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Joey Hess 2018-11-09 13:04:14 -04:00
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doc/bugs/annex_get_-J_16_via_ssh_stalls_/comment_29_c18ec0797bd55780a0851c3b0c71b184._comment Normal file
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 29"
date="2018-11-06T20:01:08Z"
content="""
whoohoo! thanks! am I reading changelog correctly that fix should be \"applied\" on remote side (`git-annex-shell`) and not on local (`git annex get`)?
"""]]

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doc/bugs/multiple_ssh_prompts__44___and_thread_blocked_indefinitely_in_an___63____63____63___transaction.mdwn Normal file
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### Please describe the problem.
Originally reported (so more details could be found there) in [datalad issue #2988].
While trying to `annex get` on local cluster, over ssh without a ssh-agent, I was prompted for password multiple times, although previous version didn't do it:
[[!format sh """
[yhalchen@discovery7 QA]$ git annex version | head -n1 ; git annex get -J2 sub-qa/
git-annex version: 6.20180926-gc906aaf
get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2Xs4_dwi.nii.gz get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2_dwi.nii.gz (from origin...)
(from origin...)
yoh@falkor.datalad.org's password: yoh@falkor.datalad.org's password:
"""]]
and when I try an "imputated" from NeuroDebian .deb package recent build of git-annex then I am observing
[[!format sh """
[yhalchen@discovery7 QA]$ export PATH=/ihome/yhalchen/7.20181105+git22-g4c7236c58/usr/lib/git-annex.linux:$PATH
[yhalchen@discovery7 QA]$ git annex version | head -n1 ; git annex get -J2 sub-qa/
git-annex version: 7.20181105+git22-g4c7236c58-1~ndall+1
get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2Xs4_dwi.nii.gz get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2_dwi.nii.gz (transfer already in progress, or unable to take transfer lock)
Unable to access these remotes: origin
Try making some of these repositories available:
6384a551-a41d-4290-b186-9258befede97 -- bids@rolando:/inbox/BIDS/dbic/QA
7d9ed214-3e5f-4cc8-ac88-f397145b2d4c -- yoh@falkor:/srv/datasets.datalad.org/www/dbic/QA [origin]
ba8f2cea-f229-422c-82be-6580e5e07ed5 -- yoh@smaug:/mnt/datasets/datalad/crawl/dbic/QA
failed
get sub-qa/ses-20161128/func/sub-qa_ses-20161128_task-rest_acq-p2Xs4X35mm_bold.nii.gz (from origin...)
(from origin...)
thread blocked indefinitely in an MVar operation
thread blocked indefinitely in an STM transaction
Unable to access these remotes: origin
Unable to access these remotes: origin
Try making some of these repositories available:
6384a551-a41d-4290-b186-9258befede97 -- bids@rolando:/inbox/BIDS/dbic/QA
7d9ed214-3e5f-4cc8-ac88-f397145b2d4c -- yoh@falkor:/srv/datasets.datalad.org/www/dbic/QA [origin]
ba8f2cea-f229-422c-82be-6580e5e07ed5 -- yoh@smaug:/mnt/datasets/datalad/crawl/dbic/QA
failed
Try making some of these repositories available:
6384a551-a41d-4290-b186-9258befede97 -- bids@rolando:/inbox/BIDS/dbic/QA
7d9ed214-3e5f-4cc8-ac88-f397145b2d4c -- yoh@falkor:/srv/datasets.datalad.org/www/dbic/QA [origin]
ba8f2cea-f229-422c-82be-6580e5e07ed5 -- yoh@smaug:/mnt/datasets/datalad/crawl/dbic/QA
failed
git-annex: thread blocked indefinitely in an STM transaction
"""]]
so smells like may be recent fixes caused some other locking problems
This is on an NFS mounted partition, but remains the same when run under `/tmp`
Running a significantly more outdated version I found laying around (6.20170815+gitg22da64d0f-1~ndall+1) shows a single password prompt
[[!meta author=yoh]]

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doc/forum/Getting__58___hGetChar__58___illegal_operation___40__handle_is_closed__41__/comment_1_9ff60145d7dfb6785bb11f2a23040948._comment Normal file
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 1"
date="2018-11-06T22:16:39Z"
content="""
FWIW -- observed similar one while testing [the fresh fix](http://git-annex.branchable.com/bugs/annex_get_-J_16_via_ssh_stalls_/#comment-2abcda07d2832b923f1e7aa12778b734) under -J10 over ssh:
[[!format sh \"\"\"
get sourcedata/sub-emmet/ses-20180521/fmap/sub-emmet_ses-20180521_acq-topupXb0X3mm_dir-AP_epi.dicom.tgz (from origin...)
Lost connection (fd:90: hGetChar: illegal operation (handle is closed))
Unable to access these remotes: origin
Try making some of these repositories available:
...
failed
\"\"\"]]
"""]]

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doc/forum/assistant_to_have_synced_folders/comment_5_6db901470af7dc7e1da90839fc08c121._comment Normal file
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[[!comment format=mdwn
username="andrew"
avatar="http://cdn.libravatar.org/avatar/acc0ece1eedf07dd9631e7d7d343c435"
subject="comment 5"
date="2018-11-08T13:06:55Z"
content="""
Could you post the output to `git annex version` are you on latest git-annex? As well can you post any information you are willing to share from `.git/config` on each of the repos in question. Also I would recommend creating two new repos from the web interface of git annex assistant (locally) and see if they behave as expected.
"""]]

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doc/forum/assistant_to_have_synced_folders/comment_6_0ec093a51b3dab465907074beb423848._comment Normal file
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[[!comment format=mdwn
username="andrew"
avatar="http://cdn.libravatar.org/avatar/acc0ece1eedf07dd9631e7d7d343c435"
subject="comment 6"
date="2018-11-08T13:10:23Z"
content="""
Also you said “i always have to run git annex sync do get the new files or repo A in repo B”, did you mean you have to run `git annex sync --content`? Or did you mean you are just getting the filenames in sync without the content?
"""]]

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doc/todo/Retire_Esqueleto_as_a_dependency/comment_2_3a3143db7124fe8790b23fdc820a7eed._comment Normal file
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[[!comment format=mdwn
username="seantparsons"
avatar="http://cdn.libravatar.org/avatar/616fb81847630239dd1ab099138cb685"
subject="comment 2"
date="2018-11-06T22:50:25Z"
content="""
I've pushed the fix needed to my branch: [[https://github.com/seanparsons/git-annex/tree/remove-esqueleto]]
This seems certianly wrong; it's lost the NOT.
Well spotted, I even remember double checking the not equal syntax, that should be fixed now.
Is there any way to verify the same or equivilant SQL gets generated?
I don't believe so, but I'm not an expert in either project I mostly just turned the \"fix compile errors until there are none\" crank.
Not clear from persistent's documentation if deleteWhere with two Filters combines them with AND or OR?
From the docs relating to the `Filter` type ([[http://hackage.haskell.org/package/persistent-2.9.0/docs/Database-Persist.html#v:-124--124-.]]):
If you are looking for an (&&.) operator to do (A AND B AND (C OR D)) you can use the (++) operator instead as there is no (&&.).
That seems pretty conclusive multiple entries in a list are combined with `FilterAnd`.
Do we know that an empty Filter list matches everything as used below instead of nothing? Not clear to me from the documentation.
Yup, the type hint indicates that it relates to the table: https://www.yesodweb.com/book/persistent#persistent_delete
it would be good to expand the test suite to test the SQL code in isolation
I can probably look at adding some more tests this weekend.
"""]]