setIdFromNames.cpp

Program that renames all SIds that also have names specified. The new identifiers will be derived from the name, with all invalid characters removed.

/**
 * @file    setIdFromNames.cpp
 * @brief   Utility program, renaming all SIds that also have 
 *          names specified. The new id will be derived from 
 *          the name, with all invalid characters removed. 
 * @author  Frank T. Bergmann
 *
 * <!--------------------------------------------------------------------------
 * This sample program is distributed under a different license than the rest
 * of libSBML.  This program uses the open-source MIT license, as follows:
 *
 * Copyright (c) 2013-2018 by the California Institute of Technology
 * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
 * and the University of Heidelberg (Germany), with support from the National
 * Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
 *
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the "Software"),
 * to deal in the Software without restriction, including without limitation
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
 * and/or sell copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 * DEALINGS IN THE SOFTWARE.
 *
 * Neither the name of the California Institute of Technology (Caltech), nor
 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
 * of Heidelberg, nor the names of any contributors, may be used to endorse
 * or promote products derived from this software without specific prior
 * written permission.
 * ------------------------------------------------------------------------ -->
 */


#include <iostream>
#include <sstream>
#include <vector>
#include <string>

#include <sbml/SBMLTypes.h>
#include <sbml/common/extern.h>
#include <sbml/common/operationReturnValues.h>
#include "util.h"


using namespace std;
LIBSBML_CPP_NAMESPACE_USE


/** 
 * The NameIdTransformer class transforms the id of a given SBase 
 * element by replacing it with a string derived from the name. 
 * 
 * It won't do anything if the name is the same as the id, or if 
 * no name is set. 
 */ 
class NameIdTransformer : public IdentifierTransformer
{
public:
    NameIdTransformer(const vector<string> &ids) 
    : IdentifierTransformer()
    , existingIds(ids)
    {
    }

    /** 
     * The actual transform implementation
     */
    int transform(SBase* element)
    {
        // return in case we don't have a valid element
        if (element == NULL || element->getTypeCode() == SBML_LOCAL_PARAMETER)  
            return LIBSBML_OPERATION_SUCCESS;

        // or if there is nothing to do
        if (!element->isSetName() || element->getId() == element->getName())            
            return LIBSBML_OPERATION_SUCCESS;

        // find the new id
        string newId = getValidIdForName(element->getName());

        // set it
        element->setId(newId);

        // remember it
        existingIds.push_back(newId);
        
        return LIBSBML_OPERATION_SUCCESS;
            
    }

private: 

    /** 
     * Cleans the name, so it represents a valid SId
     * 
     * Taken from COPASI (released under the artistic license)
     * https://github.com/copasi/COPASI/blob/master/copasi/utilities/utility.cpp
     */ 
    std::string nameToSbmlId(const std::string & name)
    {
    // We convert all non allowed characters to '_'
    // letter ::= 'a'..'z','A'..'Z'
    // digit  ::= '0'..'9'
    // idChar ::= letter | digit | '_'
    // SId    ::= (letter | '_' ) idChar*
    
    std::ostringstream IdStream;
    
    std::string::const_iterator it = name.begin();
    std::string::const_iterator end = name.end();
    
    if ('0' <= *it && *it <= '9')
        {
        IdStream << '_';
        }
    
    for (; it != end; ++it)
        {
        // second, third or forth character of a multi-byte encoding
        if (0x80 == (*it & 0xc0))
            {
            continue;
            }
    
        if (('0' <= *it && *it <= '9') ||
            ('a' <= *it && *it <= 'z') ||
            ('A' <= *it && *it <= 'Z'))
            {
            IdStream << *it;
            }
        else
            {
            IdStream << '_';
            }
        }
    
    std::string Id = IdStream.str();
    
    if (Id[Id.length() - 1] != '_')
        {
        return Id;
        }
    
    return Id.substr(0, Id.length() - 1);
    }
    
    /** 
     * Generates the id out of the name, and ensures it is unique. 
     * It does so by appending numbers to the original name. 
     */ 
    string getValidIdForName(const string& name)
    {
        string base = nameToSbmlId(name);
        string id(base);
        int count = 1;
        while (containsId(id))
        {
            std::ostringstream idStream;
            idStream << base << "_" << count;
            id = idStream.str();
            ++count;
            
        }
        return id;
    }
    
    /** 
     * Checks whether the given id is already in the vector. 
     */  
    bool containsId(string &id)
    {
        vector<string>::const_iterator it = existingIds.begin();
        while(it != existingIds.end())
        {
            if ((*it) == id) return true;
            ++it;
        }
        return false;
    }
    
    vector<string> existingIds;
};

/**
 * Returns a list of all ids from the given list of elements
 */
vector<string> getAllIds(List* allElements)
{
    vector<string> result; 
    if (allElements == NULL || allElements->getSize() == 0) 
        return result;
    
    for (unsigned long int i = 0; i < allElements->getSize(); ++i)
    {
        const SBase* current = static_cast<const SBase*>(allElements->get(i));
        if (current->isSetId() && current->getTypeCode() != SBML_LOCAL_PARAMETER)
        {           
            result.push_back(current->getId());
        }
    }
    
    return result;
}

BEGIN_C_DECLS

int
main (int argc, char* argv[])
{
    if (argc != 3)
    {
        cout << endl << "Usage: setIdFromNames filename output" << endl << endl;
        return 1;
    }
    
    const char* filename   = argv[1];
    const char* output     = argv[2];
    
        
    SBMLDocument* document;
    SBMLReader reader;
#ifdef __BORLANDC__
    unsigned long start, stop;
#else
    unsigned long long start, stop;
#endif
    
    start    = getCurrentMillis();
    document = reader.readSBML(filename);
    stop     = getCurrentMillis();
    
    unsigned int errors = document->getNumErrors(LIBSBML_SEV_ERROR);
    
    cout << endl;
    cout << "            filename: " << filename              << endl;
    cout << "      read time (ms): " << stop - start          << endl;
    
    if (errors > 0)
    {
        cout << "            error(s): " << errors << endl;
        document->printErrors(cerr);
        delete document;
        return errors;
    }
    
    start = stop;
    
    // get a list of all elements, as we will need to know all identifiers
    // so that we don't create duplicates. 
    List* allElements = document->getAllElements(); 
    
    // get a list of all ids
    const vector<string>& allIds = getAllIds(allElements);
    
    // create the transformer with the ids
    NameIdTransformer trans(allIds);
    
    // rename the identifiers (using the elements we already gathered before)
    document->getModel()->renameIDs(allElements, &trans);    
    stop     = getCurrentMillis();
    cout << "    rename time (ms): " << stop - start          << endl;
    start = stop;
    
    // write to file
    writeSBMLToFile(document, output);
    stop     = getCurrentMillis();
    cout << "     write time (ms): " << stop - start          << endl;   
    cout << endl;
    
    delete document;
    return errors;
}

END_C_DECLS