Fixes for NCF-150, bugs in libsrc4 with handling strings in non-netCDF-4 HDF5 files. Added new test in nc_test4 to verify fixes.

h5_test/tst_h_dimscales.c

@@ -223,7 +223,6 @@ main()
 	       if (datasetid > 0)
 	       {
 		  H5Dclose(datasetid);
-		  datasetid = 0;
 	       }
 	       
 	       if ((datasetid = H5Dopen(grpid, obj_name)) < 0) ERR;

libsrc4/nc4file.c

@@ -772,10 +772,11 @@ get_type_info2(NC_HDF5_FILE_INFO_T *h5, hid_t datasetid,
       {
 	 if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
 	    return NC_EHDFERR;
-	 if (is_str)
+	 /* Make sure fixed-len strings will work like variable-len strings */
+	 if (is_str || H5Tget_size(hdf_typeid) > 1)
 	    t = NUM_TYPES - 1;
 	 else
-	    t = 0;
+	     t = 0;
       }
       else if (class == H5T_INTEGER || class == H5T_FLOAT)
       {
@@ -895,6 +896,9 @@ read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
    {
       dims[0] = 0;
    }
+   else if (att->xtype == NC_STRING) {
+       dims[0] = att_npoints;
+   }
    else if (att->xtype == NC_CHAR)
    {
       /* NC_CHAR attributes are written as a scalar in HDF5, of type
@@ -913,8 +917,8 @@ read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
    } 
    else
    {
-      /* All netcdf attributes are 1-D only. */
-      if (att_ndims != 1)
+      /* All netcdf attributes are scalar or 1-D only. */
+      if (att_ndims > 1)
 	 BAIL(NC_EATTMETA);
 
       /* Read the size of this attribute. */
@@ -1859,9 +1863,9 @@ nc4_rec_read_types(NC_GRP_INFO_T *grp)
 	 
 	res = H5Literate(grp->hdf_grpid, H5_INDEX_NAME, H5_ITER_INC, 
 			 &idx, nc4_rec_read_types_cb, (void *)grp);
-	if (res<0)
-	    return NC_EHDFERR;
     }
+    if (res<0)
+	return NC_EHDFERR;
     return NC_NOERR; /* everything worked! */
 }
 

libsrc4/nc4hdf.c

@@ -834,6 +834,7 @@ nc4_get_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp,
 
    hid_t file_spaceid = 0, mem_spaceid = 0;
    hid_t xfer_plistid = 0;
+   hid_t hdf_datasetid;
    size_t file_type_size;
 
    hsize_t *xtend_size = NULL, count[NC_MAX_VAR_DIMS];
@@ -993,6 +994,23 @@ nc4_get_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp,
 	 num_spaces++;
 #endif
       }
+
+      /* Fix bug when reading HDF5 files with variable of type
+       * fixed-length string.  We need to make it look like a
+       * variable-length string, because that's all netCDF-4 data
+       * model supports, lacking anonymous dimensions.  So
+       * variable-length strings are in allocated memory that user has
+       * to free, which we allocate here. */
+      if(var->type_info->class == H5T_STRING && 
+	 H5Tget_size(var->type_info->hdf_typeid) > 1 &&
+	 !H5Tis_variable_str(var->type_info->hdf_typeid)) {
+	  hsize_t fstring_len;
+	  if ((fstring_len = H5Tget_size(var->type_info->hdf_typeid)) < 0)
+	      BAIL(NC_EHDFERR);
+      	  if (!(*(char **)data = malloc(1 + fstring_len)))
+      	      BAIL(NC_ENOMEM);
+	  bufr = *(char **)data;
+      }
    
 #ifndef HDF5_CONVERT   
       /* Are we going to convert any data? (No converting of compound or
@@ -1016,7 +1034,8 @@ nc4_get_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp,
       }
       else
 #endif /* ifndef HDF5_CONVERT */
-         bufr = data;
+	  if(!bufr)
+	      bufr = data;
 
       /* Get the HDF type of the data in memory. */
 #ifdef HDF5_CONVERT

nc_test4/Makefile.am

@@ -20,7 +20,7 @@ tst_enums tst_coords tst_coords2 tst_coords3 tst_vars3 tst_vars4	\
 tst_chunks tst_chunks2 tst_utf8 tst_fills tst_fills2 tst_fillbug	\
 tst_xplatform tst_xplatform2 tst_h_atts2 tst_endian_fill tst_atts	\
 t_type cdm_sea_soundings tst_camrun tst_vl tst_atts1 tst_atts2		\
-tst_vars2 tst_files5 tst_files6 tst_sync
+tst_vars2 tst_files5 tst_files6 tst_sync tst_h_strbug
 
 check_PROGRAMS = $(NC4_TESTS)
 

nc_test4/tst_h_strbug.c

@@ -0,0 +1,193 @@
+/* This is part of the netCDF package.  Copyright 2005 University
+   Corporation for Atmospheric Research/Unidata See COPYRIGHT file for
+   conditions of use.
+
+   This program tests fixes for bugs reported with accessing
+   fixed-length scalar string variables and variable-length scalar
+   string attributes from HDF5 files through the netCDF-4 API.
+
+   Here's a HDF5 sample programs:
+   http://hdf.ncsa.uiuc.edu/training/other-ex5/sample-programs/strings.c
+*/
+
+#include <config.h>
+#include <nc_tests.h>
+#include <err_macros.h>
+#include <hdf5.h>
+
+#define FILE_NAME "tst_h_strbug.h5"
+#define VS_ATT_NAME "vsatt"
+#define FS_ATT_NAME "fsatt"
+#define VS_VAR_NAME "vsvar"
+#define FS_VAR_NAME "fsvar"
+#define V1D_VAR_NAME "v1dvar"
+#define FSTR_LEN 20
+#define DIM1      4
+#define RANK      1
+
+int
+main()
+{
+    char *vs    = "variable-length string";
+    char fsdata[]   = "fixed-length string";
+    char *v1ddata[DIM1] = {"strings","of","variable","length"};
+    int i;
+    char ch;
+
+    printf("\n*** Creating file for checking fix to bugs in accessing strings from HDF5 non-netcdf-4 file.\n");
+    {
+	hid_t fileid, scalar_spaceid, vstypeid, fstypeid, vsattid, fsattid, vsdsetid, fsdsetid;
+	hid_t class;
+	size_t type_size = FSTR_LEN;
+	hid_t v1dattid, v1ddsetid;
+	hid_t v1dspaceid;
+	hsize_t dims[1] = {DIM1};
+
+	if ((scalar_spaceid = H5Screate(H5S_SCALAR)) < 0) ERR;
+	if ((v1dspaceid = H5Screate_simple(RANK, dims, NULL)) < 0) ERR;
+	
+	/* Create variable-length and fixed-length string types. */
+	if ((vstypeid =  H5Tcopy(H5T_C_S1)) < 0) ERR;
+	if (H5Tset_size(vstypeid, H5T_VARIABLE) < 0) ERR;
+	
+	if ((fstypeid =  H5Tcopy(H5T_C_S1)) < 0) ERR;
+	if (H5Tset_size(fstypeid, type_size) < 0) ERR;
+
+	/* Create new file, using default properties. */
+	if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) ERR;
+	
+	/* Create scalar datasets of variable- and fixed-length strings. */
+	if ((vsdsetid = H5Dcreate (fileid, VS_VAR_NAME, vstypeid, scalar_spaceid, 
+				   H5P_DEFAULT)) < 0) ERR;
+	if (H5Dwrite (vsdsetid, vstypeid, H5S_ALL, H5S_ALL, H5P_DEFAULT, &vs)) ERR;
+	if ((fsdsetid = H5Dcreate (fileid, FS_VAR_NAME, fstypeid, scalar_spaceid, 
+				   H5P_DEFAULT)) < 0) ERR;
+	if (H5Dwrite (fsdsetid, fstypeid, H5S_ALL, H5S_ALL, H5P_DEFAULT, &fsdata)) ERR;
+
+	/* Create 1D dataset of variable-length strings. */
+	if ((v1ddsetid = H5Dcreate (fileid, V1D_VAR_NAME, vstypeid, v1dspaceid, 
+				   H5P_DEFAULT)) < 0) ERR;
+	if (H5Dwrite (v1ddsetid, vstypeid, H5S_ALL, H5S_ALL, H5P_DEFAULT, &v1ddata)) ERR;
+	
+	/* Write scalar global attributes of these types. */
+	if ((vsattid = H5Acreate(fileid, VS_ATT_NAME, vstypeid, scalar_spaceid, 
+				 H5P_DEFAULT)) < 0) ERR;
+	if (H5Awrite(vsattid, vstypeid, &vs) < 0) ERR;
+	if ((fsattid = H5Acreate(fileid, FS_ATT_NAME, fstypeid, scalar_spaceid, 
+				 H5P_DEFAULT)) < 0) ERR;
+	if (H5Awrite(fsattid, fstypeid, &fsdata) < 0) ERR;
+	
+	/* Close up. */
+	if (H5Aclose(vsattid) < 0) ERR;
+	if (H5Aclose(fsattid) < 0) ERR;
+	if (H5Sclose(scalar_spaceid) < 0) ERR;
+	if (H5Sclose(v1dspaceid) < 0) ERR;
+	if (H5Tclose(vstypeid) < 0) ERR;
+	if (H5Tclose(fstypeid) < 0) ERR;
+	if (H5Dclose(vsdsetid) < 0) ERR;
+	if (H5Dclose(fsdsetid) < 0) ERR;
+	if (H5Dclose(v1ddsetid) < 0) ERR;
+	if (H5Fclose(fileid) < 0) ERR;
+    }
+
+    printf("*** Checking reading variable-length HDF5 string var through netCDF-4 API...");
+    {
+	int ncid, varid, ndims;
+	nc_type type;
+	char *data_in;
+	if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+	if (nc_inq_varid(ncid, VS_VAR_NAME, &varid)) ERR;
+	if (nc_inq_vartype(ncid, varid, &type)) ERR;
+	if (type != NC_STRING) ERR;
+	if (nc_inq_varndims(ncid, varid, &ndims )) ERR;
+	if (ndims != 0) ERR;
+	if (nc_get_var_string(ncid, varid, &data_in)) ERR;
+	if (strcmp(vs, data_in)) ERR;
+	if (nc_free_string(1, &data_in)) ERR;
+	if (nc_close(ncid)) ERR;
+    }
+    SUMMARIZE_ERR;
+
+    printf("*** Checking reading fixed-length HDF5 string var through netCDF-4 API...");
+    {
+    	int ncid, varid, ndims;
+    	nc_type type;
+    	char *data_in;
+    	if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+    	if (nc_inq_varid(ncid, FS_VAR_NAME, &varid)) ERR;
+    	if (nc_inq_vartype(ncid, varid, &type)) ERR;
+    	if (type != NC_STRING) ERR;
+    	if (nc_inq_varndims(ncid, varid, &ndims )) ERR;
+    	if (ndims != 0) ERR;
+    	if (nc_get_var_string(ncid, varid, &data_in)) ERR;
+    	if (strcmp(fsdata, data_in)) ERR;
+	if (nc_free_string(1, &data_in)) ERR;
+    	if (nc_close(ncid)) ERR;
+    }
+    SUMMARIZE_ERR;
+
+    printf("*** Checking reading variable-length HDF5 string att through netCDF-4 API...");
+    {
+	int ncid, varid, ndims;
+	nc_type type;
+	size_t len;
+	char *data_in;
+	if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+	if (nc_inq_att(ncid, NC_GLOBAL, VS_ATT_NAME, &type, &len)) ERR;
+	if (type != NC_STRING) ERR;
+	if (len != 1) ERR;
+        if (nc_get_att_string(ncid, NC_GLOBAL, VS_ATT_NAME, &data_in)) ERR;
+	if (strcmp(vs, data_in)) ERR;
+	if (nc_free_string(1, &data_in)) ERR;
+	if (nc_close(ncid)) ERR;
+    }
+    SUMMARIZE_ERR;
+
+    printf("*** Checking reading fixed-length HDF5 string att through netCDF-4 API...");
+    {
+	int ncid, varid, ndims;
+	nc_type type;
+	size_t len;
+	char *data_in;
+	if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+	if (nc_inq_att(ncid, NC_GLOBAL, FS_ATT_NAME, &type, &len)) ERR;
+	if (type != NC_CHAR) ERR;
+	if (len != FSTR_LEN) ERR;
+	if (!(data_in = malloc(len))) ERR;
+        /* if (nc_get_att_string(ncid, NC_GLOBAL, FS_ATT_NAME, &data_in)) ERR; */
+        if (nc_get_att_text(ncid, NC_GLOBAL, FS_ATT_NAME, data_in)) ERR;
+	if (strcmp(fsdata, data_in)) ERR;
+	free(data_in);
+	if (nc_close(ncid)) ERR;
+    }
+    SUMMARIZE_ERR;
+
+    printf("*** Checking reading variable-length HDF5 strings var through netCDF-4 API...");
+    {
+    	int ncid, varid, ndims;
+    	nc_type type;
+	int *dimids;
+	size_t nstrings;
+    	char **data_in;
+    	if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+    	if (nc_inq_varid(ncid, V1D_VAR_NAME, &varid)) ERR;
+    	if (nc_inq_vartype(ncid, varid, &type)) ERR;
+    	if (type != NC_STRING) ERR;
+    	if (nc_inq_varndims(ncid, varid, &ndims )) ERR;
+    	if (ndims != RANK) ERR;
+	if (!(dimids = malloc(ndims * sizeof(int)))) ERR;
+    	if (nc_inq_vardimid(ncid, varid, dimids)) ERR;
+	if (nc_inq_dimlen(ncid, dimids[0], &nstrings)) ERR;
+	if (!(data_in = (char **)malloc(nstrings * sizeof(char *)))) ERR;
+    	if (nc_get_var_string(ncid, varid, data_in)) ERR;
+	for (i = 0; i < nstrings; i++) {
+	    if(strcmp(v1ddata[i], data_in[i])) ERR;
+	}
+    	if (nc_free_string(nstrings, data_in)) ERR;
+	free(data_in);
+	free(dimids);
+    	if (nc_close(ncid)) ERR;
+    }
+    SUMMARIZE_ERR;
+    FINAL_RESULTS;
+}

ncdump/nccopy.c

@@ -52,7 +52,7 @@ static int option_write_diskless = 0; /* default, don't write output to diskless
 static int
 get_grpid(int igrp, int parid, int *ogrpp) {
     int stat = NC_NOERR;
-    int ogid;			/* like igrp but in output file */
+    int ogid = parid;		/* like igrp but in output file */
 #ifdef USE_NETCDF4
     int inparid;
 
@@ -63,13 +63,10 @@ get_grpid(int igrp, int parid, int *ogrpp) {
 	NC_CHECK(nc_inq_grpname(igrp, grpname));
 	NC_CHECK(nc_inq_grp_ncid(parid, grpname, &ogid));
     } else if(stat == NC_ENOGRP) { /* root group */
-	ogid = parid;
 	stat = NC_NOERR;
     } else {
 	NC_CHECK(stat);
     }
-#else
-    ogid = parid;
 #endif	/* USE_NETCDF4 */
     *ogrpp = ogid;
     return stat;
@@ -88,8 +85,8 @@ nc_inq_parid(int ncid, const char *fullname, int *locidp) {
     char *last_slash;
     if(parent == NULL) {
 	NC_CHECK(NC_ENOMEM);
-    }
-    last_slash = strrchr(parent, '/');
+    } else
+	last_slash = strrchr(parent, '/');
     if(last_slash == parent) {	/* parent is root */
 	free(parent);
 	parent = strdup(slash);

ncdump/ncdump.c

@@ -908,7 +908,7 @@ pr_attx(
     )
 {
     ncatt_t att;			/* attribute */
-    char *attvals;
+    char *attvals = "";
     int attvalslen = 0;
 
     NC_CHECK( nc_inq_attname(ncid, varid, ia, att.name) );