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Fix for github Issue #1388 can't delete renamed dense attribute with corder tracking enabled #4462

Merged
merged 4 commits into from
May 17, 2024
Merged

Fix for github Issue #1388 can't delete renamed dense attribute with corder tracking enabled #4462

merged 4 commits into from
May 17, 2024

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@vchoi-hdfgroup vchoi-hdfgroup commented May 3, 2024 •
edited

The problem occurs in step 3(b) below which will delete the attribute with corder x
from the creation order index v2 B-tree.

The rename sequence in H5A__dense_rename() occurs in the following order:

  1. The old attribute with corder x was removed from the creation order index v2 B-tree
  2. The new renamed attribute was inserted via H5A__dense_insert():
    (a) insert the attribute with new name j into the name index v2 B-tree
    (b) insert the attribute with corder x into the creation order index v2 B-tree
  3. The old attribute was removed via H5A__dense_remove():
    (a) remove the attribute with old name k from the name index v2 B-tree
    (b) remove the attribute with coorder x from the creation order index v2 B-tree

Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove()
won't delete the attribute with corder x from the creation order index v2 B-tree.

vchoi-hdfgroup and others added 2 commits May 3, 2024 18:50
@vchoi-hdfgroup
Fix for github issue HDFGroup#1388: can't delete renamed dense attrib…
ab536b7 
…ute with corder tracking enabled

The problem occurs in step 3(b) below which will delete the attribute with corder x
from the creation order index v2 B-tree.

The rename sequence in H5A__dense_rename() occurs in the following order:
1) The old attribute with corder x was removed from the creation order index v2 B-tree
2) The new renamed attribute was inserted via H5A__dense_insert():
(a) insert the attribute with new name j into the name index v2 B-tree
(b) insert the attribute with corder x into the creation order index v2 B-tree
3) The old attribute was removed via H5A__dense_remove():
(a) remove the attribute with old name k from the name index v2 B-tree
(b) remove the attribute with coorder x from the creation order index v2 B-tree

Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove()
won't delete the attribute with corder x from the creation order index v2 B-tree.
@vchoi-hdfgroup
Merge branch 'HDFGroup:develop' into issue_1388_develop
cb24e76
@byrnHDF byrnHDF added Component - C Library Core C library issues (usually in the src directory) Type - Bug Please report security issues to help@hdfgroup.org instead of creating an issue on GitHub labels May 6, 2024
@derobins derobins added Merge - To 1.14 This needs to be merged to HDF5 1.14 Priority - 1. High 🔼 These are important issues that should be resolved in the next release labels May 9, 2024
@lrknox lrknox merged commit 757ca52 into HDFGroup:develop May 17, 2024
58 checks passed
lrknox pushed a commit to lrknox/hdf5 that referenced this pull request May 20, 2024
@vchoi-hdfgroup @lrknox
Fix for github Issue HDFGroup#1388 can't delete renamed dense attribu…
e441451 
…te with corder tracking enabled (HDFGroup#4462)

* Fix for github issue HDFGroup#1388: can't delete renamed dense attribute with corder tracking enabled

The problem occurs in step 3(b) below which will delete the attribute with corder x
from the creation order index v2 B-tree.

The rename sequence in H5A__dense_rename() occurs in the following order:
1) The old attribute with corder x was removed from the creation order index v2 B-tree
2) The new renamed attribute was inserted via H5A__dense_insert():
(a) insert the attribute with new name j into the name index v2 B-tree
(b) insert the attribute with corder x into the creation order index v2 B-tree
3) The old attribute was removed via H5A__dense_remove():
(a) remove the attribute with old name k from the name index v2 B-tree
(b) remove the attribute with coorder x from the creation order index v2 B-tree

Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove()
won't delete the attribute with corder x from the creation order index v2 B-tree.
lrknox added a commit that referenced this pull request May 23, 2024
@lrknox
Sync develop changes May 6 - May 20 to hdf5_1_14 (#4503)
86f603e 
* win32defs: Fix Wundef warning (#4467)

* Refactor error handling code to eliminate internal ID calls (#4453)

All calls to the H5I routines are now made in API routines (sometimes in
FUNC_ENTER/LEAVE_* macros), except for some calls to H5E_clear_stack() within
the library, but I'm planning to remove those over time.

Also, made all the library internal error messages into static const variables,
instead of malloc'ing them, which means that they can just be referenced
and not copied.

Several new and updated auto-generated header files were necessary to enable
this.

* CMake: Fix mingw/fortran build (#4466)

* Update for blosc2 in plugins and prefix hdf5 cmake varnames (#4468)

* Fix an issue where compound datatype member IDs can be leaked during conversion (#4459)

Also fixes issues with handling of partially initialized datatypes during library shutdown

* H5Group: Fix operator= (#4473)

Closes #4472

* Fix github issue #2523: doxygen -- fix grammatically incorrect sentence alias (#4474)

* Remove env step not used by CI in testing (#4476)

* Add H5fortkit dependecy for H5Rff.F90 (#4482)

* Properly clean up cache when failing to load an object header (#4477)

* Properly clean up cache when failing to load an object header

* Don't check message type a second time in H5G__open_oid if the first attempt returns error

* Add more asserts to H5O__assert() to avoid segfaults

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Add a missing image from the original document (#4490)

* Disable EOF checks for SWMR readers in more cases. (#4489)

Fixes a race condition where the reader opens the file and sets its EOF from the
file's size (from the stat() call in the driver open callback).  Then, before
the reader can read the file's superblock, a SWMR writer races in, extends the
file, and closes the file, writing an updated superblock with the 'writer' and
'SWMR writer' flags in the superblock off (appropriately).  Then the reader
proceeds to read the superblock, and flags the EOF as wrong.  Taking out the
check for the 'writer' and 'SWMR writer' flags will cause SWMR readers to avoid
flagging the file as incorrect.

* Remove unnecessary fortran install (#4498)

* Only one version of binaries is produced for platforms (#4496)

* Fix for github issue #2220. (#4497)

Document the limitation in the Passthrough Conncector section of the VOL Connector Author Guide.
The limitation is posted by Neil in the github issue on Dec 22, 2022.

* Release asset tarballs with no version filenames (#4494)

* Improve spec. reading superblock into cache (a little) by using v2 size (#4491)

* Improve spec. reading superblock into cache (a little) by using v2 size

Instead of reading the absolute minimal possible, use the likely value of
a v2+ superblock w/8-byte addresses & lengths.

* Fix for github Issue #1388 can't delete renamed dense attribute with corder tracking enabled (#4462)

* Fix for github issue #1388: can't delete renamed dense attribute with corder tracking enabled

The problem occurs in step 3(b) below which will delete the attribute with corder x
from the creation order index v2 B-tree.

The rename sequence in H5A__dense_rename() occurs in the following order:
1) The old attribute with corder x was removed from the creation order index v2 B-tree
2) The new renamed attribute was inserted via H5A__dense_insert():
(a) insert the attribute with new name j into the name index v2 B-tree
(b) insert the attribute with corder x into the creation order index v2 B-tree
3) The old attribute was removed via H5A__dense_remove():
(a) remove the attribute with old name k from the name index v2 B-tree
(b) remove the attribute with coorder x from the creation order index v2 B-tree

Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove()
won't delete the attribute with corder x from the creation order index v2 B-tree.

* Fix/revert a libtool sed hack (#4501)

* Revert "Remove Autotools sed hack (#3848)"

This reverts commit 8b3ffde.

* Fix libtool sed cleanup on MacOS

Convert sed -i line to sed > libtool.bak && mv libtool.bak libtool
to avoid non-portable -i option.

* Update src/H5public.h

* Set H5 specific vars immediately if legacy find (#4512)

* Correct find process vars (vs in-line build)

* Correct SZIP find

* Everything is libaec 1.0.6 or newer

* Correct option help text
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@qkoziol qkoziol qkoziol approved these changes

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Component - C Library Core C library issues (usually in the src directory) Merge - To 1.14 This needs to be merged to HDF5 1.14 Priority - 1. High 🔼 These are important issues that should be resolved in the next release Type - Bug Please report security issues to help@hdfgroup.org instead of creating an issue on GitHub
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