Merge pull request #109 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit '0f94a43c46186eba3a536ab3b60433f469b5672c':
  Update with changes from buildbot process
  Remove duplicate block
  Update with latest changes used in buildbot process
  Re-merge HDFFV-9942 to new folder structure
  Correct dir reference
  Split tools code - remove old change
  Add new file to ignore
  Split tools into src and test - update locations
  Split tools into src and test - update with new files or locations
  Split tools into src and test - add folders
  Split tools into src and test - remove folders
  Split the code into src and test
  Add error log for dlopen

1 files changed, 1802 insertions, 0 deletions

diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
new file mode 100644
index 0000000..562cfd5
--- /dev/null
+++ b/tools/src/h5dump/h5dump.c
@@ -0,0 +1,1802 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "h5dump.h"
+#include "h5dump_ddl.h"
+#include "h5dump_xml.h"
+
+/* Name of tool */
+#define PROGRAMNAME "h5dump"
+
+static const char   *driver = NULL;      /* The driver to open the file with. */
+const char          *outfname=NULL;
+static int           doxml = 0;
+static int           useschema = 1;
+static const char   *xml_dtd_uri = NULL;
+
+/* module-scoped variables for XML option */
+#define DEFAULT_XSD     "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd"
+#define DEFAULT_DTD     "http://www.hdfgroup.org/HDF5/XML/DTD/HDF5-File.dtd"
+
+/* Standard DDL output */
+static const dump_functions ddl_function_table = {
+    dump_group,
+    dump_named_datatype,
+    dump_dataset,
+    dump_dataspace,
+    dump_datatype,
+    dump_attr_cb,
+    dump_data
+};
+
+/* XML output */
+static const dump_functions xml_function_table = {
+    xml_dump_group,
+    xml_dump_named_datatype,
+    xml_dump_dataset,
+    xml_dump_dataspace,
+    xml_dump_datatype,
+    xml_dump_attr,
+    xml_dump_data
+};
+
+/* internal functions */
+static void     init_prefix(char **prfx, size_t prfx_len);
+
+/* a structure for handling the order command-line parameters come in */
+struct handler_t {
+    void (*func)(hid_t, const char *, void *, int, const char *);
+    char *obj;
+    struct subset_t *subset_info;
+};
+
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters. The long-named ones can be partially spelled. When
+ * adding more, make sure that they don't clash with each other.
+ */
+/* The following initialization makes use of C language cancatenating */
+/* "xxx" "yyy" into "xxxyyy". */
+static const char *s_opts = "hn*peyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o*b*F:s:S:A*q:z:m:RECM:O*N:vG:";
+static struct long_options l_opts[] = {
+    { "help", no_arg, 'h' },
+    { "hel", no_arg, 'h' },
+    { "contents", optional_arg, 'n' },
+    { "properties", no_arg, 'p' },
+    { "superblock", no_arg, 'B' },
+    { "boot-block", no_arg, 'B' },
+    { "boot-bloc", no_arg, 'B' },
+    { "boot-blo", no_arg, 'B' },
+    { "boot-bl", no_arg, 'B' },
+    { "boot-b", no_arg, 'B' },
+    { "boot", no_arg, 'B' },
+    { "boo", no_arg, 'B' },
+    { "bo", no_arg, 'B' },
+    { "header", no_arg, 'H' },
+    { "heade", no_arg, 'H' },
+    { "head", no_arg, 'H' },
+    { "hea", no_arg, 'H' },
+    { "object-ids", no_arg, 'i' },
+    { "object-id", no_arg, 'i' },
+    { "object-i", no_arg, 'i' },
+    { "object", no_arg, 'i' },
+    { "objec", no_arg, 'i' },
+    { "obje", no_arg, 'i' },
+    { "obj", no_arg, 'i' },
+    { "ob", no_arg, 'i' },
+    { "version", no_arg, 'V' },
+    { "versio", no_arg, 'V' },
+    { "versi", no_arg, 'V' },
+    { "vers", no_arg, 'V' },
+    { "ver", no_arg, 'V' },
+    { "ve", no_arg, 'V' },
+    { "attribute", require_arg, 'a' },
+    { "attribut", require_arg, 'a' },
+    { "attribu", require_arg, 'a' },
+    { "attrib", require_arg, 'a' },
+    { "attri", require_arg, 'a' },
+    { "attr", require_arg, 'a' },
+    { "att", require_arg, 'a' },
+    { "at", require_arg, 'a' },
+    { "block", require_arg, 'k' },
+    { "bloc", require_arg, 'k' },
+    { "blo", require_arg, 'k' },
+    { "bl", require_arg, 'k' },
+    { "count", require_arg, 'c' },
+    { "coun", require_arg, 'c' },
+    { "cou", require_arg, 'c' },
+    { "co", require_arg, 'c' },
+    { "dataset", require_arg, 'd' },
+    { "datase", require_arg, 'd' },
+    { "datas", require_arg, 'd' },
+    { "datatype", require_arg, 't' },
+    { "datatyp", require_arg, 't' },
+    { "dataty", require_arg, 't' },
+    { "datat", require_arg, 't' },
+    { "filedriver", require_arg, 'f' },
+    { "filedrive", require_arg, 'f' },
+    { "filedriv", require_arg, 'f' },
+    { "filedri", require_arg, 'f' },
+    { "filedr", require_arg, 'f' },
+    { "filed", require_arg, 'f' },
+    { "file", require_arg, 'f' },
+    { "fil", require_arg, 'f' },
+    { "fi", require_arg, 'f' },
+    { "group", require_arg, 'g' },
+    { "grou", require_arg, 'g' },
+    { "gro", require_arg, 'g' },
+    { "gr", require_arg, 'g' },
+    { "output", optional_arg, 'o' },
+    { "outpu", optional_arg, 'o' },
+    { "outp", optional_arg, 'o' },
+    { "out", optional_arg, 'o' },
+    { "ou", optional_arg, 'o' },
+    { "soft-link", require_arg, 'l' },
+    { "soft-lin", require_arg, 'l' },
+    { "soft-li", require_arg, 'l' },
+    { "soft-l", require_arg, 'l' },
+    { "soft", require_arg, 'l' },
+    { "sof", require_arg, 'l' },
+    { "start", require_arg, 's' },
+    { "star", require_arg, 's' },
+    { "sta", require_arg, 's' },
+    { "stride", require_arg, 'S' },
+    { "strid", require_arg, 'S' },
+    { "string", no_arg, 'r' },
+    { "strin", no_arg, 'r' },
+    { "use-dtd", no_arg, 'u' },
+    { "use-dt", no_arg, 'u' },
+    { "use-d", no_arg, 'u' },
+    { "use-", no_arg, 'u' },
+    { "use", no_arg, 'u' },
+    { "us", no_arg, 'u' },
+    { "u", no_arg, 'u' },
+    { "width", require_arg, 'w' },
+    { "widt", require_arg, 'w' },
+    { "wid", require_arg, 'w' },
+    { "wi", require_arg, 'w' },
+    { "xml-dtd", require_arg, 'D' },
+    { "xml-dt", require_arg, 'D' },
+    { "xml-d", require_arg, 'D' },
+    { "xml-ns", require_arg, 'X' },
+    { "xml-n", require_arg, 'X' },
+    { "xml", no_arg, 'x' },
+    { "xm", no_arg, 'x' },
+    { "onlyattr", optional_arg, 'A' },
+    { "escape", no_arg, 'e' },
+    { "noindex", no_arg, 'y' },
+    { "binary", optional_arg, 'b' },
+    { "form", require_arg, 'F' },
+    { "sort_by", require_arg, 'q' },
+    { "sort_order", require_arg, 'z' },
+    { "format", require_arg, 'm' },
+    { "region", no_arg, 'R' },
+    { "enable-error-stack", no_arg, 'E' },
+    { "packed-bits", require_arg, 'M' },
+    { "no-compact-subset", no_arg, 'C' },
+    { "ddl", optional_arg, 'O' },
+    { "any_path", require_arg, 'N' },
+    { "vds-view-first-missing", no_arg, 'v' },
+    { "vds-gap-size", require_arg, 'G' },
+    { NULL, 0, '\0' }
+};
+
+
+/*-------------------------------------------------------------------------
+ * Function:    leave
+ *
+ * Purpose:     Shutdown MPI & HDF5 and call exit()
+ *
+ * Return:      Does not return
+ *
+ * Programmer:  Quincey Koziol
+ *              Saturday, 31. January 2004
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+leave(int ret)
+{
+    h5tools_close();
+
+    HDexit(ret);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    usage
+ *
+ * Purpose:     Print the usage message about dumper
+ *
+ * Return:      void
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(const char *prog)
+{
+    FLUSHSTREAM(rawoutstream);
+    PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] files\n", prog);
+    PRINTVALSTREAM(rawoutstream, "  OPTIONS\n");
+    PRINTVALSTREAM(rawoutstream, "     -h,   --help         Print a usage message and exit\n");
+    PRINTVALSTREAM(rawoutstream, "     -V,   --version      Print version number and exit\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- File Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "     -n,   --contents     Print a list of the file contents and exit\n");
+    PRINTVALSTREAM(rawoutstream, "                          Optional value 1 also prints attributes.\n");
+    PRINTVALSTREAM(rawoutstream, "     -B,   --superblock   Print the content of the super block\n");
+    PRINTVALSTREAM(rawoutstream, "     -H,   --header       Print the header only; no data is displayed\n");
+    PRINTVALSTREAM(rawoutstream, "     -f D, --filedriver=D Specify which driver to open the file with\n");
+    PRINTVALSTREAM(rawoutstream, "     -o F, --output=F     Output raw data into file F\n");
+    PRINTVALSTREAM(rawoutstream, "     -b B, --binary=B     Binary file output, of form B\n");
+    PRINTVALSTREAM(rawoutstream, "     -O F, --ddl=F        Output ddl text into file F\n");
+    PRINTVALSTREAM(rawoutstream, "                          Use blank(empty) filename F to suppress ddl display\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Object Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "     -a P, --attribute=P  Print the specified attribute\n");
+    PRINTVALSTREAM(rawoutstream, "                          If an attribute name contains a slash (/), escape the\n");
+    PRINTVALSTREAM(rawoutstream, "                          slash with a preceding backslash (\\).\n");
+    PRINTVALSTREAM(rawoutstream, "                          (See example section below.)\n");
+    PRINTVALSTREAM(rawoutstream, "     -d P, --dataset=P    Print the specified dataset\n");
+    PRINTVALSTREAM(rawoutstream, "     -g P, --group=P      Print the specified group and all members\n");
+    PRINTVALSTREAM(rawoutstream, "     -l P, --soft-link=P  Print the value(s) of the specified soft link\n");
+    PRINTVALSTREAM(rawoutstream, "     -t P, --datatype=P   Print the specified named datatype\n");
+    PRINTVALSTREAM(rawoutstream, "     -N P, --any_path=P   Print any attribute, dataset, group, datatype, or link that matches P\n");
+    PRINTVALSTREAM(rawoutstream, "                          P can be the absolute path or just a relative path.\n");
+    PRINTVALSTREAM(rawoutstream, "     -A,   --onlyattr     Print the header and value of attributes\n");
+    PRINTVALSTREAM(rawoutstream, "                          Optional value 0 suppresses printing attributes.\n");
+    PRINTVALSTREAM(rawoutstream, "     --vds-view-first-missing Set the VDS bounds to first missing mapped elements.\n");
+    PRINTVALSTREAM(rawoutstream, "     --vds-gap-size=N     Set the missing file gap size, N=non-negative integers\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Object Property Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "     -i,   --object-ids   Print the object ids\n");
+    PRINTVALSTREAM(rawoutstream, "     -p,   --properties   Print dataset filters, storage layout and fill value\n");
+    PRINTVALSTREAM(rawoutstream, "     -M L, --packedbits=L Print packed bits as unsigned integers, using mask\n");
+    PRINTVALSTREAM(rawoutstream, "                          format L for an integer dataset specified with\n");
+    PRINTVALSTREAM(rawoutstream, "                          option -d. L is a list of offset,length values,\n");
+    PRINTVALSTREAM(rawoutstream, "                          separated by commas. Offset is the beginning bit in\n");
+    PRINTVALSTREAM(rawoutstream, "                          the data value and length is the number of bits of\n");
+    PRINTVALSTREAM(rawoutstream, "                          the mask.\n");
+    PRINTVALSTREAM(rawoutstream, "     -R,   --region       Print dataset pointed by region references\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Formatting Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "     -e,   --escape       Escape non printing characters\n");
+    PRINTVALSTREAM(rawoutstream, "     -r,   --string       Print 1-byte integer datasets as ASCII\n");
+    PRINTVALSTREAM(rawoutstream, "     -y,   --noindex      Do not print array indices with the data\n");
+    PRINTVALSTREAM(rawoutstream, "     -m T, --format=T     Set the floating point output format\n");
+    PRINTVALSTREAM(rawoutstream, "     -q Q, --sort_by=Q    Sort groups and attributes by index Q\n");
+    PRINTVALSTREAM(rawoutstream, "     -z Z, --sort_order=Z Sort groups and attributes by order Z\n");
+    PRINTVALSTREAM(rawoutstream, "     --enable-error-stack Prints messages from the HDF5 error stack as they\n");
+    PRINTVALSTREAM(rawoutstream, "                          occur.\n");
+    PRINTVALSTREAM(rawoutstream, "     --no-compact-subset  Disable compact form of subsetting and allow the use\n");
+    PRINTVALSTREAM(rawoutstream, "                          of \"[\" in dataset names.\n");
+    PRINTVALSTREAM(rawoutstream, "     -w N, --width=N      Set the number of columns of output. A value of 0 (zero)\n");
+    PRINTVALSTREAM(rawoutstream, "                          sets the number of columns to the maximum (65535).\n");
+    PRINTVALSTREAM(rawoutstream, "                          Default width is 80 columns.\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- XML Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "     -x,   --xml          Output in XML using Schema\n");
+    PRINTVALSTREAM(rawoutstream, "     -u,   --use-dtd      Output in XML using DTD\n");
+    PRINTVALSTREAM(rawoutstream, "     -D U, --xml-dtd=U    Use the DTD or schema at U\n");
+    PRINTVALSTREAM(rawoutstream, "     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML\n");
+    PRINTVALSTREAM(rawoutstream, "                          \":\": no namespace, default: \"hdf5:\"\n");
+    PRINTVALSTREAM(rawoutstream, "                          E.g., to dump a file called `-f', use h5dump -- -f\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Subsetting Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream, " Subsetting is available by using the following options with a dataset\n");
+    PRINTVALSTREAM(rawoutstream, " option. Subsetting is done by selecting a hyperslab from the data.\n");
+    PRINTVALSTREAM(rawoutstream, " Thus, the options mirror those for performing a hyperslab selection.\n");
+    PRINTVALSTREAM(rawoutstream, " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n");
+    PRINTVALSTREAM(rawoutstream, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n");
+    PRINTVALSTREAM(rawoutstream, " each dimension. START is optional and will default to 0 in each dimension.\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      -s START,  --start=START    Offset of start of subsetting selection\n");
+    PRINTVALSTREAM(rawoutstream, "      -S STRIDE, --stride=STRIDE  Hyperslab stride\n");
+    PRINTVALSTREAM(rawoutstream, "      -c COUNT,  --count=COUNT    Number of blocks to include in selection\n");
+    PRINTVALSTREAM(rawoutstream, "      -k BLOCK,  --block=BLOCK    Size of block in hyperslab\n");
+    PRINTVALSTREAM(rawoutstream, "  START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n");
+    PRINTVALSTREAM(rawoutstream, "      number of dimensions in the dataspace being queried\n");
+    PRINTVALSTREAM(rawoutstream, "      (Alternate compact form of subsetting is described in the Reference Manual)\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Option Argument Conventions ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "  D - is the file driver to use in opening the file. Acceptable values\n");
+    PRINTVALSTREAM(rawoutstream, "      are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n");
+    PRINTVALSTREAM(rawoutstream, "      the file driver flag, the file will be opened with each driver in\n");
+    PRINTVALSTREAM(rawoutstream, "      turn and in the order specified above until one driver succeeds\n");
+    PRINTVALSTREAM(rawoutstream, "      in opening the file.\n");
+    PRINTVALSTREAM(rawoutstream, "      See examples below for family, split, and multi driver special file name usage.\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  F - is a filename.\n");
+    PRINTVALSTREAM(rawoutstream, "  P - is the full path from the root group to the object.\n");
+    PRINTVALSTREAM(rawoutstream, "  N - is an integer greater than 1.\n");
+    PRINTVALSTREAM(rawoutstream, "  T - is a string containing the floating point format, e.g '%%.3f'\n");
+    PRINTVALSTREAM(rawoutstream, "  U - is a URI reference (as defined in [IETF RFC 2396],\n");
+    PRINTVALSTREAM(rawoutstream, "        updated by [IETF RFC 2732])\n");
+    PRINTVALSTREAM(rawoutstream, "  B - is the form of binary output: NATIVE for a memory type, FILE for the\n");
+    PRINTVALSTREAM(rawoutstream, "        file type, LE or BE for pre-existing little or big endian types.\n");
+    PRINTVALSTREAM(rawoutstream, "        Must be used with -o (output file) and it is recommended that\n");
+    PRINTVALSTREAM(rawoutstream, "        -d (dataset) is used. B is an optional argument, defaults to NATIVE\n");
+    PRINTVALSTREAM(rawoutstream, "  Q - is the sort index type. It can be \"creation_order\" or \"name\" (default)\n");
+    PRINTVALSTREAM(rawoutstream, "  Z - is the sort order type. It can be \"descending\" or \"ascending\" (default)\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Examples ---------------\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  1) Attribute foo of the group /bar_none in file quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -a /bar_none/foo quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "     Attribute \"high/low\" of the group /bar_none in the file quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -a \"/bar_none/high\\/low\" quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  2) Selecting a subset from dataset /foo in file quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /foo -s \"0,1\" -S \"1,1\" -c \"2,3\" -k \"2,2\" quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  3) Saving dataset 'dset' in file quux.h5 to binary file 'out.bin'\n");
+    PRINTVALSTREAM(rawoutstream, "        using a little-endian type\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /dset -b LE -o out.bin quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  4) Display two packed bits (bits 0-1 and bits 4-6) in the dataset /dset\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /dset -M 0,1,4,3 quux.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  5) Dataset foo in files file1.h5 file2.h5 file3.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /foo file1.h5 file2.h5 file3.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  6) Dataset foo in split files splitfile-m.h5 splitfile-r.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /foo -f split splitfile\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  7) Dataset foo in multi files mf-s.h5, mf-b.h5, mf-r.h5, mf-g.h5, mf-l.h5 and mf-o.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /foo -f multi mf\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  8) Dataset foo in family files fam00000.h5 fam00001.h5 and fam00002.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "      h5dump -d /foo -f family fam%%05d.h5\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: table_list_add
+ *
+ * Purpose: Add a new set of tables
+ *
+ * Return: index of added table on success, -1 on failure
+ *
+ * Programmer: Neil Fortner, nfortne2@hdfgroup.org
+ *             Adapted from trav_addr_add in h5trav.c by Quincey Koziol
+ *
+ * Date: October 13, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+ssize_t
+table_list_add(hid_t oid, unsigned long file_no)
+{
+    size_t      idx;         /* Index of table to use */
+    find_objs_t info;
+
+    /* Allocate space if necessary */
+    if(table_list.nused == table_list.nalloc) {
+        h5dump_table_items_t    *tmp_ptr;
+
+        table_list.nalloc = MAX(1, table_list.nalloc * 2);
+        if(NULL == (tmp_ptr = (h5dump_table_items_t *)HDrealloc(table_list.tables, table_list.nalloc * sizeof(table_list.tables[0]))))
+            return -1;
+        table_list.tables = tmp_ptr;
+    } /* end if */
+
+    /* Append it */
+    idx = table_list.nused++;
+    table_list.tables[idx].fileno = file_no;
+    table_list.tables[idx].oid = oid;
+    if(H5Iinc_ref(oid) < 0) {
+        table_list.nused--;
+        return -1;
+    }
+    if(init_objs(oid, &info, &table_list.tables[idx].group_table,
+                 &table_list.tables[idx].dset_table, &table_list.tables[idx].type_table) < 0) {
+        H5Idec_ref(oid);
+        table_list.nused--;
+        return -1;
+    }
+
+#ifdef H5DUMP_DEBUG
+    dump_tables(&info);
+#endif /* H5DUMP_DEBUG */
+
+    return((ssize_t) idx);
+} /* end table_list_add() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: table_list_visited
+ *
+ * Purpose: Check if a table already exists for the specified fileno
+ *
+ * Return: The index of the matching table, or -1 if no matches found
+ *
+ * Programmer: Neil Fortner, nfortne2@hdfgroup.org
+ *             Adapted from trav_addr_visited in h5trav.c by Quincey Koziol
+ *
+ * Date: October 13, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+H5_ATTR_PURE ssize_t
+table_list_visited(unsigned long file_no)
+{
+    size_t u;           /* Local index variable */
+
+    /* Look for table */
+    for(u = 0; u < table_list.nused; u++)
+        /* Check for fileno value already in array */
+        if(table_list.tables[u].fileno == file_no)
+            return((ssize_t) u);
+
+    /* Didn't find table */
+    return(-1);
+} /* end table_list_visited() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: table_list_free
+ *
+ * Purpose: Frees the table list
+ *
+ * Return: void
+ *
+ * Programmer: Neil Fortner, nfortne2@hdfgroup.org
+ *
+ * Date: October 13, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+table_list_free(void)
+{
+    size_t u;           /* Local index variable */
+
+    /* Iterate over tables */
+    for(u = 0; u < table_list.nused; u++) {
+        /* Release object id */
+        if(H5Idec_ref(table_list.tables[u].oid) < 0)
+            h5tools_setstatus(EXIT_FAILURE);
+
+        /* Free each table */
+        free_table(table_list.tables[u].group_table);
+        HDfree(table_list.tables[u].group_table);
+        free_table(table_list.tables[u].dset_table);
+        HDfree(table_list.tables[u].dset_table);
+        free_table(table_list.tables[u].type_table);
+        HDfree(table_list.tables[u].type_table);
+    }
+
+    /* Free the table list */
+    HDfree(table_list.tables);
+    table_list.tables = NULL;
+    table_list.nalloc = table_list.nused = 0;
+} /* end table_list_free() */
+
+/*-------------------------------------------------------------------------
+ * Function:    set_binary_form
+ *
+ * Purpose: set the binary form of output by translating from a string input
+ *          parameter to a integer return value
+ *
+ * Return: integer form of binary output or -1 if none found
+ *
+ * Programmer:  Pedro Vicente Nunes
+ *             June 28, 2006
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+set_binary_form(const char *form)
+{
+    int bform = -1;
+
+    if (HDstrcmp(form,"NATIVE") == 0 || HDstrcmp(form,"MEMORY") == 0) {
+        /* native form */
+        bform = 0;
+    }
+    else if (HDstrcmp(form,"FILE") == 0) /* file type form */
+        bform = 1;
+    else if (HDstrcmp(form,"LE") == 0) /* convert to little endian */
+        bform = 2;
+    else if (HDstrcmp(form,"BE") == 0) /* convert to big endian */
+        bform = 3;
+
+    return bform;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    set_sort_by
+ *
+ * Purpose: set the "by" form of sorting by translating from a string input
+ *          parameter to a H5_index_t return value
+ *          current sort values are [creation_order | name]
+ *
+ * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found
+ *
+ * Programmer:  Pedro Vicente Nunes
+ *              October 1, 2007
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static H5_index_t
+set_sort_by(const char *form)
+{
+    H5_index_t idx_type = H5_INDEX_UNKNOWN;
+
+    if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */
+        idx_type = H5_INDEX_NAME;
+    else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */
+        idx_type = H5_INDEX_CRT_ORDER;
+
+    return idx_type;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    set_sort_order
+ *
+ * Purpose: set the order of sorting by translating from a string input
+ *          parameter to a H5_iter_order_t return value
+ *          current order values are [ascending | descending ]
+ *
+ * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found
+ *
+ * Programmer:  Pedro Vicente Nunes
+ *              October 1, 2007
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static H5_iter_order_t
+set_sort_order(const char *form)
+{
+    H5_iter_order_t iter_order = H5_ITER_UNKNOWN;
+
+    if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */
+        iter_order = H5_ITER_INC;
+    else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */
+        iter_order = H5_ITER_DEC;
+
+    return iter_order;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_hsize_list
+ *
+ * Purpose:     Parse a list of comma or space separated integers and return
+ *              them in a list. The string being passed into this function
+ *              should be at the start of the list you want to parse. You are
+ *              responsible for freeing the array returned from here.
+ *
+ *              Lists in the so-called "terse" syntax are separated by
+ *              semicolons (;). The lists themselves can be separated by
+ *              either commas (,) or white spaces.
+ *
+ * Return:      <none>
+ *
+ * Programmer:  Bill Wendling
+ *              Tuesday, 6. February 2001
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+parse_hsize_list(const char *h_list, subset_d *d)
+{
+    hsize_t        *p_list;
+    const char     *ptr;
+    unsigned int    size_count = 0;
+    unsigned int    i = 0;
+    unsigned int    last_digit = 0;
+
+    if (!h_list || !*h_list || *h_list == ';')
+        return;
+
+    /* count how many integers do we have */
+    for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
+        if (HDisdigit(*ptr)) {
+            if (!last_digit)
+                /* the last read character wasn't a digit */
+                size_count++;
+
+            last_digit = 1;
+        }
+        else
+            last_digit = 0;
+
+    if (size_count == 0)
+        /* there aren't any integers to read */
+        return;
+
+    /* allocate an array for the integers in the list */
+    p_list = (hsize_t *)HDcalloc(size_count, sizeof(hsize_t));
+
+    for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
+        if(HDisdigit(*ptr)) {
+            /* we should have an integer now */
+            p_list[i++] = (hsize_t)HDstrtoull(ptr, NULL, 0);
+
+            while (HDisdigit(*ptr))
+                /* scroll to end of integer */
+                ptr++;
+        }
+    d->data = p_list;
+    d->len = size_count;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_subset_params
+ *
+ * Purpose:     Parse the so-called "terse" syntax for specifying subsetting
+ *              parameters.
+ *
+ * Return:      Success:    struct subset_t object
+ *              Failure:    NULL
+ *
+ * Programmer:  Bill Wendling
+ *              Tuesday, 6. February 2001
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static struct subset_t *
+parse_subset_params(char *dset)
+{
+    struct subset_t *s = NULL;
+    char   *brace;
+
+    if (!disable_compact_subset && ((brace = HDstrrchr(dset, '[')) != NULL)) {
+        *brace++ = '\0';
+
+        s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t));
+        parse_hsize_list(brace, &s->start);
+
+        while (*brace && *brace != ';')
+            brace++;
+
+        if (*brace) brace++;
+
+        parse_hsize_list(brace, &s->stride);
+
+        while (*brace && *brace != ';')
+            brace++;
+
+        if (*brace) brace++;
+
+        parse_hsize_list(brace, &s->count);
+
+        while (*brace && *brace != ';')
+            brace++;
+
+        if (*brace) brace++;
+
+        parse_hsize_list(brace, &s->block);
+    }
+
+    return s;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_mask_list
+ *
+ * Purpose:     Parse a list of comma or space separated integers and fill
+ *              the packed_bits list and counter. The string being passed into this function
+ *              should be at the start of the list you want to parse.
+ *
+ * Return:      Success:        SUCCEED
+ *
+ *              Failure:        FAIL
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+parse_mask_list(const char *h_list)
+{
+    int                soffset_value;
+    unsigned           offset_value;
+    int                slength_value;
+    unsigned           length_value;
+    unsigned long long temp_mask;
+    const char        *ptr = NULL;
+
+    /* sanity check */
+    HDassert(h_list);
+
+    HDmemset(packed_mask,0,sizeof(packed_mask));
+
+    packed_bits_num = 0;
+    /* scan in pair of offset,length separated by commas. */
+    ptr = h_list;
+    while (*ptr) {
+        /* scan for an offset which is an unsigned int */
+        if (!HDisdigit(*ptr)) {
+            error_msg("Bad mask list(%s)\n", h_list);
+            return FAIL;
+        }
+        soffset_value = HDatoi(ptr);
+        offset_value = (unsigned)soffset_value;
+        if (soffset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) {
+            error_msg("Packed Bit offset value(%d) must be between 0 and %u\n",
+                    soffset_value, (unsigned)(PACKED_BITS_SIZE_MAX - 1));
+            return FAIL;
+        }
+
+        /* skip to end of integer */
+        while (HDisdigit(*++ptr))
+            ;
+        /* Look for the common separator */
+        if (*ptr++ != ',') {
+            error_msg("Bad mask list(%s), missing expected comma separator.\n", h_list);
+            return FAIL;
+        }
+
+        /* scan for a length which is a positive int */
+        if (!HDisdigit(*ptr)) {
+            error_msg("Bad mask list(%s)\n", h_list);
+            return FAIL;
+        }
+        slength_value = HDatoi(ptr);
+        if (slength_value <= 0) {
+            error_msg("Packed Bit length value(%d) must be positive.\n", slength_value);
+            return FAIL;
+        }
+        length_value = (unsigned)slength_value;
+        if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX) {
+            error_msg("Packed Bit offset+length value(%u) too large. Max is %u\n",
+                       offset_value+length_value, (unsigned)PACKED_BITS_SIZE_MAX);
+            return FAIL;
+        }
+
+        /* skip to end of int */
+        while (HDisdigit(*++ptr))
+            ;
+
+        /* store the offset,length pair */
+        if (packed_bits_num >= PACKED_BITS_MAX) {
+            /* too many requests */
+            error_msg("Too many masks requested (max. %d). Mask list(%s)\n", PACKED_BITS_MAX, h_list);
+            return FAIL;
+        }
+        packed_offset[packed_bits_num] = offset_value;
+        packed_length[packed_bits_num] = length_value;
+        /* create the bit mask by left shift 1's by length, then negate it. */
+        /* After packed_mask is calculated, packed_length is not needed but  */
+        /* keep it for debug purpose. */
+        temp_mask = ~0ULL;
+        if(length_value < (int)(8 *sizeof(unsigned long long))) {
+            temp_mask = temp_mask << length_value;
+            packed_mask[packed_bits_num] = ~temp_mask;
+        }
+        else
+            packed_mask[packed_bits_num] = temp_mask;
+        packed_bits_num++;
+
+        /* skip a possible comma separator */
+        if (*ptr == ',') {
+            if (!(*++ptr)) {
+                /* unexpected end of string */
+                error_msg("Bad mask list(%s), unexpected end of string.\n", h_list);
+                return FAIL;
+            }
+        }
+    }
+    HDassert(packed_bits_num <= PACKED_BITS_MAX);
+    if (packed_bits_num == 0) {
+        /* got no masks! */
+        error_msg("Bad mask list(%s)\n", h_list);
+        return FAIL;
+    }
+    return SUCCEED;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    free_handler
+ *
+ * Purpose:     Convenience function to free the handler_t structures. Needs a
+ *              length variable (LEN) to know how many in the array it needs
+ *              to free
+ *
+ * Return:      Nothing
+ *
+ * Programmer:  Bill Wendling
+ *              Tuesday, 20. February 2001
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+free_handler(struct handler_t *hand, int len)
+{
+    int i;
+
+    if(hand) {
+        for (i = 0; i < len; i++) {
+            if(hand[i].obj) {
+                HDfree(hand[i].obj);
+                hand[i].obj=NULL;
+            }
+
+            if (hand[i].subset_info) {
+                if(hand[i].subset_info->start.data)
+                    HDfree(hand[i].subset_info->start.data);
+                if(hand[i].subset_info->stride.data)
+                    HDfree(hand[i].subset_info->stride.data);
+                if(hand[i].subset_info->count.data)
+                    HDfree(hand[i].subset_info->count.data);
+                if(hand[i].subset_info->block.data)
+                    HDfree(hand[i].subset_info->block.data);
+
+                HDfree(hand[i].subset_info);
+                hand[i].subset_info=NULL;
+            }
+        }
+
+        HDfree(hand);
+    }
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    parse_command_line
+ *
+ * Purpose:     Parse the command line for the h5dumper.
+ *
+ * Return:      Success:    A pointer to an array of handler_t structures.
+ *                          These contain all the information needed to dump
+ *                          the necessary object.
+ *
+ *              Failure:    Exits program with EXIT_FAILURE value.
+ *
+ * Programmer:  Bill Wendling
+ *              Tuesday, 20. February 2001
+ *
+ * Modifications:
+ *  pvn June, 1, 2006. Add a switch for binary output
+ *
+ *-------------------------------------------------------------------------
+ */
+static struct handler_t *
+parse_command_line(int argc, const char *argv[])
+{
+    struct handler_t   *hand = NULL;
+    struct handler_t   *last_dset = NULL;
+    int                 i;
+    int                 opt;
+    int                 last_was_dset = FALSE;
+
+     /* no arguments */
+    if (argc == 1) {
+        usage(h5tools_getprogname());
+        goto error;
+    }
+
+    /* this will be plenty big enough to hold the info */
+    if((hand = (struct handler_t *)HDcalloc((size_t)argc, sizeof(struct handler_t)))==NULL) {
+        goto error;
+    }
+
+    /* parse command line options */
+    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+parse_start:
+        switch ((char)opt) {
+        case 'R':
+            display_region = TRUE;
+            region_output = TRUE;
+            break;
+        case 'B':
+            display_bb = TRUE;
+            last_was_dset = FALSE;
+            break;
+        case 'n':
+            display_fi = TRUE;
+            last_was_dset = FALSE;
+            if ( opt_arg != NULL) {
+                h5trav_set_verbose(HDatoi(opt_arg));
+            }
+            break;
+        case 'p':
+            display_dcpl = TRUE;
+            break;
+        case 'y':
+            display_ai = FALSE;
+            break;
+        case 'e':
+            display_escape = TRUE;
+            break;
+        case 'H':
+            display_data = FALSE;
+            display_attr_data = FALSE;
+            last_was_dset = FALSE;
+            break;
+        case 'A':
+            if ( opt_arg != NULL) {
+                if(0 == HDatoi(opt_arg)) include_attrs = FALSE;
+            }
+            else {
+                display_data = FALSE;
+                display_attr_data = TRUE;
+                last_was_dset = FALSE;
+            }
+            break;
+        case 'i':
+            display_oid = TRUE;
+            last_was_dset = FALSE;
+            break;
+        case 'r':
+            display_char = TRUE;
+            break;
+        case 'V':
+            print_version(h5tools_getprogname());
+            free_handler(hand, argc);
+            hand = NULL;
+            h5tools_setstatus(EXIT_SUCCESS);
+            goto done;
+            break;
+        case 'w':
+            {
+                int sh5tools_nCols = HDatoi(opt_arg);
+
+                if (sh5tools_nCols <= 0)
+                    h5tools_nCols = 65535;
+                else
+                    h5tools_nCols = (unsigned)sh5tools_nCols;
+                last_was_dset = FALSE;
+            }
+            break;
+        case 'N':
+            display_all = 0;
+
+            for (i = 0; i < argc; i++)
+                if (!hand[i].func) {
+                    hand[i].func = handle_paths;
+                    hand[i].obj = HDstrdup(opt_arg);
+                    break;
+                }
+
+            last_was_dset = FALSE;
+            break;
+        case 'a':
+            display_all = 0;
+
+            for (i = 0; i < argc; i++)
+                if (!hand[i].func) {
+                    hand[i].func = handle_attributes;
+                    hand[i].obj = HDstrdup(opt_arg);
+                    break;
+                }
+
+            last_was_dset = FALSE;
+            break;
+        case 'd':
+            display_all = 0;
+
+            for (i = 0; i < argc; i++)
+                if (!hand[i].func) {
+                    hand[i].func = handle_datasets;
+                    hand[i].obj = HDstrdup(opt_arg);
+                    hand[i].subset_info = parse_subset_params(hand[i].obj);
+                    last_dset = &hand[i];
+                    break;
+                }
+
+            last_was_dset = TRUE;
+            break;
+        case 'f':
+            driver = opt_arg;
+            break;
+        case 'g':
+            display_all = 0;
+
+            for (i = 0; i < argc; i++)
+                if (!hand[i].func) {
+                    hand[i].func = handle_groups;
+                    hand[i].obj = HDstrdup(opt_arg);
+                    break;
+                }
+
+            last_was_dset = FALSE;
+            break;
+        case 'l':
+            display_all = 0;
+
+            for (i = 0; i < argc; i++)
+                if (!hand[i].func) {
+                    hand[i].func = handle_links;
+                    hand[i].obj = HDstrdup(opt_arg);
+                    break;
+                }
+
+            last_was_dset = FALSE;
+            break;
+        case 't':
+            display_all = 0;
+
+            for (i = 0; i < argc; i++)
+                if (!hand[i].func) {
+                    hand[i].func = handle_datatypes;
+                    hand[i].obj = HDstrdup(opt_arg);
+                    break;
+                }
+
+            last_was_dset = FALSE;
+            break;
+
+        case 'O':
+            if (h5tools_set_output_file(opt_arg, 0) < 0) {
+                usage(h5tools_getprogname());
+                goto error;
+            }
+            break;
+
+        case 'o':
+            if ( bin_output ) {
+                if (h5tools_set_data_output_file(opt_arg, 1) < 0) {
+                    usage(h5tools_getprogname());
+                    goto error;
+                }
+            }
+            else {
+                if(display_attr_data && !display_data) {
+                    if (h5tools_set_attr_output_file(opt_arg, 0) < 0) {
+                        usage(h5tools_getprogname());
+                        goto error;
+                    }
+                }
+                if(display_data || display_all) {
+                    if (h5tools_set_data_output_file(opt_arg, 0) < 0) {
+                        usage(h5tools_getprogname());
+                        goto error;
+                    }
+                }
+            }
+
+            usingdasho = TRUE;
+            last_was_dset = FALSE;
+            outfname = opt_arg;
+            break;
+
+        case 'b':
+            if ( opt_arg != NULL) {
+                if ( ( bin_form = set_binary_form(opt_arg)) < 0) {
+                    /* failed to set binary form */
+                    usage(h5tools_getprogname());
+                    goto error;
+                }
+            }
+            bin_output = TRUE;
+            if (outfname!=NULL) {
+                if (h5tools_set_data_output_file(outfname, 1) < 0)  {
+                    /* failed to set output file */
+                    usage(h5tools_getprogname());
+                    goto error;
+                }
+
+                last_was_dset = FALSE;
+            }
+            break;
+
+        case 'q':
+            if ( ( sort_by = set_sort_by(opt_arg)) < 0) {
+                /* failed to set "sort by" form */
+                usage(h5tools_getprogname());
+                goto error;
+            }
+            break;
+
+        case 'z':
+            if ( ( sort_order = set_sort_order(opt_arg)) < 0) {
+                /* failed to set "sort order" form */
+                usage(h5tools_getprogname());
+                goto error;
+            }
+            break;
+
+        case 'M':
+            if (!last_was_dset) {
+                error_msg("option `-%c' can only be used after --dataset option\n", opt);
+                goto error;
+            }
+            if (parse_mask_list(opt_arg) != SUCCEED){
+                usage(h5tools_getprogname());
+                goto error;
+            }
+            display_packed_bits = TRUE;
+            break;
+        case 'v':
+            display_vds_first = TRUE;
+            break;
+        case 'G':
+            vds_gap_size = HDatoi(opt_arg);
+            if (vds_gap_size < 0) {
+                usage(h5tools_getprogname());
+                goto error;
+            }
+            break;
+
+        /** begin XML parameters **/
+        case 'x':
+            /* select XML output */
+            doxml = TRUE;
+            useschema = TRUE;
+            h5tools_dump_header_format = NULL;
+            dump_function_table = &xml_function_table;
+            h5tools_nCols = 0;
+            break;
+        case 'u':
+            doxml = TRUE;
+            useschema = FALSE;
+            xmlnsprefix = "";
+            h5tools_dump_header_format = NULL;
+            dump_function_table = &xml_function_table;
+            h5tools_nCols = 0;
+            break;
+        case 'D':
+            /* specify alternative XML DTD or schema */
+            /* To Do: check format of this value?  */
+            xml_dtd_uri = opt_arg;
+            h5tools_nCols = 0;
+            break;
+
+        case 'm':
+            /* specify alternative floating point printing format */
+            fp_format = opt_arg;
+            h5tools_nCols = 0;
+            break;
+
+        case 'X':
+            /* specify XML namespace (default="hdf5:"), or none */
+            /* To Do: check format of this value?  */
+            if (!useschema) {
+                usage(h5tools_getprogname());
+                goto error;
+            }
+            if (HDstrcmp(opt_arg,":") == 0)
+                xmlnsprefix = "";
+            else
+                xmlnsprefix = opt_arg;
+            h5tools_nCols = 0;
+            break;
+        /** end XML parameters **/
+
+        /** begin subsetting parameters **/
+        case 's':
+        case 'S':
+        case 'c':
+        case 'k': {
+            struct subset_t *s;
+
+            if (!last_was_dset) {
+                error_msg("option `-%c' can only be used after --dataset option\n", opt);
+                goto error;
+            }
+
+            if (last_dset->subset_info) {
+                /*
+                 * This overrides the "terse" syntax if they actually mixed
+                 * the two.
+                 */
+                s = last_dset->subset_info;
+            }
+            else {
+                last_dset->subset_info = s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t));
+            }
+
+            /*
+             * slightly convoluted, but...we are only interested in options
+             * for subsetting: "--start", "--stride", "--count", and "--block"
+             * which can come in any order. If we run out of parameters (EOF)
+             * or run into one which isn't a subsetting parameter (NOT s, S,
+             * c, or K), then we exit the do-while look, set the subset_info
+             * to the structure we've been filling. If we've reached the end
+             * of the options, we exit the parsing (goto parse_end) otherwise,
+             * since we've "read" the next option, we need to parse it. So we
+             * jump to the beginning of the switch statement (goto parse_start).
+             */
+            do {
+                switch ((char)opt) {
+                case 's':
+                    if (s->start.data) {
+                        HDfree(s->start.data);
+                        s->start.data = NULL;
+                    }
+                    parse_hsize_list(opt_arg, &s->start);
+                    break;
+                case 'S':
+                    if (s->stride.data) {
+                        HDfree(s->stride.data);
+                        s->stride.data = NULL;
+                    }
+                    parse_hsize_list(opt_arg, &s->stride);
+                    break;
+                case 'c':
+                    if (s->count.data) {
+                        HDfree(s->count.data);
+                        s->count.data = NULL;
+                    }
+                    parse_hsize_list(opt_arg, &s->count);
+                    break;
+                case 'k':
+                    if (s->block.data) {
+                        HDfree(s->block.data);
+                        s->block.data = NULL;
+                    }
+                    parse_hsize_list(opt_arg, &s->block);
+                    break;
+                default:
+                    goto end_collect;
+                }
+            } while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF);
+
+end_collect:
+            last_was_dset = FALSE;
+
+            if (opt != EOF)
+                goto parse_start;
+            else
+                goto parse_end;
+        }
+        /** end subsetting parameters **/
+
+        case 'E':
+            enable_error_stack = TRUE;
+            break;
+        case 'C':
+            disable_compact_subset = TRUE;
+            break;
+        case 'h':
+            usage(h5tools_getprogname());
+            free_handler(hand, argc);
+            hand = NULL;
+            h5tools_setstatus(EXIT_SUCCESS);
+            goto done;
+        case '?':
+        default:
+            usage(h5tools_getprogname());
+            goto error;
+        }
+    }
+
+parse_end:
+    /* check for file name to be processed */
+    if (argc <= opt_ind) {
+        error_msg("missing file name\n");
+        usage(h5tools_getprogname());
+        goto error;
+    }
+done:
+    return hand;
+
+error:
+    if (hand) {
+        free_handler(hand, argc);
+        hand = NULL;
+    }
+    h5tools_setstatus(EXIT_FAILURE);
+
+    return hand;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    main
+ *
+ * Purpose:     HDF5 dumper
+ *
+ * Return:      Success:    0
+ *              Failure:    1
+ *
+ * Programmer:  Ruey-Hsia Li
+ *
+ * Modifications:
+ *        Albert Cheng
+ *        30. September 2000
+ *        Add the -o option--output file for datasets raw data
+ *
+ *        REMcG
+ *        November 2000
+ *        Changes to support XML.
+ *
+ *        Bill Wendling
+ *        Wednesday, 10. January 2001
+ *        Modified the way command line parameters are interpreted. They go
+ *        through one function call now (get_option).
+ *
+ *        Bill Wendling
+ *        Tuesday, 20. February 2001
+ *        Moved command line parsing to separate function. Made various
+ *        "display_*" flags global.
+ *
+ *        REMcG
+ *        August 2003
+ *        Major upgrade to XML support.
+ *
+ *        Pedro Vicente
+ *        September 2007
+ *        list objects in requested order (creation order or alphabetically)
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, const char *argv[])
+{
+    hid_t               fid = -1;
+    hid_t               gid = -1;
+    H5E_auto2_t         func;
+    H5E_auto2_t         tools_func;
+    H5O_info_t          oi;
+    struct handler_t   *hand = NULL;
+    int                 i;
+    unsigned            u;
+    void               *edata;
+    void               *tools_edata;
+    char               *fname = NULL;
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+    h5tools_dump_header_format = &h5tools_standardformat;
+    dump_function_table = &ddl_function_table;
+    dump_indent = 0;
+
+    /* Disable error reporting */
+    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /* Initialize h5tools lib */
+    h5tools_init();
+
+    /* Disable tools error reporting */
+    H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
+    H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL);
+
+    if((hand = parse_command_line(argc, argv))==NULL) {
+        goto done;
+    }
+
+    if (bin_output && outfname == NULL) {
+        error_msg("binary output requires a file name, use -o <filename>\n");
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
+    if (enable_error_stack) {
+        H5Eset_auto2(H5E_DEFAULT, func, edata);
+        H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
+    }
+
+    /* Check for conflicting options */
+    if (doxml) {
+        if (!display_all) {
+            error_msg("option \"%s\" not available for XML\n",
+                    "to display selected objects");
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+        else if (display_bb) {
+            error_msg("option \"%s\" not available for XML\n", "--boot-block");
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+        else if (display_oid == 1) {
+            error_msg("option \"%s\" not available for XML\n", "--object-ids");
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+        else if (display_char == TRUE) {
+            error_msg("option \"%s\" not available for XML\n", "--string");
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+        else if (usingdasho) {
+            error_msg("option \"%s\" not available for XML\n", "--output");
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+    }
+    else {
+        if (xml_dtd_uri) {
+            warn_msg("option \"%s\" only applies with XML: %s\n", "--xml-dtd", xml_dtd_uri);
+        }
+    }
+
+    if (argc <= opt_ind) {
+        error_msg("missing file name\n");
+        usage(h5tools_getprogname());
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
+
+    while(opt_ind < argc) {
+        fname = HDstrdup(argv[opt_ind++]);
+
+        fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, driver, NULL, 0);
+
+        if (fid < 0) {
+            error_msg("unable to open file \"%s\"\n", fname);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+
+        /* allocate and initialize internal data structure */
+        init_prefix(&prefix, prefix_len);
+
+        /* Prepare to find objects that might be targets of a reference */
+        fill_ref_path_table(fid);
+
+        if(doxml) {
+            /* initialize XML */
+            /* reset prefix! */
+            HDstrcpy(prefix, "");
+
+            /* make sure the URI is initialized to something */
+            if (xml_dtd_uri == NULL) {
+                if (useschema) {
+                    xml_dtd_uri = DEFAULT_XSD;
+                }
+                else {
+                    xml_dtd_uri = DEFAULT_DTD;
+                    xmlnsprefix = "";
+                }
+            }
+            else {
+                if (useschema && HDstrcmp(xmlnsprefix,"")) {
+                    error_msg("Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n");
+                    h5tools_setstatus(EXIT_FAILURE);
+                    goto done;
+                }
+            }
+        }
+
+        /* Get object info for root group */
+        if(H5Oget_info_by_name(fid, "/", &oi, H5P_DEFAULT) < 0) {
+            error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+
+        /* Initialize object tables */
+        if(table_list_add(fid, oi.fileno) < 0) {
+            error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
+        }
+        group_table = table_list.tables[0].group_table;
+        dset_table = table_list.tables[0].dset_table;
+        type_table = table_list.tables[0].type_table;
+
+        /* does there exist unamed committed datatype */
+        for (u = 0; u < type_table->nobjs; u++)
+            if (!type_table->objs[u].recorded) {
+                unamedtype = 1;
+                break;
+            } /* end if */
+
+        /* start to dump - display file header information */
+        if (!doxml) {
+            begin_obj(h5tools_dump_header_format->filebegin, fname, h5tools_dump_header_format->fileblockbegin);
+        }
+        else {
+            PRINTVALSTREAM(rawoutstream, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+
+            /* alternative first element, depending on schema or DTD. */
+            if (useschema) {
+                if (HDstrcmp(xmlnsprefix,"") == 0) {
+                    PRINTSTREAM(rawoutstream, "<HDF5-File xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"%s\">\n",
+                            xml_dtd_uri);
+                }
+                else {
+                    /*  TO DO: make -url option work in this case (may need new option) */
+                    char *ns;
+                    char *indx;
+
+                    ns = HDstrdup(xmlnsprefix);
+                    indx = HDstrrchr(ns,(int)':');
+                    if (indx) *indx = '\0';
+
+                    PRINTSTREAM(rawoutstream, "<%sHDF5-File xmlns:%s=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\" "
+                            "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" "
+                            "xsi:schemaLocation=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File "
+                            "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\">\n",xmlnsprefix,ns);
+                    HDfree(ns);
+                }
+            }
+            else {
+                PRINTSTREAM(rawoutstream, "<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n", xml_dtd_uri);
+                PRINTVALSTREAM(rawoutstream, "<HDF5-File>\n");
+            }
+        }
+
+        if (!doxml) {
+            if (display_fi) {
+                PRINTVALSTREAM(rawoutstream, "\n");
+                dump_fcontents(fid);
+                end_obj(h5tools_dump_header_format->fileend,h5tools_dump_header_format->fileblockend);
+                PRINTVALSTREAM(rawoutstream, "\n");
+                goto done;
+            }
+
+            if (display_bb)
+                dump_fcpl(fid);
+        }
+
+        if(display_all) {
+            if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) {
+                error_msg("unable to open root group\n");
+                h5tools_setstatus(EXIT_FAILURE);
+            }
+            else {
+                if (!doxml)
+                    dump_indent += COL;
+                dump_function_table->dump_group_function(gid, "/" );
+                if (!doxml)
+                    dump_indent -= COL;
+                PRINTVALSTREAM(rawoutstream, "\n");
+            }
+
+            if(H5Gclose(gid) < 0) {
+                error_msg("unable to close root group\n");
+                h5tools_setstatus(EXIT_FAILURE);
+            }
+
+        }
+        else {
+            /* Note: this option is not supported for XML */
+            if(doxml) {
+                error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+                h5tools_setstatus(EXIT_FAILURE);
+                goto done;
+            } /* end if */
+
+            for(i = 0; i < argc; i++) {
+                if(hand[i].func) {
+                    hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1, NULL);
+                }
+            }
+            PRINTVALSTREAM(rawoutstream, "\n");
+        }
+
+        if (!doxml) {
+            end_obj(h5tools_dump_header_format->fileend, h5tools_dump_header_format->fileblockend);
+            PRINTVALSTREAM(rawoutstream, "\n");
+        }
+        else {
+            PRINTSTREAM(rawoutstream, "</%sHDF5-File>\n", xmlnsprefix);
+        }
+        /* Free tables for objects */
+        table_list_free();
+
+        if(fid >=0)
+            if (H5Fclose(fid) < 0)
+                h5tools_setstatus(EXIT_FAILURE);
+
+        if(prefix) {
+            HDfree(prefix);
+            prefix = NULL;
+        }
+        if(fname) {
+            HDfree(fname);
+            fname = NULL;
+        }
+    } /* end while */
+
+    if(hand)
+        free_handler(hand, argc);
+
+    /* To Do:  clean up XML table */
+
+    leave(h5tools_getstatus());
+
+done:
+    /* Free tables for objects */
+    table_list_free();
+
+    if(fid >=0)
+        if (H5Fclose(fid) < 0)
+            h5tools_setstatus(EXIT_FAILURE);
+
+    if(prefix) {
+        HDfree(prefix);
+        prefix = NULL;
+    }
+    if(fname) {
+        HDfree(fname);
+        fname = NULL;
+    }
+
+    if(hand)
+        free_handler(hand, argc);
+
+    /* To Do:  clean up XML table */
+
+    H5Eset_auto2(H5E_DEFAULT, func, edata);
+
+    leave(h5tools_getstatus());
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    h5_fileaccess
+ *
+ * Purpose: Returns a file access template which is the default template
+ *      but with a file driver set according to the constant or
+ *      environment variable HDF5_DRIVER
+ *
+ * Return:  Success:    A file access property list
+ *
+ *      Failure:    -1
+ *
+ * Programmer:  Robb Matzke
+ *              Thursday, November 19, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t
+h5_fileaccess(void)
+{
+    static const char *multi_letters = "msbrglo";
+    const char  *val = NULL;
+    const char  *name;
+    char         s[1024];
+    hid_t        fapl = -1;
+
+    /* First use the environment variable, then the constant */
+    val = HDgetenv("HDF5_DRIVER");
+#ifdef HDF5_DRIVER
+    if (!val) val = HDF5_DRIVER;
+#endif
+
+    if ((fapl=H5Pcreate(H5P_FILE_ACCESS))<0) return -1;
+    if (!val || !*val) return fapl; /*use default*/
+
+    HDstrncpy(s, val, sizeof s);
+    s[sizeof(s)-1] = '\0';
+    if (NULL==(name=HDstrtok(s, " \t\n\r"))) return fapl;
+
+    if (!HDstrcmp(name, "sec2")) {
+        /* Unix read() and write() system calls */
+        if (H5Pset_fapl_sec2(fapl)<0) return -1;
+    }
+    else if (!HDstrcmp(name, "stdio")) {
+        /* Standard C fread() and fwrite() system calls */
+        if (H5Pset_fapl_stdio(fapl)<0) return -1;
+    }
+    else if (!HDstrcmp(name, "core")) {
+        /* In-core temporary file with 1MB increment */
+        if (H5Pset_fapl_core(fapl, 1024*1024, FALSE)<0) return -1;
+    }
+    else if (!HDstrcmp(name, "split")) {
+        /* Split meta data and raw data each using default driver */
+        if (H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0)
+            return -1;
+    }
+    else if (!HDstrcmp(name, "multi")) {
+        /* Multi-file driver, general case of the split driver */
+        H5FD_mem_t      memb_map[H5FD_MEM_NTYPES];
+        hid_t           memb_fapl[H5FD_MEM_NTYPES];
+        const char     *memb_name[H5FD_MEM_NTYPES];
+        char            sv[H5FD_MEM_NTYPES][1024];
+        haddr_t         memb_addr[H5FD_MEM_NTYPES];
+        H5FD_mem_t      mt;
+
+        HDmemset(memb_map, 0, sizeof memb_map);
+        HDmemset(memb_fapl, 0, sizeof memb_fapl);
+        HDmemset(memb_name, 0, sizeof memb_name);
+        HDmemset(memb_addr, 0, sizeof memb_addr);
+
+        HDassert(HDstrlen(multi_letters)==H5FD_MEM_NTYPES);
+        for (mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
+            memb_fapl[mt] = H5P_DEFAULT;
+            memb_map[mt] = mt;
+            sprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
+            memb_name[mt] = sv[mt];
+            memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
+        }
+
+        if (H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0)
+            return -1;
+    }
+    else if (!HDstrcmp(name, "family")) {
+        hsize_t fam_size = 100*1024*1024; /*100 MB*/
+
+        /* Family of files, each 1MB and using the default driver */
+        if ((val=HDstrtok(NULL, " \t\n\r")))
+            fam_size = (hsize_t)(HDstrtod(val, NULL) * 1024*1024);
+        if (H5Pset_fapl_family(fapl, fam_size, H5P_DEFAULT)<0)
+            return -1;
+    }
+    else if (!HDstrcmp(name, "log")) {
+        long log_flags = H5FD_LOG_LOC_IO;
+
+        /* Log file access */
+        if ((val = HDstrtok(NULL, " \t\n\r")))
+            log_flags = HDstrtol(val, NULL, 0);
+
+        if (H5Pset_fapl_log(fapl, NULL, (unsigned)log_flags, 0) < 0)
+            return -1;
+    }
+    else if (!HDstrcmp(name, "direct")) {
+        /* Substitute Direct I/O driver with sec2 driver temporarily because
+         * some output has sec2 driver as the standard. */
+        if (H5Pset_fapl_sec2(fapl)<0) return -1;
+    }
+    else {
+        /* Unknown driver */
+        return -1;
+    }
+
+    return fapl;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    init_prefix
+ *
+ * Purpose:     allocate and initialize prefix
+ *
+ * Return:      void
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+init_prefix(char **prfx, size_t prfx_len)
+{
+    HDassert(prfx_len > 0);
+    *prfx = (char *)HDcalloc(prfx_len, 1);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:    add_prefix
+ *
+ * Purpose:     Add object to prefix
+ *
+ * Return:      void
+ *
+ *-------------------------------------------------------------------------
+ */
+void
+add_prefix(char **prfx, size_t *prfx_len, const char *name)
+{
+    size_t new_len = HDstrlen(*prfx) + HDstrlen(name) + 2;
+
+    /* Check if we need more space */
+    if(*prfx_len <= new_len) {
+        *prfx_len = new_len + 1;
+        *prfx = (char *)HDrealloc(*prfx, *prfx_len);
+    }
+
+    /* Append object name to prefix */
+    HDstrcat(HDstrcat(*prfx, "/"), name);
+} /* end add_prefix */
+