SBMLHttpResolverExample.cpp

Example of the definition and use of an SBMLHttpResolver for working with SBML “comp” files.

Example of the definition and use of an SBMLHttpResolver for working with SBML “comp” files.

/**
 * @file    SBMLHttpResolverExample.cpp
 * @brief   Example of the definition of an SBMLHttpResolver, and how one would 
 *          use it.
 * @author  Frank 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.
 * ------------------------------------------------------------------------ -->
 *
 * @class SBMLHttpResolver
 * @brief resolves HTTP documents, based on 
 * http://stackoverflow.com/questions/9786150/save-curl-content-result-into-a-string-in-c
 */
 
#include <iostream>
#include <string>
 
#include <curl/curl.h>
 
#include <sbml/SBMLTypes.h>
#include <sbml/packages/comp/common/CompExtensionTypes.h>
#include <sbml/packages/comp/util/SBMLResolver.h>
#include <sbml/packages/comp/util/SBMLResolverRegistry.h>
#include <sbml/packages/comp/util/SBMLUri.h>
 
LIBSBML_CPP_NAMESPACE_USE
using namespace std;
 
 
static size_t WriteCallback(void *contents, size_t size,
                            size_t nmemb, void *userp)
{
    ((std::string*)userp)->append((char*)contents, size * nmemb);
    return size * nmemb;
}
 
 
class LIBSBML_EXTERN SBMLHttpResolver : public SBMLResolver
{
public:
 
    /**
     * Creates a new SBMLHttpResolver object.
     */
    SBMLHttpResolver ()
    {
    }
 
 
    /**
     * Copy constructor; creates a copy of an SBMLHttpResolver object.
     *
     * @param c the SBMLHttpResolver object to copy.
     *
     * @throws @if python ValueError @else SBMLConstructorException @endif@~
     * Thrown if the argument @p orig is @c NULL.
     */
    SBMLHttpResolver(const SBMLHttpResolver& c)
    {
 
    }
 
 
    /**
     * Destroy this SBMLHttpResolver object.
     */
    virtual ~SBMLHttpResolver ()
    {
    }
 
 
    /**
     * Assignment operator for SBMLHttpResolver.
     *
     * @param rhs The object whose values are used as the basis of the
     * assignment.
     *
     * @throws @if python ValueError @else SBMLConstructorException @endif@~
     * Thrown if the argument @p rhs is @c NULL.
     */
    SBMLHttpResolver& operator=(const SBMLHttpResolver& rhs)
    {
        return *this;
    }
 
 
    /**
     * Creates and returns a deep copy of this SBMLHttpResolver object.
     *
     * @return a (deep) copy of this SBMLHttpResolver object.
     */
    virtual SBMLHttpResolver* clone() const
    {
        return new SBMLHttpResolver(*this);
    }
 
    /**
     * resolve the document for the given uri
     *
     * @param uri the uri to the target document
     * @param baseUri base uri, in case the uri is a relative one
     *
     * @return  the document, if this resolver can resolve the document or NULL.
     */
    virtual SBMLDocument* resolve(const std::string &uri,
                                  const std::string& baseUri="") const
    {
        SBMLUri * resolved = resolveUri(uri, baseUri);
        if (resolved == NULL)
            return NULL;
 
        CURL *curl;
        CURLcode res;
        std::string readBuffer;
 
        curl = curl_easy_init();
        if(curl) 
        {
            curl_easy_setopt(curl, CURLOPT_URL, resolved->getUri().c_str());
            curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, WriteCallback);
            curl_easy_setopt(curl, CURLOPT_WRITEDATA, &readBuffer);
            res = curl_easy_perform(curl);
            curl_easy_cleanup(curl);
 
            if (res == CURLE_OK)
                return readSBMLFromString(readBuffer.c_str());
 
            // here is where errors could be handled, like
            // as would occur whenever a network issue arrises.      
        }
 
        // something went wrong ... 
        return NULL;
    }
 
 
    /**
     * resolve the full uri for the given uri without actually reading the document
     *
     * @param uri the uri to the target document
     * @param baseUri base uri, in case the uri is a relative one
     *
     * @return  the full uri to the document, if this resolver can resolve the document or NULL.
     */
    virtual SBMLUri* resolveUri(const std::string &sUri,
                                const std::string& sBaseUri="") const
    {
        SBMLUri uri(sUri);
 
        if (uri.getScheme() != "http")
        {
            // this example just displays how to resolve http uris, so if we don't have one of those, 
            // bail
            return NULL;
        }
 
        // here we could get fancy and construct relative uris ... but for 
        // now this is good enough :) 
 
        return new SBMLUri(uri);
    }
 
 
protected:
 
private:
 
};
 
 
int resolveModelFromUri(const std::string& uri)
{
    // create an external document to test
    SBMLDocument doc(new CompPkgNamespaces());
    CompSBMLDocumentPlugin* plugin = (CompSBMLDocumentPlugin*)doc.getPlugin("comp");
  
    // create an external model definition 
    ExternalModelDefinition *external = plugin->createExternalModelDefinition();
    external->setSource(uri);
 
    Model* model = external->getReferencedModel();
    if (model == NULL)
    {
        // bummer something went wrong ... 
        return -1;
    }
 
    // do something with the model
    if (model->isSetId())
        cout << "resolved: " << model->getId() << endl;
    else
        cout << "resolved: " << uri << endl;
 
    if (model->isSetNotes())
        cout << model->getNotesString() << endl << endl;
 
    // all good
    return 0;
}
 
int main(void)
{
    // create http resolver 
    SBMLHttpResolver resolver;
 
    // the resolver can of course already be used: 
 
    SBMLDocument* originalBM1 =
        resolver.resolve("http://www.ebi.ac.uk/biomodels/models-main/publ/BIOMD0000000001/BIOMD0000000001.xml.origin");
    if (originalBM1 != NULL)
    {
        if (originalBM1->getModel()->isSetId())
            cout << "resolved: " << originalBM1->getModel()->getId() << endl;
        else 
            cout << "resolved: " << "BIOMD0000000001.xml.origin" << endl;
    }
    else
    {
        cout << "an error occured while trying to resolve the document. " << endl;
    }
 
    // but usually what one would do would be to 
    // add it to the registry
    SBMLResolverRegistry::getInstance().addResolver(&resolver);
 
    // and then go from there ...
    if (resolveModelFromUri("http://www.ebi.ac.uk/biomodels/models-main/publ/BIOMD0000000001/BIOMD0000000001.xml.origin") != 0 )
    {
        cout << "Comp V1 does not support L2V1 documents!" << endl;
    }
 
    if (resolveModelFromUri("http://www.ebi.ac.uk/biomodels-main/download?mid=BMID000000063853") != 0 )
    {
        cout << "something went wrong while getting the l3v1." << endl;
    }
 
    if (resolveModelFromUri("http://sbml.svn.sourceforge.net/viewvc/sbml/branches/libsbml-packages/comp/src/sbml/packages/comp/util/test/test-data/subdir/new_aggregate.xml?revision=16695") != 0 )
    {
        cout << "something went wrong while getting the l3v1 comp model." << endl;
    }
 
    cout << "done!";
 
    return 0;
}