Split tools into src and test - add folders

3 files changed, 548 insertions, 0 deletions

diff --git a/tools/src/h5format_convert/CMakeLists.txt b/tools/src/h5format_convert/CMakeLists.txt
new file mode 100644
index 0000000..957055d
--- /dev/null
+++ b/tools/src/h5format_convert/CMakeLists.txt
@@ -0,0 +1,39 @@
+cmake_minimum_required (VERSION 3.1.0)
+PROJECT (HDF5_TOOLS_SRC_H5FC)
+
+#-----------------------------------------------------------------------------
+# Setup include Directories
+#-----------------------------------------------------------------------------
+INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
+
+# --------------------------------------------------------------------
+# Add the h5format_convert executables
+# --------------------------------------------------------------------
+add_executable (h5format_convert ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c)
+TARGET_NAMING (h5format_convert STATIC)
+TARGET_C_PROPERTIES (h5format_convert STATIC " " " ")
+target_link_libraries (h5format_convert  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5format_convert PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5format_convert")
+
+set (H5_DEP_EXECUTABLES h5format_convert)
+
+##############################################################################
+##############################################################################
+###           I N S T A L L A T I O N                                      ###
+##############################################################################
+##############################################################################
+
+#-----------------------------------------------------------------------------
+# Rules for Installation of tools using make Install target
+#-----------------------------------------------------------------------------
+
+#INSTALL_PROGRAM_PDB (h5format_convert ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+
+install (
+    TARGETS
+        h5format_convert
+    EXPORT
+        ${HDF5_EXPORTED_TARGETS}
+    RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+)
diff --git a/tools/src/h5format_convert/Makefile.am b/tools/src/h5format_convert/Makefile.am
new file mode 100644
index 0000000..e2d1acf
--- /dev/null
+++ b/tools/src/h5format_convert/Makefile.am
@@ -0,0 +1,35 @@
+#
+# 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.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+#
+# HDF5 Library Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+# Include src directory
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
+
+# These are our main targets, the tools
+bin_PROGRAMS=h5format_convert
+
+# Add h5format_convert specific linker flags here
+h5format_convert_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+
+# All programs rely on hdf5 library and h5tools library
+LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+
+include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c
new file mode 100644
index 0000000..8ce28dd
--- /dev/null
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -0,0 +1,474 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Programmer:  Vailin Choi; Feb 2015
+ */
+
+
+/*
+ * We include the private header file so we can get to the uniform
+ * programming environment it declares.  
+ * HDF5 API functions (except for H5G_basename())
+ */
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+#include "h5trav.h"
+
+/* Name of tool */
+#define PROGRAMNAME "h5format_convert"
+
+static char *fname_g = NULL;
+static char *dname_g = NULL;
+static int dset_g = FALSE;
+static int noop_g = FALSE;
+static int verbose_g = 0;
+
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters.
+ */
+static const char *s_opts = "hVvd:n";
+static struct long_options l_opts[] = {
+        { "help", no_arg, 'h' },
+	{ "hel", no_arg, 'h'},
+	{ "he", no_arg, 'h'},
+        { "version", no_arg, 'V' },
+	{ "version", no_arg, 'V' },
+	{ "versio", no_arg, 'V' },
+	{ "versi", no_arg, 'V' },
+	{ "vers", no_arg, 'V' },
+        { "verbose", no_arg, 'v' },
+        { "verbos", no_arg, 'v' },
+        { "verbo", no_arg, 'v' },
+        { "verb", no_arg, 'v' },
+        { "dname", require_arg, 'd' },
+        { "dnam", require_arg, 'd' },
+        { "dna", require_arg, 'd' },
+        { "dn", require_arg, 'd' },
+        { "noop", no_arg, 'n' },
+        { "noo", no_arg, 'n' },
+        { "no", no_arg, 'n' },
+        { NULL, 0, '\0' }
+};
+
+
+/*-------------------------------------------------------------------------
+ * Function: usage
+ *
+ * Purpose: print usage
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog) 
+{
+    HDfprintf(stdout, "usage: %s [OPTIONS] file_name\n", prog);
+    HDfprintf(stdout, "  OPTIONS\n");
+    HDfprintf(stdout, "   -h, --help                Print a usage message and exit\n");
+    HDfprintf(stdout, "   -V, --version             Print version number and exit\n");
+    HDfprintf(stdout, "   -v, --verbose             Turn on verbose mode\n");
+    HDfprintf(stdout, "   -d dname, --dname=dataset_name    Pathname for the dataset\n");
+    HDfprintf(stdout, "   -n, --noop                Perform all the steps except the actual conversion\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout, "Examples of use:\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout, "h5format_convert -d /group/dataset file_name\n");
+    HDfprintf(stdout, "  Convert the dataset </group/dataset> in the HDF5 file <file_name>:\n");
+    HDfprintf(stdout, "    a. chunked dataset: convert the chunk indexing type to version 1 B-tree\n");
+    HDfprintf(stdout, "    b. compact/contiguous dataset: downgrade the layout version to 3\n");
+    HDfprintf(stdout, "    c. virtual dataset: no action\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout, "h5format_convert file_name\n");
+    HDfprintf(stdout, "  Convert all datasets in the HDF5 file <file_name>:\n");
+    HDfprintf(stdout, "    a. chunked dataset: convert the chunk indexing type to version 1 B-tree\n");
+    HDfprintf(stdout, "    b. compact/contiguous dataset: downgrade the layout version to 3\n");
+    HDfprintf(stdout, "    c. virtual dataset: no action\n");
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout, "h5format_convert -n -d /group/dataset file_name\n");
+    HDfprintf(stdout, "  Go through all the steps except the actual conversion when \n");
+    HDfprintf(stdout, "  converting the dataset </group/dataset> in the HDF5 file <file_name>.\n");
+} /* usage() */
+
+/*-------------------------------------------------------------------------
+ * Function: parse_command_line
+ *
+ * Purpose: parse command line input
+ *
+ * Return: Success: 0
+ *  	   Failure: 1
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+parse_command_line(int argc, const char **argv) 
+{
+    int opt;
+
+     /* no arguments */
+    if (argc == 1) {
+        usage(h5tools_getprogname());
+	h5tools_setstatus(EXIT_FAILURE);
+        goto error;
+    }
+
+    /* parse command line options */
+    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+	switch((char) opt) {
+	    case 'h':
+		usage(h5tools_getprogname());
+		h5tools_setstatus(EXIT_SUCCESS);
+		goto error;
+
+	    case 'V':
+		print_version(h5tools_getprogname());
+		h5tools_setstatus(EXIT_SUCCESS);
+		goto error;
+
+	    case 'v':
+		verbose_g = TRUE;
+		break;
+
+	    case 'd': /* -d dname */
+		if(opt_arg != NULL && *opt_arg)
+		    dname_g = HDstrdup(opt_arg);
+		if(dname_g == NULL) {
+		    h5tools_setstatus(EXIT_FAILURE);
+		    error_msg("No dataset name\n", opt_arg);
+		    usage(h5tools_getprogname());
+		    goto error;
+		}
+		dset_g = TRUE;
+		break;
+
+	    case 'n': /* -n */
+		noop_g = TRUE;
+		break;
+
+	    default:
+		h5tools_setstatus(EXIT_FAILURE);
+		usage(h5tools_getprogname());
+		goto error;
+		break;
+	} /* switch */
+    } /* while */
+
+    if (argc <= opt_ind) {
+        error_msg("missing file name\n");
+        usage(h5tools_getprogname());
+	h5tools_setstatus(EXIT_FAILURE);
+        goto error;
+    }
+
+    fname_g = HDstrdup(argv[opt_ind]);
+
+    return(0);
+
+error:
+    return(-1); ;
+} /* parse_command_line() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: leave
+ *
+ * Purpose: Close HDF5
+ *
+ * Return: Does not return
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+leave(int ret)
+{
+    h5tools_close();
+
+    HDexit(ret);
+} /* leave() */
+
+/*-------------------------------------------------------------------------
+ * Function: convert()
+ *
+ * Purpose: To downgrade a dataset's indexing type or layout version:
+ *		For chunked:
+ *		  Downgrade the chunk indexing type to version 1 B-tree
+ *	    	  If type is already version 1 B-tree, no further action
+ *		For compact/contiguous:
+ *		  Downgrade the layout version from 4 to 3
+ *		  If version is already <= 3, no further action
+ *		For virtual:
+ *		  No further action
+ *
+ * Return: Success: 0
+ *  	   Failure: 1
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+convert(hid_t fid, const char *dname)
+{
+    hid_t dcpl = -1;
+    hid_t did = -1;
+    H5D_layout_t layout_type;
+    H5D_chunk_index_t idx_type;
+
+    /* Open the dataset */
+    if((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0) {
+	error_msg("unable to open dataset \"%s\"\n", dname);
+	h5tools_setstatus(EXIT_FAILURE);
+	goto error;
+
+    } else if(verbose_g)
+	HDfprintf(stdout, "Open the dataset\n");
+
+    /* Get the dataset's creation property list */
+    if((dcpl = H5Dget_create_plist(did)) < 0) {
+	error_msg("unable to get the dataset creation property list\n");
+	h5tools_setstatus(EXIT_FAILURE);
+	goto error;
+    }
+
+    /* Get the dataset's layout */
+    if((layout_type = H5Pget_layout(dcpl)) < 0) {
+	error_msg("unable to get the dataset layout type\n");
+	h5tools_setstatus(EXIT_FAILURE);
+	goto error;
+
+    } else if(verbose_g)
+	HDfprintf(stdout, "Retrieve the dataset's layout\n");
+
+    switch(layout_type) {
+	case H5D_CHUNKED:
+	    if(verbose_g)
+		HDfprintf(stdout, "Dataset is a chunked dataset\n");
+
+	    /* Get the dataset's chunk indexing type */
+	    if(H5Dget_chunk_index_type(did, &idx_type) < 0) {
+		error_msg("unable to get the chunk indexing type for \"%s\"\n", dname);
+		h5tools_setstatus(EXIT_FAILURE);
+		goto error;
+	    } else if(verbose_g)
+		HDfprintf(stdout, "Retrieve the dataset's chunk indexing type\n");
+
+	    if(idx_type == H5D_CHUNK_IDX_BTREE) {
+		if(verbose_g)
+		    HDfprintf(stdout, "Dataset's chunk indexing type is already version 1 B-tree: no further action\n");
+		h5tools_setstatus(EXIT_SUCCESS);
+		goto done;
+	    } else if (verbose_g)
+		HDfprintf(stdout, "Dataset's chunk indexing type is not version 1 B-tree\n");
+	    break;
+
+	case H5D_CONTIGUOUS:
+	    if(verbose_g)
+		HDfprintf(stdout, "Dataset is a contiguous dataset: downgrade layout version as needed\n");
+	    break;
+
+        case H5D_COMPACT:
+	    if(verbose_g)
+		HDfprintf(stdout, "Dataset is a compact dataset: downgrade layout version as needed\n");
+	    break;
+
+        case H5D_VIRTUAL:
+	    if(verbose_g)
+		HDfprintf(stdout, "No further action for virtual dataset\n");
+	    goto done;
+
+        case H5D_NLAYOUTS:
+        case H5D_LAYOUT_ERROR:
+	default:
+	    error_msg("unknown layout type for \"%s\"\n", dname);
+	    h5tools_setstatus(EXIT_FAILURE);
+	    goto error;
+
+    } /* end switch */
+
+    /* No further action if it is a noop */
+    if(noop_g) {
+	if(verbose_g)
+	    HDfprintf(stdout, "Not converting the dataset\n");
+	h5tools_setstatus(EXIT_SUCCESS);
+	goto done;
+    }
+
+    if(verbose_g)
+	HDfprintf(stdout, "Converting the dataset...\n");
+
+    /* Downgrade the dataset */
+    if(H5Dformat_convert(did) < 0) {
+	error_msg("unable to downgrade dataset \"%s\"\n", dname);
+	h5tools_setstatus(EXIT_FAILURE);
+	goto error;
+    } else if(verbose_g)
+	HDfprintf(stdout, "Done\n");
+
+done:
+    /* Close the dataset */
+    if(H5Dclose(did) < 0) {
+        error_msg("unable to close dataset \"%s\"\n", dname);
+        h5tools_setstatus(EXIT_FAILURE);
+	goto error;
+    } else if(verbose_g)
+	HDfprintf(stdout, "Close the dataset\n");
+    
+    /* Close the dataset creation property list */
+    if(H5Pclose(dcpl) < 0) {
+        error_msg("unable to close dataset creation property list\n");
+        h5tools_setstatus(EXIT_FAILURE);
+	goto error;
+    } else if(verbose_g)
+	printf("Close the dataset creation property list\n");
+
+    return(0);
+
+error:
+    if(verbose_g)
+	HDfprintf(stdout, "Error encountered\n");
+
+    H5E_BEGIN_TRY {
+        H5Pclose(dcpl);
+        H5Dclose(did);
+    } H5E_END_TRY;
+
+    return(-1);
+} /* convert() */
+
+/*-------------------------------------------------------------------------
+ * Function: convert_dsets_cb()
+ *
+ * Purpose:  The callback routine from the traversal to convert the
+ *	     chunk indexing type of the dataset object.
+ *
+ * Return: Success: 0
+ *  	   Failure: 1
+ *-------------------------------------------------------------------------
+ */
+static int
+convert_dsets_cb(const char *path, const H5O_info_t *oi, const char *already_visited, void *_fid)
+{
+    hid_t fid = *(hid_t *)_fid;
+
+    /* If the object has already been seen then just return */
+    if(NULL == already_visited) {
+        if(oi->type == H5O_TYPE_DATASET) {
+	    if(verbose_g)
+		HDfprintf(stdout, "Going to process dataset:%s...\n", path);
+	    if(convert(fid, path) < 0)
+		goto error;
+	} /* end if */
+    } /* end if */
+
+    return 0;
+
+error:
+    return -1;
+} /* end convert_dsets_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: To convert the chunk indexing type of a dataset in a file to
+ *	    version 1 B-tree.
+ *
+ * Return: Success: 0
+ *  	   Failure: 1
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, const char *argv[])
+{
+    H5E_auto2_t func;
+    void *edata;
+    hid_t fid = -1;
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
+    /* Disable error reporting */
+    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /* Initialize h5tools lib */
+    h5tools_init();
+
+    /* Parse command line options */
+    if(parse_command_line(argc, argv) < 0)
+	goto done;
+    else if(verbose_g)
+	HDfprintf(stdout, "Process command line options\n");
+
+    if(noop_g && verbose_g)
+	HDfprintf(stdout, "It is noop...\n");
+
+    /* Open the HDF5 file */
+    if((fid = h5tools_fopen(fname_g, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0)) < 0) {
+	error_msg("unable to open file \"%s\"\n", fname_g);
+	h5tools_setstatus(EXIT_FAILURE);
+	goto done;
+    } else if(verbose_g)
+	HDfprintf(stdout, "Open the file %s\n", fname_g);
+
+    if(dset_g) { /* Convert a specified dataset in the file */
+	if(verbose_g)
+	    HDfprintf(stdout, "Going to process dataset: %s...\n", dname_g);
+	if(convert(fid, dname_g) < 0)
+	    goto done;
+    } else { /* Convert all datasets in the file */
+	if(verbose_g)
+	    HDfprintf(stdout, "Processing all datasets in the file...\n");
+	if(h5trav_visit(fid, "/", TRUE, TRUE, convert_dsets_cb, NULL, &fid) < 0)
+	    goto done;
+    } /* end else */
+
+    if(verbose_g) {
+        if(noop_g) {
+            HDfprintf(stdout, "Not processing the file's superblock...\n");
+            h5tools_setstatus(EXIT_SUCCESS);
+            goto done;
+        } /* end if */
+        HDfprintf(stdout, "Processing the file's superblock...\n");
+    } /* end if */
+
+    /* Process superblock */
+    if(H5Fformat_convert(fid) < 0) {
+        error_msg("unable to convert file's superblock\"%s\"\n", fname_g);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    } /* end if */
+
+done:
+    /* Close the file */
+    if(fid >= 0) {
+	if(H5Fclose(fid) < 0) {
+	    error_msg("unable to close file \"%s\"\n", fname_g);
+	    h5tools_setstatus(EXIT_FAILURE);
+	} else if(verbose_g)
+	    HDfprintf(stdout, "Close the file\n");
+    }  /* end if */
+
+    if(fname_g)
+	HDfree(fname_g);
+    if(dname_g)
+	HDfree(dname_g);
+    
+    H5Eset_auto2(H5E_DEFAULT, func, edata);
+    leave(h5tools_getstatus());
+
+} /* end main() */
+