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* Check for overflow when calculating on-disk attribute data size (#2459)Egbert Eich2023-03-021-0/+0
| | | | | | | | | | | | | | | | | * 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
* Onion VFD (#1953)Dana Robinson2022-08-0210-0/+54
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Onion VFD feature * Fixes onion VFD errors with non-sec2 backing store VFDs * Disables the onion VFD tests w/ ph5diff * Disables non-sec2 VFDs as onion VFD backing stores * Committing clang-format changes * Formatted source * Typo * Adds onion VFD tools tests to CMake * Fixes for v16 API compatibility * Memset structs to avoid bad frees on errors * H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE * Properly decodes checksums on BE machines * Be more careful about uint64_t to haddr_t/hsize_t conversions * Another fix for BE data comparison * Removed double underscores from onion constants * Replace hard-coded onion header string w/ constant * Fixes cleanup paths in H5FD__onion_ingest_history() * Fixed use of size_t revision numbers * Fix h5dump revision count format string Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes a stack overflow in the h5dump test generator (#1903)Dana Robinson2022-07-182-5/+5
| | | | | | | | | | | | | * Fixes a stack overflow in the h5dump test generator The opaque type size was declared to be the size of the "buffer of two opaque elements", causing a memcpy call in H5Dwrite to read outside the buffer, dumping garbage into the file. Note that this only affected the test generator and not h5dump itself. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move error-stack text to top of usage display (#1564)Allen Byrne2022-04-018-16/+32
| | | | | | | | | * Move error-stack text to top of usage display * Add optional tag ti list * format changes * Revert incorrect change
* VFD plugins (#602)jhendersonHDF2021-09-2913-0/+78
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* Tools long double updates (#522)Allen Byrne2021-04-159-41/+1246
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#405)bmribler2021-03-192-0/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) Description Checked against buffer size to prevent segfault, in case of data corruption. + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode Platforms tested: Linux/64 (jelly) * Accidentally left in another occurrence of the previous patch from user after a more correct fix was applied, that is the check now accounted for the previous advance of the buffer pointer. Removed it. * Typo * Fixed format issues. * Added test. * Changed arguments to ADD_H5_TEST * Fixing arguments to ADD_H5_TEST again. * Fixing arguments again. * Took out the CMake changes until Allen can help. * Added files: tCVE_2018_11206_fill_old.h5 tCVE_2018_11206_fill_new.h5 * Revert "Took out the CMake changes until Allen can help." This reverts commit c21324d6e0044994c5cd24b0671e7d1dd41096cc. * Revert "Fixing arguments again." This reverts commit 5832a70674339e4b524749adde5a181f8c3a446a. * Revert "Fixing arguments to ADD_H5_TEST again." This reverts commit b45de823c22ce83a388d46466ef7c04b66ff05ed. * Revert "Changed arguments to ADD_H5_TEST" This reverts commit 16719824f57e52158451ddd261788c0dcaa3ec55. * Added first argument to ADD_H5_TEST for HDFFV-10480 fix. * Changed argument 0 to 1 * Revert "Changed argument 0 to 1" This reverts commit b343d6613ba681b43248dd5820e96389984ebcf7. * Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix." This reverts commit b8a0f9a9e8ec8e6c6ff38d33195d63edff76a563. * Added first argument and corrected the second. * Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049 * Improved error messages.
* Fix display of long double in tools (#469)Allen Byrne2021-03-174-0/+63
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Primary change is HDFFV-11212 - new refs and JNI (#372)Allen Byrne2021-02-251-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments
* HDFFV-11096 replace backticks with doublequotesAllen Byrne2020-10-048-16/+16
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* HDFFV-11096 fix typo in h5dump usage textAllen Byrne2020-10-038-8/+8
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* Tools refactorAllen Byrne2020-07-152-6/+6
| | | | | | Move error_stack setup to tools library Add structure for h5dump properties Eliminate duplicated h5diff functions Use properties structure in place of argument lists.
* Added VOL command-line options to (p)h5diff, h5ls, h5dump, and h5mkgrp.Dana Robinson2020-04-2113-0/+78
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* Updated test ddl files so CMake passes after h5dump failures.Dana Robinson2020-04-061-9/+9
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* Updated tools dump output when dataset offset is undefined.Dana Robinson2020-04-021-1/+1
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* Misc changes for h5dump VOL changes.Dana Robinson2020-03-301-1/+1
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* HDFFV-10976,-10980 Init obj_type before calling H5Rget_obj_type3Allen Byrne2019-12-201-1/+1
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* HDFFV-10980 - h5diff uses new ref APIsAllen Byrne2019-12-1919-0/+484
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* HDFFV-10876 fix compare referenceAllen Byrne2019-12-081-2/+2
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* Add missing quotesAllen Byrne2019-12-071-2/+2
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* Correct indentationAllen Byrne2019-12-071-15/+15
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* HDFFV-10876 Update dump to match DDL specAllen Byrne2019-12-059-1372/+1372
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* Add extra lineAllen Byrne2019-12-042-0/+2
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* Adjust whitespaceAllen Byrne2019-12-042-4/+4
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* Update h5ls help and rework dump_mem routines for attrsAllen Byrne2019-12-047-38/+41
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* Update data output referenceAllen Byrne2019-12-032-12/+32
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* Update reference files to latest outputAllen Byrne2019-12-027-1509/+1185
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* HDFFV-10876 Update h5dump and h5ls for new ref api.Allen Byrne2019-11-0717-1093/+1173
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* HDFFV-10876 h5dump OPAQUE size should be optionalAllen Byrne2019-08-271-1/+0
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* Squashed commit of the following:Larry Knox2019-07-2513-0/+125
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* HDFFV-9407 Add testAllen Byrne2019-06-241-0/+0
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* HDFFV-10632 - split stderr and stdout in cmakeAllen Byrne2018-12-0323-25/+0
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-2/+2
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* Add test file with unwritten datasetsAllen Byrne2018-07-242-0/+329
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* Fix for HDFFV-10333:Vailin Choi2018-07-112-0/+5
| | | | | | | | | 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
* HDFFV-10384 Add opt arg to helpAllen Byrne2018-02-158-16/+16
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* HDFFV-10188 emu insists on printing non-native descriptionAllen Byrne2017-08-231-1/+1
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* HDFFV-10188 Add tests and filesAllen Byrne2017-08-213-0/+40
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* HDFFV-10188 enable null space testAllen Byrne2017-08-211-0/+39
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* HDFFV-10256 Add testAllen Byrne2017-08-012-0/+20
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* HDFFV-10186 xml test also needs endianess aware filesAllen Byrne2017-05-102-0/+103
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* Fix reference file contentsAllen Byrne2017-05-101-1/+1
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* HDFFV-10186 Add endianess to bitfield and fix testsAllen Byrne2017-05-102-0/+293
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* Use correct var types for dataAllen Byrne2017-05-042-16/+16
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* Final merge of page buffering branch to developQuincey Koziol2017-03-147-71/+20
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* HDFFV-10118 fix dataAllen Byrne2017-01-201-6/+15
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* HDFFV-10118 change h5ls to not display extra infoAllen Byrne2017-01-201-22/+6
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* HDFFV-10118 fixed plugin tests for toolsAllen Byrne2017-01-203-3/+3
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* HDFFV-9994 - correct reference fileAllen Byrne2017-01-171-20/+26
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* HDFFV-9994 add UD tests for toolsAllen Byrne2017-01-173-0/+47
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