setIdFromNames.cpp

Program that renames all SIds that also have names specified.

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 allElements;
    delete document;
    return errors;
}
 
END_C_DECLS