Commit Graph

3716 Commits

Author SHA1 Message Date
jhendersonHDF
34fcb9c5a4
Fix several spelling/grammar issues (#3621) 2023-10-03 09:01:28 -07:00
Dana Robinson
a03506b089
Remove unnecessary assignment in test generator (#3603)
Fixes what looks like a copy/paste/modify error in the format convert
test file generator, where an array element is assigned one value
and them immediately overwritten by another value.

Fixes Coverity issue 1542285
2023-09-27 09:57:02 -05:00
Dana Robinson
d8fbc56f78
Fix potential uninitialized variable (#3602)
Moves a union initialization up a bit so it's performed before code
that can jump to the cleanup target, where file descriptors could
be checked without being initialized.

This could only happen in test code and only in an out-of-memory
situation.

Fixes Coverity 1542254
2023-09-27 09:56:25 -05:00
Allen Byrne
1529ec0ab3
Develop tools move (#3580)
Reorganizes the tools files to support the VOL tests
2023-09-26 13:46:55 -07:00
Scot Breitenfeld
a87ca572fe
Replaces HDgetenv with getenv (#3599) 2023-09-26 13:11:22 -07:00
Dana Robinson
58f3d6664e
Use HDoff_t with lseek consistently (#3600)
lseek on Windows uses __int64 for both the offset and return type
instead of off_t like most POSIX systems. This changes ensures we
use HDoff_t (which is typdef'd correctly on Windows) w/ lseek.
2023-09-26 11:38:07 -07:00
Dana Robinson
44a00ef876
Strip HD prefix from string/char C API calls (#3540)
* Strip HD prefix from string/char C API calls

* HD(f)(put|get)(s|c)
* HDstr*
* HDv*printf
* HD(s)(print|scan)f
* HDperror

But NOT:

* HDstrcase*
* HDvasprintf
* HDstrtok_r
* HDstrndup

As those are not C99 and have portability work-around
implementations. They will be handled later.

* Fix th5_system.c screwup
2023-09-15 15:13:18 -07:00
Dana Robinson
aa849f07e3
Remove HD prefix from math functions (#3538) 2023-09-14 10:54:00 -07:00
Dana Robinson
ae1379094b
hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491) 2023-09-05 11:50:06 -07:00
vchoi-hdfgroup
e7bb05a886
Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with segmenetation fault. (#3427)
It is because the object in the testfile points back to the root group.
When the tool tries to traverse the object, it goes back to the root group and then back again.
2023-08-25 08:13:04 -05:00
jhendersonHDF
14645ae83e
Avoid H5Ocopy in h5repack for variable-length string types (#3419) 2023-08-24 08:53:05 -07:00
Allen Byrne
67246efd6a
Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] (#3353) 2023-08-24 08:45:38 -07:00
jhendersonHDF
f61522ec4d
Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407) 2023-08-22 09:03:04 -07:00
jhendersonHDF
915cadb44f
Make h5dump spacing consistent when printing VLEN datatype (#3351) 2023-08-04 09:02:40 -07:00
Sean McBride
07df0d252c
Fixes the last of the -Wextra-semi-stmt warnings (#3326)
* Fixed extra semi warning by adjusting alternative macro definitions

* Find-replace H5E_END_TRY; -> H5E_END_TRY

* Made H5Epush_goto a do-while loop, fixed indentation

* Made GOTOERROR and ERRMSG do-while loops

* Made Hgoto_error and Hgoto_done  do-while loops

* Made vrfy_cint_type and vrfy_ctype  do-while loops

* Made TEST_TYPE_CONTIG and others do-while loops

* Removed extraneous semi-colons

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-08-02 17:46:26 -05:00
jhendersonHDF
f5c3963c18
Fix h5repack for variable-length datatyped datasets (#3331) 2023-08-02 13:19:21 -07:00
jhendersonHDF
74352dfda8
Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314) 2023-08-01 23:14:32 -05:00
Sean McBride
553e1cd311
Another round of fixing -Wextra-semi-stmt warnings (#3264)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-07-24 16:18:04 -05:00
Scot Breitenfeld
1706355ee1
removed the use of encoded single apostrophe (#3261)
* removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read

* updated sanitizer paragraph
* fixed brief description for H5Fget_info
2023-07-20 09:01:58 -05:00
jhendersonHDF
aab497a631
Fix some warnings in developer builds (#3247)
* Fix some warnings in developer builds

* Switch approach to Winline flag
2023-07-18 04:27:07 -07:00
Jan-Willem Blokland
305ac88865
ROS3: (feature) Temporary security credentials (#3030)
- Implemented support for AWS temporary security credentials.
  For this kind of credentials also a session/security token
  should be included in the request by adding the
  x-amz-security-token header.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-07-14 15:15:11 -05:00
Dana Robinson
7196d1e4c2
Remove HD from HDis* (e.g., isalpha) (#3212)
* HDisalnum
* HDisalpha
* HDiscntrl
* HDisdigit
* HDisgraph
* HDislower
* HDisprint
* HDispunct
* HDisspace
* HDisupper
* HDisxdigit
2023-06-29 12:47:16 -07:00
Dana Robinson
39e6bf48c9
Remove HD from HDmem* calls (#3211) 2023-06-29 12:33:46 -07:00
Dana Robinson
fd933f30b1
Remove programmer/date from comments (#3210)
* Removes Programmer: and Date: fields
* Fixes a few Modifications: fields leftover from previous work
2023-06-29 12:13:29 -07:00
Dana Robinson
fd56a593b7
Remove HD from C std lib file ops (#3206)
* HDfclose
* HDferror
* HDfeof
* HDfflush
* HDfopen
* HDfread
* HDfwrite
2023-06-29 08:19:31 -07:00
Dana Robinson
8aef67f0ae
Remove HD from strto* calls (#3204)
* HDstrtod
* HDstrtol
* HDstrtoll
* HDstrtoul
* HDstrtoull
* HDstrtoumax
2023-06-29 08:18:49 -07:00
Dana Robinson
9f430d15b0
Rename HDexit() and related to exit(), etc. (#3202)
* HDatexit
* HDexit
* HD_exit
2023-06-29 08:18:01 -07:00
Dana Robinson
dd39b54c95
Rename HDato*() to ato*() (#3201) 2023-06-29 06:33:09 -07:00
Dana Robinson
a90bdbbcfc
Remove HD from protected POSIX calls (#3203)
These calls are non-C99 but protected by ifdefs and have no Windows
equivalents:
* HDalarm
* HDasprintf
* HDclock_gettime
* HDfcntl
* HDgethostname
* HDgetrusage
* HDsymlink
2023-06-29 06:32:40 -07:00
Dana Robinson
aebac33a1f
Remove HD from memory allocate/free calls (#3195)
* HDcalloc
* HDfree
* HDmalloc
* HDrealloc
2023-06-28 15:48:12 -07:00
Dana Robinson
96d89bcae7
Rename HDsystem() to system() (#3197)
system() is only used in the iopipe test and the things it calls
(which are POSIX-y) are protected by an ifdef.
2023-06-28 13:01:26 -07:00
mattjala
d87efd3a46
Add note about HDF5_VOL_CONNECTOR to tools usage (#3159) 2023-06-28 09:56:35 -07:00
Dana Robinson
187ea8a9ae
Rename HD(f)printf() to (f)printf() (#3194) 2023-06-28 08:31:32 -07:00
Dana Robinson
7a44581a84
Rename HDassert() to assert() (#3191)
* Change HDassert to assert

* Fix bin/make_err
2023-06-28 07:31:56 -07:00
Dana Robinson
d81e751d41
Remove HDva_(arg|copy|end|start) (#3184) 2023-06-27 17:43:23 -07:00
Sean McBride
65d8c93470
Many fixes to various compiler warnings (#3124)
* Fixed various -Wmissing-variable-declarations by adding static keyword
* In a few cases, renamed the variable suffix from _g to _s.
* Fixed some -Wmissing-variable-declarations by using different declaration macros
* Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero
* Fixed various -Wcomma warnings
* Fixed clang -Wstrict-prototypes warnings
* Fixed various -Wunused-variable warnings
* Updated some casts to fix the only 3 -Wcast-qual warnings
* Fixed the only -Wsometimes-uninitialized warning
2023-06-18 22:13:38 -07:00
Sean McBride
68eba3da69
Many clang -Wextra-semi-stmt fixes (#2537)
* Adds semicolons to function-like macros
* Adds a do..while(0) loop to some macros
* Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
2023-06-15 21:49:02 -07:00
Allen Byrne
c961ef98ff
Add h5copy help test and verify consistency (#2902)
* Add autotools test for help
2023-05-17 10:41:01 -05:00
Dana Robinson
265494b5b9
Remove "the the" from comments and docs (#2865) 2023-05-01 09:06:39 -07:00
jhendersonHDF
e6db9b25d3
Fix ROS3 VFD anonymous credential usage with h5dump and h5ls (#2798) 2023-04-24 08:21:12 -07:00
Allen Byrne
445fcab52f
Add no subsets option to h5diff like h5dump #2688 (#2756) 2023-04-18 11:21:18 -07:00
Quincey Koziol
49a71463a0
Comment cleanup (#2689)
* Clean up content and redundant logging in comments.
2023-04-11 09:41:32 -05:00
Dana Robinson
1ad030f669
Remove dead code hidden behind #ifdef LATER (#2686) 2023-04-10 11:39:46 -07:00
Allen Byrne
fc91e8856f
Fix #2598 sanitize leak (#2660) 2023-04-07 10:35:51 -07:00
Allen Byrne
cb679af19d
Make sure that ONLY_SHARED_LIBS option is correctly set (#2544) 2023-03-13 16:24:49 -05:00
Allen Byrne
42d1e89755
GH issue #1142, print must have verbose on first (#2540) 2023-03-13 16:23:33 -05:00
Egbert Eich
b16ec83d4b
Check for overflow when calculating on-disk attribute data size (#2459)
* Remove duplicate code

Signed-off-by: Egbert Eich <eich@suse.com>

* Add test case for CVE-2021-37501

Bogus sizes in this test case causes the on-disk data size
calculation in H5O__attr_decode() to overflow so that the
calculated size becomes 0. This causes the read to overflow
and h5dump to segfault.
This test case was crafted, the test file was not directly
generated by HDF5.
Test case from:
https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md
2023-03-02 11:17:49 -06:00
Dana Robinson
5ce275145c
Fix uninitialized variable in pio_engine.c (#2463) 2023-02-13 10:36:17 -08:00
Dana Robinson
02b93cad26
Fix a possible uninitialized variable in pio_perf (#2461) 2023-02-13 08:10:47 -08:00
Quincey Koziol
90d20764f4
Determine if native connector is terminal (#2397)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

* Use API routine to determine if native connector is terminal.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-01-09 13:49:29 -08:00