Fix rename bug name dim same as existing var

include/nc4internal.h

@@ -153,7 +153,7 @@ typedef struct NC_VAR_INFO
    nc_bool_t created;           /* Variable has already been created (_not_ that it was just created) */
    nc_bool_t written_to;        /* True if variable has data written to it */
    struct NC_TYPE_INFO *type_info;
-   int atts_not_read;           /* If true, the atts have not yet been read. */
+   int atts_read;               /* If true, the atts have been read. */
    nc_bool_t meta_read;         /* True if this vars metadata has been completely read. */
    nc_bool_t coords_read;       /* True if this var has hidden coordinates att, and it has been read. */
    NCindex *att; 		/* NCindex<NC_ATT_INFO_T*> */
@@ -229,7 +229,7 @@ typedef struct NC_GRP_INFO
    void *format_grp_info;
    struct NC_FILE_INFO *nc4_info;
    struct NC_GRP_INFO *parent;
-   int atts_not_read;
+   int atts_read;               /* True if atts have been read for this group. */
    NCindex* children;		/* NCindex<struct NC_GRP_INFO*> */
    NCindex* dim;		/* NCindex<NC_DIM_INFO_T> * */
    NCindex* att;		/* NCindex<NC_ATT_INFO_T> * */

libhdf4/hdf4file.c

@@ -415,6 +415,7 @@ nc4_var_list_add_full(NC_GRP_INFO_T* grp, const char* name, int ndims, nc_type x
    (*var)->created = NC_TRUE;
    (*var)->written_to = NC_TRUE;
    (*var)->format_var_info = format_var_info;
+   (*var)->atts_read = 1;
 
    /* Fill special type_info struct for variable type information. */
    if ((retval = nc4_set_var_type(xtype, endianness, type_size, type_name,
@@ -630,6 +631,7 @@ NC_HDF4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
    assert(nc4_info && nc4_info->root_grp);
    h5 = nc4_info;
    h5->no_write = NC_TRUE;
+   h5->root_grp->atts_read = 1;
 
    /* Allocate data to hold HDF4 specific file data. */
    if (!(hdf4_file = malloc(sizeof(NC_HDF4_FILE_INFO_T))))

libhdf5/hdf5attr.c

@@ -27,13 +27,14 @@ static int
 getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
             NCindex **attlist)
 {
-   NC_VAR_INFO_T* var;
    int retval;
 
+   assert(grp && attlist);
+
    if (varid == NC_GLOBAL)
    {
       /* Do we need to read the atts? */
-      if (grp->atts_not_read)
+      if (!grp->atts_read)
          if ((retval = nc4_read_atts(grp, NULL)))
             return retval;
 
@@ -43,12 +44,14 @@ getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
    }
    else
    {
+      NC_VAR_INFO_T *var;
+
       if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
          return NC_ENOTVAR;
       assert(var->hdr.id == varid);
 
       /* Do we need to read the atts? */
-      if (var->atts_not_read)
+      if (!var->atts_read)
          if ((retval = nc4_read_atts(grp, var)))
             return retval;
 

libhdf5/hdf5create.c

@@ -66,6 +66,7 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
       BAIL(retval);
    nc4_info = NC4_DATA(nc);
    assert(nc4_info && nc4_info->root_grp);
+   nc4_info->root_grp->atts_read = 1;
 
    /* Add struct to hold HDF5-specific file metadata. */
    if (!(nc4_info->format_file_info = calloc(1, sizeof(NC_HDF5_FILE_INFO_T))))

libhdf5/hdf5file.c

@@ -727,7 +727,7 @@ NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
    if (nattsp)
    {
       /* Do we need to read the atts? */
-      if (grp->atts_not_read)
+      if (!grp->atts_read)
          if ((retval = nc4_read_atts(grp, NULL)))
             return retval;
 

libhdf5/hdf5grp.c

@@ -67,6 +67,11 @@ NC4_def_grp(int parent_ncid, const char *name, int *new_ncid)
       return retval;
    if (!(g->format_grp_info = calloc(1, sizeof(NC_HDF5_GRP_INFO_T))))
       return NC_ENOMEM;
+
+   /* For new groups, there are no atts to read from file. */
+   g->atts_read = 1;
+
+   /* Return the ncid to the user. */
    if (new_ncid)
       *new_ncid = grp->nc4_info->controller->ext_ncid | g->hdr.id;
 

libhdf5/hdf5internal.c

@@ -385,7 +385,7 @@ delete_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
  * @param dim Pointer to dimension info struct.
  *
  * @return ::NC_NOERR No error.
- * @author Quincey Koziol
+ * @author Quincey Koziol, Ed Hartnett
  */
 int
 nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
@@ -406,14 +406,14 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
    hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
    hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
 
-   /* Detach dimscales from the [new] coordinate variable */
+   /* Detach dimscales from the [new] coordinate variable. */
    if (var->dimscale_attached)
    {
       int dims_detached = 0;
       int finished = 0;
       int d;
 
-      /* Loop over all dimensions for variable */
+      /* Loop over all dimensions for variable. */
       for (d = 0; d < var->ndims && !finished; d++)
       {
          /* Is there a dimscale attached to this axis? */
@@ -439,7 +439,8 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
 
                      /* Find dataset ID for dimension */
                      if (dim1->coord_var)
-                        dim_datasetid = ((NC_HDF5_VAR_INFO_T *)(dim1->coord_var->format_var_info))->hdf_datasetid;
+                        dim_datasetid = ((NC_HDF5_VAR_INFO_T *)
+                                         (dim1->coord_var->format_var_info))->hdf_datasetid;
                      else
                         dim_datasetid = hdf5_dim1->hdf_dimscaleid;
 
@@ -450,7 +451,8 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
                      if (dim_datasetid > 0)
                      {
                         LOG((3, "detaching scale from %s", var->hdr.name));
-                        if (H5DSdetach_scale(hdf5_var->hdf_datasetid, dim_datasetid, d) < 0)
+                        if (H5DSdetach_scale(hdf5_var->hdf_datasetid,
+                                             dim_datasetid, d) < 0)
                            BAIL(NC_EHDFERR);
                      }
                      var->dimscale_attached[d] = NC_FALSE;
@@ -462,7 +464,7 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
          }
       } /* next variable dimension */
 
-      /* Release & reset the array tracking attached dimscales */
+      /* Release & reset the array tracking attached dimscales. */
       free(var->dimscale_attached);
       var->dimscale_attached = NULL;
       need_to_reattach_scales++;
@@ -476,31 +478,32 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
          BAIL(NC_EHDFERR);
       hdf5_dim->hdf_dimscaleid = 0;
 
-      /* Now delete the dimscale's dataset
-         (it will be recreated later, if necessary) */
+      /* Now delete the dimscale's dataset (it will be recreated
+         later, if necessary). */
       if (H5Gunlink(hdf5_grp->hdf_grpid, dim->hdr.name) < 0)
          return NC_EDIMMETA;
    }
 
-   /* Attach variable to dimension */
+   /* Attach variable to dimension. */
    var->dimscale = NC_TRUE;
    dim->coord_var = var;
 
    /* Check if this variable used to be a coord. var */
    if (need_to_reattach_scales || (var->was_coord_var && grp != NULL))
    {
-      /* Reattach the scale everywhere it is used. */
-      /* (Recall that netCDF dimscales are always 1-D) */
+      /* Reattach the scale everywhere it is used. (Recall that netCDF
+       * dimscales are always 1-D) */
       if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
                                         var->dimids[0], hdf5_var->hdf_datasetid)))
          return retval;
 
-      /* Set state transition indicator (cancels earlier transition) */
+      /* Set state transition indicator (cancels earlier
+       * transition). */
       var->was_coord_var = NC_FALSE;
    }
-   else
-      /* Set state transition indicator */
-      var->became_coord_var = NC_TRUE;
+
+   /* Set state transition indicator */
+   var->became_coord_var = NC_TRUE;
 
 exit:
    return retval;
@@ -837,7 +840,7 @@ nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
    if (varid == NC_GLOBAL)
    {
       /* Do we need to read the atts? */
-      if (my_grp->atts_not_read)
+      if (!my_grp->atts_read)
          if ((retval = nc4_read_atts(my_grp, NULL)))
             return retval;
 
@@ -849,7 +852,7 @@ nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
          return NC_ENOTVAR;
 
       /* Do we need to read the var attributes? */
-      if (my_var->atts_not_read)
+      if (!my_var->atts_read)
          if ((retval = nc4_read_atts(my_grp, my_var)))
             return retval;
 

libhdf5/hdf5open.c

@@ -1308,7 +1308,7 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
    H5Iinc_ref(hdf5_var->hdf_datasetid); /* Increment number of objects using ID */
    incr_id_rc++; /* Indicate that we've incremented the ref. count (for errors) */
    var->created = NC_TRUE;
-   var->atts_not_read = 1;   /* Don't read var atts until user asks for one. */
+   var->atts_read = 0;
 
    /* Try and read the dimids from the COORDINATES attribute. If it's
     * not present, we will have to do dimsscale matching to locate the
@@ -2112,9 +2112,9 @@ nc4_read_atts(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
 
    /* Remember that we have read the atts for this var or group. */
    if (var)
-      var->atts_not_read = 0;
+      var->atts_read = 1;
    else
-      grp->atts_not_read = 0;
+      grp->atts_read = 1;
 
    return NC_NOERR;
 }
@@ -2569,9 +2569,6 @@ rec_read_metadata(NC_GRP_INFO_T *grp)
          BAIL(retval);
    }
 
-   /* Defer the reading of global atts until someone asks for one. */
-   grp->atts_not_read = 1;
-
    /* When reading existing file, mark all variables as written. */
    for (i = 0; i < ncindexsize(grp->vars); i++)
       ((NC_VAR_INFO_T *)ncindexith(grp->vars, i))->written_to = NC_TRUE;

libhdf5/hdf5var.c

@@ -410,6 +410,7 @@ NC4_def_var(int ncid, const char *name, nc_type xtype,
 
    var->is_new_var = NC_TRUE;
    var->meta_read = NC_TRUE;
+   var->atts_read = NC_TRUE;
 
    /* Point to the type, and increment its ref. count */
    var->type_info = type;

nc_test4/tst_rename2.c

@@ -25,6 +25,10 @@ See \ref copyright file for more info.
 #define DIM_X "x"
 #define DIM_Y "y"
 #define DIM_Z "z"
+#define VAR_NAME_START "lon"
+#define VAR_NAME_END "lo"
+#define DIM_NAME_START "lon"
+#define DIM_NAME_END "lo"
 
 #define DIM1_LEN 4
 #define NDIM1 1
@@ -147,5 +151,89 @@ main(int argc, char **argv)
       SUMMARIZE_ERR;
 
    } /* next format */
+
+#define FILE_NAME1 "tst_dims_foo1.nc"
+#define DIM_NAME "lat_T42"
+#define VAR_NAME DIM_NAME
+#define DIM_NAME2 "lat"
+#define VAR_NAME2 DIM_NAME2
+#define RANK_lat_T42 1
+   fprintf(stderr,"*** test renaming with sync...");
+   {
+      int ncid, dimid, varid;
+      char file_name[NC_MAX_NAME + 1];
+      char name[NC_MAX_NAME + 1];
+
+      /* Create file with dim and associated coordinate var. */
+      sprintf(file_name, "%s_sync.nc", TEST_NAME);
+      nc_set_log_level(4);
+      if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
+      if (nc_def_dim(ncid, DIM_NAME_END, DIM1_LEN, &dimid)) ERR;
+      if (nc_def_var(ncid, DIM_NAME_END, NC_INT, NDIM1, &dimid, &varid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
+      if (nc_def_dim(ncid, DIM_NAME_START, DIM1_LEN, &dimid)) ERR;
+      if (nc_def_var(ncid, DIM_NAME_END, NC_INT, NDIM1, &dimid, &varid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
+      if (nc_rename_dim(ncid, dimid, DIM_NAME_END)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Reopen file and check, */
+      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
+      if (nc_inq_dimid(ncid, DIM_NAME_END, &dimid)) ERR;
+      if (nc_inq_varid(ncid, DIM_NAME_END, &varid)) ERR;
+      if (nc_inq_dimname(ncid, dimid, name)) ERR;
+      if (strcmp(name, DIM_NAME_END)) ERR;
+      if (nc_inq_varname(ncid, varid, name)) ERR;
+      if (strcmp(name, DIM_NAME_END)) ERR;
+      if (nc_close(ncid)) ERR;
+   }
+   SUMMARIZE_ERR;
+   fprintf(stderr,"*** test renaming with sync...");
+   {
+      int ncid, dimid, varid;
+      char file_name[NC_MAX_NAME + 1];
+      char name[NC_MAX_NAME + 1];
+
+      /* Create file with dim and associated coordinate var. */
+      sprintf(file_name, "%s_sync.nc", TEST_NAME);
+      if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
+      if (nc_def_dim(ncid, DIM_NAME_START, DIM1_LEN, &dimid)) ERR;
+      if (nc_def_var(ncid, VAR_NAME_START, NC_INT, NDIM1, &dimid, &varid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      nc_set_log_level(4);
+      /* Open the file and rename the var. */
+      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
+      if (nc_inq_dimid(ncid, DIM_NAME_START, &dimid)) ERR;
+      if (nc_inq_varid(ncid, VAR_NAME_START, &varid)) ERR;
+      if (nc_rename_var(ncid, varid, VAR_NAME_END)) ERR;
+
+      /* Sync to disk. Now the file has one dim and one var. The dim
+       * is a dimscale only dataset, and the var is a dataset with a
+       * dimscale attached pointing to the dim. */
+      /* if (nc_sync(ncid)) ERR; */
+      if (nc_close(ncid)) ERR;
+      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
+      /* Now rename the dim to the same name as the var. After this
+       * there will be one dataset, called DIM_NAME_END, which will be
+       * a dimscale. */
+      if (nc_rename_dim(ncid, dimid, DIM_NAME_END)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Reopen file and check, */
+      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
+      if (nc_inq_dimid(ncid, DIM_NAME_END, &dimid)) ERR;
+      if (nc_inq_varid(ncid, VAR_NAME_END, &varid)) ERR;
+      if (nc_inq_dimname(ncid, dimid, name)) ERR;
+      if (strcmp(name, DIM_NAME_END)) ERR;
+      if (nc_inq_varname(ncid, varid, name)) ERR;
+      if (strcmp(name, VAR_NAME_END)) ERR;
+      if (nc_close(ncid)) ERR;
+   }
+   SUMMARIZE_ERR;
    FINAL_RESULTS;
 }