More refactoring to completely (?) mimic previous library behavior for scanning contents of the file

RELEASE_NOTES.md

@@ -7,6 +7,9 @@ Recent releases include references to Jira issue identifiers for more informatio
 ## 4.3.1 Released TBD
 
 
+* Corrected behavior of nc_inq_unlimdim and nv_inq_unlimdims to report dimids
+  in same order as nc_inq_dimids
+
 * Addressed an issue reported by Jeff Whitaker regarding `nc_inq_nvars` returning an incorrect number of dimensions (this issue was introduced in 4.3.1-rc5).  Integrated a test contributed by Jeff Whitaker.
 
 ### 4.3.1-rc5 Released 2013-12-06

include/nc4internal.h

@@ -97,16 +97,22 @@ typedef enum {VAR, DIM, ATT} NC_OBJ_T;
  * as the netCDF dimid. */
 #define NC_DIMID_ATT_NAME "_Netcdf4Dimid"
 
+/* Generic doubly-linked list node */
+typedef struct NC_LIST_NODE
+{
+   void *next;
+   void *prev;
+} NC_LIST_NODE_T;
+
 /* This is a struct to handle the dim metadata. */
 typedef struct NC_DIM_INFO
 {
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    char *name;
    size_t len;
    int dimid;
    int unlimited;
    int extended;
-   struct NC_DIM_INFO *next;
-   struct NC_DIM_INFO *prev;
    hid_t hdf_dimscaleid;
    HDF5_OBJID_T hdf5_objid;
    struct NC_VAR_INFO *coord_var; /* The coord var, if it exists. */
@@ -115,10 +121,9 @@ typedef struct NC_DIM_INFO
 
 typedef struct NC_ATT_INFO
 {
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    int len;
    char *name;
-   struct NC_ATT_INFO *next;
-   struct NC_ATT_INFO *prev;
    int dirty;
    int created;
    nc_type xtype;
@@ -133,15 +138,14 @@ typedef struct NC_ATT_INFO
 /* This is a struct to handle the var metadata. */
 typedef struct NC_VAR_INFO
 {
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    char *name;
    char *hdf5_name; /* used if different from name */
    int ndims;
    int *dimids;
    NC_DIM_INFO_T **dim;
    int varid;
    int natts;
-   struct NC_VAR_INFO *next;
-   struct NC_VAR_INFO *prev;
    int dirty;
    int created;         /* Variable has already been created (_not_ that it was just created) */
    int written_to;
@@ -174,8 +178,7 @@ typedef struct NC_VAR_INFO
 
 typedef struct NC_FIELD_INFO
 {
-   struct NC_FIELD_INFO *next;
-   struct NC_FIELD_INFO *prev;
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    nc_type nctype;
    hid_t hdf_typeid;
    hid_t native_typeid;
@@ -188,16 +191,14 @@ typedef struct NC_FIELD_INFO
 
 typedef struct NC_ENUM_MEMBER_INFO
 {
-   struct NC_ENUM_MEMBER_INFO *next;
-   struct NC_ENUM_MEMBER_INFO *prev;
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    char *name;
    void *value;
 } NC_ENUM_MEMBER_INFO_T;
 
 typedef struct NC_TYPE_INFO
 {
-   struct NC_TYPE_INFO *next;
-   struct NC_TYPE_INFO *prev;
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    nc_type nc_typeid;
    hid_t hdf_typeid;
    hid_t native_typeid;
@@ -219,11 +220,10 @@ typedef struct NC_TYPE_INFO
  * parthenogenesis. */
 typedef struct NC_GRP_INFO
 {
+   NC_LIST_NODE_T l;            /* Use generic doubly-linked list (must be first) */
    int nc_grpid;
    struct NC_GRP_INFO *parent;
    struct NC_GRP_INFO *children;
-   struct NC_GRP_INFO *next; /* points to siblings */
-   struct NC_GRP_INFO *prev; /* points to siblings */
    NC_VAR_INFO_T *var;
    NC_DIM_INFO_T *dim;
    NC_ATT_INFO_T *att;
@@ -291,16 +291,10 @@ int nc4_convert_type(const void *src, void *dest,
 /* These functions do HDF5 things. */
 int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
 int nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset);
-int pg_var(NC_PG_T pg, NC *nc, int ncid, int varid, nc_type xtype, int is_long, void *ip);
-int nc4_pg_var1(NC_PG_T pg, NC *nc, int ncid, int varid, const size_t *indexp, 
-		nc_type xtype, int is_long, void *ip);
 int nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp, 
 		 const size_t *countp, nc_type xtype, int is_long, void *op);
 int nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp, 
 		 const size_t *countp, nc_type xtype, int is_long, void *op);
-int nc4_pg_varm(NC_PG_T pg, NC *nc, int ncid, int varid, const size_t *startp, 
-		const size_t *countp, const ptrdiff_t *stridep,
-		const ptrdiff_t *imapp, nc_type xtype, int is_long, void *op);
 int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
 int nc4_rec_detect_need_to_preserve_dimids(NC_GRP_INFO_T *grp, int *bad_coord_orderp);
 int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order);
@@ -341,9 +335,9 @@ int nc4_get_hdf_typeid(NC_HDF5_FILE_INFO_T *h5, nc_type xtype,
 int nc4_nc4f_list_add(NC *nc, const char *path, int mode);
 int nc4_var_list_add(NC_VAR_INFO_T **list, NC_VAR_INFO_T **var);
 int nc4_var_list_del(NC_VAR_INFO_T **list, NC_VAR_INFO_T *var);
-int nc4_dim_list_add(NC_DIM_INFO_T **list);
+int nc4_dim_list_add(NC_DIM_INFO_T **list, NC_DIM_INFO_T **dim);
 int nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim);
-int nc4_att_list_add(NC_ATT_INFO_T **list);
+int nc4_att_list_add(NC_ATT_INFO_T **list, NC_ATT_INFO_T **att);
 int nc4_type_list_add(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T **new_type);
 int nc4_field_list_add(NC_FIELD_INFO_T **list, int fieldid, const char *name,
 		       size_t offset, hid_t field_hdf_typeid, hid_t native_typeid, 

libsrc/memio.c

@@ -103,7 +103,6 @@ memio_new(const char* path, int ioflags, off_t initialsize, ncio** nciopp, NCMEM
     int status = NC_NOERR;
     ncio* nciop = NULL;
     NCMEMIO* memio = NULL;
-    int openfd = -1;
 
     if(pagesize == 0) {
 
@@ -156,15 +155,20 @@ memio_new(const char* path, int ioflags, off_t initialsize, ncio** nciopp, NCMEM
     memio->persist = fIsSet(ioflags,NC_WRITE);
 
     if(nciopp) *nciopp = nciop;
+    else {
+        free((char*)nciop->path);
+        free(nciop);
+    }
     if(memiop) *memiop = memio;
+    else free(memio);
 
 done:
-    if(openfd >= 0) close(openfd);
     return status;
 
 fail:
     if(nciop != NULL) {
         if(nciop->path != NULL) free((char*)nciop->path);
+        free(nciop);
     }
     goto done;
 }

libsrc4/nc3stub.c

@@ -294,11 +294,6 @@ nc3_inq_unlimdim(int ncid, int *unlimdimidp) {abort();}
 int
 nc3_show_metadata(int ncid) {abort();}
 
-#ifdef IGNORE
-int
-nc3_delete_mp(const char * path, int basepe) {abort();}
-#endif
-
 int
 nc3_put_att_text(int ncid, int varid, const char *name,
 		size_t len, const char *op) {abort();}

libsrc4/nc4attr.c

@@ -234,7 +234,7 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
       attlist = &grp->att;
    else
    {
-      for (var = grp->var; var; var = var->next)
+      for (var = grp->var; var; var = var->l.next)
 	 if (var->varid == varid)
 	 {
 	    attlist = &var->att;
@@ -243,7 +243,7 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
       if (!var)
 	 return NC_ENOTVAR;
    }
-   for (att = *attlist; att; att = att->next)
+   for (att = *attlist; att; att = att->l.next)
       if (!strcmp(att->name, norm_name))
 	 break;
 
@@ -299,20 +299,16 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
    if (new_att)
    {
       LOG((3, "adding attribute %s to the list...", norm_name));
-      if ((res = nc4_att_list_add(attlist)))
+      if ((res = nc4_att_list_add(attlist, &att)))
 	 BAIL (res);
-      /* Find this att's entry in the list (the last one). */
-      for (att=*attlist; att->next; att=att->next)
-	 ;
    }
 
    /* Now fill in the metadata. */
    att->dirty++;
    if (att->name)
       free(att->name);
-   if (!(att->name = malloc((strlen(norm_name) + 1) * sizeof(char))))
+   if (!(att->name = strdup(norm_name)))
       return NC_ENOMEM;
-   strcpy(att->name, norm_name);
    att->xtype = file_type;
 
    /* If this att has vlen or string data, release it before we lose the length value. */
@@ -333,8 +329,8 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
    }
 
    att->len = len;
-   if (att->prev)
-      att->attnum = att->prev->attnum + 1;
+   if (att->l.prev)
+      att->attnum = ((NC_ATT_INFO_T *)att->l.prev)->attnum + 1;
    else
       att->attnum = 0;
    if (type)
@@ -415,7 +411,7 @@ nc4_put_att(int ncid, NC *nc, int varid, const char *name,
       /* Mark the var and all its atts as dirty, so they get
        * rewritten. */
       var->dirty++;
-      for (varatt = var->att; varatt; varatt = varatt->next)
+      for (varatt = var->att; varatt; varatt = varatt->l.next)
 	 varatt->dirty++;
    }
 
@@ -645,7 +641,7 @@ NC4_rename_att(int ncid, int varid, const char *name,
    }
    else
    {
-      for (var = grp->var; var; var = var->next)
+      for (var = grp->var; var; var = var->l.next)
 	 if (var->varid == varid)
 	 {
 	    list = var->att;
@@ -654,14 +650,14 @@ NC4_rename_att(int ncid, int varid, const char *name,
       if (!var)
 	 return NC_ENOTVAR;
    }
-   for (att = list; att; att = att->next)
+   for (att = list; att; att = att->l.next)
       if (!strncmp(att->name, norm_newname, NC_MAX_NAME))
 	 return NC_ENAMEINUSE;
 
    /* Normalize name and find the attribute. */
    if ((retval = nc4_normalize_name(name, norm_name)))
       return retval;
-   for (att = list; att; att = att->next)
+   for (att = list; att; att = att->l.next)
       if (!strncmp(att->name, norm_name, NC_MAX_NAME))
 	 break;
    if (!att)
@@ -758,7 +754,7 @@ NC4_del_att(int ncid, int varid, const char *name)
    }
    else
    {
-      for(var = grp->var; var; var = var->next)
+      for(var = grp->var; var; var = var->l.next)
       {
 	 if (var->varid == varid)
 	 {
@@ -775,7 +771,7 @@ NC4_del_att(int ncid, int varid, const char *name)
    }
 
    /* Now find the attribute by name or number. */
-   for (att = *attlist; att; att = att->next)
+   for (att = *attlist; att; att = att->l.next)
       if (!strcmp(att->name, name))
 	 break;
 
@@ -789,7 +785,7 @@ NC4_del_att(int ncid, int varid, const char *name)
 	 BAIL(NC_EATTMETA);
 
    /* Renumber all following attributes. */
-   for (natt = att->next; natt; natt = natt->next)
+   for (natt = att->l.next; natt; natt = natt->l.next)
       natt->attnum--;
 
    /* Delete this attribute from this list. */

libsrc4/nc4dim.c

@@ -48,7 +48,7 @@ NC4_inq_unlimdim(int ncid, int *unlimdimidp)
    *unlimdimidp = -1;
    for (g = grp; g && !found; g = g->parent)
    {
-      for (dim = g->dim; dim; dim = dim->next)
+      for (dim = g->dim; dim; dim = dim->l.next)
       {
 	 if (dim->unlimited)
 	 {
@@ -98,7 +98,7 @@ NC4_def_dim(int ncid, const char *name, size_t len, int *idp)
    {
       /* Only one limited dimenson for strict nc3. */
       if (len == NC_UNLIMITED)
-	 for (dim = grp->dim; dim; dim = dim->next)
+	 for (dim = grp->dim; dim; dim = dim->l.next)
 	    if (dim->unlimited)
 	       return NC_EUNLIMIT;
 
@@ -123,26 +123,25 @@ NC4_def_dim(int ncid, const char *name, size_t len, int *idp)
 	 return NC_EDIMSIZE;
 
    /* Make sure the name is not already in use. */
-   for (dim = grp->dim; dim; dim = dim->next)
+   for (dim = grp->dim; dim; dim = dim->l.next)
       if (!strncmp(dim->name, norm_name, NC_MAX_NAME))
 	 return NC_ENAMEINUSE;
 
    /* Add a dimension to the list. The ID must come from the file
     * information, since dimids are visible in more than one group. */
-   nc4_dim_list_add(&grp->dim);
-   grp->dim->dimid = grp->nc4_info->next_dimid++;
+   nc4_dim_list_add(&grp->dim, &dim);
+   dim->dimid = grp->nc4_info->next_dimid++;
 
    /* Initialize the metadata for this dimension. */
-   if (!(grp->dim->name = malloc((strlen(norm_name) + 1) * sizeof(char))))
+   if (!(dim->name = strdup(norm_name)))
       return NC_ENOMEM;
-   strcpy(grp->dim->name, norm_name);
-   grp->dim->len = len;
+   dim->len = len;
    if (len == NC_UNLIMITED)
-      grp->dim->unlimited++;
+      dim->unlimited++;
 
    /* Pass back the dimid. */
    if (idp)
-      *idp = grp->dim->dimid;
+      *idp = dim->dimid;
 
    return retval;
 }
@@ -180,7 +179,7 @@ NC4_inq_dimid(int ncid, const char *name, int *idp)
 
    /* Go through each dim and check for a name match. */
    for (g = grp; g && !finished; g = g->parent)
-      for (dim = g->dim; dim; dim = dim->next)
+      for (dim = g->dim; dim; dim = dim->l.next)
 	 if (!strncmp(dim->name, norm_name, NC_MAX_NAME))
 	 {
 	    if (idp)
@@ -301,12 +300,12 @@ NC4_rename_dim(int ncid, int dimid, const char *name)
       return retval;
 
    /* Make sure the new name is not already in use in this group. */
-   for (dim = grp->dim; dim; dim = dim->next)
+   for (dim = grp->dim; dim; dim = dim->l.next)
       if (!strncmp(dim->name, norm_name, NC_MAX_NAME))
 	 return NC_ENAMEINUSE;
 
    /* Find the dim. */
-   for (dim = grp->dim; dim; dim = dim->next)
+   for (dim = grp->dim; dim; dim = dim->l.next)
       if (dim->dimid == dimid)
 	 break;
    if (!dim)
@@ -393,7 +392,7 @@ NC4_inq_unlimdims(int ncid, int *nunlimdimsp, int *unlimdimidsp)
    /* Get our dim info. */
    assert(h5);
    {
-      for (dim=grp->dim; dim; dim=dim->next)
+      for (dim=grp->dim; dim; dim=dim->l.next)
       {
 	 if (dim->unlimited)
 	 {