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Feature #2474 sonarqube_findings_ncutil #2512

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merged 9 commits into from
Apr 18, 2023
Merged

Feature #2474 sonarqube_findings_ncutil #2512

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d13c9f3
#2474 Avoid the devision by 0
Apr 14, 2023
816c629
#2474 Check if n_alloc is a negative value
Apr 14, 2023
d3644ea
@2474 Check if E is not allocated before accessing it
Apr 14, 2023
bcf2341
#2474 Sets n at write_job_aggr_seeps and write_job_aggr_seeps_mpr
Apr 14, 2023
3e65a97
#2474 Initialize n to 0
Apr 14, 2023
a766cab
@2474 Changed long pointer to LongArray
Apr 14, 2023
b197624
#2474 Use LongArray for NetCDF API
Apr 14, 2023
422baa3
#2474 Changed 0 to nullptr
Apr 14, 2023
af6712c
#2474 Assign FO_Node instead of calling memcpy
Apr 15, 2023
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3 changes: 2 additions & 1 deletion src/basic/vx_math/nti.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,8 @@ y = ca2;
// reduce x and y as much as possible
//

n = (y*L_over_b - x*L_over_a)/( L_over_a*L_over_a + L_over_b*L_over_b );
n = (0 == L_over_a && 0 == L_over_b) ?
0 : (y*L_over_b - x*L_over_a)/( L_over_a*L_over_a + L_over_b*L_over_b );

x += n*L_over_a;
y -= n*L_over_b;
Expand Down
9 changes: 7 additions & 2 deletions src/basic/vx_util/two_d_array.h
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Expand Up @@ -274,7 +274,7 @@ T TwoD_Array<T>::operator()(int _x, int _y) const

{

return ( E[two_to_one(_x, _y)] );
return ( get(_x, _y) );

}

Expand All @@ -287,6 +287,11 @@ T TwoD_Array<T>::get(int _x, int _y) const

{

if (E == nullptr) {
mlog << Error << "\nTwoD_Array<T>::get(x,y) -> E is not initialized\n\n";
exit ( 1 );
}

return ( E[two_to_one(_x, _y)] );

}
Expand All @@ -301,7 +306,7 @@ bool TwoD_Array<T>::s_is_on(int _x, int _y) const

{

return ( (bool) (E[two_to_one(_x, _y)]) );
return ( (bool) (E == nullptr) ? false : (E[two_to_one(_x, _y)]) );

}

Expand Down
8 changes: 4 additions & 4 deletions src/libcode/vx_data2d_nc_met/met_file.cc
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Expand Up @@ -413,7 +413,7 @@ double fill_value;
double missing_value = get_var_missing_value(var);
get_var_fill_value(var, fill_value);

status = get_nc_data(var, &d, (long *)a);
status = get_nc_data(var, &d, a);

if ( !status ) {

Expand Down Expand Up @@ -579,10 +579,10 @@ plane.set_size(Nx, Ny);
clock_t clock_time;
double nc_time;

long dim[dimCount], cur[dimCount];
LongArray dim, cur;
for (int index=0; index<dimCount; index++) {
dim[index] = 1;
cur[index] = (b[index] == vx_data2d_star) ? 0 : b[index];
dim.add(1);
cur.add((b[index] == vx_data2d_star) ? 0 : b[index]);
}
dim[x_slot] = Nx;
dim[y_slot] = Ny;
Expand Down
10 changes: 5 additions & 5 deletions src/libcode/vx_data2d_nc_pinterp/pinterp_file.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -571,7 +571,7 @@ double d = bad_data_double;
double missing_value = get_var_missing_value(var);
get_var_fill_value(var, fill_value);

status = get_nc_data(var, &d, (long *)a);
status = get_nc_data(var, &d, a);

if ( !status ) {

Expand Down Expand Up @@ -743,12 +743,12 @@ plane.set_size(Nx, Ny);
//
double d[Ny];

long offsets[dim_count];
long lengths[dim_count];
LongArray offsets;
LongArray lengths;

for (int k=0; k<dim_count; k++) {
offsets[k] = (a[k] == vx_data2d_star) ? 0 : a[k];
lengths[k] = 1;
offsets.add((a[k] == vx_data2d_star) ? 0 : a[k]);
lengths.add(1);
}
lengths[y_slot] = Ny;

Expand Down
18 changes: 10 additions & 8 deletions src/libcode/vx_data2d_nccf/nccf_file.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -902,7 +902,7 @@ double NcCfFile::getData(NcVar * var, const LongArray & a) const
double missing_value = get_var_missing_value(var);
get_var_fill_value(var, fill_value);

status = get_nc_data(var, &d, (long *)a);
status = get_nc_data(var, &d, a);

if (!status)
{
Expand Down Expand Up @@ -1049,11 +1049,11 @@ bool NcCfFile::getData(NcVar * v, const LongArray & a, DataPlane & plane) const
double *d = new double[plane_size];

size_t dim_size;
long offsets[dim_count];
long lengths[dim_count];
LongArray offsets;
LongArray lengths;
for (int k=0; k<dim_count; k++) {
offsets[k] = (a[k] == vx_data2d_star) ? 0 : a[k];
lengths[k] = 1;
offsets.add((a[k] == vx_data2d_star) ? 0 : a[k]);
lengths.add(1);
dim_size = v->getDim(k).getSize();
if (dim_size < offsets[k]) {
mlog << Error << "\n" << method_name
Expand Down Expand Up @@ -3202,9 +3202,11 @@ LatLonData NcCfFile::get_data_from_lat_lon_vars(NcVar *lat_var, NcVar *lon_var,
bool lat_first = false;
if (two_dim_coord) {
lat_first = (lat_counts == get_dim_size(lat_var, 0));
long cur[2], length[2];
cur[0] = cur[1] = 0;
length[0] = length[1] = 1;
LongArray cur, length; // {0,0}, {1,1}
cur.add(0);
cur.add(0);
length.add(1);
length.add(1);
if (lat_first) length[0] = lat_counts;
else length[1] = lat_counts;
get_nc_data(lat_var,lat_values, length, cur);
Expand Down
30 changes: 22 additions & 8 deletions src/libcode/vx_nc_obs/nc_obs_util.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -603,10 +603,17 @@ void NetcdfObsVars::read_header_data(MetPointHeader &hdr_data) {
float *hdr_lon_block = new float[buf_size];
float *hdr_elv_block = new float[buf_size];

long offsets[2] = { 0, 0 };
long lengths[2] = { 1, 1 };
long offsets_1D[1] = { 0 };
long lengths_1D[1] = { 1 };
LongArray offsets; // = { 0, 0 };
LongArray lengths; // = { 1, 1 };
LongArray offsets_1D; // = { 0 };
LongArray lengths_1D; // = { 1 };

offsets.add(0);
offsets.add(0);
lengths.add(1);
lengths.add(1);
offsets_1D.add(0);
lengths_1D.add(1);

for(int i_start=0; i_start<nhdr_count; i_start+=buf_size) {
buf_size = ((nhdr_count-i_start) > NC_BUFFER_SIZE_32K)
Expand Down Expand Up @@ -821,10 +828,14 @@ void NetcdfObsVars::read_header_data(MetPointHeader &hdr_data) {
bool NetcdfObsVars::read_obs_data(int buf_size, int offset,
int qty_len, float *obs_arr, int *qty_idx_arr, char *obs_qty_buf) {
bool result = true;
long offsets[2] = { offset, 0 };
long lengths[2] = { buf_size, 1 };
LongArray offsets; // = { offset, 0 };
LongArray lengths; // = { buf_size, 1 };
const char *method_name = "read_obs_data() -> ";

offsets.add(offset);
offsets.add(0);
lengths.add(buf_size);
lengths.add(1);
if (IS_VALID_NC(obs_arr_var)) {
// Read the current observation message
lengths[1] = OBS_ARRAY_LEN;
Expand Down Expand Up @@ -921,8 +932,8 @@ void NetcdfObsVars::read_pb_hdr_data(MetPointHeader &hdr_data) {
return;
}

long offsets[1] = { 0 };
long lengths[1] = { 1 };
LongArray offsets; // = { 0 };
LongArray lengths; // = { 1 };
bool has_hdr_prpt_typ_var = !IS_INVALID_NC(hdr_prpt_typ_var);
bool has_hdr_irpt_typ_var = !IS_INVALID_NC(hdr_irpt_typ_var);
bool has_hdr_inst_typ_var = !IS_INVALID_NC(hdr_inst_typ_var);
Expand All @@ -931,6 +942,9 @@ void NetcdfObsVars::read_pb_hdr_data(MetPointHeader &hdr_data) {
if (has_hdr_irpt_typ_var) hdr_data.irpt_typ_array.extend(pb_hdr_count);
if (has_hdr_inst_typ_var) hdr_data.inst_typ_array.extend(pb_hdr_count);

offsets.add(0);
lengths.add(1);

// Read PB report type
int buf_size = ((pb_hdr_count > NC_BUFFER_SIZE_32K)
? NC_BUFFER_SIZE_32K : (pb_hdr_count));
Expand Down
48 changes: 27 additions & 21 deletions src/libcode/vx_nc_util/nc_utils.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -1278,7 +1278,7 @@ float get_float_var(NcVar * var, const int index) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, int *data, const long *curs) {
bool get_nc_data(NcVar *var, int *data, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_int, curs);

return(return_status);
Expand Down Expand Up @@ -1307,23 +1307,23 @@ bool get_nc_data(NcVar *var, int *data, const long dim, const long cur) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, int *data, const long *dims, const long *curs) {
bool get_nc_data(NcVar *var, int *data, const LongArray &dims, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_int, dims, curs);

return(return_status);
}

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, short *data, const long *curs) {
bool get_nc_data(NcVar *var, short *data, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, (short)bad_data_int, curs);

return(return_status);
}

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, short *data, const long *dims, const long *curs) {
bool get_nc_data(NcVar *var, short *data, const LongArray &dims, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, (short)bad_data_int, dims, curs);

return(return_status);
Expand Down Expand Up @@ -1421,13 +1421,13 @@ bool get_nc_data(NcVar *var, float *data) {
for (int idx=0; idx<cell_count; idx++) {
ushort_data[idx] =(unsigned short)packed_data[idx];
}
copy_nc_data_t(var, data, ushort_data, cell_count,
copy_nc_data_t(var, data, ushort_data, cell_count,
"ushort", add_offset, scale_factor,
has_missing, (unsigned short)missing_value);
delete [] ushort_data;
}
else {
copy_nc_data_t(var, data, packed_data, cell_count,
copy_nc_data_t(var, data, packed_data, cell_count,
"short", add_offset, scale_factor,
has_missing, missing_value);
}
Expand Down Expand Up @@ -1496,15 +1496,15 @@ bool get_nc_data(NcVar *var, float *data) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, float *data, const long *curs) {
bool get_nc_data(NcVar *var, float *data, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_float, curs);

return(return_status);
}

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, float *data, const long *dims, const long *curs) {
bool get_nc_data(NcVar *var, float *data, const LongArray &dims, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_float, dims, curs);

return(return_status);
Expand All @@ -1521,7 +1521,7 @@ bool get_nc_data(NcVar *var, float *data, const long dim, const long cur) {
////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcFile *nc, const char *var_name, double *data,
const long *dims, const long *curs) {
const LongArray &dims, const LongArray &curs) {

//
// Retrieve the input variables
Expand Down Expand Up @@ -1620,13 +1620,13 @@ bool get_nc_data(NcVar *var, double *data) {
for (int idx=0; idx<cell_count; idx++) {
ushort_data[idx] =(unsigned short)packed_data[idx];
}
copy_nc_data_t(var, data, ushort_data, cell_count,
copy_nc_data_t(var, data, ushort_data, cell_count,
"ushort", add_offset, scale_factor,
has_missing, (unsigned short)missing_value);
delete [] ushort_data;
}
else {
copy_nc_data_t(var, data, packed_data, cell_count,
copy_nc_data_t(var, data, packed_data, cell_count,
"short", add_offset, scale_factor,
has_missing, missing_value);
}
Expand Down Expand Up @@ -1692,7 +1692,7 @@ bool get_nc_data(NcVar *var, double *data) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, double *data, const long *curs) {
bool get_nc_data(NcVar *var, double *data, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_double, curs);
return(return_status);
}
Expand All @@ -1707,7 +1707,8 @@ bool get_nc_data(NcVar *var, double *data, const long dim, const long cur) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, double *data, const long *dims, const long *curs) {
bool get_nc_data(NcVar *var, double *data, const LongArray &dims,
const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_double, dims, curs);

return(return_status);
Expand Down Expand Up @@ -1795,7 +1796,7 @@ bool get_nc_data(NcVar *var, unsigned short *data) {
////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcFile *nc, const char *var_name, char *data,
const long *dims, const long *curs) {
const LongArray &dims, const LongArray &curs) {

//
// Retrieve the input variables
Expand All @@ -1814,7 +1815,7 @@ bool get_nc_data(NcVar *var, char *data, const long dim, const long cur) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, char *data, const long *dims, const long *curs) {
bool get_nc_data(NcVar *var, char *data, const LongArray &dims, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, bad_data_char, dims, curs);

return(return_status);
Expand All @@ -1833,7 +1834,7 @@ bool get_nc_data(NcVar *var, ncbyte *data) {
////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcFile *nc, const char *var_name, ncbyte *data,
const long *dims, const long *curs) {
const LongArray &dims, const LongArray &curs) {

//
// Retrieve the input variables
Expand All @@ -1852,7 +1853,7 @@ bool get_nc_data(NcVar *var, ncbyte *data, const long dim, const long cur) {

////////////////////////////////////////////////////////////////////////

bool get_nc_data(NcVar *var, ncbyte *data, const long *dims, const long *curs) {
bool get_nc_data(NcVar *var, ncbyte *data, const LongArray &dims, const LongArray &curs) {
bool return_status = get_nc_data_(var, data, (ncbyte)bad_data_char, dims, curs);

return(return_status);
Expand All @@ -1867,7 +1868,7 @@ int get_index_at_nc_data(NcVar *var, double value, const string dim_name, bool i
if (IS_VALID_NC_P(var)) {
int data_size = get_data_size(var);
double *values = new double[data_size];

if (get_nc_data(var, values)) {
unixtime ut;
int sec_per_unit;
Expand Down Expand Up @@ -1935,14 +1936,19 @@ bool get_nc_data_to_array(NcVar *var, StringArray *array_buf) {
<< GET_NC_NAME_P(var) << "\n\n";
}
else {
long offsets[2] = { 0, 0 };
long lengths[2] = { 1, 1 };
LongArray offsets; // { 0, 0 };
LongArray lengths; // { 1, 1 };
NcDim count_dim = var->getDim(dim_count-2);
NcDim str_dim = var->getDim(dim_count-1);
int count = get_dim_size(&count_dim);
int str_len = get_dim_size(&str_dim);
lengths[1] = str_len;
char str_buffer[str_len+1];

offsets.add(0);
offsets.add(0);
lengths.add(1);
lengths.add(str_len);

result = true;
for (int idx=0; idx<count; idx++) {
if(!get_nc_data(var, str_buffer, lengths, offsets)) {
Expand Down
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