceMgr::instance(), Debug::isFlagSet(), DString::left(), DString::lower(), DString::mid(), Dir::mkdir(), DString::npos, Portable::openInputStream(), Portable::openOutputStream(), p, CommentScanner::parseCommentBlock(), Dir::remove(), replaceFormulas(), Dir::rmdir(), Dir::setCurrent(), split(), DString::str(), DString::stripWhiteSpace(), Portable::system(), theTranslator, and Translator::trCiteReferences().

Referenced by parseInput().

getFormulas()

DString CitationManager::getFormulas ( const DString & s )

private

Definition at line 237 of file cite.cpp.

{
  if (s.empty()) return s;
  DString result;
  result.reserve(s.length()+32);
  DString formula;
  formula.reserve(256);
  bool insideFormula = false;
  int citeFormulaCnt = 1;
  const char *ps=s.data();
  char c = 0;
  while ((c=*ps++))
  {
    if (insideFormula)
    {
      switch (c)
      {
        case '\\':
          formula+=c;
          c = *ps++;
          formula+=c;
          break;
        case '\n':
          formula+=c;
          result+='$';
          result+=formula;
          insideFormula = false;
          formula.clear();
          break;
        case '$':
          {
            const size_t idLen = 30;
            char id[idLen];
            snprintf(id,idLen,"%s%06d",g_formulaMarker.c_str(),citeFormulaCnt);
            p->formulaCite.emplace(citeFormulaCnt,std::string("\\f$") + formula.str() + "\\f$");
            citeFormulaCnt++;
            // need { and } due to the capitalization rules of bibtex.
            result+='{';
            result+=id;
            result+='}';
            insideFormula = false;
            formula.clear();
          }
          break;
        default:
          formula+=c;
          break;
      }
    }
    else
    {
      switch (c)
      {
        case '\\':
          result+=c;
          c = *ps++;
          result+=c;
          break;
        case '$':
          insideFormula = true;
          break;
        default:
          result+=c;
          break;
      }
    }
  }
  if (insideFormula)
  {
    result+=formula;
    formula.clear();
  }
  return result;
}

References DString::clear(), DString::data(), DString::empty(), g_formulaMarker, DString::length(), p, DString::reserve(), and DString::str().

Referenced by generatePage(), and ~CitationManager().

insert()

void CitationManager::insert

(

const DString &

label

)

Insert a citation identified by label into the database.

Definition at line 96 of file cite.cpp.

{
  DString lowerCaseLabel = label.lower();
  p->entries.emplace(lowerCaseLabel.str(),std::make_unique<CiteInfoImpl>(lowerCaseLabel));
}

References DString::lower(), p, and DString::str().

Referenced by addCite(), and insertCrossReferencesForBibFile().

insertCrossReferencesForBibFile()

void CitationManager::insertCrossReferencesForBibFile ( const DString & bibFile )

private

Definition at line 132 of file cite.cpp.

{
  // sanity checks
  if (bibFile.empty())
  {
    return;
  }
  FileInfo fi(bibFile.str());
  if (!fi.exists())
  {
    err("bib file {} not found!\n",bibFile);
    return;
  }
  std::ifstream f = Portable::openInputStream(bibFile);
  if (!f.is_open())
  {
    err("could not open file {} for reading\n",bibFile);
    return;
  }
 
  // search for citation cross references
  DString citeName;
 
  std::string lineStr;
  int lineCount = 0;
  while (getline(f,lineStr))
  {
    size_t i = DString::npos;
    DString line(lineStr);
    lineCount++;
    if (line.stripWhiteSpace().startsWith("@"))
    {
      // assumption entry like: "@book { name," or "@book { name" (spaces optional)
      size_t j = line.find('{');
      // when no {, go hunting for it
      while (j==DString::npos && getline(f,lineStr))
      {
        line = lineStr;
        lineCount++;
        j = line.find('{');
      }
      // search for the name
      citeName = "";
      if (!f.eof() && j!=DString::npos) // to prevent something like "@manual ," and no { found
      {
        size_t k = line.find(',',j);
        j++;
        // found a line "@....{.....,...." or "@.....{....."
        //                     ^=j  ^=k               ^=j   k=-1
        while (!f.eof() && citeName.empty())
        {
          if (k!=DString::npos)
          {
            citeName = line.mid(j,k-j);
          }
          else
          {
            citeName = line.mid(j);
          }
          citeName = citeName.stripWhiteSpace();
          j = 0;
          if (citeName.empty() && getline(f,lineStr))
          {
            line = lineStr;
            lineCount++;
            k = line.find(',');
          }
        }
      }
      //printf("citeName = #%s#\n",qPrint(citeName));
      if (!citeName.empty())
      {
        std::string lCiteName = citeName.lower().str();
        auto it = p->citePosition.find(lCiteName);
        if (it != p->citePosition.end())
        {
          warn(bibFile,lineCount,"multiple use of citation name '{}', (first occurrence: {}, line {})",
               lCiteName,it->second.fileName,it->second.lineNr);
        }
        else
        {
          p->citePosition.emplace(lCiteName,CitePosition(bibFile,lineCount));
        }
      }
    }
    else if ((i=line.find("crossref"))!=DString::npos && !citeName.empty()) /* assumption cross reference is on one line and the only item */
    {
      size_t j = line.find('{',i);
      size_t k = line.find('}',i);
      if (j!=DString::npos && k!=DString::npos && j>i && k>j)
      {
        DString crossrefName = line.mid(j+1,k-j-1);
        // check if the reference with the cross reference is used
        // insert cross reference when cross reference has not yet been added.
        if (find(citeName) && !find(crossrefName)) // not found yet
        {
          insert(crossrefName);
        }
      }
    }
  }
}

References CitePosition::CitePosition(), DString::empty(), err, FileInfo::exists(), find(), DString::find(), insert(), lineCount, DString::lower(), DString::mid(), DString::npos, Portable::openInputStream(), p, DString::startsWith(), DString::str(), DString::stripWhiteSpace(), and warn.

Referenced by generatePage(), and ~CitationManager().

instance()

CitationManager & CitationManager::instance ( )

static

Definition at line 86 of file cite.cpp.

{
  static CitationManager ct;
  return ct;
}

References CitationManager().

Referenced by addCite(), clearAll(), DocAnchor::DocAnchor(), DocCite::DocCite(), DocCite::getText(), LatexDocVisitor::operator()(), TextDocVisitor::operator()(), parseInput(), substituteLatexKeywords(), writeLatexMakefile(), and writeMakeBat().

latexBibFiles()

DString CitationManager::latexBibFiles

(

)

lists the bibtex cite files in a comma separated list

Definition at line 572 of file cite.cpp.

{
  DString result;
  StringVector citeDataList = Config_getList(CITE_BIB_FILES);
  int i = 0;
  for (const auto &bibdata : citeDataList)
  {
    DString bibFile = getBibFile(bibdata);
    FileInfo fi(bibFile.str());
    if (fi.exists() && !bibFile.empty())
    {
      if (i) result += ",";
      i++;
      result += bibTmpFile;
      result += DString().setNum(i);
    }
  }
  return result;
}

References bibTmpFile, Config_getList, DString::DString(), DString::empty(), FileInfo::exists(), getBibFile(), DString::setNum(), and DString::str().

Referenced by substituteLatexKeywords().

replaceFormulas()

DString CitationManager::replaceFormulas ( const DString & s )

private

Definition at line 312 of file cite.cpp.

{
  if (s.empty()) return s;
  DString t;
  size_t pos=0;
  size_t i = DString::npos;
  while ((i=s.find(g_formulaMarker,pos))!=DString::npos)
  {
    t += s.mid(pos,i-pos);
    int markerSize = static_cast<int>( g_formulaMarker.length());
    int markerId = atoi(s.mid(i+markerSize,6).data());
    auto it = p->formulaCite.find(markerId);
    if (it != p->formulaCite.end()) t += it->second;
    pos = i + markerSize+6;
  }
  t += s.mid(pos);
  //printf("replaceFormulas(%s)=%s\n",qPrint(s),qPrint(t));
  return t;
}

References DString::data(), DString::empty(), DString::find(), g_formulaMarker, DString::mid(), DString::npos, and p.

Referenced by generatePage(), and ~CitationManager().

Member Data Documentation

p

std::unique_ptr<Private> CitationManager::p

private

Definition at line 123 of file cite.h.

Referenced by CitationManager(), clear(), empty(), find(), generatePage(), getFormulas(), insert(), insertCrossReferencesForBibFile(), and replaceFormulas().

---

The documentation for this class was generated from the following files:

• src/cite.h
• src/cite.cpp