[svn-r776] Fixed references, object references should be working now.

10 files changed, 143 insertions, 87 deletions

diff --git a/src/H5.c b/src/H5.c
index 8e35cc9..6cbd1bb 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -1944,7 +1944,7 @@ H5_trace (hbool_t returning, const char *func, const char *type, ...)
                 fprintf(out, "NULL");
             }
 	    } else {
-            href_t ref = va_arg (ap, href_t);
+            hobj_ref_t ref = va_arg (ap, hobj_ref_t);
             fprintf (out, "Reference Object=%p", &ref);
 	    }
 	    break;
diff --git a/src/H5D.c b/src/H5D.c
index dde94a2..f7bc440 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -2261,6 +2261,32 @@ H5D_typeof (H5D_t *dset)
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5D_get_file
+ *
+ * Purpose:	Returns the dataset's file pointer.
+ *
+ * Return:	Success:	Ptr to the dataset's file pointer.
+ *
+ *		Failure:	NULL
+ *
+ * Programmer:	Quincey Koziol
+ *              Thursday, October 22, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+H5F_t *
+H5D_get_file (const H5D_t *dset)
+{
+    FUNC_ENTER (H5D_get_file, NULL);
+    assert (dset);
+    assert (dset->ent.file);
+    FUNC_LEAVE (dset->ent.file);
+}
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5D_init_storage
  *
  * Purpose:	Initialize the data for a new dataset.  If a selection is
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index f89e9b3..6aeb421 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -83,5 +83,6 @@ H5T_t *H5D_typeof (H5D_t *dset);
 H5S_t *H5D_get_space(H5D_t *dset);
 H5D_t * H5D_new(const H5D_create_t *create_parms);
 herr_t H5D_open_oid(H5D_t *dataset, H5G_entry_t *ent);
+H5F_t * H5D_get_file(const H5D_t *dset);
 
 #endif
diff --git a/src/H5O.c b/src/H5O.c
index d03d5fa..0902b1c 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -1044,13 +1044,6 @@ H5O_find_in_ohdr(H5F_t *f, const haddr_t *addr, const H5O_class_t **type_p,
     assert(addr && H5F_addr_defined(addr));
     assert(type_p);
 
-#ifdef QAK
-    printf("%s: addr=",FUNC);
-    H5F_addr_print(stdout,addr);
-    printf("\n%s: f=%p, addr=%p\n",FUNC,f,addr);
-    printf("%s: f->shared=%p\n",FUNC,f->shared);
-    printf("%s: H5AC_HASH=%lu\n",FUNC,(unsigned long)H5AC_HASH(f,addr));
-#endif /* QAK */
     /* Load the object header */
     if (NULL == (oh = H5AC_find(f, H5AC_OHDR, addr, NULL, NULL))) {
 	HRETURN_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL,
diff --git a/src/H5Odtype.c b/src/H5Odtype.c
index 482725e..26d42f1 100644
--- a/src/H5Odtype.c
+++ b/src/H5Odtype.c
@@ -218,6 +218,15 @@ H5O_dtype_decode_helper(const uint8 **pp, H5T_t *dt)
         }
         break;
 
+    case H5T_POINTER:
+        dt->u.atomic.order = H5T_ORDER_NONE;
+        dt->u.atomic.prec = 8 * dt->size;
+        dt->u.atomic.offset = 0;
+        dt->u.atomic.lsb_pad = H5T_PAD_ZERO;
+        dt->u.atomic.msb_pad = H5T_PAD_ZERO;
+        dt->u.atomic.u.r.rtype = flags & 0x0f;
+        break;
+
     default:
         if (flags) {
             HRETURN_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, FAIL,
@@ -457,6 +466,10 @@ H5O_dtype_encode_helper(uint8 **pp, const H5T_t *dt)
         }
         break;
 
+    case H5T_POINTER:
+        flags |= (dt->u.atomic.u.r.rtype & 0x0f);
+        break;
+        
     default:
         /*nothing */
         break;
diff --git a/src/H5R.c b/src/H5R.c
index f936202..a7d79c7 100644
--- a/src/H5R.c
+++ b/src/H5R.c
@@ -20,6 +20,7 @@ static char		RcsId[] = "@(#)$Revision$";
 #include <H5Iprivate.h>		/* ID Functions */
 #include <H5Dprivate.h>		/* Datasets */
 #include <H5Eprivate.h>		/* Error handling */
+#include <H5Fprivate.h>		/* Files */
 #include <H5Gprivate.h>		/* Groups */
 #include <H5Rprivate.h>		/* References */
 #include <H5Sprivate.h>		/* Dataspaces */
@@ -32,10 +33,10 @@ static herr_t		H5R_init_interface(void);
 static void		H5R_term_interface(void);
 
 /* Static functions */
-static herr_t H5R_create(href_t *ref, H5G_entry_t *loc, const char *name,
+static herr_t H5R_create(void *ref, H5G_entry_t *loc, const char *name,
         H5R_type_t ref_type, H5S_t *space);
-static hid_t H5R_dereference(H5D_t *dset, href_t *ref);
-static H5S_t * H5R_get_space(href_t *ref);
+static hid_t H5R_dereference(H5D_t *dset, H5R_type_t ref_type, void *_ref);
+static H5S_t * H5R_get_space(void *ref);
 
 
 /*--------------------------------------------------------------------------
@@ -98,7 +99,7 @@ H5R_term_interface(void)
     Creates a particular kind of reference for the user
  USAGE
     herr_t H5R_create(ref, loc, name, ref_type, space)
-        href_t *ref;        OUT: Reference created
+        void *ref;          OUT: Reference created
         H5G_entry_t *loc;   IN: File location used to locate object pointed to
         const char *name;   IN: Name of object at location LOC_ID of object
                                     pointed to
@@ -119,14 +120,14 @@ H5R_term_interface(void)
  REVISION LOG
 --------------------------------------------------------------------------*/
 static herr_t
-H5R_create(href_t *ref, H5G_entry_t *loc, const char *name, H5R_type_t ref_type, H5S_t __unused__ *space)
+H5R_create(void *_ref, H5G_entry_t *loc, const char *name, H5R_type_t ref_type, H5S_t __unused__ *space)
 {
     H5G_stat_t sb;              /* Stat buffer for retrieving OID */
     herr_t ret_value = FAIL;
 
     FUNC_ENTER(H5R_create, FAIL);
 
-    assert(ref);
+    assert(_ref);
     assert(loc);
     assert(name);
     assert(ref_type>H5R_BADTYPE || ref_type<H5R_MAXTYPE);
@@ -134,9 +135,29 @@ H5R_create(href_t *ref, H5G_entry_t *loc, const char *name, H5R_type_t ref_type,
     if (H5G_get_objinfo (loc, name, 0, &sb)<0)
         HGOTO_ERROR (H5E_REFERENCE, H5E_NOTFOUND, FAIL, "unable to stat object");
 
-    /* Set information for reference */
-    ref->oid[0]=sb.objno[0];
-    ref->oid[1]=sb.objno[1];
+    switch(ref_type) {
+        case H5R_OBJECT:
+        {
+            hobj_ref_t *ref=(hobj_ref_t *)_ref; /* Get pointer to correct type of reference struct */
+            uint8 *p;       /* Pointer to OID to store */
+
+            /* Set information for reference */
+            p=(uint8 *)ref->oid;
+            H5F_addr_encode(loc->file,&p,(const haddr_t *)sb.objno);
+            break;
+        }
+
+        case H5R_DATASET_REGION:
+        case H5R_INTERNAL:
+            HRETURN_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL,
+                  "Dataset region and internal references are not supported yet");
+
+        case H5R_BADTYPE:
+        case H5R_MAXTYPE:
+            assert("unknown reference type" && 0);
+            HRETURN_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL,
+                  "internal error (unknown reference type)");
+    } /* end switch */
 
     /* Return success */
     ret_value=SUCCEED;
@@ -153,7 +174,7 @@ done:
     Creates a particular kind of reference for the user
  USAGE
     herr_t H5Rcreate(ref, loc_id, name, ref_type, space_id)
-        href_t *ref;        OUT: Reference created
+        void *ref;          OUT: Reference created
         hid_t loc_id;       IN: Location ID used to locate object pointed to
         const char *name;   IN: Name of object at location LOC_ID of object
                                     pointed to
@@ -174,7 +195,7 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 herr_t
-H5Rcreate(href_t *ref, hid_t loc_id, const char *name, H5R_type_t ref_type, hid_t space_id)
+H5Rcreate(void *ref, hid_t loc_id, const char *name, H5R_type_t ref_type, hid_t space_id)
 {
     H5G_entry_t *loc = NULL;        /* File location */
     H5S_t	*space = NULL;          /* Pointer to dataspace containing region */
@@ -214,7 +235,8 @@ done:
  USAGE
     hid_t H5R_dereference(ref)
         H5D_t *dset;        IN: Dataset reference object is in.
-        href_t *ref;        IN: Reference to open.
+        H5R_type_t ref_type;    IN: Type of reference
+        void *ref;          IN: Reference to open.
         
  RETURNS
     Valid ID on success, FAIL on failure
@@ -228,17 +250,19 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 static hid_t
-H5R_dereference(H5D_t *dset, href_t *ref)
+H5R_dereference(H5D_t *dset, H5R_type_t ref_type, void *_ref)
 {
     H5D_t *dataset;             /* Pointer to dataset to open */
+    hobj_ref_t *ref=(hobj_ref_t *)_ref; /* Only object references currently supported */
     H5G_entry_t ent;            /* Symbol table entry */
+    uint8 *p;                   /* Pointer to OID to store */
     hid_t ret_value = FAIL;
 
     FUNC_ENTER(H5R_dereference, FAIL);
 
     assert(ref);
+    assert(ref_type==H5R_OBJECT);
 
-printf("%s: ref->oid=%ld-%ld\n",FUNC,(long)ref->oid[0],ref->oid[1]);
     /*
      * Switch on object type, when we implement that feature, always try to
      *  open a dataset for now
@@ -251,9 +275,10 @@ printf("%s: ref->oid=%ld-%ld\n",FUNC,(long)ref->oid[0],ref->oid[1]);
 
     /* Initialize the symbol table entry */
     HDmemset(&ent,0,sizeof(H5G_entry_t));
-    HDmemcpy(&(ent.header),ref->oid,sizeof(haddr_t));
     ent.type=H5G_NOTHING_CACHED;
-/* ent.file=ref->file; */
+    ent.file=H5D_get_file(dset);
+    p=(uint8 *)ref->oid;
+    H5F_addr_decode(ent.file,(const uint8 **)&p,&(ent.header));
 
     /* Open the dataset object */
     if (H5D_open_oid(dataset, &ent) < 0) {
@@ -266,7 +291,6 @@ printf("%s: ref->oid=%ld-%ld\n",FUNC,(long)ref->oid[0],ref->oid[1]);
         HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
 		      "can't register dataset");
     }
-printf("%s: ret_value=%ld\n",FUNC,(long)ret_value);
 
 done:
     FUNC_LEAVE(ret_value);
@@ -281,7 +305,8 @@ done:
  USAGE
     hid_t H5Rdereference(ref)
         hid_t dataset;      IN: Dataset reference object is in.
-        href_t *ref;        IN: Reference to open.
+        H5R_type_t ref_type;    IN: Type of reference to create
+        void *ref;          IN: Reference to open.
         
  RETURNS
     Valid ID on success, FAIL on failure
@@ -294,22 +319,24 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 hid_t
-H5Rdereference(hid_t dataset, href_t *ref)
+H5Rdereference(hid_t dataset, H5R_type_t ref_type, void *_ref)
 {
     H5D_t		   *dset = NULL;	/* dataset object */
     hid_t ret_value = FAIL;
 
     FUNC_ENTER(H5Rdereference, FAIL);
-    H5TRACE2("i","i*r",dataset,ref);
+    H5TRACE2("i","i*r",dataset,_ref);
 
     /* Check args */
     if (H5I_DATASET != H5I_get_type(dataset) || NULL == (dset = H5I_object(dataset)))
         HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
-    if(ref==NULL)
+    if(ref_type<=H5R_BADTYPE || ref_type>=H5R_MAXTYPE)
+        HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type");
+    if(_ref==NULL)
         HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer");
 
     /* Create reference */
-    if ((ret_value=H5R_dereference(dset, ref))<0)
+    if ((ret_value=H5R_dereference(dset, ref_type, _ref))<0)
         HGOTO_ERROR (H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable dereference object");
 
 done:
@@ -324,7 +351,7 @@ done:
     Retrieves a dataspace with the region pointed to selected.
  USAGE
     H5S_t *H5R_get_space(ref)
-        href_t *ref;        IN: Reference to open.
+        void *ref;        IN: Reference to open.
         
  RETURNS
     Pointer to the dataspace on success, NULL on failure
@@ -338,7 +365,7 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 static H5S_t *
-H5R_get_space(href_t __unused__ *ref)
+H5R_get_space(void __unused__ *ref)
 {
     H5S_t *ret_value = NULL;
 
@@ -360,7 +387,7 @@ done:
     Retrieves a dataspace with the region pointed to selected.
  USAGE
     hid_t H5Rget_space(ref)
-        href_t *ref;        IN: Reference to open.
+        void *ref;        IN: Reference to open.
         
  RETURNS
     Valid ID on success, FAIL on failure
@@ -374,7 +401,7 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 hid_t
-H5Rget_space(href_t *ref)
+H5Rget_space(void *ref)
 {
     H5S_t *space = NULL;
     hid_t ret_value = FAIL;
diff --git a/src/H5Rpublic.h b/src/H5Rpublic.h
index 4882444..ebb7771 100644
--- a/src/H5Rpublic.h
+++ b/src/H5Rpublic.h
@@ -31,12 +31,19 @@ typedef enum {
     H5R_MAXTYPE                 /* highest type in group (Invalid as true type)*/
 } H5R_type_t;
 
-/* Reference structure for user's code */
+#ifdef LATER
+/* Generic reference structure for user's code */
 typedef struct {
     unsigned long oid[2];       /* OID of object referenced */
     unsigned long region[2];    /* heap ID of region in object */
     unsigned long file[2];      /* heap ID of external filename */
 } href_t;
+#endif /* LATER */
+
+/* Object reference structure for user's code */
+typedef struct {
+    unsigned long oid[2];       /* OID of object referenced */
+} hobj_ref_t;
 
 /* Publicly visible datastructures */
 
@@ -45,10 +52,10 @@ extern "C" {
 #endif
 
 /* Functions in H5R.c */
-herr_t H5Rcreate(href_t *ref, hid_t loc_id, const char *name,
+herr_t H5Rcreate(void *ref, hid_t loc_id, const char *name,
         H5R_type_t ref_type, hid_t space_id);
-hid_t H5Rdereference(hid_t dataset, href_t *ref);
-hid_t H5Rget_space(href_t *ref);
+hid_t H5Rdereference(hid_t dataset, H5R_type_t ref_type, void *ref);
+hid_t H5Rget_space(void *ref);
 
 #ifdef __cplusplus
 }
diff --git a/src/H5T.c b/src/H5T.c
index 575d98f..d583f3d 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -220,14 +220,6 @@ H5T_init_interface(void)
     dt->u.atomic.prec = 8*dt->size;
     dt->u.atomic.offset = 0;
 
-    /* Object pointer (i.e. object header address in file) */
-    dt = H5I_object (H5T_STD_PTR_OBJ_g = H5Tcopy (H5T_NATIVE_INT_g));
-    dt->type = H5T_POINTER;
-    dt->state = H5T_STATE_IMMUTABLE;
-    dt->size = sizeof(haddr_t);
-    dt->u.atomic.u.r.rtype = H5R_OBJECT;
-    dt->u.atomic.prec = 8*dt->size;
-    dt->u.atomic.offset = 0;
 
     /*------------------------------------------------------------
      * IEEE Types
@@ -607,6 +599,29 @@ H5T_init_interface(void)
 		      "can't initialize H5T layer");
     }
 
+    /*------------------------------------------------------------
+     * Pointer types
+     *------------------------------------------------------------ 
+     */
+    /* Object pointer (i.e. object header address in file) */
+    if (NULL==(dt = H5MM_calloc(sizeof(H5T_t)))) {
+        HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed");
+    }
+    dt->state = H5T_STATE_IMMUTABLE;
+    H5F_addr_undef (&(dt->ent.header));
+    dt->type = H5T_POINTER;
+    dt->size = sizeof(haddr_t);
+    dt->u.atomic.order = H5T_ORDER_NONE;
+    dt->u.atomic.offset = 0;
+    dt->u.atomic.prec = 8 * dt->size;
+    dt->u.atomic.lsb_pad = H5T_PAD_ZERO;
+    dt->u.atomic.msb_pad = H5T_PAD_ZERO;
+    dt->u.atomic.u.r.rtype = H5R_OBJECT;
+    if ((H5T_STD_PTR_OBJ_g = H5I_register(H5I_DATATYPE, dt)) < 0) {
+	HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
+		      "unable to initialize H5T layer");
+    }
+
     /*
      * Register conversion functions beginning with the most general and
      * ending with the most specific.
@@ -4398,36 +4413,23 @@ H5T_find(const H5T_t *src, const H5T_t *dst, H5T_bkg_t need_bkg,
 
     FUNC_ENTER(H5T_find, NULL);
 
-#ifdef QAK
-    printf("%s: check 1.0\n",FUNC);
-#endif /* QAK */
     if (!noop_cdata.stats &&
 	NULL==(noop_cdata.stats = H5MM_calloc (sizeof(H5T_stats_t)))) {
 	HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
 		       "memory allocation failed");
     }
 
-#ifdef QAK
-    printf("%s: check 2.0, src->type=%d, dst->type=%d\n",
-	   FUNC, (int)src->type, (int)dst->type);
-#endif /* QAK */
     /* No-op case */
     if (need_bkg<H5T_BKG_YES && 0==H5T_cmp(src, dst)) {
 	*pcdata = &noop_cdata;
 	HRETURN(H5T_conv_noop);
     }
     
-#ifdef QAK
-    printf("%s: check 3.0\n", FUNC);
-#endif /* QAK */
     /* Find it */
     if (NULL == (path = H5T_path_find(NULL, src, dst, TRUE, NULL))) {
 	HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL,
 		      "unable to create conversion path");
     }
-#ifdef QAK
-    printf("%s: path=%p\n", FUNC, path);
-#endif /* QAK */
 
     if ((ret_value=path->func)) {
 	*pcdata = &(path->cdata);
@@ -4495,9 +4497,6 @@ H5T_path_find(const char *name, const H5T_t *src, const H5T_t *dst,
             HRETURN(H5T_path_g[md]);
         }
     }
-#ifdef QAK
-    printf("%s: check 2.0, create=%d, md=%d\n", FUNC, (int)create, md);
-#endif /* QAK */
 
     /* Insert */
     if (create) {
@@ -4524,18 +4523,9 @@ H5T_path_find(const char *name, const H5T_t *src, const H5T_t *dst,
             HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
                    "memory allocation failed");
         }
-#ifdef QAK
-	printf("%s: check 3.0, src=%p, dst=%p\n", FUNC, src, dst);
-	printf("%s: check 3.0, src->type=%d, dst->type=%d\n",
-	       FUNC, (int)src->type, (int)dst->type);
-#endif /* QAK */
         path->src = H5T_copy(src, H5T_COPY_ALL);
         path->dst = H5T_copy(dst, H5T_COPY_ALL);
 
-#ifdef QAK
-	printf("%s: check 3.5, func=%p, name=%s\n",
-	       FUNC, func, (name!=NULL ? name : "NULL"));
-#endif /* QAK */
         /* Associate a function with the path if possible */
         if (func) {
             HDstrncpy (path->name, name, H5T_NAMELEN);
@@ -4601,9 +4591,6 @@ H5T_path_find(const char *name, const H5T_t *src, const H5T_t *dst,
             }
         }
     }
-#ifdef QAK
-    printf("%s: leaving path=%p\n", FUNC, path);
-#endif /* QAK */
     FUNC_LEAVE(path);
 }
 
diff --git a/src/H5private.h b/src/H5private.h
index 2d42902..2b976e0 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -177,19 +177,6 @@ typedef int intn;
 typedef unsigned uintn;
 
 /*
- * Status return values for the `herr_t' type.
- * Since some unix/c routines use 0 and -1 (or more precisely, non-negative
- * vs. negative) as their return code, and some assumption had been made in
- * the code about that, it is important to keep these constants the same
- * values.  When checking the success or failure of an integer-valued
- * function, remember to compare against zero and not one of these two
- * values.
- */
-#define SUCCEED         0
-#define FAIL            (-1)
-#define UFAIL           (unsigned)(-1)
-
-/*
  * File addresses.
  */
 typedef struct {
diff --git a/src/H5public.h b/src/H5public.h
index 2e07a24..04550c0 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -45,6 +45,21 @@
  */
 typedef int herr_t;
 
+
+/*
+ * Status return values for the `herr_t' type.
+ * Since some unix/c routines use 0 and -1 (or more precisely, non-negative
+ * vs. negative) as their return code, and some assumption had been made in
+ * the code about that, it is important to keep these constants the same
+ * values.  When checking the success or failure of an integer-valued
+ * function, remember to compare against zero and not one of these two
+ * values.
+ */
+#define SUCCEED         0
+#define FAIL            (-1)
+#define UFAIL           (unsigned)(-1)
+
+
 /*
  * Boolean type.  Successful return values are zero (false) or positive
  * (true). The typical true value is 1 but don't bet on it.  Boolean