diff options
Diffstat (limited to 'tools')
24 files changed, 829 insertions, 218 deletions
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c index 6b75aa3..531cdcd 100644 --- a/tools/h5dump/h5dumpgentest.c +++ b/tools/h5dump/h5dumpgentest.c @@ -35,6 +35,7 @@ #define FILE2 "tdset.h5" #define FILE3 "tattr.h5" #define FILE4 "tslink.h5" +#define FILE4_1 "tsoftlinks.h5" #define FILE5 "thlink.h5" #define FILE6 "tcompound.h5" #define FILE7 "tall.h5" @@ -94,7 +95,7 @@ #define FILE61 "textlinksrc.h5" #define FILE62 "textlinktar.h5" #define FILE63 "textlinkfar.h5" -#define FILE64 "tarray8.h5" +/*#define FILE64 "tarray8.h5"*/ #define FILE65 "tattrreg.h5" #define FILE66 "file_space.h5" @@ -213,7 +214,8 @@ typedef struct s1_t { #define ARRAY3_DIM2 3 /* VL string datatype name */ -#define VLSTR_TYPE "vl_string_type" +/* TODO remove complier error not used, remove the link when everything is OK */ +/* #define VLSTR_TYPE "vl_string_type" */ /* "File 41" macros */ /* Name of dataset to create in datafile */ @@ -466,6 +468,246 @@ static void gent_softlink(void) H5Fclose(fid); } +/*------------------------------------------------------------------------- + * Function: gent_softlink2 + * + * Purpose: Create soft links to various objects. + * Return: + * SUCCEED + * FAIL + * Programmer: Jonathan Kim + * Date: May 26, 2010 + *-------------------------------------------------------------------------*/ +#define NX 4 +#define NY 2 +static int gent_softlink2(void) +{ + hid_t fileid1; + hid_t grp1=0, grp2=0; + hid_t tid; + hid_t dset1, dset2; + hid_t datatype, dataspace; + hsize_t dimsf[2]; /* dataset dimensions */ + herr_t status=SUCCEED; + int data1[NX][NY] = {{0,0},{1,1},{2,2},{3,3}}; + int data2[NX][NY] = {{0,0},{0,1},{0,2},{3,3}}; + + /*----------------------------------------------------------------------- + * FILE + *------------------------------------------------------------------------*/ + /* Create a new file */ + fileid1 = H5Fcreate(FILE4_1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + if (fileid1 < 0) + { + fprintf(stderr, "Error: %s> H5Fcreate failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /*----------------------------------------------------------------------- + * Groups + *------------------------------------------------------------------------*/ + grp1 = H5Gcreate2(fileid1, "group1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (grp1 < 0) + { + fprintf(stderr, "Error: %s> H5Gcreate2 failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + grp2 = H5Gcreate2(fileid1, "group_empty", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (grp2 < 0) + { + fprintf(stderr, "Error: %s> H5Gcreate2 failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /*----------------------------------------------------------------------- + * Named datatype + *------------------------------------------------------------------------*/ + tid = H5Tcopy(H5T_NATIVE_INT); + status = H5Tcommit2(fileid1, "dtype", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Tcommit2 failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /*----------------------------------------------------------------------- + * Datasets + *------------------------------------------------------------------------*/ + /* + * Describe the size of the array and create the data space for fixed + * size dataset. + */ + dimsf[0] = NX; + dimsf[1] = NY; + dataspace = H5Screate_simple(2, dimsf, NULL); + + /* + * Define datatype for the data in the file. + * We will store little endian INT numbers. + */ + datatype = H5Tcopy(H5T_NATIVE_INT); + + /*--------------- + * dset1 + */ + /* Create a new dataset as sample object */ + dset1 = H5Dcreate2(fileid1, "/dset1", datatype, dataspace, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (dset1 < 0) + { + fprintf(stderr, "Error: %s> H5Dcreate2 failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + status = H5Dwrite(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data1); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Dwrite failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /*--------------- + * dset2 + */ + /* Create a new dataset as sample object */ + dset2 = H5Dcreate2(fileid1, "/dset2", datatype, dataspace, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (dset2 < 0) + { + fprintf(stderr, "Error: %s> H5Dcreate2 failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + status = H5Dwrite(dset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data2); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Dwrite failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /*----------------------------------------------------------------------- + * Soft links + *------------------------------------------------------------------------*/ + /* + * create various soft links under '/' root + */ + /* link to dset1 */ + status = H5Lcreate_soft("/dset1", fileid1, "soft_dset1", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* link to data type */ + status = H5Lcreate_soft("/dtype", fileid1, "soft_dtype", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* link to group1 */ + status = H5Lcreate_soft("/group1", fileid1, "soft_group1", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* link to empty group */ + status = H5Lcreate_soft("/group_empty", fileid1, "soft_empty_grp", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* dangling link */ + status = H5Lcreate_soft("not_yet", fileid1, "soft_dangle", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /*----------------------------------------- + * create various soft links under a group + */ + /* link to dset1 */ + status = H5Lcreate_soft("/dset1", grp1, "soft_dset1", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* link to dset2 */ + status = H5Lcreate_soft("/dset2", grp1, "soft_dset2", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* link to data type */ + status = H5Lcreate_soft("/dtype", grp1, "soft_dtype", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* link to empty group */ + status = H5Lcreate_soft("/group_empty", grp1, "soft_empty_grp", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + + /* dangling link */ + status = H5Lcreate_soft("not_yet", grp1, "soft_dangle", H5P_DEFAULT, H5P_DEFAULT); + if (status < 0) + { + fprintf(stderr, "Error: %s> H5Lcreate_soft failed.\n", FILE4_1); + status = FAIL; + goto out; + } + +out: + /* + * Close/release resources. + */ + H5Sclose(dataspace); + H5Gclose(grp1); + H5Gclose(grp2); + H5Tclose(datatype); + H5Dclose(dset1); + H5Dclose(dset2); + H5Fclose(fileid1); + + return status; +} + /* / @@ -1661,7 +1903,7 @@ static void gent_objref(void) hid_t sid1; /* Dataspace ID */ hid_t tid1; /* Datatype ID */ hsize_t dims1[] = {SPACE1_DIM1}; - hobj_ref_t *wbuf, /* buffer to write to disk */ + hobj_ref_t *wbuf, /* buffer to write to disk */ *rbuf, /* buffer read from disk */ *tbuf; /* temp. buffer read from disk */ uint32_t *tu32; /* Temporary pointer to uint32 data */ @@ -1669,9 +1911,9 @@ static void gent_objref(void) const char *write_comment = "Foo!"; /* Comments for group */ /* Allocate write & read buffers */ - wbuf = malloc(sizeof(hobj_ref_t) * SPACE1_DIM1); - rbuf = malloc(sizeof(hobj_ref_t) * SPACE1_DIM1); - tbuf = malloc(sizeof(hobj_ref_t) * SPACE1_DIM1); + wbuf = (hobj_ref_t*) malloc(sizeof(hobj_ref_t) * SPACE1_DIM1); + rbuf = (hobj_ref_t*) malloc(sizeof(hobj_ref_t) * SPACE1_DIM1); + tbuf = (hobj_ref_t*) malloc(sizeof(hobj_ref_t) * SPACE1_DIM1); /* Create file */ fid1 = H5Fcreate(FILE16, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); @@ -1779,10 +2021,10 @@ static void gent_datareg(void) int i; /* counting variables */ /* Allocate write & read buffers */ - wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1); - rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1); - dwbuf=malloc(sizeof(uint8_t)*SPACE2_DIM1*SPACE2_DIM2); - drbuf=calloc(sizeof(uint8_t),SPACE2_DIM1*SPACE2_DIM2); + wbuf = (hdset_reg_ref_t*) calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1); + rbuf = (hdset_reg_ref_t*) malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1); + dwbuf = (uint8_t*) malloc(sizeof(uint8_t)*SPACE2_DIM1*SPACE2_DIM2); + drbuf = (uint8_t*) calloc(sizeof(uint8_t),SPACE2_DIM1*SPACE2_DIM2); /* Create file */ fid1 = H5Fcreate(FILE17, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); @@ -1888,10 +2130,10 @@ static void gent_attrreg(void) int i; /* counting variables */ /* Allocate write & read buffers */ - wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1); - rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1); - dwbuf=malloc(sizeof(uint8_t)*SPACE2_DIM1*SPACE2_DIM2); - drbuf=calloc(sizeof(uint8_t),SPACE2_DIM1*SPACE2_DIM2); + wbuf = (hdset_reg_ref_t*) calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1); + rbuf = (hdset_reg_ref_t*) malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1); + dwbuf = (uint8_t*) malloc(sizeof(uint8_t)*SPACE2_DIM1*SPACE2_DIM2); + drbuf = (uint8_t*) calloc(sizeof(uint8_t),SPACE2_DIM1*SPACE2_DIM2); /* Create file */ fid1 = H5Fcreate(FILE65, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); @@ -2961,7 +3203,7 @@ static void gent_array8(void) hsize_t sdims[] = {F64_DIM0}; hsize_t tdims[] = {F64_DIM1}; int wdata[(F64_DIM1) * sizeof(int)]; /* Write buffer */ - int i; + unsigned int i; /* * Initialize data. i is the element in the dataspace, j and k the @@ -5655,7 +5897,7 @@ static void gent_longlinks(void) assert(gid >= 0); /* Construct very long file name */ - objname = HDmalloc((size_t)(F51_MAX_NAME_LEN + 1)); + objname = (char*) HDmalloc((size_t)(F51_MAX_NAME_LEN + 1)); assert(objname); for(u = 0; u < F51_MAX_NAME_LEN; u++) objname[u] = 'a'; @@ -5919,7 +6161,7 @@ gent_hyperslab(void) double *buf; int i, ret; - buf = malloc(32 * 4097 * sizeof(double) ); + buf = (double*) malloc(32 * 4097 * sizeof(double) ); for(i = 0; i < 32 * 4097; i++) buf[i] = 1; @@ -6526,6 +6768,7 @@ int main(void) gent_group(); gent_attribute(); gent_softlink(); + gent_softlink2(); gent_dataset(); gent_hardlink(); gent_extlink(); diff --git a/tools/h5ls/CMakeLists.txt b/tools/h5ls/CMakeLists.txt index 840f80e..fe9f927 100644 --- a/tools/h5ls/CMakeLists.txt +++ b/tools/h5ls/CMakeLists.txt @@ -43,6 +43,16 @@ IF (BUILD_TESTING) textlinksrc-5.ls textlinksrc-6.ls textlinksrc-7.ls + textlinksrc-1-old.ls + textlinksrc-2-old.ls + textlinksrc-3-old.ls + textlinksrc-6-old.ls + textlinksrc-7-old.ls + tsoftlinks-1.ls + tsoftlinks-2.ls + tsoftlinks-3.ls + tsoftlinks-4.ls + tsoftlinks-5.ls tgroup.ls tgroup-1.ls tgroup-2.ls @@ -75,6 +85,7 @@ IF (BUILD_TESTING) tnestedcomp.h5 tsaf.h5 tslink.h5 + tsoftlinks.h5 tstr.h5 tudlink.h5 tvldtypes1.h5 @@ -116,39 +127,93 @@ IF (BUILD_TESTING) ) ENDMACRO (ADD_H5_TEST file) + # test the help syntax ADD_H5_TEST (help-1 0 -w80 -h) ADD_H5_TEST (help-2 0 -w80 --help) ADD_H5_TEST (help-3 0 -w80 -?) + + # test simple command ADD_H5_TEST (tall-1 0 -w80 tall.h5) ADD_H5_TEST (tall-2 0 -w80 -r -d tall.h5) ADD_H5_TEST (tgroup 0 -w80 tgroup.h5) ADD_H5_TEST (tgroup-3 0 -w80 tgroup.h5/g1) + + # test for displaying groups + # The following combination of arguments is expected to return an error message + # and return value 1 ADD_H5_TEST (tgroup-1 1 -w80 -r -g tgroup.h5) ADD_H5_TEST (tgroup-2 0 -w80 -g tgroup.h5/g1) + + # test for displaying simple space datasets ADD_H5_TEST (tdset-1 0 -w80 -r -d tdset.h5) + + # test for displaying soft links (dangle) ADD_H5_TEST (tslink-1 0 -w80 -r tslink.h5) + + # test for displaying more soft links with --follow-symlinks + ADD_H5_TEST (tsoftlinks-1 0 --follow-symlinks tsoftlinks.h5) + ADD_H5_TEST (tsoftlinks-2 0 --follow-symlinks -r tsoftlinks.h5) + ADD_H5_TEST (tsoftlinks-3 0 --follow-symlinks tsoftlinks.h5/group1) + ADD_H5_TEST (tsoftlinks-4 0 --follow-symlinks -r tsoftlinks.h5/group1) + ADD_H5_TEST (tsoftlinks-5 0 --follow-symlinks tsoftlinks.h5/soft_dset1) + + # test for displaying external and user-defined links with --follow-symlinks ADD_H5_TEST (textlink-1 0 -w80 -r textlink.h5) - ADD_H5_TEST (textlinksrc-1 0 -w80 -Er textlinksrc.h5) - ADD_H5_TEST (textlinksrc-2 0 -w80 -Erv textlinksrc.h5/ext_link5) - ADD_H5_TEST (textlinksrc-3 0 -w80 -Er textlinksrc.h5/ext_link1) + ADD_H5_TEST (textlinksrc-1 0 -w80 --follow-symlinks -r textlinksrc.h5) + ADD_H5_TEST (textlinksrc-2 0 -w80 --follow-symlinks -rv textlinksrc.h5/ext_link5) + ADD_H5_TEST (textlinksrc-3 0 -w80 --follow-symlinks -r textlinksrc.h5/ext_link1) ADD_H5_TEST (textlinksrc-4 0 -w80 -r textlinksrc.h5) ADD_H5_TEST (textlinksrc-5 0 -w80 -r textlinksrc.h5/ext_link1) - ADD_H5_TEST (textlinksrc-6 0 -w80 -E textlinksrc.h5) - ADD_H5_TEST (textlinksrc-7 0 -w80 -E textlinksrc.h5/ext_link1) + ADD_H5_TEST (textlinksrc-6 0 -w80 --follow-symlinks textlinksrc.h5) + ADD_H5_TEST (textlinksrc-7 0 -w80 --follow-symlinks textlinksrc.h5/ext_link1) ADD_H5_TEST (tudlink-1 0 -w80 -r tudlink.h5) + + # test for displaying external links with -E + # the option -E will be depriciated but keep it for backward compatibility + ADD_H5_TEST (textlinksrc-1-old 0 -w80 -Er textlinksrc.h5) + ADD_H5_TEST (textlinksrc-2-old 0 -w80 -Erv textlinksrc.h5/ext_link5) + ADD_H5_TEST (textlinksrc-3-old 0 -w80 -Er textlinksrc.h5/ext_link1) + ADD_H5_TEST (textlinksrc-6-old 0 -w80 -E textlinksrc.h5) + ADD_H5_TEST (textlinksrc-7-old 0 -w80 -E textlinksrc.h5/ext_link1) + + # tests for hard links ADD_H5_TEST (thlink-1 0 -w80 thlink.h5) + + # tests for compound data types ADD_H5_TEST (tcomp-1 0 -w80 -r -d tcompound.h5) + + #test for the nested compound type ADD_H5_TEST (tnestcomp-1 0 -w80 -r -d tnestedcomp.h5) + + # test for loop detection ADD_H5_TEST (tloop-1 0 -w80 -r -d tloop.h5) + + # test for string ADD_H5_TEST (tstr-1 0 -w80 -r -d tstr.h5) + + # test test file created from lib SAF team ADD_H5_TEST (tsaf 0 -w80 -r -d tsaf.h5) + + # test for variable length data types ADD_H5_TEST (tvldtypes1 0 -w80 -r -d tvldtypes1.h5) + + # test for array data types ADD_H5_TEST (tarray1 0 -w80 -r -d tarray1.h5) + + # test for empty data ADD_H5_TEST (tempty 0 -w80 -d tempty.h5) + + # test for all dataset types written to attributes + # enable -S for avoiding printing NATIVE types ADD_H5_TEST (tattr2 0 -w80 -v -S tattr2.h5) + + # test for non-existing file ADD_H5_TEST (nosuchfile 1 nosuchfile.h5) + IF (WORDS_BIGENDIAN) + # test for variable length data types in verbose mode ADD_H5_TEST (tvldtypes2be 0 -v tvldtypes1.h5) + # test for dataset region references data types in verbose mode ADD_H5_TEST (tdataregbe 0 -v tdatareg.h5) ELSE (WORDS_BIGENDIAN) ADD_H5_TEST (tvldtypes2le 0 -v tvldtypes1.h5) diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c index c856642..835af10 100644 --- a/tools/h5ls/h5ls.c +++ b/tools/h5ls/h5ls.c @@ -34,23 +34,24 @@ #define NAME_BUF_SIZE 2048 -/* Struct to keep track of external link targets visited */ -typedef struct elink_trav_t { +/* Struct to keep track of symbolic link targets visited */ +typedef struct symlink_trav_t { size_t nalloc; size_t nused; struct { + H5L_type_t type; char *file; char *path; } *objs; -} elink_trav_t; +} symlink_trav_t; /* Struct to pass through to visitors */ typedef struct { const char *fname; /* Filename */ hid_t fid; /* File ID */ hid_t gid; /* Group ID */ - hbool_t ext_target; /* Whether this is the target of an external link */ - elink_trav_t *elink_list; /* List of visited external links */ + hbool_t symlink_target; /* Whether this is the target of an symbolic link */ + symlink_trav_t *symlink_list; /* List of visited symbolic links */ int base_len; /* Length of base path name, if not root */ int name_start; /* # of leading characters to strip off path names on output */ }iter_t; @@ -64,6 +65,7 @@ static hbool_t label_g = FALSE; /* label compound values? */ static hbool_t string_g = FALSE; /* print 1-byte numbers as ASCII? */ static hbool_t fullname_g = FALSE; /* print full path names */ static hbool_t recursive_g = FALSE; /* recursive descent listing */ +static hbool_t follow_symlink_g = FALSE; /* follow symbolic links */ static hbool_t follow_elink_g = FALSE; /* follow external links */ static hbool_t grp_literal_g = FALSE; /* list group, not contents */ static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */ @@ -111,30 +113,46 @@ usage (void) { fprintf(stderr, "\ usage: %s [OPTIONS] [OBJECTS...]\n\ - OPTIONS\n\ - -h, -?, --help Print a usage message and exit\n\ - -a, --address Print addresses for raw data\n\ - -d, --data Print the values of datasets\n\ - -e, --errors Show all HDF5 error reporting\n\ - -E, --external Allow traversal into external files\n\ - -f, --full Print full path names instead of base names\n\ - -g, --group Show information about a group, not its contents\n\ - -l, --label Label members of compound datasets\n\ - -r, --recursive List all groups recursively, avoiding cycles\n\ - -s, --string Print 1-byte integer datasets as ASCII\n\ - -S, --simple Use a machine-readable output format\n\ - -wN, --width=N Set the number of columns of output\n\ - -v, --verbose Generate more verbose output\n\ - -V, --version Print version number and exit\n\ - --vfd=DRIVER Use the specified virtual file driver\n\ - -x, --hexdump Show raw data in hexadecimal format\n\ + OPTIONS\n\ + -h, -?, --help Print a usage message and exit\n\ + -a, --address Print addresses for raw data\n\ + -d, --data Print the values of datasets\n\ + -e, --errors Show all HDF5 error reporting\n\ + --follow-symlinks Follow symbolic links (soft links and external links)\n\ + to display target object information.\n\ + Without this option, h5ls identifies a symbolic link\n\ + as a soft link or external link and prints the value\n\ + assigned to the symbolic link; it does not provide any\n\ + information regarding the target object or determine\n\ + whether the link is a dangling link.\n\ + -f, --full Print full path names instead of base names\n\ + -g, --group Show information about a group, not its contents\n\ + -l, --label Label members of compound datasets\n\ + -r, --recursive List all groups recursively, avoiding cycles\n\ + -s, --string Print 1-byte integer datasets as ASCII\n\ + -S, --simple Use a machine-readable output format\n\ + -wN, --width=N Set the number of columns of output\n\ + -v, --verbose Generate more verbose output\n\ + -V, --version Print version number and exit\n\ + --vfd=DRIVER Use the specified virtual file driver\n\ + -x, --hexdump Show raw data in hexadecimal format\n\ \n\ - OBJECTS\n\ - Each object consists of an HDF5 file name optionally followed by a\n\ - slash and an object name within the file (if no object is specified\n\ - within the file then the contents of the root group are displayed).\n\ - The file name may include a printf(3C) integer format such as\n\ - \"%%05d\" to open a file family.\n", + OBJECTS\n\ + Each object consists of an HDF5 file name optionally followed by a\n\ + slash and an object name within the file (if no object is specified\n\ + within the file then the contents of the root group are displayed).\n\ + The file name may include a printf(3C) integer format such as\n\ + \"%%05d\" to open a file family.\n\ +\n\ + Deprecated Options\n\ + The following options have been deprecated in HDF5. While they remain\n\ + available, they have been superseded as indicated and may be removed\n\ + from HDF5 in the future. Use the indicated replacement option in all\n\ + new work; where possible, existing scripts, et cetera, should also be\n\ + updated to use the replacement option.\n\ +\n\ + -E or --external Follow external links.\n\ + Replaced by --follow-symlinks.\n", h5tools_getprogname()); } @@ -469,6 +487,9 @@ display_precision(hid_t type, int ind) case H5T_NPAD: plsb_s = "unknown"; break; + default: + ; + break; } } if (H5Tget_offset(type)+prec<8*H5Tget_size(type)) { @@ -486,6 +507,9 @@ display_precision(hid_t type, int ind) case H5T_NPAD: pmsb_s = "unknown"; break; + default: + ; + break; } } if (plsb_s || pmsb_s) { @@ -646,6 +670,9 @@ display_float_type(hid_t type, int ind) case H5T_NORM_ERROR: norm_s = ", unknown normalization"; break; + default: + ; + break; } printf("\n%*s(significant for %lu bit%s at bit %lu%s)", ind, "", (unsigned long)msize, 1==msize?"":"s", (unsigned long)mpos, @@ -672,6 +699,9 @@ display_float_type(hid_t type, int ind) case H5T_NPAD: pad_s = "unknown"; break; + default: + ; + break; } printf("\n%*s(internal padding bits are %s)", ind, "", pad_s); } @@ -786,7 +816,7 @@ display_enum_type(hid_t type, int ind) /* Get the names and raw values of all members */ name = calloc(nmembs, sizeof(char*)); - value = calloc(nmembs, MAX(H5Tget_size(type), dst_size)); + value = (unsigned char *)calloc(nmembs, MAX(H5Tget_size(type), dst_size)); for (i=0; i<nmembs; i++) { name[i] = H5Tget_member_name(type, i); H5Tget_member_value(type, i, value+i*H5Tget_size(type)); @@ -889,6 +919,9 @@ display_string_type(hid_t type, int UNUSED ind) case H5T_STR_ERROR: pad_s = "unknown-format"; break; + default: + ; + break; } /* Character set */ @@ -917,6 +950,9 @@ display_string_type(hid_t type, int UNUSED ind) case H5T_CSET_ERROR: cset_s = "unknown-character-set"; break; + default: + ; + break; } if (H5Tis_variable_str(type)) { @@ -1054,7 +1090,7 @@ display_array_type(hid_t type, int ind) if (H5T_ARRAY!=H5Tget_class(type)) return FALSE; ndims = H5Tget_array_ndims(type); if (ndims) { - dims = malloc(ndims*sizeof(dims[0])); + dims = (hsize_t *)malloc(ndims*sizeof(dims[0])); H5Tget_array_dims2(type, dims); /* Print dimensions */ @@ -1701,7 +1737,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void iter_t *iter = (iter_t*)_iter; /* Print the link's name, either full name or base name */ - if(!iter->ext_target) + if(!iter->symlink_target) display_obj_name(stdout, iter, name, ""); /* Check object information */ @@ -1709,7 +1745,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void printf("Unknown type(%d)", (int)oinfo->type); obj_type = H5O_TYPE_UNKNOWN; } - if(iter->ext_target) + if(iter->symlink_target) fputc('{', stdout); if(obj_type >= 0 && dispatch_g[obj_type].name) fputs(dispatch_g[obj_type].name, stdout); @@ -1718,7 +1754,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void if(first_seen) { printf(", same as "); display_string(stdout, first_seen, TRUE); - if(!iter->ext_target) + if(!iter->symlink_target) printf("\n"); } /* end if */ else { @@ -1735,7 +1771,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void /* List the first line of information for the object. */ if(obj_type >= 0 && dispatch_g[obj_type].list1) (dispatch_g[obj_type].list1)(obj); - if(!iter->ext_target || (verbose_g > 0)) + if(!iter->symlink_target || (verbose_g > 0)) putchar('\n'); /* Show detailed information about the object, beginning with information @@ -1787,18 +1823,18 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void } /* end else */ done: - if(iter->ext_target) { + if(iter->symlink_target) { fputs("}\n", stdout); - iter->ext_target = FALSE; + iter->symlink_target = FALSE; } return 0; } /* end list_obj() */ /*------------------------------------------------------------------------- - * Function: elink_trav_add + * Function: symlink_visit_add * - * Purpose: Add an external link to visited data structure + * Purpose: Add an symbolic link to visited data structure * * Return: 0 on success, -1 on failure * @@ -1807,16 +1843,26 @@ done: * * Date: September 5, 2008 * + * Modified: + * Jonathan Kim + * - Renamed from elink_trav_add to symlink_visit_add for both soft and + * external links. (May 25, 2010) + * - Add type parameter to distingush between soft and external link for + * sure, which prevent from mixing up visited link when the target names + * are same between the soft and external link, as code marks with the + * target name. (May 25,2010) + * *------------------------------------------------------------------------- */ static herr_t -elink_trav_add(elink_trav_t *visited, const char *file, const char *path) +symlink_visit_add(symlink_trav_t *visited, H5L_type_t type, const char *file, const char *path) { size_t idx; /* Index of address to use */ void *tmp_ptr; /* Allocate space if necessary */ - if(visited->nused == visited->nalloc) { + if(visited->nused == visited->nalloc) + { visited->nalloc = MAX(1, visited->nalloc * 2); if(NULL == (tmp_ptr = HDrealloc(visited->objs, visited->nalloc * sizeof(visited->objs[0])))) return -1; @@ -1825,24 +1871,36 @@ elink_trav_add(elink_trav_t *visited, const char *file, const char *path) /* Append it */ idx = visited->nused++; - if(NULL == (visited->objs[idx].file = HDstrdup(file))) { - visited->nused--; - return -1; + + visited->objs[idx].type = type; + visited->objs[idx].file = NULL; + visited->objs[idx].path = NULL; + + if (type == H5L_TYPE_EXTERNAL) + { + if(NULL == (visited->objs[idx].file = HDstrdup(file))) + { + visited->nused--; + return -1; + } } - if(NULL == (visited->objs[idx].path = HDstrdup(path))) { + + if(NULL == (visited->objs[idx].path = HDstrdup(path))) + { visited->nused--; - HDfree (visited->objs[idx].file); + if (visited->objs[idx].file) + HDfree (visited->objs[idx].file); return -1; } return 0; -} /* end elink_trav_add() */ +} /* end symlink_visit_add() */ /*------------------------------------------------------------------------- - * Function: elink_trav_visited + * Function: symlink_is_visited * - * Purpose: Check if an external link has already been visited + * Purpose: Check if an symbolic link has already been visited * * Return: TRUE/FALSE * @@ -1851,22 +1909,41 @@ elink_trav_add(elink_trav_t *visited, const char *file, const char *path) * * Date: September 5, 2008 * + * Modified: + * Jonathan Kim + * - Renamed from elink_trav_visited to symlink_is_visited for both soft and + * external links. (May 25, 2010) + * - Add type parameter to distingush between soft and external link for + * sure, which prevent from mixing up visited link when the target names + * are same between the soft and external link, as code marks with the + * target name. (May 25,2010) + * *------------------------------------------------------------------------- */ static hbool_t -elink_trav_visited(elink_trav_t *visited, const char *file, const char *path) +symlink_is_visited(symlink_trav_t *visited, H5L_type_t type, const char *file, const char *path) { - size_t u; /* Local index variable */ + size_t u; /* Local index variable */ - /* Look for elink */ + /* Look for symlink */ for(u = 0; u < visited->nused; u++) - /* Check for elink value already in array */ - if(!HDstrcmp(visited->objs[u].file, file) && !HDstrcmp(visited->objs[u].path, path)) - return(TRUE); - - /* Didn't find elink */ + { + /* Check for symlink values already in array */ + /* check type and path pair to distingush between symbolic links */ + if ((visited->objs[u].type == type) && !HDstrcmp(visited->objs[u].path, path)) + { + /* if external link, file need to be matched as well */ + if (visited->objs[u].type == H5L_TYPE_EXTERNAL) + { + if (!HDstrcmp(visited->objs[u].file, file)) + return (TRUE); + } + return (TRUE); + } + } + /* Didn't find symlink */ return(FALSE); -} /* end elink_trav_visited() */ +} /* end symlink_is_visited() */ /*------------------------------------------------------------------------- @@ -1886,7 +1963,7 @@ elink_trav_visited(elink_trav_t *visited, const char *file, const char *path) static herr_t list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) { - char *buf; + char *buf=NULL; iter_t *iter = (iter_t*)_iter; /* Print the link's name, either full name or base name */ @@ -1894,18 +1971,52 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) switch(linfo->type) { case H5L_TYPE_SOFT: - if((buf = HDmalloc(linfo->u.val_size)) == NULL) + if((buf = (char*)HDmalloc(linfo->u.val_size)) == NULL) goto done; if(H5Lget_val(iter->fid, name, buf, linfo->u.val_size, H5P_DEFAULT) < 0) { - HDfree(buf); goto done; } /* end if */ HDfputs("Soft Link {", stdout); HDfputs(buf, stdout); - HDfree(buf); - HDfputs("}\n", stdout); + HDfputc('}', stdout); + if(follow_symlink_g) + { + hbool_t orig_grp_literal = grp_literal_g; + HDfputc(' ', stdout); + + /* Check if we have already seen this softlink */ + if(symlink_is_visited(iter->symlink_list, linfo->type, NULL, buf)) + { + HDfputs("{Already Visited}\n", stdout); + goto done; + } + + /* Add this link to the list of seen softlinks */ + if(symlink_visit_add(iter->symlink_list, linfo->type, NULL, buf) < 0) + goto done; + + /* Adjust user data to specify that we are operating on the + * target of an soft link */ + iter->symlink_target = TRUE; + + /* Prevent recursive listing of soft link target if + * recursive_g is off */ + if(!recursive_g) + grp_literal_g = TRUE; + /* Recurse through the soft link */ + if(visit_obj(iter->fid, name, iter) < 0) + { + grp_literal_g = orig_grp_literal; + goto done; + } + + grp_literal_g = orig_grp_literal; + } + else + HDfputc('\n', stdout); + break; case H5L_TYPE_EXTERNAL: @@ -1913,16 +2024,13 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) const char *filename; const char *path; - if((buf = HDmalloc(linfo->u.val_size)) == NULL) + if((buf = (char*)HDmalloc(linfo->u.val_size)) == NULL) goto done; - if(H5Lget_val(iter->fid, name, buf, linfo->u.val_size, H5P_DEFAULT) < 0) { - HDfree(buf); + if(H5Lget_val(iter->fid, name, buf, linfo->u.val_size, H5P_DEFAULT) < 0) goto done; - } /* end if */ - if(H5Lunpack_elink_val(buf, linfo->u.val_size, NULL, &filename, &path) < 0) { - HDfree(buf); + + if(H5Lunpack_elink_val(buf, linfo->u.val_size, NULL, &filename, &path) < 0) goto done; - } /* end if */ HDfputs("External Link {", stdout); HDfputs(filename, stdout); @@ -1933,27 +2041,28 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) HDfputc('}', stdout); /* Recurse through the external link */ - if(follow_elink_g) { + /* keep the follow_elink_g for backward compatibility with -E */ + if(follow_symlink_g || follow_elink_g) + { hbool_t orig_grp_literal = grp_literal_g; - HDfputc(' ', stdout); /* Check if we have already seen this elink */ - if(elink_trav_visited(iter->elink_list, filename, path)) { + if(symlink_is_visited(iter->symlink_list, linfo->type, filename, path)) + { HDfputs("{Already Visited}\n", stdout); - HDfree(buf); goto done; } /* Add this link to the list of seen elinks */ - if(elink_trav_add(iter->elink_list, filename, path) < 0) { - HDfree(buf); + if(symlink_visit_add(iter->symlink_list, linfo->type, filename, path) < 0) + { goto done; } /* Adjust user data to specify that we are operating on the * target of an external link */ - iter->ext_target = TRUE; + iter->symlink_target = TRUE; /* Prevent recursive listing of external link target if * recursive_g is off */ @@ -1962,7 +2071,6 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) /* Recurse through the external link */ if(visit_obj(iter->fid, name, iter) < 0) { - HDfree(buf); grp_literal_g = orig_grp_literal; goto done; } @@ -1972,7 +2080,6 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) else HDfputc('\n', stdout); - HDfree(buf); } break; @@ -1982,6 +2089,8 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter) } /* end switch */ done: + if (buf) + HDfree(buf); return 0; } /* end list_lnk() */ @@ -2008,9 +2117,9 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) /* Retrieve info for object to list */ if(H5Oget_info_by_name(file, oname, &oi, H5P_DEFAULT) < 0) { - if(iter->ext_target) { + if(iter->symlink_target) { HDfputs("{**NOT FOUND**}\n", stdout); - iter->ext_target = FALSE; + iter->symlink_target = FALSE; } else display_obj_name(stdout, iter, oname, "**NOT FOUND**"); @@ -2020,7 +2129,7 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) /* Check for group iteration */ if(H5O_TYPE_GROUP == oi.type && !grp_literal_g) { /* Get ID for group */ - if(!iter->ext_target && (iter->gid = H5Gopen2(file, oname, H5P_DEFAULT)) < 0) { + if(!iter->symlink_target && (iter->gid = H5Gopen2(file, oname, H5P_DEFAULT)) < 0) { fprintf(stderr, "%s: unable to open '%s' as group\n", iter->fname, oname); return 0; /* Previously "continue", when this code was in main(). * We don't "continue" here in order to close the file @@ -2032,10 +2141,10 @@ visit_obj(hid_t file, const char *oname, iter_t *iter) iter->name_start = iter->base_len; /* Specified name is a group. List the complete contents of the group. */ - h5trav_visit(file, oname, (hbool_t) (display_root_g || iter->ext_target), recursive_g, list_obj, list_lnk, iter); + h5trav_visit(file, oname, (hbool_t) (display_root_g || iter->symlink_target), recursive_g, list_obj, list_lnk, iter); /* Close group */ - if(!iter->ext_target) + if(!iter->symlink_target) H5Gclose(iter->gid); } /* end if */ else { @@ -2211,6 +2320,8 @@ main(int argc, const char *argv[]) data_g = TRUE; } else if(!HDstrcmp(argv[argno], "--errors")) { show_errors_g = TRUE; + } else if(!HDstrcmp(argv[argno], "--follow-symlinks")) { + follow_symlink_g = TRUE; } else if(!HDstrcmp(argv[argno], "--external")) { follow_elink_g = TRUE; } else if(!HDstrcmp(argv[argno], "--full")) { @@ -2381,7 +2492,7 @@ main(int argc, const char *argv[]) while(argno < argc) { H5L_info_t li; iter_t iter; - elink_trav_t elink_list; + symlink_trav_t symlink_list; size_t u; fname = HDstrdup(argv[argno++]); @@ -2443,12 +2554,12 @@ main(int argc, const char *argv[]) iter.fname = fname; iter.fid = file; iter.gid = -1; - iter.ext_target = FALSE; - iter.elink_list = &elink_list; + iter.symlink_target = FALSE; + iter.symlink_list = &symlink_list; - /* Initialize list of visited external links */ - elink_list.nused = elink_list.nalloc = 0; - elink_list.objs = NULL; + /* Initialize list of visited symbolic links */ + symlink_list.nused = symlink_list.nalloc = 0; + symlink_list.objs = NULL; /* Check for root group as object name */ if(HDstrcmp(oname, root_name)) { @@ -2477,11 +2588,14 @@ main(int argc, const char *argv[]) if(x) HDfree(oname); - for(u=0; u < elink_list.nused; u++) { - HDfree(elink_list.objs[u].file); - HDfree(elink_list.objs[u].path); + for(u=0; u < symlink_list.nused; u++) + { + if (symlink_list.objs[u].type == H5L_TYPE_EXTERNAL) + HDfree(symlink_list.objs[u].file); + + HDfree(symlink_list.objs[u].path); } - HDfree(elink_list.objs); + HDfree(symlink_list.objs); } /* end while */ if (err_openfile) diff --git a/tools/h5ls/testh5ls.sh.in b/tools/h5ls/testh5ls.sh.in index 367e539..40dcaa4 100644 --- a/tools/h5ls/testh5ls.sh.in +++ b/tools/h5ls/testh5ls.sh.in @@ -129,17 +129,32 @@ TOOLTEST tdset-1.ls 0 -w80 -r -d tdset.h5 # test for displaying soft links TOOLTEST tslink-1.ls 0 -w80 -r tslink.h5 -# test for displaying external and user-defined links +# test for displaying more soft links with --follow-symlinks +TOOLTEST tsoftlinks-1.ls 0 --follow-symlinks tsoftlinks.h5 +TOOLTEST tsoftlinks-2.ls 0 --follow-symlinks -r tsoftlinks.h5 +TOOLTEST tsoftlinks-3.ls 0 --follow-symlinks tsoftlinks.h5/group1 +TOOLTEST tsoftlinks-4.ls 0 --follow-symlinks -r tsoftlinks.h5/group1 +TOOLTEST tsoftlinks-5.ls 0 --follow-symlinks tsoftlinks.h5/soft_dset1 + +# test for displaying external and user-defined links with --follow-symlinks TOOLTEST textlink-1.ls 0 -w80 -r textlink.h5 -TOOLTEST textlinksrc-1.ls 0 -w80 -Er textlinksrc.h5 -TOOLTEST textlinksrc-2.ls 0 -w80 -Erv textlinksrc.h5/ext_link5 -TOOLTEST textlinksrc-3.ls 0 -w80 -Er textlinksrc.h5/ext_link1 +TOOLTEST textlinksrc-1.ls 0 -w80 --follow-symlinks -r textlinksrc.h5 +TOOLTEST textlinksrc-2.ls 0 -w80 --follow-symlinks -rv textlinksrc.h5/ext_link5 +TOOLTEST textlinksrc-3.ls 0 -w80 --follow-symlinks -r textlinksrc.h5/ext_link1 TOOLTEST textlinksrc-4.ls 0 -w80 -r textlinksrc.h5 TOOLTEST textlinksrc-5.ls 0 -w80 -r textlinksrc.h5/ext_link1 -TOOLTEST textlinksrc-6.ls 0 -w80 -E textlinksrc.h5 -TOOLTEST textlinksrc-7.ls 0 -w80 -E textlinksrc.h5/ext_link1 +TOOLTEST textlinksrc-6.ls 0 -w80 --follow-symlinks textlinksrc.h5 +TOOLTEST textlinksrc-7.ls 0 -w80 --follow-symlinks textlinksrc.h5/ext_link1 TOOLTEST tudlink-1.ls 0 -w80 -r tudlink.h5 +# test for displaying external links with -E +# the option -E will be depriciated but keep it for backward compatibility +TOOLTEST textlinksrc-1-old.ls 0 -w80 -Er textlinksrc.h5 +TOOLTEST textlinksrc-2-old.ls 0 -w80 -Erv textlinksrc.h5/ext_link5 +TOOLTEST textlinksrc-3-old.ls 0 -w80 -Er textlinksrc.h5/ext_link1 +TOOLTEST textlinksrc-6-old.ls 0 -w80 -E textlinksrc.h5 +TOOLTEST textlinksrc-7-old.ls 0 -w80 -E textlinksrc.h5/ext_link1 + # tests for hard links TOOLTEST thlink-1.ls 0 -w80 thlink.h5 diff --git a/tools/testfiles/help-1.ls b/tools/testfiles/help-1.ls index 4c45570..1b5de0c 100644 --- a/tools/testfiles/help-1.ls +++ b/tools/testfiles/help-1.ls @@ -2,27 +2,43 @@ output for 'h5ls -w80 -h' ############################# usage: h5ls [OPTIONS] [OBJECTS...] - OPTIONS - -h, -?, --help Print a usage message and exit - -a, --address Print addresses for raw data - -d, --data Print the values of datasets - -e, --errors Show all HDF5 error reporting - -E, --external Allow traversal into external files - -f, --full Print full path names instead of base names - -g, --group Show information about a group, not its contents - -l, --label Label members of compound datasets - -r, --recursive List all groups recursively, avoiding cycles - -s, --string Print 1-byte integer datasets as ASCII - -S, --simple Use a machine-readable output format - -wN, --width=N Set the number of columns of output - -v, --verbose Generate more verbose output - -V, --version Print version number and exit - --vfd=DRIVER Use the specified virtual file driver - -x, --hexdump Show raw data in hexadecimal format + OPTIONS + -h, -?, --help Print a usage message and exit + -a, --address Print addresses for raw data + -d, --data Print the values of datasets + -e, --errors Show all HDF5 error reporting + --follow-symlinks Follow symbolic links (soft links and external links) + to display target object information. + Without this option, h5ls identifies a symbolic link + as a soft link or external link and prints the value + assigned to the symbolic link; it does not provide any + information regarding the target object or determine + whether the link is a dangling link. + -f, --full Print full path names instead of base names + -g, --group Show information about a group, not its contents + -l, --label Label members of compound datasets + -r, --recursive List all groups recursively, avoiding cycles + -s, --string Print 1-byte integer datasets as ASCII + -S, --simple Use a machine-readable output format + -wN, --width=N Set the number of columns of output + -v, --verbose Generate more verbose output + -V, --version Print version number and exit + --vfd=DRIVER Use the specified virtual file driver + -x, --hexdump Show raw data in hexadecimal format - OBJECTS - Each object consists of an HDF5 file name optionally followed by a - slash and an object name within the file (if no object is specified - within the file then the contents of the root group are displayed). - The file name may include a printf(3C) integer format such as - "%05d" to open a file family. + OBJECTS + Each object consists of an HDF5 file name optionally followed by a + slash and an object name within the file (if no object is specified + within the file then the contents of the root group are displayed). + The file name may include a printf(3C) integer format such as + "%05d" to open a file family. + + Deprecated Options + The following options have been deprecated in HDF5. While they remain + available, they have been superseded as indicated and may be removed + from HDF5 in the future. Use the indicated replacement option in all + new work; where possible, existing scripts, et cetera, should also be + updated to use the replacement option. + + -E or --external Follow external links. + Replaced by --follow-symlinks. diff --git a/tools/testfiles/help-2.ls b/tools/testfiles/help-2.ls index 522cb5a..6f7e75d 100644 --- a/tools/testfiles/help-2.ls +++ b/tools/testfiles/help-2.ls @@ -2,27 +2,43 @@ output for 'h5ls -w80 -help' ############################# usage: h5ls [OPTIONS] [OBJECTS...] - OPTIONS - -h, -?, --help Print a usage message and exit - -a, --address Print addresses for raw data - -d, --data Print the values of datasets - -e, --errors Show all HDF5 error reporting - -E, --external Allow traversal into external files - -f, --full Print full path names instead of base names - -g, --group Show information about a group, not its contents - -l, --label Label members of compound datasets - -r, --recursive List all groups recursively, avoiding cycles - -s, --string Print 1-byte integer datasets as ASCII - -S, --simple Use a machine-readable output format - -wN, --width=N Set the number of columns of output - -v, --verbose Generate more verbose output - -V, --version Print version number and exit - --vfd=DRIVER Use the specified virtual file driver - -x, --hexdump Show raw data in hexadecimal format + OPTIONS + -h, -?, --help Print a usage message and exit + -a, --address Print addresses for raw data + -d, --data Print the values of datasets + -e, --errors Show all HDF5 error reporting + --follow-symlinks Follow symbolic links (soft links and external links) + to display target object information. + Without this option, h5ls identifies a symbolic link + as a soft link or external link and prints the value + assigned to the symbolic link; it does not provide any + information regarding the target object or determine + whether the link is a dangling link. + -f, --full Print full path names instead of base names + -g, --group Show information about a group, not its contents + -l, --label Label members of compound datasets + -r, --recursive List all groups recursively, avoiding cycles + -s, --string Print 1-byte integer datasets as ASCII + -S, --simple Use a machine-readable output format + -wN, --width=N Set the number of columns of output + -v, --verbose Generate more verbose output + -V, --version Print version number and exit + --vfd=DRIVER Use the specified virtual file driver + -x, --hexdump Show raw data in hexadecimal format - OBJECTS - Each object consists of an HDF5 file name optionally followed by a - slash and an object name within the file (if no object is specified - within the file then the contents of the root group are displayed). - The file name may include a printf(3C) integer format such as - "%05d" to open a file family. + OBJECTS + Each object consists of an HDF5 file name optionally followed by a + slash and an object name within the file (if no object is specified + within the file then the contents of the root group are displayed). + The file name may include a printf(3C) integer format such as + "%05d" to open a file family. + + Deprecated Options + The following options have been deprecated in HDF5. While they remain + available, they have been superseded as indicated and may be removed + from HDF5 in the future. Use the indicated replacement option in all + new work; where possible, existing scripts, et cetera, should also be + updated to use the replacement option. + + -E or --external Follow external links. + Replaced by --follow-symlinks. diff --git a/tools/testfiles/help-3.ls b/tools/testfiles/help-3.ls index 22ad865..939c8eb 100644 --- a/tools/testfiles/help-3.ls +++ b/tools/testfiles/help-3.ls @@ -2,27 +2,43 @@ output for 'h5ls -w80 -?' ############################# usage: h5ls [OPTIONS] [OBJECTS...] - OPTIONS - -h, -?, --help Print a usage message and exit - -a, --address Print addresses for raw data - -d, --data Print the values of datasets - -e, --errors Show all HDF5 error reporting - -E, --external Allow traversal into external files - -f, --full Print full path names instead of base names - -g, --group Show information about a group, not its contents - -l, --label Label members of compound datasets - -r, --recursive List all groups recursively, avoiding cycles - -s, --string Print 1-byte integer datasets as ASCII - -S, --simple Use a machine-readable output format - -wN, --width=N Set the number of columns of output - -v, --verbose Generate more verbose output - -V, --version Print version number and exit - --vfd=DRIVER Use the specified virtual file driver - -x, --hexdump Show raw data in hexadecimal format + OPTIONS + -h, -?, --help Print a usage message and exit + -a, --address Print addresses for raw data + -d, --data Print the values of datasets + -e, --errors Show all HDF5 error reporting + --follow-symlinks Follow symbolic links (soft links and external links) + to display target object information. + Without this option, h5ls identifies a symbolic link + as a soft link or external link and prints the value + assigned to the symbolic link; it does not provide any + information regarding the target object or determine + whether the link is a dangling link. + -f, --full Print full path names instead of base names + -g, --group Show information about a group, not its contents + -l, --label Label members of compound datasets + -r, --recursive List all groups recursively, avoiding cycles + -s, --string Print 1-byte integer datasets as ASCII + -S, --simple Use a machine-readable output format + -wN, --width=N Set the number of columns of output + -v, --verbose Generate more verbose output + -V, --version Print version number and exit + --vfd=DRIVER Use the specified virtual file driver + -x, --hexdump Show raw data in hexadecimal format - OBJECTS - Each object consists of an HDF5 file name optionally followed by a - slash and an object name within the file (if no object is specified - within the file then the contents of the root group are displayed). - The file name may include a printf(3C) integer format such as - "%05d" to open a file family. + OBJECTS + Each object consists of an HDF5 file name optionally followed by a + slash and an object name within the file (if no object is specified + within the file then the contents of the root group are displayed). + The file name may include a printf(3C) integer format such as + "%05d" to open a file family. + + Deprecated Options + The following options have been deprecated in HDF5. While they remain + available, they have been superseded as indicated and may be removed + from HDF5 in the future. Use the indicated replacement option in all + new work; where possible, existing scripts, et cetera, should also be + updated to use the replacement option. + + -E or --external Follow external links. + Replaced by --follow-symlinks. diff --git a/tools/testfiles/textlinksrc-1-old.ls b/tools/testfiles/textlinksrc-1-old.ls new file mode 100644 index 0000000..5e81dec --- /dev/null +++ b/tools/testfiles/textlinksrc-1-old.ls @@ -0,0 +1,19 @@ +############################# + output for 'h5ls -w80 -Er textlinksrc.h5' +############################# +/ Group +/ext_link1 External Link {textlinktar.h5//group} {Group} +/ext_link1/dset Dataset {6} +/ext_link1/elink_t1 External Link {textlinksrc.h5//} {Group} +/ext_link1/elink_t1/ext_link1 External Link {textlinktar.h5//group} {Already Visited} +/ext_link1/elink_t1/ext_link2 External Link {textlinktar.h5//dset} {Dataset {6}} +/ext_link1/elink_t1/ext_link3 External Link {textlinktar.h5//type} {Type} +/ext_link1/elink_t1/ext_link4 External Link {textlinktar.h5//group/elink_t2} {**NOT FOUND**} +/ext_link1/elink_t1/ext_link5 External Link {textlinktar.h5//empty_group} {Group} +/ext_link1/elink_t2 External Link {textlinksrc.h5//ext_link4} {**NOT FOUND**} +/ext_link1/subgroup Group +/ext_link1/subgroup/link_to_group Group, same as /ext_link1 +/ext_link2 External Link {textlinktar.h5//dset} {Already Visited} +/ext_link3 External Link {textlinktar.h5//type} {Already Visited} +/ext_link4 External Link {textlinktar.h5//group/elink_t2} {Already Visited} +/ext_link5 External Link {textlinktar.h5//empty_group} {Already Visited} diff --git a/tools/testfiles/textlinksrc-1.ls b/tools/testfiles/textlinksrc-1.ls index 5e81dec..f39eec9 100644 --- a/tools/testfiles/textlinksrc-1.ls +++ b/tools/testfiles/textlinksrc-1.ls @@ -1,5 +1,5 @@ ############################# - output for 'h5ls -w80 -Er textlinksrc.h5' + output for 'h5ls -w80 --follow-symlinks -r textlinksrc.h5' ############################# / Group /ext_link1 External Link {textlinktar.h5//group} {Group} diff --git a/tools/testfiles/textlinksrc-2-old.ls b/tools/testfiles/textlinksrc-2-old.ls new file mode 100644 index 0000000..acdc3d2 --- /dev/null +++ b/tools/testfiles/textlinksrc-2-old.ls @@ -0,0 +1,8 @@ +############################# + output for 'h5ls -w80 -Erv textlinksrc.h5/ext_link5' +############################# +Opened "textlinksrc.h5" with sec2 driver. +ext_link5 External Link {textlinktar.h5//empty_group} {Group + Location: 3:1832 + Links: 1 +} diff --git a/tools/testfiles/textlinksrc-2.ls b/tools/testfiles/textlinksrc-2.ls index acdc3d2..ea99be8 100644 --- a/tools/testfiles/textlinksrc-2.ls +++ b/tools/testfiles/textlinksrc-2.ls @@ -1,5 +1,5 @@ ############################# - output for 'h5ls -w80 -Erv textlinksrc.h5/ext_link5' + output for 'h5ls -w80 --follow-symlinks -rv textlinksrc.h5/ext_link5' ############################# Opened "textlinksrc.h5" with sec2 driver. ext_link5 External Link {textlinktar.h5//empty_group} {Group diff --git a/tools/testfiles/textlinksrc-3-old.ls b/tools/testfiles/textlinksrc-3-old.ls new file mode 100644 index 0000000..a86ca32 --- /dev/null +++ b/tools/testfiles/textlinksrc-3-old.ls @@ -0,0 +1,14 @@ +############################# + output for 'h5ls -w80 -Er textlinksrc.h5/ext_link1' +############################# +ext_link1 External Link {textlinktar.h5//group} {Group} +/dset Dataset {6} +/elink_t1 External Link {textlinksrc.h5//} {Group} +/elink_t1/ext_link1 External Link {textlinktar.h5//group} {Already Visited} +/elink_t1/ext_link2 External Link {textlinktar.h5//dset} {Dataset {6}} +/elink_t1/ext_link3 External Link {textlinktar.h5//type} {Type} +/elink_t1/ext_link4 External Link {textlinktar.h5//group/elink_t2} {**NOT FOUND**} +/elink_t1/ext_link5 External Link {textlinktar.h5//empty_group} {Group} +/elink_t2 External Link {textlinksrc.h5//ext_link4} {**NOT FOUND**} +/subgroup Group +/subgroup/link_to_group Group, same as /ext_link1 diff --git a/tools/testfiles/textlinksrc-3.ls b/tools/testfiles/textlinksrc-3.ls index a86ca32..bd173f3 100644 --- a/tools/testfiles/textlinksrc-3.ls +++ b/tools/testfiles/textlinksrc-3.ls @@ -1,5 +1,5 @@ ############################# - output for 'h5ls -w80 -Er textlinksrc.h5/ext_link1' + output for 'h5ls -w80 --follow-symlinks -r textlinksrc.h5/ext_link1' ############################# ext_link1 External Link {textlinktar.h5//group} {Group} /dset Dataset {6} diff --git a/tools/testfiles/textlinksrc-6-old.ls b/tools/testfiles/textlinksrc-6-old.ls new file mode 100644 index 0000000..e1b8b74 --- /dev/null +++ b/tools/testfiles/textlinksrc-6-old.ls @@ -0,0 +1,8 @@ +############################# + output for 'h5ls -w80 -E textlinksrc.h5' +############################# +ext_link1 External Link {textlinktar.h5//group} {Group} +ext_link2 External Link {textlinktar.h5//dset} {Dataset {6}} +ext_link3 External Link {textlinktar.h5//type} {Type} +ext_link4 External Link {textlinktar.h5//group/elink_t2} {**NOT FOUND**} +ext_link5 External Link {textlinktar.h5//empty_group} {Group} diff --git a/tools/testfiles/textlinksrc-6.ls b/tools/testfiles/textlinksrc-6.ls index e1b8b74..6cda888 100644 --- a/tools/testfiles/textlinksrc-6.ls +++ b/tools/testfiles/textlinksrc-6.ls @@ -1,5 +1,5 @@ ############################# - output for 'h5ls -w80 -E textlinksrc.h5' + output for 'h5ls -w80 --follow-symlinks textlinksrc.h5' ############################# ext_link1 External Link {textlinktar.h5//group} {Group} ext_link2 External Link {textlinktar.h5//dset} {Dataset {6}} diff --git a/tools/testfiles/textlinksrc-7-old.ls b/tools/testfiles/textlinksrc-7-old.ls new file mode 100644 index 0000000..9249d0c --- /dev/null +++ b/tools/testfiles/textlinksrc-7-old.ls @@ -0,0 +1,4 @@ +############################# + output for 'h5ls -w80 -E textlinksrc.h5/ext_link1' +############################# +ext_link1 External Link {textlinktar.h5//group} {Group} diff --git a/tools/testfiles/textlinksrc-7.ls b/tools/testfiles/textlinksrc-7.ls index 9249d0c..528c4c5 100644 --- a/tools/testfiles/textlinksrc-7.ls +++ b/tools/testfiles/textlinksrc-7.ls @@ -1,4 +1,4 @@ ############################# - output for 'h5ls -w80 -E textlinksrc.h5/ext_link1' + output for 'h5ls -w80 --follow-symlinks textlinksrc.h5/ext_link1' ############################# ext_link1 External Link {textlinktar.h5//group} {Group} diff --git a/tools/testfiles/tgroup-1.ls b/tools/testfiles/tgroup-1.ls index 5401cd7..8d38e0f 100644 --- a/tools/testfiles/tgroup-1.ls +++ b/tools/testfiles/tgroup-1.ls @@ -4,27 +4,43 @@ Error: 'recursive' option not compatible with 'group info' option! usage: h5ls [OPTIONS] [OBJECTS...] - OPTIONS - -h, -?, --help Print a usage message and exit - -a, --address Print addresses for raw data - -d, --data Print the values of datasets - -e, --errors Show all HDF5 error reporting - -E, --external Allow traversal into external files - -f, --full Print full path names instead of base names - -g, --group Show information about a group, not its contents - -l, --label Label members of compound datasets - -r, --recursive List all groups recursively, avoiding cycles - -s, --string Print 1-byte integer datasets as ASCII - -S, --simple Use a machine-readable output format - -wN, --width=N Set the number of columns of output - -v, --verbose Generate more verbose output - -V, --version Print version number and exit - --vfd=DRIVER Use the specified virtual file driver - -x, --hexdump Show raw data in hexadecimal format + OPTIONS + -h, -?, --help Print a usage message and exit + -a, --address Print addresses for raw data + -d, --data Print the values of datasets + -e, --errors Show all HDF5 error reporting + --follow-symlinks Follow symbolic links (soft links and external links) + to display target object information. + Without this option, h5ls identifies a symbolic link + as a soft link or external link and prints the value + assigned to the symbolic link; it does not provide any + information regarding the target object or determine + whether the link is a dangling link. + -f, --full Print full path names instead of base names + -g, --group Show information about a group, not its contents + -l, --label Label members of compound datasets + -r, --recursive List all groups recursively, avoiding cycles + -s, --string Print 1-byte integer datasets as ASCII + -S, --simple Use a machine-readable output format + -wN, --width=N Set the number of columns of output + -v, --verbose Generate more verbose output + -V, --version Print version number and exit + --vfd=DRIVER Use the specified virtual file driver + -x, --hexdump Show raw data in hexadecimal format - OBJECTS - Each object consists of an HDF5 file name optionally followed by a - slash and an object name within the file (if no object is specified - within the file then the contents of the root group are displayed). - The file name may include a printf(3C) integer format such as - "%05d" to open a file family. + OBJECTS + Each object consists of an HDF5 file name optionally followed by a + slash and an object name within the file (if no object is specified + within the file then the contents of the root group are displayed). + The file name may include a printf(3C) integer format such as + "%05d" to open a file family. + + Deprecated Options + The following options have been deprecated in HDF5. While they remain + available, they have been superseded as indicated and may be removed + from HDF5 in the future. Use the indicated replacement option in all + new work; where possible, existing scripts, et cetera, should also be + updated to use the replacement option. + + -E or --external Follow external links. + Replaced by --follow-symlinks. diff --git a/tools/testfiles/tsoftlinks-1.ls b/tools/testfiles/tsoftlinks-1.ls new file mode 100644 index 0000000..fc57da9 --- /dev/null +++ b/tools/testfiles/tsoftlinks-1.ls @@ -0,0 +1,13 @@ +############################# + output for 'h5ls --follow-symlinks tsoftlinks.h5' +############################# +dset1 Dataset {4, 2} +dset2 Dataset {4, 2} +dtype Type +group1 Group +group_empty Group +soft_dangle Soft Link {not_yet} {**NOT FOUND**} +soft_dset1 Soft Link {/dset1} {Dataset {4, 2}} +soft_dtype Soft Link {/dtype} {Type} +soft_empty_grp Soft Link {/group_empty} {Group} +soft_group1 Soft Link {/group1} {Group} diff --git a/tools/testfiles/tsoftlinks-2.ls b/tools/testfiles/tsoftlinks-2.ls new file mode 100644 index 0000000..3566f70 --- /dev/null +++ b/tools/testfiles/tsoftlinks-2.ls @@ -0,0 +1,24 @@ +############################# + output for 'h5ls --follow-symlinks -r tsoftlinks.h5' +############################# +/ Group +/dset1 Dataset {4, 2} +/dset2 Dataset {4, 2} +/dtype Type +/group1 Group +/group1/soft_dangle Soft Link {not_yet} {**NOT FOUND**} +/group1/soft_dset1 Soft Link {/dset1} {Dataset {4, 2}} +/group1/soft_dset2 Soft Link {/dset2} {Dataset {4, 2}} +/group1/soft_dtype Soft Link {/dtype} {Type} +/group1/soft_empty_grp Soft Link {/group_empty} {Group} +/group_empty Group +/soft_dangle Soft Link {not_yet} {Already Visited} +/soft_dset1 Soft Link {/dset1} {Already Visited} +/soft_dtype Soft Link {/dtype} {Already Visited} +/soft_empty_grp Soft Link {/group_empty} {Already Visited} +/soft_group1 Soft Link {/group1} {Group} +/soft_group1/soft_dangle Soft Link {not_yet} {Already Visited} +/soft_group1/soft_dset1 Soft Link {/dset1} {Already Visited} +/soft_group1/soft_dset2 Soft Link {/dset2} {Already Visited} +/soft_group1/soft_dtype Soft Link {/dtype} {Already Visited} +/soft_group1/soft_empty_grp Soft Link {/group_empty} {Already Visited} diff --git a/tools/testfiles/tsoftlinks-3.ls b/tools/testfiles/tsoftlinks-3.ls new file mode 100644 index 0000000..2face70 --- /dev/null +++ b/tools/testfiles/tsoftlinks-3.ls @@ -0,0 +1,8 @@ +############################# + output for 'h5ls --follow-symlinks tsoftlinks.h5/group1' +############################# +soft_dangle Soft Link {not_yet} {**NOT FOUND**} +soft_dset1 Soft Link {/dset1} {Dataset {4, 2}} +soft_dset2 Soft Link {/dset2} {Dataset {4, 2}} +soft_dtype Soft Link {/dtype} {Type} +soft_empty_grp Soft Link {/group_empty} {Group} diff --git a/tools/testfiles/tsoftlinks-4.ls b/tools/testfiles/tsoftlinks-4.ls new file mode 100644 index 0000000..c1f4568 --- /dev/null +++ b/tools/testfiles/tsoftlinks-4.ls @@ -0,0 +1,8 @@ +############################# + output for 'h5ls --follow-symlinks -r tsoftlinks.h5/group1' +############################# +/soft_dangle Soft Link {not_yet} {**NOT FOUND**} +/soft_dset1 Soft Link {/dset1} {Dataset {4, 2}} +/soft_dset2 Soft Link {/dset2} {Dataset {4, 2}} +/soft_dtype Soft Link {/dtype} {Type} +/soft_empty_grp Soft Link {/group_empty} {Group} diff --git a/tools/testfiles/tsoftlinks-5.ls b/tools/testfiles/tsoftlinks-5.ls new file mode 100644 index 0000000..6e915e1 --- /dev/null +++ b/tools/testfiles/tsoftlinks-5.ls @@ -0,0 +1,4 @@ +############################# + output for 'h5ls --follow-symlinks tsoftlinks.h5/soft_dset1' +############################# +soft_dset1 Soft Link {/dset1} {Dataset {4, 2}} diff --git a/tools/testfiles/tsoftlinks.h5 b/tools/testfiles/tsoftlinks.h5 Binary files differnew file mode 100644 index 0000000..01ea922 --- /dev/null +++ b/tools/testfiles/tsoftlinks.h5 |