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Raito Bezarius 64a2f038b1 fix(local-store): invalidate phantom referrers at garbage collection time 
Sometimes, a path can disappear from the `ValidPaths` table (I have 23
such cases on my 1.4TB Nix store).

When this occurs and you try to run a garbage collection,
`queryReferrers` will report no referrer because it's performing a
*RIGHT JOIN* between `Refs` and `ValidPaths`, finally, when you issue
the deletion SQL statement, this will throw an uncaught exception from
SQLite side regarding a foreign key violation because `reference` in
`Refs` is a foreign key to `ValidPaths` (which we are trying to delete).

Why can this happen?

Two reasons:

* `PRAGMA foreign_keys=off;` will disable deletion on cascade.
* Trigger recursion *limits*, a deletion on cascade is a *trigger*, when
  a delete is issued and it triggers a bunch of deletion on cascade,
  there's a documented limit by SQLite: https://www.sqlite.org/limits.html#max_trigger_depth

  > Recursion limit on foreign key actions. The SQLITE_MAX_TRIGGER_DEPTH
  > and SQLITE_LIMIT_TRIGGER_DEPTH settings determine the maximum
  > allowable depth of trigger program recursion. For the purposes of
  > these limits, foreign key actions are considered trigger programs. The
  > PRAGMA recursive_triggers setting does not affect the operation of
  > foreign key actions. It is not possible to disable recursive foreign
  > key actions.

As I do not see easy ways to solve the root cause, garbage collection
should be self-healing in that regards, so I propose to invalidate
phantom referrers as we go.

As part of a work improving the consistency of the SQLite database, it
would make sense to count how many times this happen and try to find
ways to reproduce this issue.

Change-Id: I055a8a1d8c0e44d4388a411abe8e5a5e385f7b55
Signed-off-by: Raito Bezarius <raito@lix.systems>
2024-12-01 17:17:13 +01:00
..
ca
tests: move nix-shell related tests to subdir
2024-10-13 23:12:45 -07:00
common
fix(local-store): invalidate phantom referrers at garbage collection time
2024-12-01 17:17:13 +01:00
config
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
dyn-drv
remove the autoconf+Make buildsystem
2024-05-07 17:04:30 -06:00
flakes
tests/functional/flakes: test with UTF-8 bullets
2024-10-30 08:21:58 -07:00
lang
libexpr: Deprecate overriding __sub and the like
2024-11-28 18:15:52 +01:00
nested-sandboxing
chore: rebrand Nix to Lix when it makes sense
2024-06-01 20:31:24 +02:00
nix-shell
nix-shell: stop using dynamic format strings!!
2024-10-13 23:12:45 -07:00
plugins
Include rearrangement: rest
2024-11-18 12:31:19 -08:00
repl_characterization
libexpr: handle debug trace frames as parent pointer list
2024-11-28 15:12:22 +00:00
test-libstoreconsumer
Include rearrangement: rest
2024-11-18 12:31:19 -08:00
add.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
bad.tar.xz
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
bash-profile.sh
chore: remove monolithic coreutils requirement
2024-10-30 15:12:35 +04:00
big-derivation-attr.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
binary-cache-build-remote.sh
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2023-12-01 12:06:43 -05:00
binary-cache.sh
chore: rebrand Nix to Lix when it makes sense
2024-06-01 20:31:24 +02:00
brotli.sh
Put functional tests in tests/functional
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build-delete.sh
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2023-12-01 12:06:43 -05:00
build-dry.sh
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2023-12-01 12:06:43 -05:00
build-hook-ca-fixed.nix
Merge pull request #9032 from Ma27/structured-attrs-env-vars
2024-03-07 10:46:47 +01:00
build-hook-ca-floating.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
build-hook.nix
Merge pull request #9032 from Ma27/structured-attrs-env-vars
2024-03-07 10:46:47 +01:00
build-jobless.sh
libstore: diagnose local build failure in goal
2024-08-25 19:55:47 +02:00
build-remote-content-addressed-fixed.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
build-remote-content-addressed-floating.sh
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2023-12-01 12:06:43 -05:00
build-remote-input-addressed.sh
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2023-12-01 12:06:43 -05:00
build-remote-trustless-after.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
build-remote-trustless-should-fail-0.sh
chore: rebrand Nix to Lix when it makes sense
2024-06-01 20:31:24 +02:00
build-remote-trustless-should-pass-0.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
build-remote-trustless-should-pass-1.sh
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build-remote-trustless-should-pass-2.sh
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build-remote-trustless-should-pass-3.sh
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2023-12-01 12:06:43 -05:00
build-remote-trustless.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
build-remote.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
build.sh
fix build test error count checks
2024-10-05 16:21:19 +00:00
case-hack.sh
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2023-12-01 12:06:43 -05:00
case.nar
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2023-12-01 12:06:43 -05:00
check-refs.nix
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2023-12-01 12:06:43 -05:00
check-refs.sh
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2023-12-01 12:06:43 -05:00
check-reqs.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
check-reqs.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
check.nix
libstore: report all differing outputs rather than just the first
2024-10-29 18:34:54 +01:00
check.sh
feat: Add temp-dir setting
2024-11-06 18:11:47 -08:00
common.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
completions.sh
Merge pull request #8817 from iFreilicht/flake-update-lock-overhaul
2024-03-25 17:36:24 -06:00
compression-levels.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
compute-levels.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
config.nix.in
chore: remove monolithic coreutils requirement
2024-10-30 15:12:35 +04:00
config.sh
Rename nix show-config to nix config show
2024-05-03 16:26:16 +02:00
db-migration.sh
chore: rebrand Nix to Lix when it makes sense
2024-06-01 20:31:24 +02:00
debugger.sh
Merge pull request #9933 from pennae/debugger-fix
2024-03-04 08:57:44 +01:00
dependencies.builder0.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
dependencies.nix
libutil: handle json builder log messages with unexpected format
2024-10-15 11:15:42 +02:00
dependencies.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
derivation-json.sh
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2023-12-01 12:06:43 -05:00
dummy
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2023-12-01 12:06:43 -05:00
dump-db.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
eval-store.sh
Merge pull request #9589 from obsidiansystems/floating-content-addressing-derivations-eval-store
2024-03-04 07:15:08 +01:00
eval.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
eval.sh
distinguish between throws & errors during throw
2024-07-04 17:43:03 -06:00
experimental-features.sh
libexpr/flake: allow automatic rejection of configuration options from flakes
2024-06-30 19:28:14 +02:00
export-graph.nix
Put functional tests in tests/functional
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export-graph.sh
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export.sh
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2023-12-01 12:06:43 -05:00
extra-sandbox-profile.nix
libstore: Fix sandbox=relaxed
2024-05-08 19:31:43 +00:00
extra-sandbox-profile.sh
libstore: Fix sandbox=relaxed
2024-05-08 19:31:43 +00:00
failing.nix
Merge pull request #9032 from Ma27/structured-attrs-env-vars
2024-03-07 10:46:47 +01:00
fetchClosure.sh
Add pre-commit checks
2024-03-29 22:57:40 -07:00
fetchers.sh
Reapply "libfetchers: make attribute / URL query handling consistent"
2024-08-01 15:41:30 -07:00
fetchGit.sh
libfetchers/git: restore compat with builtins.fetchGit from 2.3
2024-09-28 14:52:06 +02:00
fetchGitRefs.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
fetchGitSubmodules.sh
treewide: Stop using URL literals
2024-08-17 15:48:10 +00:00
fetchMercurial.sh
treewide: Stop using URL literals
2024-08-17 15:48:10 +00:00
fetchPath.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
fetchTree-file.sh
chore: rebrand Nix to Lix when it makes sense
2024-06-01 20:31:24 +02:00
fetchurl.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
filter-source.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
filter-source.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
fixed.builder1.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
fixed.builder2.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
fixed.nix
Merge pull request #9662 from shlevy/flat-fixed-references-assert
2024-03-04 07:50:02 +01:00
fixed.sh
Merge pull request #9662 from shlevy/flat-fixed-references-assert
2024-03-04 07:50:02 +01:00
fmt.sh
fix(nix fmt): remove the default "." argument
2024-09-26 14:32:29 -07:00
fmt.simple.sh
fix(nix fmt): remove the default "." argument
2024-09-26 14:32:29 -07:00
fod-failing.nix
store: guess the URL of failing fixed-output derivations
2024-06-27 22:44:16 -07:00
function-trace.sh
Add pre-commit checks
2024-03-29 22:57:40 -07:00
gc-auto.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
gc-concurrent2.builder.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
gc-concurrent.builder.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
gc-concurrent.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
gc-concurrent.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
gc-non-blocking.sh
gc: refactor the gc server thread out into a class without changing it
2024-07-19 20:55:55 +00:00
gc-runtime.nix
gc: Find roots using libproc on Darwin
2024-04-25 23:24:21 -04:00
gc-runtime.sh
gc: Find roots using libproc on Darwin
2024-04-25 23:24:21 -04:00
gc.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
hash-check.nix
Remove ancient let from 2 test files
2024-10-14 17:19:22 +04:00
hash.sh
Revert "Reject weak hash algorithms as SRIs, and warn in any other cases"
2024-11-01 11:59:59 +00:00
hermetic.nix
Merge pull request #9032 from Ma27/structured-attrs-env-vars
2024-03-07 10:46:47 +01:00
ifd.nix
Merge branch '2.18-maintenance' into ifd-buildStore-2.18
2024-01-11 07:21:16 -05:00
import-derivation.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
import-derivation.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
impure-derivations.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
impure-derivations.sh
chore: rebrand Nix to Lix when it makes sense
2024-06-01 20:31:24 +02:00
impure-eval.sh
Merge pull request #4093 from matthewbauer/eval-system
2024-03-04 07:21:01 +01:00
init.sh
Fix failing darwin tests
2024-05-06 18:56:40 +02:00
install-darwin.sh
change shebangs of all .sh scripts to bash
2024-06-24 14:00:43 -07:00
lang-test-infra.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
lang.sh
tests/functional-lang: Small cleanup of flagfiles handling
2024-10-18 11:40:04 +00:00
legacy-ssh-store.sh
"but doctor, I AM the untrusted store": nix doctor had wrong trustedness
2024-04-08 15:40:12 -07:00
linux-sandbox-cert-test.nix
Add pre-commit checks
2024-03-29 22:57:40 -07:00
linux-sandbox.sh
libstore/build: copy ca-certificates too
2024-05-31 07:54:18 +00:00
local-store.sh
"but doctor, I AM the untrusted store": nix doctor had wrong trustedness
2024-04-08 15:40:12 -07:00
logging.sh
Merge pull request #9637 from 9999years/fix-logging-test-on-macos
2024-03-04 07:26:34 +01:00
meson.build
fix(local-store): invalidate phantom referrers at garbage collection time
2024-12-01 17:17:13 +01:00
misc.sh
libutil/args: warn on unknown settings after parsing all flags
2024-05-30 03:07:21 +00:00
multiple-outputs.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
multiple-outputs.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
nar-access.nix
Add pre-commit checks
2024-03-29 22:57:40 -07:00
nar-access.sh
Merge pull request #9288 from edolstra/fix-nar-access-test
2024-03-04 05:27:18 +01:00
nested-sandboxing.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
nix_path.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
nix-build-examples.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
nix-build.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
nix-channel.sh
Add pre-commit checks
2024-03-29 22:57:40 -07:00
nix-collect-garbage-d.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
nix-collect-garbage-dry-run.sh
Fix dry-run flag for nix-collect-garbage
2024-07-09 13:55:05 +00:00
nix-copy-ssh-common.sh
Merge pull request #9604 from obsidiansystems/test-substitute-on-destination
2024-03-07 03:34:00 +01:00
nix-copy-ssh-ng.sh
Merge pull request #9604 from obsidiansystems/test-substitute-on-destination
2024-03-07 03:34:00 +01:00
nix-copy-ssh.sh
Merge pull request #9604 from obsidiansystems/test-substitute-on-destination
2024-03-07 03:34:00 +01:00
nix-daemon-untrusting.sh
change shebangs of all .sh scripts to bash
2024-06-24 14:00:43 -07:00
nix-profile.sh
libfetchers: log fetches by URL just before they happen
2024-05-24 15:15:42 -06:00
optimise-store.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
output-normalization.sh
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2023-12-01 12:06:43 -05:00
parallel.builder.sh
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2023-12-01 12:06:43 -05:00
parallel.nix
Put functional tests in tests/functional
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parallel.sh
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2023-12-01 12:06:43 -05:00
pass-as-file.sh
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2023-12-01 12:06:43 -05:00
path-from-hash-part.sh
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2023-12-01 12:06:43 -05:00
path.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
phantom-referrers-gc.sh
fix(local-store): invalidate phantom referrers at garbage collection time
2024-12-01 17:17:13 +01:00
placeholders.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
plugins.sh
tests: don't build test plugin shared libs on static builds
2024-05-12 23:04:21 +02:00
post-hook.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
pure-eval.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
pure-eval.sh
treewide: Stop using URL literals
2024-08-17 15:48:10 +00:00
push-to-store-old.sh
change shebangs of all .sh scripts to bash
2024-06-24 14:00:43 -07:00
push-to-store.sh
change shebangs of all .sh scripts to bash
2024-06-24 14:00:43 -07:00
read-only-store.sh
Add pre-commit checks
2024-03-29 22:57:40 -07:00
readfile-context.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
readfile-context.sh
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2023-12-01 12:06:43 -05:00
recursive.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
recursive.sh
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2023-12-01 12:06:43 -05:00
referrers.sh
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2023-12-01 12:06:43 -05:00
regression-484.sh
fix: good errors for failures caused by allowSubstitutes
2024-08-23 17:49:15 -07:00
remote-store.sh
"but doctor, I AM the untrusted store": nix doctor had wrong trustedness
2024-04-08 15:40:12 -07:00
repair.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
repl.sh
src/libcmd/repl.cc: allow :log /path/to/store.drv
2024-08-07 15:58:44 +03:00
restricted.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
restricted.sh
libexpr: Deprecate overriding __sub and the like
2024-11-28 18:15:52 +01:00
search.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
search.sh
cli: eat terminal codes from stdout also
2024-08-04 20:41:19 -07:00
secure-drv-outputs.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
secure-drv-outputs.sh
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2023-12-01 12:06:43 -05:00
selfref-gc.sh
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2023-12-01 12:06:43 -05:00
shell-hello.nix
Merge pull request #9648 from cole-h/nix-shell-ordering
2024-03-04 07:50:55 +01:00
shell.sh
Merge pull request #9648 from cole-h/nix-shell-ordering
2024-03-04 07:50:55 +01:00
signing.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
simple-failing.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
simple.builder.sh
Add pre-commit checks
2024-03-29 22:57:40 -07:00
simple.nix
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2023-12-01 12:06:43 -05:00
simple.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
ssh-relay.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
store-ping.sh
Merge pull request #9632 from cole-h/nix-daemon-testing
2024-03-04 08:17:32 +01:00
structured-attrs.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
structured-attrs.sh
tests: move nix-shell related tests to subdir
2024-10-13 23:12:45 -07:00
substitute-truncated-nar.sh
libutil: remove sinkToSource eof callback
2024-06-23 11:52:49 +00:00
substitute-with-invalid-ca.sh
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2023-12-01 12:06:43 -05:00
suggestions.sh
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2023-12-01 12:06:43 -05:00
supplementary-groups.sh
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2023-12-01 12:06:43 -05:00
symlink-derivation.nix
Merge pull request #10456 from NixOS/fixpermdeniedbind
2024-04-11 15:43:58 +03:00
tarball.sh
treewide: Stop using URL literals
2024-08-17 15:48:10 +00:00
test-infra.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
test-libstoreconsumer.sh
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
test-repl-characterization.sh
Implement a parser for a literate testing system for the repl
2024-03-14 14:30:38 -07:00
timeout.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
timeout.sh
tests: fix functional-timeout
2024-05-28 04:20:00 +00:00
toString-path.sh
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2023-12-01 12:06:43 -05:00
undefined-variable.nix
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2023-12-01 12:06:43 -05:00
user-envs-migration.sh
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user-envs.builder.sh
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2023-12-01 12:06:43 -05:00
user-envs.nix
Put functional tests in tests/functional
2023-12-01 12:06:43 -05:00
user-envs.sh
Merge pull request #9257 from Artturin/nixenvjsondrvpath
2024-03-04 05:59:15 +01:00
why-depends.sh
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zstd.sh
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