Merge branch 'master' of ssh://git-annex.branchable.com
This commit is contained in:
Joey Hess
commit
9adc0b3417
3 changed files with 128 additions and 0 deletions
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### Please describe the problem.
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It seems fully and correctly obtain `get` a file but it ended up in tmp/, upon attempts to reget tries to reget it with incorrect range (since fully here already):
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[[!format sh """
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$> datalad install -g http://github.com/openneurodatasets/ds000001
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install(notneeded): /mnt/btrfs/scrap/tmp/openneuro/ds000001 (dataset) [dataset <Dataset path=/mnt/btrfs/scrap/tmp/openneuro/ds000001> was already cloned from 'http://github.com/openneurodatasets/ds000001']
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[WARNING] Running get resulted in stderr output: download failed: Requested Range Not Satisfiable
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download failed: Requested Range Not Satisfiable
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git-annex: get: 1 failed
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[ERROR ] from s3-PUBLIC...; from s3-PUBLIC...; Unable to access these remotes: s3-PUBLIC; Try making some of these repositories available:; b5dd2e3d-825f-4bc2-b719-cba1059f6bfc -- root@93184394ac19:/datalad/ds000001; deaa691f-c824-4416-9bf8-a94a47dd31b5 -- [s3-PUBLIC]; ; (Note that these git remotes have annex-ignore set: origin) [get(/mnt/btrfs/scrap/tmp/openneuro/ds000001/sub-03/func/sub-03_task-balloonanalogrisktask_run-03_bold.nii.gz)]
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[WARNING] could not get some content in /mnt/btrfs/scrap/tmp/openneuro/ds000001 ['/mnt/btrfs/scrap/tmp/openneuro/ds000001/sub-03/func/sub-03_task-balloonanalogrisktask_run-03_bold.nii.gz'] [get(/mnt/btrfs/scrap/tmp/openneuro/ds000001)]
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action summary:
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get (error: 1, impossible: 1)
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install (notneeded: 1)
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1 14492 ->1.....................................:Mon 05 Nov 2018 10:36:53 PM EST:.
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smaug:/mnt/btrfs/scrap/tmp/openneuro
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$> cd ds000001
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CHANGES dataset_description.json sub-01/ sub-03/ sub-05/ sub-07/ sub-09/ sub-11/ sub-13/ sub-15/ task-balloonanalogrisktask_bold.json
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README participants.tsv sub-02/ sub-04/ sub-06/ sub-08/ sub-10/ sub-12/ sub-14/ sub-16/
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1 14493.....................................:Mon 05 Nov 2018 10:36:56 PM EST:.
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(git)smaug:/mnt/btrfs/scrap/tmp/openneuro/ds000001[master]
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$> git annex get --debug
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[2018-11-05 22:36:59.665601708] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","symbolic-ref","-q","HEAD"]
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[2018-11-05 22:36:59.669131907] process done ExitSuccess
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[2018-11-05 22:36:59.669205841] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","refs/heads/master"]
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[2018-11-05 22:36:59.672930992] process done ExitSuccess
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[2018-11-05 22:36:59.673020181] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--cached","-z","--"]
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get sub-03/func/sub-03_task-balloonanalogrisktask_run-03_bold.nii.gz [2018-11-05 22:36:59.686205786] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","git-annex"]
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[2018-11-05 22:36:59.690089151] process done ExitSuccess
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[2018-11-05 22:36:59.690165258] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
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[2018-11-05 22:36:59.693038961] process done ExitSuccess
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[2018-11-05 22:36:59.693248238] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","log","refs/heads/git-annex..4fd548ce0d4e2bc67da62795e80880a7ae1f6abc","--pretty=%H","-n1"]
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[2018-11-05 22:36:59.697945062] process done ExitSuccess
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[2018-11-05 22:36:59.698564444] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch"]
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[2018-11-05 22:36:59.698998042] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch-check=%(objectname) %(objecttype) %(objectsize)"]
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(from s3-PUBLIC...)
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[2018-11-05 22:36:59.734434115] Request {
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host = "openneuro.org.s3.amazonaws.com"
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port = 80
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secure = False
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requestHeaders = [("Range","bytes=46216487-"),("Accept-Encoding","identity"),("User-Agent","git-annex/6.20181011+git124-g94aa0e2f6-1~ndall+1")]
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path = "/ds000001/sub-03/func/sub-03_task-balloonanalogrisktask_run-03_bold.nii.gz"
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queryString = "?versionId=KKf9EeO6JyGQbKG_SyU51ehWSYeXiMX9"
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method = "GET"
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proxy = Nothing
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rawBody = False
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redirectCount = 10
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responseTimeout = ResponseTimeoutDefault
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requestVersion = HTTP/1.1
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}
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download failed: Requested Range Not Satisfiable
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(from s3-PUBLIC...)
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[2018-11-05 22:36:59.815117255] Request {
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host = "openneuro.org.s3.amazonaws.com"
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port = 80
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secure = False
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requestHeaders = [("Range","bytes=46216487-"),("Accept-Encoding","identity"),("User-Agent","git-annex/6.20181011+git124-g94aa0e2f6-1~ndall+1")]
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path = "/ds000001/sub-03/func/sub-03_task-balloonanalogrisktask_run-03_bold.nii.gz"
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queryString = "?versionId=KKf9EeO6JyGQbKG_SyU51ehWSYeXiMX9"
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method = "GET"
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proxy = Nothing
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rawBody = False
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redirectCount = 10
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responseTimeout = ResponseTimeoutDefault
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requestVersion = HTTP/1.1
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}
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download failed: Requested Range Not Satisfiable
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Unable to access these remotes: s3-PUBLIC
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Try making some of these repositories available:
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b5dd2e3d-825f-4bc2-b719-cba1059f6bfc -- root@93184394ac19:/datalad/ds000001
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deaa691f-c824-4416-9bf8-a94a47dd31b5 -- [s3-PUBLIC]
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(Note that these git remotes have annex-ignore set: origin)
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failed
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[2018-11-05 22:36:59.852095523] process done ExitSuccess
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[2018-11-05 22:36:59.85253563] process done ExitSuccess
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git-annex: get: 1 failed
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$> du -scb .git/annex/tmp/MD5E-s46216487--ec7b8fc23a313f1429e941fd94c2d268.nii.gz
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46216487 .git/annex/tmp/MD5E-s46216487--ec7b8fc23a313f1429e941fd94c2d268.nii.gz
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46216487 total
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$> md5sum .git/annex/tmp/MD5E-s46216487--ec7b8fc23a313f1429e941fd94c2d268.nii.gz
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ec7b8fc23a313f1429e941fd94c2d268 .git/annex/tmp/MD5E-s46216487--ec7b8fc23a313f1429e941fd94c2d268.nii.gz
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$> git annex version
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git-annex version: 6.20181011+git124-g94aa0e2f6-1~ndall+1
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"""]]
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Not sure why it ended up not moved into the proper location but I think upon redownload, size should be verified, if "Full" - try to proceed to checksum verification etc.
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[[!comment format=mdwn
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username="metst13@1d16544ec52801db7efb2895d3dc7a4458b8eb45"
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nickname="metst13"
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avatar="http://cdn.libravatar.org/avatar/168d629704097ddc596f75ca32a687a3"
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subject="clone to the server"
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date="2018-11-06T14:58:39Z"
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content="""
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As usually, create a directory on the server, `git init`, then `git-annex init` there.
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Add that locally: `git remote add my-server-name my-server:~/my-repo`
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`git-annex sync` locally seems to work fine and pushes data to the server.
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I needed to have this workaround before, because I could not get data from my laptop while on the server (I wasn't sure I had an open IP address for my laptop). This is mostly a basic thing in git, but I had errors with git-annex earlier and I try to be cautious now.
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"""]]
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[[!comment format=mdwn
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username="metst13@1d16544ec52801db7efb2895d3dc7a4458b8eb45"
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nickname="metst13"
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avatar="http://cdn.libravatar.org/avatar/168d629704097ddc596f75ca32a687a3"
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subject="comment 6"
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date="2018-11-06T16:10:11Z"
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content="""
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I must add that after the previous commands finished, content of the repository was not shown on the server (it was all in .git). I made
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git checkout synced/master
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and files appeared. Unfortunately it seems all timestamps were new, which I didn't like, and it was already asked here (http://git-annex.branchable.com/todo/does_not_preserve_timestamps/).
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"""]]
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