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Merge branch 'master' of ssh://git-annex.branchable.com

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Joey Hess 2019-01-05 11:27:49 -04:00
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I recently noticed that a file I thought I had on one of my repositories was missing, so I decided to get it:
chymera@clusterhost ~/ni_data/ofM.dr $ git annex get 20151226_112356_4012_1_7/2/pulseprogram
get 20151226_112356_4012_1_7/2/pulseprogram (from data0...)
git-annex-shell: failed to read git config of git repository in zenhost on /run/media/chymera/data0/ni_data; perhaps this repository is not set up correctly or has moved
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.3]
rsync failed -- run git annex again to resume file transfer
(from data1...)
git-annex-shell: failed to read git config of git repository in zenhost on /run/media/chymera/data1/ni_data; perhaps this repository is not set up correctly or has moved
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.3]
rsync failed -- run git annex again to resume file transfer
(from quiethost...)
ssh: connect to host localhost port 2225: Connection refused
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: unexplained error (code 255) at io.c(226) [Receiver=3.1.3]
rsync failed -- run git annex again to resume file transfer
(from zenhost...)
SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
32,243 100% 7.69MB/s 0:00:00 (xfr#1, to-chk=0/1)
(checksum...) ok
(recording state in git...)
chymera@clusterhost ~/ni_data/ofM.dr $ ls -lah 20151226_112356_4012_1_7/2/pdata/1/
total 468K
drwxr-sr-x 2 chymera wheel 4.0K Nov 2 2017 .
drwxr-sr-x 3 chymera wheel 4.0K Mar 20 2017 ..
-rw-r-Sr-- 1 chymera wheel 422K Mar 20 2017 2dseq
-rw-r-Sr-- 1 chymera wheel 356 Mar 20 2017 id
-rw-r-Sr-- 1 chymera wheel 420 Mar 20 2017 methreco
-rw-r-Sr-- 1 chymera wheel 349 Mar 20 2017 procs
-rw-r-Sr-- 1 chymera wheel 9.1K Mar 20 2017 reco
-rw-r-Sr-- 1 chymera wheel 8.3K Nov 2 2017 visu_pars
chymera@clusterhost ~/ni_data/ofM.dr $ ls -lah 20151226_112356_4012_1_7/2/pulseprogram
lrwxrwxrwx 1 chymera wheel 195 Dec 25 22:01 20151226_112356_4012_1_7/2/pulseprogram -> ../../../.git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
chymera@clusterhost ~/ni_data/ofM.dr $ git annex get 20151226_112356_4012_1_7/2/pulseprogram
chymera@clusterhost ~/ni_data/ofM.dr $ ls -lah 20151226_112356_4012_1_7/2/pdata/1/^C
chymera@clusterhost ~/ni_data/ofM.dr $ git annex direct
chymera@clusterhost ~/ni_data/ofM.dr $ git annex get 20151226_112356_4012_1_7/2/pulseprogram
chymera@clusterhost ~/ni_data/ofM.dr $ ls -lah 20151226_112356_4012_1_7/2/pulseprogram
lrwxrwxrwx 1 chymera wheel 195 Dec 25 22:01 20151226_112356_4012_1_7/2/pulseprogram -> ../../../.git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
chymera@clusterhost ~/ni_data/ofM.dr $ git annex drop 20151226_112356_4012_1_7/2/pulseprogram
drop 20151226_112356_4012_1_7/2/pulseprogram (locking data0...) (lockcontent failed) (checking data0...) git-annex-shell: failed to read git config of git repository in zenhost on /run/media/chymera/data0/ni_data; perhaps this repository is not set up correctly or has moved
(locking data1...) (lockcontent failed) (checking data1...) git-annex-shell: failed to read git config of git repository in zenhost on /run/media/chymera/data1/ni_data; perhaps this repository is not set up correctly or has moved
(locking quiethost...) (lockcontent failed) (checking quiethost...) ssh: connect to host localhost port 2225: Connection refused
(locking zenhost...) ok
(recording state in git...)
chymera@clusterhost ~/ni_data/ofM.dr $ git annex get 20151226_112356_4012_1_7/2/pulseprogram
get 20151226_112356_4012_1_7/2/pulseprogram (from data0...)
git-annex-shell: failed to read git config of git repository in zenhost on /run/media/chymera/data0/ni_data; perhaps this repository is not set up correctly or has moved
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.3]
rsync failed -- run git annex again to resume file transfer
(from data1...)
git-annex-shell: failed to read git config of git repository in zenhost on /run/media/chymera/data1/ni_data; perhaps this repository is not set up correctly or has moved
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.3]
rsync failed -- run git annex again to resume file transfer
(from quiethost...)
ssh: connect to host localhost port 2225: Connection refused
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: unexplained error (code 255) at io.c(226) [Receiver=3.1.3]
rsync failed -- run git annex again to resume file transfer
(from zenhost...)
SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
32,243 100% 30.75MB/s 0:00:00 (xfr#1, to-chk=0/1)
(checksum...) ok
(recording state in git...)
chymera@clusterhost ~/ni_data/ofM.dr $ ls -lah 20151226_112356_4012_1_7/2/pulseprogram
lrwxrwxrwx 1 chymera wheel 195 Dec 25 22:01 20151226_112356_4012_1_7/2/pulseprogram -> ../../../.git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
Even after git-annex states it fetched it, the symlink is still broken.
On my other remote, however, it's perfectly fine:
chymera@zenhost ~/ni_data/ofM.dr $ ls -lah 20151226_112356_4012_1_7/2/pulseprogram
lrwxrwxrwx 1 chymera wheel 195 May 23 2018 20151226_112356_4012_1_7/2/pulseprogram -> ../../../.git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624

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[[!comment format=mdwn
username="Chymera"
avatar="http://cdn.libravatar.org/avatar/555d585d6d78c68894ac90fd1e984309"
subject="comment 1"
date="2019-01-04T21:08:54Z"
content="""
Interestingly stat claims the target file is missing in both repos:
chymera@clusterhost ~/ni_data/ofM.dr $ stat .git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
stat: cannot stat '.git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624': No such file or directory
chymera@zenhost ~/ni_data/ofM.dr $ stat .git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624
stat: cannot stat '.git/annex/objects/vz/WW/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624/SHA256E-s32243--feae20d26c487947f9ad30019459464ba5a206a4ae6149a9d10fa4100c64f624': No such file or directory
But the tail command works on the file on one of the repos:
chymera@clusterhost ~/ni_data/ofM.dr $ tail -10 20151226_112356_4012_1_7/2/pulseprogram
tail: cannot open '20151226_112356_4012_1_7/2/pulseprogram' for reading: No such file or directory
chymera@zenhost ~/ni_data/ofM.dr $ tail -10 20151226_112356_4012_1_7/2/pulseprogram
exit
# 147 \"/opt/PV6.0/exp/stan/nmr/lists/pp/FLASHAngio.ppg\"
ph0 = 0
ph1 = 0
# 153 \"/opt/PV6.0/exp/stan/nmr/lists/pp/FLASHAngio.ppg\"
"""]]

8
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[[!comment format=mdwn
username="Chymera"
avatar="http://cdn.libravatar.org/avatar/555d585d6d78c68894ac90fd1e984309"
subject="comment 2"
date="2019-01-04T23:05:43Z"
content="""
turns out I need to do `git annex inidrect` and then `git annex direct` for my files to be detected, this software is really strange
"""]]