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Allow ncdump -t to handle variable length string attributes #2584

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merged 5 commits into from
Jan 18, 2023
Merged

Allow ncdump -t to handle variable length string attributes #2584

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a2bcb9d
Added an ncdump -t calendars test using variable length string
srherbener Jan 8, 2023
5175de9
Modifications to enable the use of variable length string attributes …
srherbener Jan 9, 2023
57c5766
Merge branch 'main' into feature/ncdump-dtime-vlen-units
srherbener Jan 11, 2023
4e7480f
Moved the new ncdump_tst_calendars_nc4 test to the "USE_HDF5" section.
srherbener Jan 18, 2023
94cad50
Add new test, tst_calendars_nc4.sh, to automake-based builds.
WardF Jan 18, 2023
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3 changes: 2 additions & 1 deletion ncdump/CMakeLists.txt
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Expand Up @@ -213,6 +213,7 @@ endif()
add_sh_test(ncdump tst_64bit)
add_sh_test(ncdump tst_lengths)
add_sh_test(ncdump tst_calendars)
add_sh_test(ncdump tst_calendars_nc4)
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I believe I placed this new test in the wrong section. I see the IF (USE_HDF5) section below this and I suspect that is where it belongs. I'll try moving it.

add_sh_test(ncdump run_utf8_tests)

add_sh_test(ncdump tst_nccopy3_subset)
Expand Down Expand Up @@ -242,7 +243,7 @@ endif()
endif()

SET_TESTS_PROPERTIES(ncdump_tst_nccopy3 PROPERTIES DEPENDS
"ncdump_tst_calendars;ncdump_run_utf8_tests;ncdump_tst_output;ncdump_tst_64bit;ncdump_run_tests;ncdump_tst_lengths")
"ncdump_tst_calendars;ncdump_tst_calendars_nc4;ncdump_run_utf8_tests;ncdump_tst_output;ncdump_tst_64bit;ncdump_run_tests;ncdump_tst_lengths")
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I'm going to remove this addition. I misunderstood and now am thinking that the new ncdump_tst_calendars_nc4 test does not belong here since the ncdump_tst_nccopy3 test does not depend on it.


ENDIF()

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24 changes: 15 additions & 9 deletions ncdump/nctime0.c
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Expand Up @@ -79,13 +79,18 @@ calendar_type(int ncid, int varid) {
int ncals = (sizeof calmap)/(sizeof calmap[0]);
ctype = cdMixed; /* default mixed Gregorian/Julian ala udunits */
stat = nc_inq_att(ncid, varid, CF_CAL_ATT_NAME, &catt.type, &catt.len);
if(stat == NC_NOERR && catt.type == NC_CHAR && catt.len > 0) {
char *calstr = (char *)emalloc(catt.len + 1);
if(stat == NC_NOERR && (catt.type == NC_CHAR || catt.type == NC_STRING) && catt.len > 0) {
char *calstr;
size_t cf_cal_att_name_len = strlen(CF_CAL_ATT_NAME);
strncpy(catt.name, CF_CAL_ATT_NAME, cf_cal_att_name_len);
catt.name[cf_cal_att_name_len] = '\0';
catt.tinfo = get_typeinfo(catt.type);
nc_get_att_single_string(ncid, varid, &catt, &calstr);

int itype;
NC_CHECK(nc_get_att(ncid, varid, CF_CAL_ATT_NAME, calstr));
calstr[catt.len] = '\0';
int calstr_len = strlen(calstr);
for(itype = 0; itype < ncals; itype++) {
if(strncasecmp(calstr, calmap[itype].attname, catt.len) == 0) {
if(strncasecmp(calstr, calmap[itype].attname, calstr_len) == 0) {
ctype = calmap[itype].type;
break;
}
Expand Down Expand Up @@ -204,10 +209,11 @@ get_timeinfo(int ncid1, int varid1, ncvar_t *vp) {

/* time variables must have appropriate units attribute or be a bounds variable */
nc_status = nc_inq_att(ncid, varid, "units", &uatt.type, &uatt.len);
if(nc_status == NC_NOERR && uatt.type == NC_CHAR) { /* TODO: NC_STRING? */
units = emalloc(uatt.len + 1);
NC_CHECK(nc_get_att(ncid, varid, "units", units));
units[uatt.len] = '\0';
if(nc_status == NC_NOERR && (uatt.type == NC_CHAR || uatt.type == NC_STRING)) {
strncpy(uatt.name, "units", 5);
uatt.name[5] = '\0';
uatt.tinfo = get_typeinfo(uatt.type);
nc_get_att_single_string(ncid, varid, &uatt, &units);
if(!is_valid_time_unit(units)) {
free(units);
return;
Expand Down
146 changes: 146 additions & 0 deletions ncdump/ref_times_nc4.cdl
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@@ -0,0 +1,146 @@
netcdf tst_times_nc4 {
dimensions:
time = 1 ;
bnds = 2 ;
t3 = UNLIMITED ; // (3 currently)
variables:
double t1_days(time) ;
t1_days:units = "days since 1500-1-1" ;
double t1_days_case(time) ;
t1_days_case:units = "DaYs since 1500-1-1" ;
double t1_st_days(time) ;
t1_st_days:calendar = "standard" ;
t1_st_days:units = "days since 1500-01-01 00:00:00" ;
double t1_gr_days(time) ;
t1_gr_days:calendar = "gregorian" ;
t1_gr_days:units = "days since 1500-01-01 00:00:00" ;
double t1_pg_days(time) ;
t1_pg_days:calendar = "proleptic_gregorian" ;
t1_pg_days:units = "days since 1500-01-01 00:00:00" ;
double t1_nl_days(time) ;
t1_nl_days:calendar = "noleap" ;
t1_nl_days:units = "days since 1500-01-01 00:00:00" ;
double t1_365_days(time) ;
t1_365_days:calendar = "365_day" ;
t1_365_days:units = "days since 1500-01-01 00:00:00" ;
double t1_al_days(time) ;
t1_al_days:calendar = "all_leap" ;
t1_al_days:units = "days since 1500-01-01 00:00:00" ;
double t1_366_days(time) ;
t1_366_days:calendar = "366_day" ;
t1_366_days:units = "days since 1500-01-01 00:00:00" ;
double t1_360_days(time) ;
t1_360_days:calendar = "360_day" ;
t1_360_days:units = "days since 1500-01-01 00:00:00" ;
double t1_jl_days(time) ;
t1_jl_days:calendar = "julian" ;
t1_jl_days:units = "days since 1500-01-01 00:00:00" ;
double t2_days(time) ;
string t2_days:units = "days since 2000-6-15 12:00" ;
double t2_st_days(time) ;
string t2_st_days:calendar = "standard" ;
string t2_st_days:units = "days since 2000-06-15 12:00:00" ;
double t2_gr_days(time) ;
string t2_gr_days:calendar = "gregorian" ;
string t2_gr_days:units = "days since 2000-06-15 12:00:00" ;
double t2_pg_days(time) ;
string t2_pg_days:calendar = "proleptic_gregorian" ;
string t2_pg_days:units = "days since 2000-06-15 12:00:00" ;
double t2_pgt_days(time) ;
string t2_pgt_days:calendar = "proleptic_gregorian" ;
string t2_pgt_days:units = "days since 2000-06-15T12:00:00" ;
double t2_nl_days(time) ;
string t2_nl_days:calendar = "noleap" ;
string t2_nl_days:units = "days since 2000-06-15 12:00:00" ;
double t2_365_days(time) ;
string t2_365_days:calendar = "365_day" ;
string t2_365_days:units = "days since 2000-06-15 12:00:00" ;
double t2_al_days(time) ;
string t2_al_days:calendar = "all_leap" ;
string t2_al_days:units = "days since 2000-06-15 12:00:00" ;
double t2_366_days(time) ;
string t2_366_days:calendar = "366_day" ;
string t2_366_days:units = "days since 2000-06-15 12:00:00" ;
double t2_360_days(time) ;
string t2_360_days:calendar = "360_day" ;
string t2_360_days:units = "days since 2000-06-15 12:00:00" ;
double t2_jl_days(time) ;
string t2_jl_days:calendar = "julian" ;
string t2_jl_days:units = "days since 2000-06-15 12:00:00" ;
int t3(t3) ;
t3:units = "days since 1804-1-1" ;
t3:calendar = "gregorian" ;
t3:bounds = "t3_bnds" ;
t3:time1 = 1 ; // "1804-01-02"
t3:time2 = 5, 6 ; // "1804-01-06", "1804-01-07"
t3:time3 = 7.125f, 8.75f ; // "1804-01-08 03", "1804-01-09 18"
t3:time4 = 58.5, 59.5, 60.5 ;
// "1804-02-28 12", "1804-02-29 12", "1804-03-01 12"
t3:time5 = 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120 ;
// "1804-04-10", "1804-04-11", "1804-04-12", "1804-04-13",
// "1804-04-14", "1804-04-15", "1804-04-16", "1804-04-17",
// "1804-04-18", "1804-04-19", "1804-04-20", "1804-04-21",
// "1804-04-22", "1804-04-23", "1804-04-24", "1804-04-25",
// "1804-04-26", "1804-04-27", "1804-04-28", "1804-04-29",
// "1804-04-30"
double t3_bnds(t3, bnds) ;
int t4 ;
t4:units = "days" ;
t4:att1 = 1 ;
t4:att2 = 5, 6 ;
t4:att3 = 7.125f, 8.75f ;
data:

t1_days = "2009-01-01" ;

t1_days_case = "2009-01-01" ;

t1_st_days = "2009-01-01" ;

t1_gr_days = "2009-01-01" ;

t1_pg_days = "2009-01-01" ;

t1_nl_days = "2009-01-01" ;

t1_365_days = "2009-01-01" ;

t1_al_days = "2009-01-01" ;

t1_366_days = "2009-01-01" ;

t1_360_days = "2009-01-01" ;

t1_jl_days = "2009-01-01" ;

t2_days = "2009-01-01" ;

t2_st_days = "2009-01-01" ;

t2_gr_days = "2009-01-01" ;

t2_pg_days = "2009-01-01" ;

t2_pgt_days = "2009-01-01" ;

t2_nl_days = "2009-01-01" ;

t2_365_days = "2009-01-01" ;

t2_al_days = "2009-01-01" ;

t2_366_days = "2009-01-01" ;

t2_360_days = "2009-01-01" ;

t2_jl_days = "2009-01-01" ;

t3 = "1804-01-11", "1804-01-12", "1804-01-13" ;

t3_bnds =
"1804-01-10 12", "1804-01-11 12",
"1804-01-11 12", "1804-01-12 12",
"1804-01-12 12", "1804-01-13 12" ;

t4 = _ ;
}
133 changes: 133 additions & 0 deletions ncdump/tst_calendars_nc4.cdl
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@@ -0,0 +1,133 @@
netcdf tst_calendars_nc4 { // test climate calendars and CDL time with -t option
dimensions:
time = 1;
bnds = 2 ; // for cell bounds on t3 time coordinate variable
t3 = unlimited ;
variables:
// Use fixed length string attributes for the t1 set of variables
double t1_days(time);
t1_days:units = "days since 1500-1-1";
double t1_days_case(time);
t1_days_case:units = "DaYs since 1500-1-1";
double t1_st_days(time);
t1_st_days:calendar = "standard" ; // mixed julian-gregorian
t1_st_days:units = "days since 1500-01-01 00:00:00";
double t1_gr_days(time);
t1_gr_days:calendar = "gregorian" ; // same as "standard"
t1_gr_days:units = "days since 1500-01-01 00:00:00";
double t1_pg_days(time);
t1_pg_days:calendar = "proleptic_gregorian" ;
t1_pg_days:units = "days since 1500-01-01 00:00:00";
double t1_nl_days(time);
t1_nl_days:calendar = "noleap" ;
t1_nl_days:units = "days since 1500-01-01 00:00:00";
double t1_365_days(time);
t1_365_days:calendar = "365_day" ; // same as "noleap"
t1_365_days:units = "days since 1500-01-01 00:00:00";
double t1_al_days(time);
t1_al_days:calendar = "all_leap" ;
t1_al_days:units = "days since 1500-01-01 00:00:00";
double t1_366_days(time);
t1_366_days:calendar = "366_day" ; // same as "all_leap"
t1_366_days:units = "days since 1500-01-01 00:00:00";
double t1_360_days(time);
t1_360_days:calendar = "360_day" ;
t1_360_days:units = "days since 1500-01-01 00:00:00";
double t1_jl_days(time);
t1_jl_days:calendar = "julian" ;
t1_jl_days:units = "days since 1500-01-01 00:00:00";

// Use variable length string attributes for the t2 set of variables
double t2_days(time);
string t2_days:units = "days since 2000-6-15 12:00";
double t2_st_days(time);
string t2_st_days:calendar = "standard" ; // mixed julian-gregorian
string t2_st_days:units = "days since 2000-06-15 12:00:00";
double t2_gr_days(time);
string t2_gr_days:calendar = "gregorian" ; // same as "standard"
string t2_gr_days:units = "days since 2000-06-15 12:00:00";
double t2_pg_days(time);
string t2_pg_days:calendar = "proleptic_gregorian" ;
string t2_pg_days:units = "days since 2000-06-15 12:00:00";
double t2_pgt_days(time);
string t2_pgt_days:calendar = "proleptic_gregorian" ;
string t2_pgt_days:units = "days since 2000-06-15T12:00:00";
double t2_nl_days(time);
string t2_nl_days:calendar = "noleap" ;
string t2_nl_days:units = "days since 2000-06-15 12:00:00";
double t2_365_days(time);
string t2_365_days:calendar = "365_day" ; // same as "noleap"
string t2_365_days:units = "days since 2000-06-15 12:00:00";
double t2_al_days(time); // *** no year, 07-29 12:00
string t2_al_days:calendar = "all_leap" ; // seems wrong, same as gregorian
string t2_al_days:units = "days since 2000-06-15 12:00:00";
double t2_366_days(time); // *** no year, 07-29 12:00
string t2_366_days:calendar = "366_day" ; // omits years, same as "clim"??
string t2_366_days:units = "days since 2000-06-15 12:00:00";
double t2_360_days(time);
string t2_360_days:calendar = "360_day" ; // omits years, same as "clim"??
string t2_360_days:units = "days since 2000-06-15 12:00:00";
double t2_jl_days(time);
string t2_jl_days:calendar = "julian" ;
string t2_jl_days:units = "days since 2000-06-15 12:00:00";

// double t1_none_days(time);
// t1_none_days:calendar = "none" ;
// t1_none_days:units = "days since 1500-01-01 00:00:00";
// double t2_none_days(time);
// t2_none_days:calendar = "none" ;
// t2_none_days:units = "days since 2000-06-15 12:00:00";

// test -t option on numeric attributes of a time-valued variable
int t3(t3) ;
t3:units = "days since 1804-1-1" ;
t3:calendar = "gregorian" ;
t3:bounds = "t3_bnds" ;
t3:time1 = 1 ;
t3:time2 = 5, 6 ;
t3:time3 = 7.125f, 8.75f ;
t3:time4 = 58.5, 59.5, 60.5 ;
t3:time5 = 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120 ;
double t3_bnds(t3, bnds) ; // no attributes, since a cell bounds variable

// test -t bug fix, time unit without base time should not interpret numeric atts as times
int t4 ;
t4:units = "days" ;
t4:att1 = 1 ;
t4:att2 = 5, 6 ;
t4:att3 = 7.125f, 8.75f ;

data:
// Should all represent 2009-01-01 00:00:00
t1_days = 185900;
t1_days_case = 185900;
t1_st_days = 185900;
t1_gr_days = 185900;
t1_pg_days = 185909;
t1_nl_days = 185785;
t1_365_days = 185785;
t1_366_days = 186294;
t1_al_days = 186294;
t1_360_days = 183240;
t1_jl_days = 185913;

t2_days = 3121.5;
t2_st_days = 3121.5;
t2_gr_days = 3121.5;
t2_pg_days = 3121.5;
t2_pgt_days = 3121.5;
t2_nl_days = 3119.5;
t2_365_days = 3119.5;
t2_366_days = 3127.5;
t2_al_days = 3127.5;
t2_360_days = 3075.5;
t2_jl_days = 3121.5;

// Not sure what these should represent yet ...
// t1_none_days = 185900;
// t2_none_days = 3121.5;

t3 = 10, 11, 12;
t3_bnds = 9.5, 10.5, 10.5, 11.5, 11.5, 12.5 ;
}

20 changes: 20 additions & 0 deletions ncdump/tst_calendars_nc4.sh
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#!/bin/sh

if test "x$srcdir" = x ; then srcdir=`pwd`; fi
. ../test_common.sh

# This shell script tests ncdump -t option for CF calendar attributes using netcdf4 format

set -e
echo ""
echo "*** Testing ncdump -t output for times with CF calendar attribute, netcdf4 format"
echo "*** creating netcdf4 file tst_calendars.nc from tst_calendars.cdl..."
${NCGEN} -b -k nc4 -o tst_calendars_nc4.nc $srcdir/tst_calendars_nc4.cdl
echo "*** creating tst_times_nc4.cdl from tst_calendars.nc with ncdump -t ..."
${NCDUMP} -n tst_times_nc4 -t tst_calendars_nc4.nc > tst_times_nc4.cdl
echo "*** comparing tst_times_nc4.cdl with ref_times_nc4.cdl..."
diff -b tst_times_nc4.cdl $srcdir/ref_times_nc4.cdl
echo ""
echo "*** All ncdump test output (netcdf4 format) for -t option with CF calendar atts passed!"

exit 0
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