Allow ncdump -t to handle variable length string attributes

ncdump/CMakeLists.txt

@@ -263,6 +263,7 @@ endif()
     add_sh_test(ncdump tst_ncgen4)
     add_sh_test(ncdump tst_netcdf4_4)
     add_sh_test(ncdump tst_nccopy4)
+    add_sh_test(ncdump tst_calendars_nc4)
 
     SET_TESTS_PROPERTIES(ncdump_tst_nccopy4 PROPERTIES DEPENDS "ncdump_run_ncgen_tests;ncdump_tst_output;ncdump_tst_ncgen4;ncdump_sh_tst_fillbug;ncdump_tst_netcdf4_4;ncdump_tst_h_scalar;tst_comp;tst_comp2;tst_nans;tst_opaque_data;tst_create_files;tst_special_atts")
     SET_TESTS_PROPERTIES(ncdump_tst_nccopy5 PROPERTIES DEPENDS "ncdump_tst_nccopy4")

ncdump/nctime0.c

@@ -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;
 	    }
@@ -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;

ncdump/ref_times_nc4.cdl

@@ -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 = _ ;
+}

ncdump/tst_calendars_nc4.cdl

@@ -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 ;
+}
+

ncdump/tst_calendars_nc4.sh

@@ -0,0 +1,20 @@
+#!/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

ncdump/utils.c

@@ -13,6 +13,7 @@
 #include <assert.h>
 #include <ctype.h>
 #include "utils.h"
+#include "nccomps.h"
 #ifndef isascii
 EXTERNL int isascii(int c);
 #endif
@@ -959,3 +960,38 @@ parseFQN(int ncid, const char* fqn0, VarID* idp)
 }
 #endif
 
+/*********************************************************************************/
+void nc_get_att_single_string(const int ncid, const int varid,
+                              const struct ncatt_t *att, char **str_out) {
+    if (att->type == NC_CHAR) {
+        // NC_CHAR type attribute
+        // Use a call to nc_get_att_text which expects to output the attribute value
+        // into a char * pointing to allocated memory. The number of bytes to allocate
+        // is the attribute length (which is the number of elements in a vector, 1 for
+        // scalar) times the size of each element in bytes. The attribute length is
+        // held in att->len, and the attribute element size is in att->tinfo->size.
+        *str_out = emalloc((att->len + 1) * att->tinfo->size);
+	(*str_out)[att->len] = '\0';
+        NC_CHECK(nc_get_att_text(ncid, varid, att->name, *str_out));
+    } else if (att->type == NC_STRING) {
+        // NC_STRING type attribute
+        // Use a call to nc_get_att_string which expects to output the attribute value
+        // into a vector of char pointers, where each entry points to allocated memory.
+        // The vector of char pointers needs to be allocated to the length (number of strings)
+        // times the size of each entry (size of a char *).
+        char **att_strings = emalloc((att->len + 1) * att->tinfo->size);
+        NC_CHECK(nc_get_att_string(ncid, varid, att->name, att_strings));
+        // str_out needs to be allocated to a size large enough to hold the string that
+        // the first pointer in att_strings is pointing to.
+        size_t att_str_len = strlen(att_strings[0]);
+        *str_out = emalloc((att_str_len + 1) * att->tinfo->size);
+	(*str_out)[att_str_len] = '\0';
+        strncpy(*str_out, att_strings[0], att_str_len);
+        nc_free_string(att->len, att_strings);
+    } else {
+        fprintf(stderr,"nc_get_att_single_string: unknown attribute type: %d\n", att->type);
+        fprintf(stderr,"                          must use one of:  NC_CHAR, NC_STRING\n");
+        fflush(stderr); fflush(stdout);
+        exit(2);
+    }
+}