Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop

3 files changed, 142 insertions, 279 deletions

diff --git a/c++/test/CMakeVFDTests.cmake b/c++/test/CMakeVFDTests.cmake
index 996a20f..6a8ce2c 100644
--- a/c++/test/CMakeVFDTests.cmake
+++ b/c++/test/CMakeVFDTests.cmake
@@ -55,7 +55,7 @@
             -P "${HDF_RESOURCES_DIR}/vfdTest.cmake"
       )
       set_tests_properties (CPP_VFD-${vfdname}-cpp_testhdf5 PROPERTIES DEPENDS CPP_VFD-${vfdname}-cpp_testhdf5-clear-objects)
-      set_tests_properties (CPP_VFD-${vfdname}-cpp_testhdf5 PROPERTIES TIMEOUT 30)
+      set_tests_properties (CPP_VFD-${vfdname}-cpp_testhdf5 PROPERTIES TIMEOUT ${CTEST_SHORT_TIMEOUT})
     endif ()
   endmacro ()
 
diff --git a/c++/test/tarray.cpp b/c++/test/tarray.cpp
index 6bd4ca6..fccc556 100644
--- a/c++/test/tarray.cpp
+++ b/c++/test/tarray.cpp
@@ -286,7 +286,7 @@ H5::DataType getArr()
     *dims = 5; 
     H5::ArrayType ret; 
     ret = H5::ArrayType(H5::PredType::NATIVE_INT, 1, dims); 
-    delete[] dims; 
+    delete dims; 
     return ret;
 }
 
@@ -371,7 +371,6 @@ static void test_array_info()
     s1_t rdata[SPACE1_DIM1][ARRAY1_DIM1];   // Information read in
     hsize_t sdims1[] = {SPACE1_DIM1};
     hsize_t tdims1[] = {ARRAY1_DIM1};
-    int     nmemb;      // Number of compound members
     int     ii;         // counting variables
     hsize_t idxi, idxj, idxk; // dimension indicing variables
     H5T_class_t mclass; // Datatype class for field
diff --git a/c++/test/tlinks.cpp b/c++/test/tlinks.cpp
index 6e990c9..491cd6a 100644
--- a/c++/test/tlinks.cpp
+++ b/c++/test/tlinks.cpp
@@ -31,288 +31,27 @@ using namespace H5;
 #include "h5test.h"
 #include "h5cpputil.h"  // C++ utilility header file
 
-// A lot of the definition inherited from C test links.c is left here until
-// the H5L API is implemented and tests are completed - BMR 10/19/2009
-/*
- * This file needs to access private information from the H5G package.
- * This file also needs to access the group testing code.
- */
-//#define H5G_FRIEND
-//#define H5G_TESTING
-
-//#include "h5test.h"
-//#include "H5Gpkg.h"     /* Groups */
-//#include "H5Iprivate.h" /* IDs */
-//#include "H5Lprivate.h" /* Links */
-
-/* File for external link test.  Created with gen_udlinks.c */
-#define LINKED_FILE  "be_extlink2.h5"
-
-#if 0
-const char *FILENAME[] = {
-    "links0",
-    "links1",
-    "links2",
-    "links3",
-    "links4a", /* 4 */
-    "links4b", /* 5 */
-    "links4c", /* 6 */
-    "links4d", /* 7 */
-    "links5",  /* 8 */
-    "links6",  /* 9 */
-    "links7",  /* 10 */
-    "links8",  /* 11 */
-    "extlinks0",        /* 12: main files */
-    "tmp/extlinks0",    /* 13: */
-    "extlinks1",        /* 14: target files */
-    "tmp/extlinks1",    /* 15: */
-    "extlinks2",        /* 16: */
-    "tmp/extlinks2",    /* 17: */
-    "extlinks3",        /* 18: */
-    "tmp/extlinks3",    /* 19: */
-    "extlinks4",        /* 20: */
-    "tmp/extlinks4",    /* 21: */
-    "extlinks5",        /* 22: */
-    "tmp/extlinks6",    /* 23: */
-    "extlinks7",        /* 24: */
-    "tmp/extlinks7",    /* 25: */
-    "tmp/extlinks8",    /* 26: */
-    "extlinks9",        /* 27: */
-    "tmp/extlinks9",    /* 28: */
-    "extlinks10",       /* 29: */ /* TESTS for windows */
-    "tmp/extlinks10",   /* 30: */
-    "tmp/extlinks11",   /* 31: */
-    "tmp/extlinks12",   /* 32: */
-    "extlinks13",       /* 33: */
-    "tmp/extlinks13",   /* 34: */
-    "tmp/extlinks14",   /* 35: */
-    "tmp/extlinks15",   /* 36: */
-    "extlinks16A",      /* 37: */ /* TESTS for H5P_set_elink_fapl */
-    "extlinks16B",      /* 38: */
-    "extlinks17",       /* 39: */
-    "extlinks18A",      /* 40: */
-    "extlinks18B",      /* 41: */
-    "extlinks19A",      /* 42: */
-    "extlinks19B",      /* 43: */
-    "extlinks20",       /* 44: */
-    NULL
-};
-
-#endif // 0
-
-#define TMPDIR          "tmp"
-
-#define FAMILY_SIZE     1024
-#define CORE_INCREMENT  1024
-#define NUM400          400
-
-/* do not do check_all_closed() for "ext*" files and "tmp/ext*" */
-#define EXTSTOP         12
-
-#define LINK_BUF_SIZE   1024
 #define NAME_BUF_SIZE   1024
-#define MAX_NAME_LEN    ((64*1024)+1024)
-
-/* Link type IDs */
-#define UD_HARD_TYPE 201
-#define UD_CB_TYPE H5L_TYPE_MAX
-#define UD_PLIST_TYPE 128
-#define UD_CBFAIL_TYPE UD_PLIST_TYPE
-#define UD_ERROR_TYPE 189
-#define UD_BAD_TYPE1 H5L_TYPE_HARD
-#define UD_BAD_TYPE2 (H5L_TYPE_UD_MIN - 5)
-#define UD_BAD_VERS (H5L_LINK_CLASS_T_VERS + 1)
-
-#define DEST_PROP_NAME "destination_group"
-#define REREG_TARGET_NAME "rereg_target"
-
-#define UD_CB_LINK_NAME "ud_callback_link"
-#define NEW_UD_CB_LINK_NAME "ud_callback_link2"
-#define UD_CB_TARGET "ud_target"
-#define UD_CB_TARGET_LEN 10
-
-#define LE_FILENAME "le_extlink1.h5"
-#define BE_FILENAME "be_extlink1.h5"
-
-#define ELINK_CB_FAM_SIZE (hsize_t) 100
-
 #define H5L_DIM1 100
 #define H5L_DIM2 100
 
-/* Creation order macros */
-#define CORDER_SOFT_GROUP_NAME  "corder_soft_group"
-#define CORDER_NLINKS               18
-
-/* Timestamp macros */
-#define TIMESTAMP_GROUP_1       "timestamp1"
-#define TIMESTAMP_GROUP_2       "timestamp2"
-
-/* Link iteration struct */
-typedef struct {
-    H5_iter_order_t order;      /* Direction of iteration */
-    unsigned ncalled;           /* # of times callback is entered */
-    unsigned nskipped;          /* # of links skipped */
-    int stop;                   /* # of iterations to stop after */
-    int64_t curr;               /* Current creation order value */
-    size_t max_visit;           /* Size of "visited link" flag array */
-    hbool_t *visited;           /* Pointer to array of "visited link" flags */
-} link_iter_info_t;
-
-#if 0
-/* Link visit structs */
-typedef struct {
-    const char *path;           /* Path to link */
-    H5L_type_t type;            /* Type of link */
-} link_visit_t;
-static const link_visit_t lvisit0[] = {
-    {"Dataset_zero", H5L_TYPE_HARD},
-    {"Group1", H5L_TYPE_HARD},
-    {"Group1/Dataset_one", H5L_TYPE_HARD},
-    {"Group1/Group2", H5L_TYPE_HARD},
-    {"Group1/Group2/Dataset_two", H5L_TYPE_HARD},
-    {"Group1/Group2/Type_two", H5L_TYPE_HARD},
-    {"Group1/Group2/hard_zero", H5L_TYPE_HARD},
-    {"Group1/Type_one", H5L_TYPE_HARD},
-    {"Group1/hard_one", H5L_TYPE_HARD},
-    {"Type_zero", H5L_TYPE_HARD},
-    {"ext_dangle", H5L_TYPE_EXTERNAL},
-    {"ext_one", H5L_TYPE_EXTERNAL},
-    {"hard_one", H5L_TYPE_HARD},
-    {"hard_two", H5L_TYPE_HARD},
-    {"hard_zero", H5L_TYPE_HARD},
-    {"soft_dangle", H5L_TYPE_SOFT},
-    {"soft_one", H5L_TYPE_SOFT},
-    {"soft_two", H5L_TYPE_SOFT}
-};
-static const link_visit_t lvisit1[] = {
-    {"Dataset_one", H5L_TYPE_HARD},
-    {"Group2", H5L_TYPE_HARD},
-    {"Group2/Dataset_two", H5L_TYPE_HARD},
-    {"Group2/Type_two", H5L_TYPE_HARD},
-    {"Group2/hard_zero", H5L_TYPE_HARD},
-    {"Group2/hard_zero/Dataset_zero", H5L_TYPE_HARD},
-    {"Group2/hard_zero/Group1", H5L_TYPE_HARD},
-    {"Group2/hard_zero/Type_zero", H5L_TYPE_HARD},
-    {"Group2/hard_zero/ext_dangle", H5L_TYPE_EXTERNAL},
-    {"Group2/hard_zero/ext_one", H5L_TYPE_EXTERNAL},
-    {"Group2/hard_zero/hard_one", H5L_TYPE_HARD},
-    {"Group2/hard_zero/hard_two", H5L_TYPE_HARD},
-    {"Group2/hard_zero/hard_zero", H5L_TYPE_HARD},
-    {"Group2/hard_zero/soft_dangle", H5L_TYPE_SOFT},
-    {"Group2/hard_zero/soft_one", H5L_TYPE_SOFT},
-    {"Group2/hard_zero/soft_two", H5L_TYPE_SOFT},
-    {"Type_one", H5L_TYPE_HARD},
-    {"hard_one", H5L_TYPE_HARD}
-};
-static const link_visit_t lvisit2[] = {
-    {"Dataset_two", H5L_TYPE_HARD},
-    {"Type_two", H5L_TYPE_HARD},
-    {"hard_zero", H5L_TYPE_HARD},
-    {"hard_zero/Dataset_zero", H5L_TYPE_HARD},
-    {"hard_zero/Group1", H5L_TYPE_HARD},
-    {"hard_zero/Group1/Dataset_one", H5L_TYPE_HARD},
-    {"hard_zero/Group1/Group2", H5L_TYPE_HARD},
-    {"hard_zero/Group1/Type_one", H5L_TYPE_HARD},
-    {"hard_zero/Group1/hard_one", H5L_TYPE_HARD},
-    {"hard_zero/Type_zero", H5L_TYPE_HARD},
-    {"hard_zero/ext_dangle", H5L_TYPE_EXTERNAL},
-    {"hard_zero/ext_one", H5L_TYPE_EXTERNAL},
-    {"hard_zero/hard_one", H5L_TYPE_HARD},
-    {"hard_zero/hard_two", H5L_TYPE_HARD},
-    {"hard_zero/hard_zero", H5L_TYPE_HARD},
-    {"hard_zero/soft_dangle", H5L_TYPE_SOFT},
-    {"hard_zero/soft_one", H5L_TYPE_SOFT},
-    {"hard_zero/soft_two", H5L_TYPE_SOFT}
-};
-
-typedef struct {
-    unsigned idx;               /* Index in link visit structure */
-    const link_visit_t *info;   /* Pointer to the link visit structure to use */
-} lvisit_ud_t;
-
-
-/* Object visit structs */
+// Object visit structs
 typedef struct {
     const char *path;           /* Path to object */
     H5O_type_t type;            /* Type of object */
 } obj_visit_t;
-static const obj_visit_t ovisit0_old[] = {
-    {".", H5O_TYPE_GROUP},
-    {"Dataset_zero", H5O_TYPE_DATASET},
-    {"Group1", H5O_TYPE_GROUP},
-    {"Group1/Dataset_one", H5O_TYPE_DATASET},
-    {"Group1/Group2", H5O_TYPE_GROUP},
-    {"Group1/Group2/Dataset_two", H5O_TYPE_DATASET},
-    {"Group1/Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
-    {"Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
-    {"Type_zero", H5O_TYPE_NAMED_DATATYPE}
-};
-static const obj_visit_t ovisit0_new[] = {
-    {".", H5O_TYPE_GROUP},
-    {"Dataset_zero", H5O_TYPE_DATASET},
-    {"Group1", H5O_TYPE_GROUP},
-    {"Group1/Dataset_one", H5O_TYPE_DATASET},
-    {"Group1/Group2", H5O_TYPE_GROUP},
-    {"Group1/Group2/Dataset_two", H5O_TYPE_DATASET},
-    {"Group1/Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
-    {"Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
-    {"Type_zero", H5O_TYPE_NAMED_DATATYPE}
-};
-static const obj_visit_t ovisit1_old[] = {
-    {".", H5O_TYPE_GROUP},
-    {"Dataset_one", H5O_TYPE_DATASET},
-    {"Group2", H5O_TYPE_GROUP},
-    {"Group2/Dataset_two", H5O_TYPE_DATASET},
-    {"Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
-    {"Group2/hard_zero", H5O_TYPE_GROUP},
-    {"Group2/hard_zero/Dataset_zero", H5O_TYPE_DATASET},
-    {"Group2/hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE},
-    {"Type_one", H5O_TYPE_NAMED_DATATYPE}
-};
-static const obj_visit_t ovisit1_new[] = {
-    {".", H5O_TYPE_GROUP},
-    {"Dataset_one", H5O_TYPE_DATASET},
-    {"Group2", H5O_TYPE_GROUP},
-    {"Group2/Dataset_two", H5O_TYPE_DATASET},
-    {"Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
-    {"Group2/hard_zero", H5O_TYPE_GROUP},
-    {"Group2/hard_zero/Dataset_zero", H5O_TYPE_DATASET},
-    {"Group2/hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE},
-    {"Type_one", H5O_TYPE_NAMED_DATATYPE}
-};
-static const obj_visit_t ovisit2_old[] = {
-    {".", H5O_TYPE_GROUP},
-    {"Dataset_two", H5O_TYPE_DATASET},
-    {"Type_two", H5O_TYPE_NAMED_DATATYPE},
-    {"hard_zero", H5O_TYPE_GROUP},
-    {"hard_zero/Dataset_zero", H5O_TYPE_DATASET},
-    {"hard_zero/Group1", H5O_TYPE_GROUP},
-    {"hard_zero/Group1/Dataset_one", H5O_TYPE_DATASET},
-    {"hard_zero/Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
-    {"hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE}
-};
-static const obj_visit_t ovisit2_new[] = {
-    {".", H5O_TYPE_GROUP},
-    {"Dataset_two", H5O_TYPE_DATASET},
-    {"Type_two", H5O_TYPE_NAMED_DATATYPE},
-    {"hard_zero", H5O_TYPE_GROUP},
-    {"hard_zero/Dataset_zero", H5O_TYPE_DATASET},
-    {"hard_zero/Group1", H5O_TYPE_GROUP},
-    {"hard_zero/Group1/Dataset_one", H5O_TYPE_DATASET},
-    {"hard_zero/Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
-    {"hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE}
-};
 
+// User data for callback function
 typedef struct {
     unsigned idx;               /* Index in object visit structure */
     const obj_visit_t *info;    /* Pointer to the object visit structure to use */
 } ovisit_ud_t;
-#endif
 
 static const char *FILENAME[] = {
     "link0",
     "link1.h5",
     "link2.h5",
+    "visit",
     NULL
 };
 
@@ -842,6 +581,140 @@ static void test_num_links(hid_t fapl_id, hbool_t new_format)
 } // test_num_links
 
 
+// Data for visit on the file
+static const obj_visit_t file_visit[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Data", H5O_TYPE_GROUP},
+    {"Data/Compressed_Data", H5O_TYPE_DATASET},
+    {"Data/Float_Data", H5O_TYPE_DATASET},
+};
+
+// Data for visit on the group
+static const obj_visit_t group_visit[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Compressed_Data", H5O_TYPE_DATASET},
+    {"Float_Data", H5O_TYPE_DATASET},
+};
+
+const H5std_string FILE_NAME("tvisit.h5");
+const H5std_string GROUP_NAME("/Data");
+const H5std_string DSET1_NAME("/Data/Compressed_Data");
+const H5std_string DSET2_NAME("/Data/Float_Data");
+const int RANK = 2;
+const int DIM1 = 2;
+
+// Operator function
+static int visit_obj_cb(H5Object& obj, const H5std_string name, const H5O_info_t *oinfo, void *_op_data)
+{
+    ovisit_ud_t *op_data = static_cast <ovisit_ud_t *>(_op_data);
+
+    // Check for correct object information
+    if(strcmp(op_data->info[op_data->idx].path, name.c_str())) return(H5_ITER_ERROR);
+    if(op_data->info[op_data->idx].type != oinfo->type) return(H5_ITER_ERROR);
+
+    // Advance to next location
+    op_data->idx++;
+
+    return(H5_ITER_CONT);
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    test_visit
+ *
+ * Purpose      Test H5Object::visit
+ *
+ * Return       None
+ *
+ * February 8, 2019
+ *-------------------------------------------------------------------------
+ */
+static void test_visit(hid_t fapl_id, hbool_t new_format)
+{
+    hsize_t  dims[2];
+    hsize_t  cdims[2];
+    char filename[NAME_BUF_SIZE];
+
+    if(new_format)
+        SUBTEST("H5Object::visit (w/new group format)")
+    else
+        SUBTEST("H5Object::visit")
+
+    try
+    {
+        // Use the file access template id to create a file access prop. list
+        FileAccPropList fapl(fapl_id);
+
+        // Build the hdf5 file name and create the file
+        h5_fixname(FILENAME[3], fapl_id, filename, sizeof filename);
+	    H5File *file = new H5File(filename, H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, fapl);
+
+        // Create a group
+	    Group* group = new Group(file->createGroup(GROUP_NAME));
+
+        // Create a chunked/compressed dataset within this group specified by path
+	    dims[0] = 20;
+	    dims[1] = 2;
+	    cdims[0] = 2;
+	    cdims[1] = 2;
+	    DataSpace *dataspace = new DataSpace(RANK, dims); // create new dspace
+	    DSetCreatPropList ds_creatplist;  // create dataset creation prop list
+	    ds_creatplist.setChunk(2, cdims);  // then modify it for compression
+	    ds_creatplist.setDeflate(6);
+
+	    DataSet* dataset = new DataSet(file->createDataSet(DSET1_NAME,
+                        PredType::NATIVE_INT, *dataspace, ds_creatplist));
+
+	    delete dataset;
+	    delete dataspace;
+
+	    // Create another dataset
+	    dims[0] = 5;
+	    dims[1] = 2;
+	    dataspace = new DataSpace(RANK, dims); // create second dspace
+	    dataset = new DataSet(file->createDataSet(DSET2_NAME,
+			            PredType::NATIVE_FLOAT, *dataspace));
+
+        // Close everything
+	    delete dataset;
+	    delete dataspace;
+	    delete group;
+	    delete file;
+
+	    // Reopen the file and group in the file.
+	    file = new H5File(filename, H5F_ACC_RDWR);
+	    group = new Group(file->openGroup("Data"));
+
+        // Open the group
+	    dataset = new DataSet(group->openDataSet(DSET2_NAME));
+        delete dataset;
+
+        // Visit objects in the file
+        ovisit_ud_t udata;          /* User-data for visiting */
+        udata.idx = 0;
+        udata.info = file_visit;
+
+        file->visit(H5_INDEX_NAME, H5_ITER_INC, visit_obj_cb, &udata, H5O_INFO_BASIC);
+
+        // Visit objects in the group
+        udata.idx = 0;
+        udata.info = group_visit;
+
+        group->visit(H5_INDEX_NAME, H5_ITER_INC, visit_obj_cb, &udata, H5O_INFO_BASIC);
+
+	    // Close the group and file.
+	    delete group;
+	    delete file;
+
+        PASSED();
+    } // end of try block
+    catch (Exception& E)
+    {
+  cerr << "in catch" << endl;
+        issue_fail_msg("test_visit()", __LINE__, __FILE__, E.getCDetailMsg());
+    }
+} // test_visit()
+
+
 /*-------------------------------------------------------------------------
  * Function:    test_links
  *
@@ -858,7 +731,8 @@ void test_links()
     hid_t        fapl_id, fapl2_id;    /* File access property lists */
     unsigned new_format;     /* Whether to use the new format or not */
 
-    fapl_id = h5_fileaccess();
+    if((fapl_id = h5_fileaccess()) < 0)
+        throw Exception("test_links", "Unable to get file access property list");
 
     // Output message about test being performed
     MESSAGE(5, ("Testing Various Links\n"));
@@ -891,24 +765,18 @@ void test_links()
             test_move(my_fapl_id, new_format);
             test_copy(my_fapl_id, new_format);
             test_lcpl(my_fapl_id, new_format);
+            test_visit(my_fapl_id, new_format);
         } /* end for */
 
         /* Close 2nd FAPL */
         H5Pclose(fapl2_id);
 
         h5_clean_files(FILENAME, fapl_id);
-
-        /* Test that external links can be used after a library reset.  MUST be
-        * called last so the reset doesn't interfere with the property lists.  This
-        * routine will delete its own file. */
-        /* nerrors += external_reset_register() < 0 ? 1 : 0;
- */
     }
     catch (Exception& E)
     {
         issue_fail_msg("test_links()", __LINE__, __FILE__, E.getCDetailMsg());
     }
-
 }
 
 
@@ -926,7 +794,3 @@ void cleanup_links()
     HDremove(FILENAME[0]);
     HDremove(FILENAME[1]);
 }
-
-
-
-