#57 Problem 'get-content' command

Hi,

I am downloading content from gin and everything has been going well but now I'm having issues with the files not actually being downloaded. When I check the files it still remains as a placeholder (size is 64 bytes and it should be 75MB). 'gin ls' shows everything is ok and green so I don't know what the issue is. It has been working fine until now. Any suggestions of what might be the issue?

Thanks! Sara

Depending on where the file was originally added (what operating system and which defaults it uses), the files may be added as "locked". On Windows, locked files remain as placeholders until you unlock them. On other platforms (Linux and macOS), locked files are links to the content.

To unlock a file you can run

gin unlock <path>

or

gin unlock .

to unlock everything under the current working directory (recursively).

You can save this change with a

gin commit <path>

and then pushed with

gin upload

This will make the files be unlocked the next time they're downloaded by anyone.

Thank you!

I tried this but it didn't work...

I also tried 'remove-content' and then again, 'get-content'

It displays as if there's no problem, but when I check the file, again it has not downloaded the content....

I was working on this all day (downloading content from the remote repo) and this issue just started this afternoon...

I'm sorry you're having trouble with this. I'd like to ask you to try a few diagnostic steps to see what's going on. Can you please paste the results of the following commands? Replace <filename> with the path to one of the files that present the issue:

1. gin annex whereis <filename> this should show all the locations that have the file contents (should be server and local computer)
2. gin annex info this will show us the IDs of each location and how many annexed files are locally
3. cat <filename> to see the contents of the file to determine if it's some kind of corruption or it is in fact a pointer file
4. gin annex info <filename> to show us the id of the file and some extra information

Thank you so much! Here they are:

1: whereis a_00001.tif (3 copies)

    5079b0eb-2fa6-4ca1-9af5-e6f37da5f61e -- Moberg@DESKTOP-1CV6OU3
    ba79057c-cb4b-4c87-8114-ad3318e490ec -- git@def205aad250:/data/repos/larkumlab/sara_moberg_association_formation.git [origin]
    c907c6e2-8c40-47f7-8684-d22ec1c88820 -- Moberg@DESKTOP-A8EI0PU [here]

2: trusted repositories: 0 semitrusted repositories: 24

    00000000-0000-0000-0000-000000000001 -- web
    00000000-0000-0000-0000-000000000002 -- bittorrent
    1efac426-6c58-4f77-8e1c-549bb02d9451 -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    2e1f5d5c-e353-4859-9ddc-057c49aca41f -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    41b64453-a082-412a-8bac-a93cfbd587dd -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    435cc52f-5448-4aea-b0eb-57ea519676d5 -- Moberg@DESKTOP-34JF2HD
    4d4a2581-9083-4b21-a7fd-0246333b51c4 -- git@def205aad250:/data/tmp/appdata/tmp/local-repo/1619
    4def2a49-04c3-4e80-879e-9c1307feebee -- Moberg@DESKTOP-34JF2HD
    50247185-5737-41d3-a668-4fa6dee10069 -- moberg@DESKTOP-TSB8H9C
    5079b0eb-2fa6-4ca1-9af5-e6f37da5f61e -- Moberg@DESKTOP-1CV6OU3
    564aa3b2-24d0-4f70-a803-d3d9371f8820 -- moberg@DESKTOP-TSB8H9C
    5a085806-dec1-455d-9f48-36f76c8b9b16 -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    704f5231-e7d6-48d1-926b-1c0ad2594a5d -- git@b71abff825ef:/data/tmp/appdata/tmp/local-repo/1619
    82213ca4-d8c6-418b-8df0-ab41e5dfc54a -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    91322776-5641-4ff3-bad8-2c943bd8f736 -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    972210d7-bd11-4a30-b63c-ec029a1d2388 -- Moberg@DESKTOP-A8EI0PU
    ba79057c-cb4b-4c87-8114-ad3318e490ec -- git@def205aad250:/data/repos/larkumlab/sara_moberg_association_formation.git [origin]
    bd766067-a0d8-4f5e-8644-6566bbf3e447 -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    c907c6e2-8c40-47f7-8684-d22ec1c88820 -- Moberg@DESKTOP-A8EI0PU [here]
    d52987bb-6233-4f28-8aa7-38a9f5b21bbc -- Moberg@DESKTOP-A8EI0PU
    e067b8c8-630a-433e-af09-9e7976799646 -- moberg@DESKTOP-TSB8H9C
    ec89f990-ed7a-4a26-a306-04c889edb5a4 -- git@c3d83a1cb62f:/data/tmp/appdata/tmp/local-repo/1619
    f66da87f-4cef-4408-95bb-9e65aea3438e -- moberg@DESKTOP-TSB8H9C
    faab4d47-047e-469e-91c9-905ef73f42a5 -- colombj@MacBook-Pro-4:~/github_repo/07_larkumlabrepos/sara_moberg_association_formation

untrusted repositories: 0 transfers in progress: none available local disk space: 154.35 gigabytes (+1 megabyte reserved) temporary object directory size: 57.55 megabytes (clean up with git-annex unused) local annex keys: 300 local annex size: 42.87 gigabytes annexed files in working tree: 5893 size of annexed files in working tree: 587.29 gigabytes bloom filter size: 32 mebibytes (0.1% full) backend usage:

    MD5: 5893

3: /annex/objects/MD5-s79023734--6d6402beda

4: file: a_00001.tif size: 79.02 megabytes key: MD5-s79023734--6d6402beda present: true

This last one is very strange to me, it seems as it shows the file to be present, with the content, but when I physically press on the file, the size shows as 64 bytes....

yes, everything seems normal. It's like I suspected in the beginning: the file is a pointer file but the content is available locally. It's strange that the unlocking didn't do anything. Can you try again to unlock just this file? Let's try with plain git annex (without gin).

git annex unlock a_00001.tif

and paste any output. Then check the individual file if it's there.

Good morning!

I tried unlocking using git but nothing happens.... I think it's as if it's already unlocked from the command before...

This is very strange. I had a quick look at the server-side repository and there don't seem to be any issues. Is it possible something is corrupted with the local clone? Can you try cloning it again from the server and trying to gin get and gin unlock just one of the files experiencing the issue as a test?

This worked!

I re-downloaded the whole repository and then just tried the 'get-content' command and now I have the file with its full content.

That's great news. Happy it worked out. I'd like to ask for some information so I could maybe figure out what went wrong. Do you mind sending me the following files to gin@g-node.org:

• the gin client log file: on Windows it should be at C:\Users\<User>\AppData\Local\g-node\gin
• the configuration for the repository with the issue: in the local repository, it's under .git\config

You can close the issue if everything is okay now.

Ok, great, will do!

Thanks for your help!

Cheers, Sara