* Reverted removal of H5I_REFERENCE to avoid breaking binary

  compatibility.
* Added a quick H5I_REFERENCE smoke check to test_misc19()
  in tmisc.c.

22 files changed, 157 insertions, 5 deletions

diff --git a/c++/src/H5IdComponent.cpp b/c++/src/H5IdComponent.cpp
index 457f594..284c6c5 100644
--- a/c++/src/H5IdComponent.cpp
+++ b/c++/src/H5IdComponent.cpp
@@ -174,6 +174,7 @@ H5I_type_t IdComponent::getHDFObjType() const
 ///             \li \c H5I_DATASPACE
 ///             \li \c H5I_DATASET
 ///             \li \c H5I_ATTR
+///             \li \c H5I_REFERENCE (DEPRECATED)
 ///             \li \c H5I_VFL
 ///             \li \c H5I_GENPROP_CLS
 ///             \li \c H5I_GENPROP_LST
@@ -226,6 +227,7 @@ bool IdComponent::isValid(hid_t an_id)
 ///             \li \c H5I_DATASPACE
 ///             \li \c H5I_DATASET
 ///             \li \c H5I_ATTR
+///             \li \c H5I_REFERENCE (DEPRECATED)
 ///             \li \c H5I_VFL
 ///             \li \c H5I_GENPROP_CLS
 ///             \li \c H5I_GENPROP_LST
diff --git a/c++/src/H5PropList.cpp b/c++/src/H5PropList.cpp
index dd7b21a..16a6316 100644
--- a/c++/src/H5PropList.cpp
+++ b/c++/src/H5PropList.cpp
@@ -138,6 +138,24 @@ PropList::PropList(const hid_t plist_id) : IdComponent()
               throw PropListIException("PropList constructor", "H5Pcopy failed");
           }
           break;
+        /* These should really be error cases, but changing that breaks
+         * the stated behavior and causes test failures.
+         * (DER, July 2017)
+         */
+        case H5I_BADID:
+        case H5I_FILE:
+        case H5I_GROUP:
+        case H5I_DATATYPE:
+        case H5I_DATASPACE:
+        case H5I_DATASET:
+        case H5I_ATTR:
+        case H5I_REFERENCE:
+        case H5I_VFL:
+        case H5I_ERROR_CLASS:
+        case H5I_ERROR_MSG:
+        case H5I_ERROR_STACK:
+        case H5I_NTYPES:
+        case H5I_UNINIT:
         default:
           id = H5P_DEFAULT;
           break;
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index b216d03..8a3d6c8 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -309,6 +309,7 @@ public class HDF5Constants {
     public static final int H5I_GROUP = H5I_GROUP();
     public static final int H5I_INVALID_HID = H5I_INVALID_HID();
     public static final int H5I_NTYPES = H5I_NTYPES();
+    public static final int H5I_REFERENCE = H5I_REFERENCE();
     public static final int H5I_UNINIT = H5I_UNINIT();
     public static final int H5I_VFL = H5I_VFL();
 
@@ -1195,6 +1196,8 @@ public class HDF5Constants {
 
     private static native final int H5I_NTYPES();
 
+    private static native final int H5I_REFERENCE();
+
     private static native final int H5I_UNINIT();
 
     private static native final int H5I_VFL();
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 1b97655..d4511e1 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -590,6 +590,8 @@ Java_hdf_hdf5lib_HDF5Constants_H5I_1DATASET(JNIEnv *env, jclass cls) { return H5
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5I_1ATTR(JNIEnv *env, jclass cls) { return H5I_ATTR; }
 JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5I_1REFERENCE(JNIEnv *env, jclass cls) { return H5I_REFERENCE; }
+JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5I_1VFL(JNIEnv *env, jclass cls) { return H5I_VFL; }
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5I_1INVALID_1HID(JNIEnv *env, jclass cls) { return H5I_INVALID_HID; }
diff --git a/src/H5.c b/src/H5.c
index f7826d4..59984dc 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -306,6 +306,7 @@ H5_term_library(void)
         pending += DOWN(A_top);
         pending += DOWN(D_top);
         pending += DOWN(G_top);
+        pending += DOWN(R_top);
         pending += DOWN(S_top);
         pending += DOWN(T_top);
 
diff --git a/src/H5Adeprec.c b/src/H5Adeprec.c
index c37dc3c..9221254 100644
--- a/src/H5Adeprec.c
+++ b/src/H5Adeprec.c
@@ -318,6 +318,7 @@ H5Aget_num_attrs(hid_t loc_id)
         case H5I_FILE:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5F.c b/src/H5F.c
index 8131f53..78fce2a 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -679,6 +679,7 @@ H5Fflush(hid_t object_id, H5F_scope_t scope)
         case H5I_UNINIT:
         case H5I_BADID:
         case H5I_DATASPACE:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 512439f..e52d539 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -452,6 +452,7 @@ H5F_get_objects_cb(void *obj_ptr, hid_t obj_id, void *key)
 	    case H5I_BADID:
 	    case H5I_FILE:
 	    case H5I_DATASPACE:
+	    case H5I_REFERENCE:
 	    case H5I_VFL:
 	    case H5I_GENPROP_CLS:
 	    case H5I_GENPROP_LST:
diff --git a/src/H5Gloc.c b/src/H5Gloc.c
index 8548b92..c011cdf 100644
--- a/src/H5Gloc.c
+++ b/src/H5Gloc.c
@@ -240,6 +240,9 @@ H5G_loc(hid_t loc_id, H5G_loc_t *loc)
             } /* end case */
             break;
 
+        case H5I_REFERENCE:
+            HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get group location of reference")
+
         case H5I_UNINIT:
         case H5I_BADID:
         case H5I_VFL:
diff --git a/src/H5Gname.c b/src/H5Gname.c
index a90821c..7b53668 100644
--- a/src/H5Gname.c
+++ b/src/H5Gname.c
@@ -835,6 +835,7 @@ H5G_name_replace_cb(void *obj_ptr, hid_t obj_id, void *key)
         case H5I_FILE:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5Gtest.c b/src/H5Gtest.c
index 8a7f8c4..7271cdc 100644
--- a/src/H5Gtest.c
+++ b/src/H5Gtest.c
@@ -553,6 +553,7 @@ H5G__user_path_test(hid_t obj_id, char *user_path, size_t *user_path_len, unsign
         case H5I_FILE:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5I.c b/src/H5I.c
index 42edf58..b8e47a2 100644
--- a/src/H5I.c
+++ b/src/H5I.c
@@ -451,9 +451,9 @@ H5I_nmembers(H5I_type_t type)
     FUNC_ENTER_NOAPI(FAIL)
 
     if(type <= H5I_BADID || type >= H5I_next_type)
-	HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "invalid type number")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "invalid type number")
     if(NULL == (type_ptr = H5I_id_type_list_g[type]) || type_ptr->init_count <= 0)
-	HGOTO_DONE(0);
+        HGOTO_DONE(0);
 
     /* Set return value */
     H5_CHECKED_ASSIGN(ret_value, int64_t, type_ptr->id_count, uint64_t);
diff --git a/src/H5Ipublic.h b/src/H5Ipublic.h
index 3ac2257..c737bbe 100644
--- a/src/H5Ipublic.h
+++ b/src/H5Ipublic.h
@@ -30,6 +30,8 @@
  * When adding types here, add a section to the 'misc19' test in test/tmisc.c
  * to verify that the H5I{inc|dec|get}_ref() routines work correctly with it.
  *
+ * NOTE: H5I_REFERENCE is not used by the library and has been deprecated
+ *       with a tentative removal version of 1.12.0. (DER, July 2017)
  */
 typedef enum H5I_type_t {
     H5I_UNINIT      = (-2),     /* uninitialized type                           */
@@ -40,6 +42,7 @@ typedef enum H5I_type_t {
     H5I_DATASPACE,              /* type ID for Dataspace objects                */
     H5I_DATASET,                /* type ID for Dataset objects                  */
     H5I_ATTR,                   /* type ID for Attribute objects                */
+    H5I_REFERENCE,              /* *DEPRECATED* type ID for Reference objects   */
     H5I_VFL,                    /* type ID for virtual file layer               */
     H5I_GENPROP_CLS,            /* type ID for generic property list classes    */
     H5I_GENPROP_LST,            /* type ID for generic property lists           */
diff --git a/src/H5O.c b/src/H5O.c
index 79aaddf..152e6cc 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -1081,6 +1081,7 @@ H5Oclose(hid_t object_id)
         case H5I_FILE:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
@@ -2627,6 +2628,7 @@ H5O_get_loc(hid_t object_id)
         case H5I_FILE:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5Oflush.c b/src/H5Oflush.c
index 387e0ff..9764f56 100644
--- a/src/H5Oflush.c
+++ b/src/H5Oflush.c
@@ -396,6 +396,7 @@ H5O_refresh_metadata_reopen(hid_t oid, H5G_loc_t *obj_loc, hid_t dxpl_id, hbool_
         case H5I_FILE:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5R.c b/src/H5R.c
index dc012e8..c2a10ce 100644
--- a/src/H5R.c
+++ b/src/H5R.c
@@ -71,6 +71,17 @@ hbool_t H5_PKG_INIT_VAR = FALSE;
 /* Local Variables */
 /*******************/
 
+/* Reference ID class */
+static const H5I_class_t H5I_REFERENCE_CLS[1] = {{
+    H5I_REFERENCE,		/* ID class value */
+    0,				/* Class flags */
+    0,				/* # of reserved IDs for class */
+    NULL			/* Callback routine for closing objects of this class */
+}};
+
+/* Flag indicating "top" of interface has been initialized */
+static hbool_t H5R_top_package_initialize_s = FALSE;
+
 
 
 /*--------------------------------------------------------------------------
@@ -92,6 +103,13 @@ H5R__init_package(void)
 
     FUNC_ENTER_NOAPI_NOINIT
 
+/* Initialize the atom group for the file IDs */
+    if(H5I_register_type(H5I_REFERENCE_CLS) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to initialize interface")
+
+    /* Mark "top" of interface as initialized, too */
+    H5R_top_package_initialize_s = TRUE;
+
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5R__init_package() */
@@ -99,6 +117,46 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
+    H5R_top_term_package
+ PURPOSE
+    Terminate various H5R objects
+ USAGE
+    void H5R_top_term_package()
+ RETURNS
+    void
+ DESCRIPTION
+    Release IDs for the atom group, deferring full interface shutdown
+    until later (in H5R_term_package).
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+     Can't report errors...
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+int
+H5R_top_term_package(void)
+{
+    int	n = 0;
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    if(H5R_top_package_initialize_s) {
+        if(H5I_nmembers(H5I_REFERENCE) > 0) {
+            (void)H5I_clear_type(H5I_REFERENCE, FALSE, FALSE);
+            n++; /*H5I*/
+	} /* end if */
+
+        /* Mark closed */
+        if(0 == n)
+            H5R_top_package_initialize_s = FALSE;
+    } /* end if */
+
+    FUNC_LEAVE_NOAPI(n)
+} /* end H5R__init_package() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
     H5R_term_package
  PURPOSE
     Terminate various H5R objects
@@ -120,12 +178,24 @@ done:
 int
 H5R_term_package(void)
 {
+    int	n = 0;
+
     FUNC_ENTER_NOAPI_NOINIT_NOERR
 
-    if(H5_PKG_INIT_VAR)
-        H5_PKG_INIT_VAR = FALSE;
+    if(H5_PKG_INIT_VAR) {
+        /* Sanity checks */
+        HDassert(0 == H5I_nmembers(H5I_REFERENCE));
+        HDassert(FALSE == H5R_top_package_initialize_s);
+
+        /* Destroy the reference id group */
+        n += (H5I_dec_type_ref(H5I_REFERENCE) > 0);
+
+        /* Mark closed */
+        if(0 == n)
+            H5_PKG_INIT_VAR = FALSE;
+    }
 
-    FUNC_LEAVE_NOAPI(0)
+    FUNC_LEAVE_NOAPI(n)
 } /* end H5R_term_package() */
 
 
diff --git a/src/H5T.c b/src/H5T.c
index 2f59767..a525cd5 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -1673,6 +1673,7 @@ H5Tcopy(hid_t type_id)
         case H5I_GROUP:
         case H5I_DATASPACE:
         case H5I_ATTR:
+        case H5I_REFERENCE:
         case H5I_VFL:
         case H5I_GENPROP_CLS:
         case H5I_GENPROP_LST:
diff --git a/src/H5private.h b/src/H5private.h
index ff45cec..ca4ebcf 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -2593,6 +2593,7 @@ H5_DLL int H5L_term_package(void);
 H5_DLL int H5P_term_package(void);
 H5_DLL int H5PL_term_package(void);
 H5_DLL int H5R_term_package(void);
+H5_DLL int H5R_top_term_package(void);
 H5_DLL int H5S_term_package(void);
 H5_DLL int H5S_top_term_package(void);
 H5_DLL int H5SL_term_package(void);
diff --git a/src/H5trace.c b/src/H5trace.c
index e2a746b..9fb8a72 100644
--- a/src/H5trace.c
+++ b/src/H5trace.c
@@ -1320,6 +1320,10 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
                                 fprintf(out, "%ld (attr)", (long)obj);
                                 break;
 
+                            case H5I_REFERENCE:
+                                fprintf(out, "%ld (reference)", (long)obj);
+                                break;
+
                             case H5I_VFL:
                                 fprintf(out, "%ld (file driver)", (long)obj);
                                 break;
@@ -1497,6 +1501,10 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
                                     fprintf(out, "H5I_ATTR");
                                     break;
 
+                                case H5I_REFERENCE:
+                                    fprintf(out, "H5I_REFERENCE");
+                                    break;
+
                                 case H5I_VFL:
                                     fprintf(out, "H5I_VFL");
                                     break;
diff --git a/test/links.c b/test/links.c
index 2d9bb0d..7b3e37d 100644
--- a/test/links.c
+++ b/test/links.c
@@ -7743,6 +7743,7 @@ done:
             case H5I_FILE:
             case H5I_DATASPACE:
             case H5I_ATTR:
+            case H5I_REFERENCE:
             case H5I_VFL:
             case H5I_GENPROP_CLS:
             case H5I_GENPROP_LST:
@@ -7829,6 +7830,7 @@ done:
             case H5I_FILE:
             case H5I_DATASPACE:
             case H5I_ATTR:
+            case H5I_REFERENCE:
             case H5I_VFL:
             case H5I_GENPROP_CLS:
             case H5I_GENPROP_LST:
diff --git a/test/tfile.c b/test/tfile.c
index 20b41e0..533bb24 100644
--- a/test/tfile.c
+++ b/test/tfile.c
@@ -1393,6 +1393,7 @@ test_obj_count_and_id(hid_t fid1, hid_t fid2, hid_t did, hid_t gid1,
                     case H5I_DATATYPE:
                     case H5I_DATASPACE:
                     case H5I_ATTR:
+                    case H5I_REFERENCE:
                     case H5I_VFL:
                     case H5I_GENPROP_CLS:
                     case H5I_GENPROP_LST:
diff --git a/test/tmisc.c b/test/tmisc.c
index bec80b2..22ae558 100644
--- a/test/tmisc.c
+++ b/test/tmisc.c
@@ -30,6 +30,7 @@
 #include "testhdf5.h"
 #include "H5srcdir.h"
 #include "H5Dpkg.h"         /* Datasets                 */
+#include "H5Iprivate.h"     /* IDs, can be removed when H5I_REFERENCE is gone */
 
 /* Definitions for misc. test #1 */
 #define MISC1_FILE  "tmisc1.h5"
@@ -3447,6 +3448,34 @@ test_misc19(void)
 
     HDfree(vfd_cls);
 
+/* Check H5I operations on references */
+
+    /* Reference IDs are not used by the library so there's no
+     * way of testing if incr/decr, etc. work. Instead, just
+     * do a quick smoke check to ensure that a couple of basic
+     * calls return sane values.
+     *
+     * H5I_REFERENCE has been declared deprecated with a tentative
+     * removal version of HDF5 1.12.0.
+     *
+     * Delete this entire block when H5I_REFERENCE no longer exists.
+     *
+     * The H5Iprivate.h header was included to support H5I_nmembers()
+     * so that can also probably be removed as well.
+     */
+{
+    htri_t tf;                      /* Boolean generic return   */
+    int64_t num_members;            /* Number of members in type */
+
+    tf = H5Itype_exists(H5I_REFERENCE);
+    VERIFY(tf, TRUE, "H5Itype_exists");
+
+    num_members = 999;
+    num_members = H5I_nmembers(H5I_REFERENCE);
+    VERIFY(num_members, 0, "H5Inmembers");
+
+} /* end block */
+
 } /* end test_misc19() */
 
 /****************************************************************