Cppcheck report - MOAB: src/io/WriteNC.cpp

#include "WriteNC.hpp"
#include "moab/CN.hpp"
#include "MBTagConventions.hpp"
#include "MBParallelConventions.h"
#include "moab/Interface.hpp"
#include "moab/Range.hpp"
#include "moab/WriteUtilIface.hpp"
#include "moab/FileOptions.hpp"
#include "NCWriteHelper.hpp"

#include <fstream>
#include <map>
#include <set>

#include <iostream>
#include <sstream>

#ifdef WIN32
#ifdef size_t
#undef size_t
#endif
#endif

namespace moab
{

WriterIface* WriteNC::factory( Interface* iface )
{
    return new WriteNC( iface );
}

WriteNC::WriteNC( Interface* impl )
    : mbImpl( impl ), dbgOut( stderr ),
#ifdef MOAB_HAVE_MPI
      myPcomm( NULL ),
#endif
      noMesh( false ), noVars( false ), append( false ), mGlobalIdTag( 0 ), isParallel( false ), myHelper( NULL )
{
    assert( impl != NULL );
    impl->query_interface( mWriteIface );
}

WriteNC::~WriteNC()
{
    mbImpl->release_interface( mWriteIface );
    if( myHelper != NULL ) delete myHelper;
}

//! Writes out a file
ErrorCode WriteNC::write_file( const char* file_name,
                               const bool overwrite,
                               const FileOptions& options,
                               const EntityHandle* file_set,
                               const int num_set,
                               const std::vector< std::string >&,
                               const Tag*,
                               int,
                               int )
{
    ErrorCode rval;
    // See if opts has variable(s) specified
    std::vector< std::string > var_names;
    std::vector< std::string > desired_names;
    std::vector< int > tstep_nums;
    std::vector< double > tstep_vals;

    // Get and cache predefined tag handles
    mGlobalIdTag = mbImpl->globalId_tag();

    // num set has to be 1, we will write only one set, the original file set used to load
    if( num_set != 1 ) MB_SET_ERR( MB_FAILURE, "We should write only one set (the file set used to read data into)" );

    rval = parse_options( options, var_names, desired_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );

    // Important to create some data that will be used to write the file; dimensions, variables, etc
    // new variables still need to have some way of defining their dimensions
    // maybe it will be passed as write options
    rval = process_conventional_tags( *file_set );MB_CHK_SET_ERR( rval, "Trouble processing conventional tags" );

    // Create or append the file
    if( append )
        dbgOut.tprintf( 1, "opening file %s for appending \n", file_name );
    else
        dbgOut.tprintf( 1, "creating file %s\n", file_name );
    fileName = file_name;
    int success;

    if( append )
    {
        int omode = NC_WRITE;
#ifdef MOAB_HAVE_PNETCDF
        if( isParallel )
            success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, omode, MPI_INFO_NULL, &fileId );
        else
            success = NCFUNC( open )( MPI_COMM_SELF, file_name, omode, MPI_INFO_NULL, &fileId );
#else
        // This is a regular netcdf file, open in write mode
        success = NCFUNC( open )( file_name, omode, &fileId );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name << " for appending" );
    }
    else
    {  // Case when the file is new, will be overwritten, most likely
        int cmode = overwrite ? NC_CLOBBER : NC_NOCLOBBER;
#ifdef MOAB_HAVE_PNETCDF
        if( isParallel )
            success = NCFUNC( create )( myPcomm->proc_config().proc_comm(), file_name, cmode, MPI_INFO_NULL, &fileId );
        else
            success = NCFUNC( create )( MPI_COMM_SELF, file_name, cmode, MPI_INFO_NULL, &fileId );
#else
        // This is a regular netcdf file
        success = NCFUNC( create )( file_name, cmode, &fileId );
#endif
        if( success ) MB_SET_ERR( MB_FAILURE, "Trouble creating file " << file_name << " for writing" );
    }

    if( NULL != myHelper ) delete myHelper;

    // Get appropriate helper instance for WriteNC class based on some info in the file set
    myHelper = NCWriteHelper::get_nc_helper( this, fileId, options, *file_set );
    if( NULL == myHelper )
    {
        MB_SET_ERR( MB_FAILURE, "Failed to get NCWriteHelper class instance" );
    }

    rval = myHelper->collect_mesh_info();MB_CHK_SET_ERR( rval, "Trouble collecting mesh information" );

    rval = myHelper->collect_variable_data( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble collecting variable data" );

    rval = myHelper->init_file( var_names, desired_names, append );MB_CHK_SET_ERR( rval, "Trouble initializing file" );

    rval = myHelper->write_values( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble writing values to file" );

    success = NCFUNC( close )( fileId );
    if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );

    return MB_SUCCESS;
}

ErrorCode WriteNC::parse_options( const FileOptions& opts,
                                  std::vector< std::string >& var_names,
                                  std::vector< std::string >& desired_names,
                                  std::vector< int >& tstep_nums,
                                  std::vector< double >& tstep_vals )
{
    int tmpval;
    if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
    {
        dbgOut.set_verbosity( tmpval );
        dbgOut.set_prefix( "NCWrite" );
    }

    ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
    if( MB_TYPE_OUT_OF_RANGE == rval )
        noVars = true;
    else
        noVars = false;

    rval = opts.get_strs_option( "RENAME", desired_names );
    if( MB_ENTITY_NOT_FOUND == rval )
    {
        if( !noVars )
        {
            desired_names.resize( var_names.size() );
            std::copy( var_names.begin(), var_names.end(), desired_names.begin() );
        }
    }
    // Either way
    assert( desired_names.size() == var_names.size() );

    opts.get_ints_option( "TIMESTEP", tstep_nums );
    opts.get_reals_option( "TIMEVAL", tstep_vals );
    rval = opts.get_null_option( "NOMESH" );
    if( MB_SUCCESS == rval ) noMesh = true;

    rval = opts.get_null_option( "APPEND" );
    if( MB_SUCCESS == rval ) append = true;

    if( 2 <= dbgOut.get_verbosity() )
    {
        if( !var_names.empty() )
        {
            std::cerr << "Variables requested: ";
            for( unsigned int i = 0; i < var_names.size(); i++ )
                std::cerr << var_names[i];
            std::cerr << std::endl;
        }
        if( !tstep_nums.empty() )
        {
            std::cerr << "Timesteps requested: ";
            for( unsigned int i = 0; i < tstep_nums.size(); i++ )
                std::cerr << tstep_nums[i];
            std::cerr << std::endl;
        }
        if( !tstep_vals.empty() )
        {
            std::cerr << "Time vals requested: ";
            for( unsigned int i = 0; i < tstep_vals.size(); i++ )
                std::cerr << tstep_vals[i];
            std::cerr << std::endl;
        }
    }

// FIXME: copied from ReadNC, may need revise
#ifdef MOAB_HAVE_MPI
    isParallel = ( opts.match_option( "PARALLEL", "WRITE_PART" ) != MB_ENTITY_NOT_FOUND );

    if( !isParallel )
        // Return success here, since rval still has _NOT_FOUND from not finding option
        // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel
        // before any use for myPcomm
        return MB_SUCCESS;

    int pcomm_no = 0;
    rval         = opts.get_int_option( "PARALLEL_COMM", pcomm_no );
    if( MB_TYPE_OUT_OF_RANGE == rval )
    {
        MB_SET_ERR( rval, "Invalid value for PARALLEL_COMM option" );
    }

    myPcomm = ParallelComm::get_pcomm( mbImpl, pcomm_no );
    if( 0 == myPcomm )
    {
        myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
    }

#ifndef MOAB_HAVE_PNETCDF
    const int procs = myPcomm->proc_config().proc_size();
    if( procs > 1 )
    {
        MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Attempt to launch NC writer in parallel without pnetcdf support" );
    }
#endif

    const int rank = myPcomm->proc_config().proc_rank();
    dbgOut.set_rank( rank );
#endif

    return MB_SUCCESS;
}

// This is the inverse process to create conventional tags
// Will look at <pargal_source>/src/core/fileinfo.cpp, init dim, vars, atts
ErrorCode WriteNC::process_conventional_tags( EntityHandle fileSet )
{
    ErrorCode rval;

    // Start copy
    Tag dimNamesTag      = 0;
    std::string tag_name = "__DIM_NAMES";
    const void* data     = NULL;
    int dimNamesSz       = 0;
    rval                 = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, dimNamesTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( dimNamesTag, &fileSet, 1, &data, &dimNamesSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    const char* p = static_cast< const char* >( data );
    dbgOut.tprintf( 1, "__DIM_NAMES tag has string length %d\n", dimNamesSz );

    std::size_t start = 0;

    Tag dimLensTag = 0;
    tag_name       = "__DIM_LENS";
    data           = NULL;
    int dimLensSz  = 0;
    rval           = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, dimLensTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( dimLensTag, &fileSet, 1, &data, &dimLensSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    const int* int_p = static_cast< const int* >( data );
    dbgOut.tprintf( 1, "__DIM_LENS tag has %d values\n", dimLensSz );

    int idxDim = 0;
    // Dim names are separated by '\0' in the string of __DIM_NAMES tag
    for( std::size_t i = 0; i != static_cast< std::size_t >( dimNamesSz ); i++ )
    {
        if( p[i] == '\0' )
        {
            std::string dim_name( &p[start], i - start );
            int len = int_p[idxDim];
            dimNames.push_back( dim_name );
            dimLens.push_back( len );
            dbgOut.tprintf( 2, "Dimension %s has length %d\n", dim_name.c_str(), len );
            // FIXME: Need info from moab to set unlimited dimension
            // Currently assume each file has the same number of time dimensions
            /*if ((dim_name == "time") || (dim_name == "Time"))
              insert(dim_name, *(new pcdim(dim_name, len * m_file_names.size(), true)));
            else
              insert(dim_name, *(new pcdim(dim_name, len)));*/
            start = i + 1;
            idxDim++;
        }
    }

    Tag meshTypeTag = 0;
    tag_name        = "__MESH_TYPE";
    data            = NULL;
    int meshTypeSz  = 0;
    rval            = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( meshTypeTag, &fileSet, 1, &data, &meshTypeSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    p         = static_cast< const char* >( data );
    grid_type = std::string( &p[0], meshTypeSz );
    dbgOut.tprintf( 2, "Mesh type: %s\n", grid_type.c_str() );

    // Read <__VAR_NAMES_LOCATIONS> tag
    Tag varNamesLocsTag = 0;
    tag_name            = "__VAR_NAMES_LOCATIONS";
    data                = NULL;
    int varNamesLocsSz  = 0;
    rval                = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, varNamesLocsTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    rval = mbImpl->tag_get_by_ptr( varNamesLocsTag, &fileSet, 1, &data, &varNamesLocsSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    int_p = static_cast< const int* >( data );
    std::vector< int > varNamesLocs( varNamesLocsSz );
    std::copy( int_p, int_p + varNamesLocsSz, varNamesLocs.begin() );

    Tag varNamesTag = 0;
    tag_name        = "__VAR_NAMES";
    rval            = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varNamesTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    data           = NULL;
    int varNamesSz = 0;
    rval           = mbImpl->tag_get_by_ptr( varNamesTag, &fileSet, 1, &data, &varNamesSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    dbgOut.tprintf( 2, "__VAR_NAMES tag has string length %d\n", varNamesSz );
    p = static_cast< const char* >( data );

    start      = 0;
    int idxVar = 0;
    int sz;
    // Var names are separated by '\0' in the string of __VAR_NAMES tag
    for( std::size_t i = 0; i != static_cast< std::size_t >( varNamesSz ); i++ )
    {
        if( p[i] == '\0' )
        {
            std::string var_name( &p[start], i - start );

            dbgOut.tprintf( 2, "var name: %s index %d \n", var_name.c_str(), idxVar );
            // Process var name:
            // This will create/initiate map; we will populate variableDataStruct with info about
            // dims, tags, etc reference & is important; otherwise variableDataStruct will go out of
            // scope, and deleted :(
            VarData& variableDataStruct = varInfo[var_name];
            variableDataStruct.varName  = var_name;
            variableDataStruct.entLoc   = varNamesLocs[idxVar];

            dbgOut.tprintf( 2, "at var name %s varInfo size %d \n", var_name.c_str(), (int)varInfo.size() );

            sz                    = 0;
            Tag dims_tag          = 0;
            std::string dim_names = "__" + var_name + "_DIMS";
            rval = mbImpl->tag_get_handle( dim_names.c_str(), 0, MB_TYPE_OPAQUE, dims_tag, MB_TAG_ANY );
            if( MB_SUCCESS != rval )
            {
                if( MB_TAG_NOT_FOUND == rval )
                {
                    dbgOut.tprintf( 2, "tag : %s not found, continue \n", dim_names.c_str() );
                    start = i + 1;
                    idxVar++;
                    continue;
                }
                MB_SET_ERR( rval, "Trouble getting conventional tag " << dim_names );
            }
            rval = mbImpl->tag_get_length( dims_tag, sz );MB_CHK_SET_ERR( rval, "Trouble getting size of dimensions for variable " << var_name );
            sz /= sizeof( Tag );  // The type is MB_TYPE_OPAQUE, but it is a list of tags, so we
                                  // need to divide by the size of Tag
            // sz is used for number of dimension tags in this list
            dbgOut.tprintf( 2, "var name: %s has %d dimensions \n", var_name.c_str(), sz );

            variableDataStruct.varDims.resize( sz );
            const void* ptr = NULL;
            rval            = mbImpl->tag_get_by_ptr( dims_tag, &fileSet, 1, &ptr );<--- rval is assigned

            const Tag* ptags = static_cast< const moab::Tag* >( ptr );
            for( std::size_t j = 0; j != static_cast< std::size_t >( sz ); j++ )
            {
                std::string dim_name;
                rval = mbImpl->tag_get_name( ptags[j], dim_name );MB_CHK_SET_ERR( rval, "Trouble getting dimension of variable " << var_name );
                dbgOut.tprintf( 2, "var name: %s has %s as dimension \n", var_name.c_str(), dim_name.c_str() );
                std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), dim_name );
                if( vit == dimNames.end() )
                    MB_SET_ERR( MB_FAILURE, "Dimension " << dim_name << " not found for variable " << var_name );
                variableDataStruct.varDims[j] = (int)( vit - dimNames.begin() );  // Will be used for writing
                // This will have to change to actual file dimension, for writing
            }

            // Attributes for this variable
            std::stringstream ssTagName;
            ssTagName << "__" << var_name << "_ATTRIBS";
            tag_name      = ssTagName.str();
            Tag varAttTag = 0;
            rval =<--- rval is overwritten
                mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag, MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
            const void* varAttPtr = NULL;
            int varAttSz          = 0;
            rval                  = mbImpl->tag_get_by_ptr( varAttTag, &fileSet, 1, &varAttPtr, &varAttSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
            if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag retrieved for variable %s\n", tag_name.c_str() );

            std::string attribString( (char*)varAttPtr, (char*)varAttPtr + varAttSz );
            if( attribString == "NO_ATTRIBS" )
            {
                // This variable has no attributes
                variableDataStruct.numAtts = 0;
            }
            else if( attribString == "DUMMY_VAR" )
            {
                // This variable is a dummy coordinate variable
                variableDataStruct.numAtts = 0;
                dummyVarNames.insert( variableDataStruct.varName );
            }
            else
            {
                ssTagName << "_LEN";
                tag_name         = ssTagName.str();
                Tag varAttLenTag = 0;
                rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, varAttLenTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
                int varAttLenSz = 0;
                rval            = mbImpl->tag_get_length( varAttLenTag, varAttLenSz );MB_CHK_SET_ERR( rval, "Trouble getting length of conventional tag " << tag_name );
                std::vector< int > varAttLen( varAttLenSz );
                rval = mbImpl->tag_get_data( varAttLenTag, &fileSet, 1, &varAttLen[0] );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );

                rval = process_concatenated_attribute( varAttPtr, varAttSz, varAttLen, variableDataStruct.varAtts );MB_CHK_SET_ERR( rval, "Trouble processing attributes of variable " << var_name );

                if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag metadata for variable %s\n", tag_name.c_str() );
            }
            // End attribute

            start = i + 1;
            idxVar++;
        }  // if (p[i] == '\0')
    }

    // Global attributes
    tag_name         = "__GLOBAL_ATTRIBS";
    Tag globalAttTag = 0;
    rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, globalAttTag, MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    std::vector< int > gattLen;

    const void* gattptr = NULL;
    int globalAttSz     = 0;
    rval                = mbImpl->tag_get_by_ptr( globalAttTag, &fileSet, 1, &gattptr, &globalAttSz );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );

    if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag value retrieved for %s size %d\n", tag_name.c_str(), globalAttSz );

    // <__GLOBAL_ATTRIBS_LEN>
    tag_name            = "__GLOBAL_ATTRIBS_LEN";
    Tag globalAttLenTag = 0;

    rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, globalAttLenTag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting conventional tag " << tag_name );
    int sizeGAtt = 0;
    rval         = mbImpl->tag_get_length( globalAttLenTag, sizeGAtt );MB_CHK_SET_ERR( rval, "Trouble getting length of conventional tag " << tag_name );
    gattLen.resize( sizeGAtt );
    rval = mbImpl->tag_get_data( globalAttLenTag, &fileSet, 1, &gattLen[0] );MB_CHK_SET_ERR( rval, "Trouble getting data of conventional tag " << tag_name );
    if( MB_SUCCESS == rval ) dbgOut.tprintf( 2, "Tag retrieved for variable %s\n", tag_name.c_str() );

    rval = process_concatenated_attribute( gattptr, globalAttSz, gattLen, globalAtts );MB_CHK_SET_ERR( rval, "Trouble processing global attributes" );

    return MB_SUCCESS;
}

// Reverse process from create_attrib_string
ErrorCode WriteNC::process_concatenated_attribute( const void* attPtr,
                                                   int attSz,
                                                   std::vector< int >& attLen,
                                                   std::map< std::string, AttData >& attributes )
{
    std::size_t start       = 0;
    std::size_t att_counter = 0;
    std::string concatString( (char*)attPtr, (char*)attPtr + attSz );

    for( std::size_t i = 0; i != (size_t)attSz; i++ )
    {
        if( concatString[i] == '\0' )
        {
            std::string att_name( &concatString[start], i - start );
            start = i + 1;
            while( concatString[i] != ';' )
                ++i;
            std::string data_type( &concatString[start], i - start );
            ++i;
            start = i;
            i     = attLen[att_counter];
            if( concatString[i] != ';' ) MB_SET_ERR( MB_FAILURE, "Error parsing attributes" );

            std::string data_val( &concatString[start], i - start );
            start = i + 1;

            AttData& attrib = attributes[att_name];
            attrib.attValue = data_val;
            attrib.attLen   = data_val.size();

            if( data_type == "char" )
                attrib.attDataType = NC_CHAR;
            else if( data_type == "double" )
                attrib.attDataType = NC_DOUBLE;
            else if( data_type == "float" )
                attrib.attDataType = NC_FLOAT;
            else if( data_type == "int" )
                attrib.attDataType = NC_INT;
            else if( data_type == "short" )
                attrib.attDataType = NC_SHORT;

            ++att_counter;
            dbgOut.tprintf( 2, "       Process attribute %s with value %s \n", att_name.c_str(), data_val.c_str() );
        }
    }

    return MB_SUCCESS;
}

}  // namespace moab