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Missing and duplicated files in list #10385

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cyberduck opened this issue Jul 3, 2018 · 16 comments
Closed

Missing and duplicated files in list #10385

cyberduck opened this issue Jul 3, 2018 · 16 comments

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@cyberduck
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@cyberduck cyberduck commented Jul 3, 2018

528c4d9 created the issue

I'm using Cyberduck v6.6.2 (28219) on Mac OS X 10.13.4 High Sierra.
On the sites that I have tried to use Cyberduck with, it fails to list some files and will fail to download them properly.
(It also has other strange behaviour, such as failing to list files alphabetically when I sort by filename).
The attached screenshot shows an example - here I've sorted by filename, but the files with chr19 strangely appear at the top of the list, and the file Tanzania_GWAS-2.5M_b37_chr0X_aligned.vcf.gzis missing from the view. (It is missing from the whole listing although only the top is shown in the screenshot). The second screenshot shows the output of ls done in sftp` in the same folder, correctly listing the contents of the folder.

Digging a bit further, it appears both programs correctly list 104 files, but Cyberduck has duplicated information for some files. Specifically, the top 4 files in the Cyberduck listing (Tanzania_GWAS-2.5M_b37_chr19_aligned.vcf.gz, Tanzania_GWAS-2.5M_b37_chr19_aligned.vcf.gz.tbi, Tanzania_GWAS-2.5M_b37_chr19.vcf.gz and Tanzania_GWAS-2.5M_b37_chr0X.vcf.gz.tbi) all appear again further down the list. The associated information e.g. file size is also repeated. Presumably these duplicate entries replace those for the missing files.


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@cyberduck
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@cyberduck cyberduck commented Jul 9, 2018

@dkocher commented

Please post the transcript from the log drawer (⌘-L).

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@cyberduck cyberduck commented Jul 10, 2018

528c4d9 commented

I've attached the log drawer output (log.txt) from this sequence of operations:
1: connect to the server
2: navigate to the relevant folder
3: double-click on it.

@cyberduck
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@cyberduck cyberduck commented Feb 14, 2019

@dkocher commented

Can you let us know if you still have this bug with the current release.

@cyberduck
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@cyberduck cyberduck commented Feb 15, 2019

528c4d9 commented

This is still an issue in the updated version of Cyberduck, as shown in the attached screenshot.
Best,
Gavin.

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@cyberduck cyberduck commented Feb 15, 2019

@dkocher commented

I suppose it is not possible to get a temporary account on the server to reproduce the issue?

@cyberduck
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@cyberduck cyberduck commented Feb 15, 2019

528c4d9 commented

I can ask about this - can you send your public key?
Thanks,
g.

@cyberduck
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@cyberduck cyberduck commented Feb 15, 2019

@dkocher commented

Replying to [comment:9 gavinband]:

I can ask about this - can you send your public key?
Thanks,
g.

-----BEGIN PGP PUBLIC KEY BLOCK-----
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WCoQsIzYE0Xcpni/JdQYHqfrgn6bpPMyjFwGCgYgJA0qsUz5PAc01WGuaUHkBy+d
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iDIAA/4kYypTf1EJSjEgyPKzzPCkbfr/GNzadLt8SoV0rtg2EyJpSKe5Mt67E26d
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KTRLt56e2pNz9WzbWGS2wfomlL+g5mNC/qjz89KB2VJGsmDNFLQsRGF2aWQgS29j
aGVyIChTd2l0emVybGFuZCkgPGRrb2NoZXJAc3Vkby5jaD6IXwQTEQIAHwIbAwQL
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bncv7y/OloIZZ5+LmE/o2c0sAJ9Axb+uei4jksGwSyarZrgyIIL0FbQna2V5YmFz
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LZZJAQrc1Bo1nIQRAJ4+DX+v1pr2iGn3BbnZhsh+j1heWQ==
=w3zG
-----END PGP PUBLIC KEY BLOCK-----

@cyberduck
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@cyberduck cyberduck commented Feb 18, 2019

528c4d9 commented

Hi, do you have an ssh public key for this, rather than a gpg one?
Thanks,
g.

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@cyberduck cyberduck commented Feb 23, 2019

@dkocher commented

Replying to [comment:11 gavinband]:

Hi, do you have an ssh public key for this, rather than a gpg one?
Thanks,
g.

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDplFjFCWXZmp9/Dy30JsZdP8QcKBqhjVReiBrBEolpbywdbqqZyHFcVFyyPb92d2+4p6++M0cddMVPQ1MEZjXd8PTpm9XR09wrHq0DrHvkArhI+2lpsZ3wm2DxeGl3mhv8U8jXgcMLjjGF+mDN2t0p58+Qawb7qfWUMjUQN2BhmKCT5fgzKu0dKUtZi7FSfU6U1223pwB2k8iGdYeLftNvEe0aZiTsa695IqjL1rUMRpiTlnn/ip2CiJZlZjem2rnnPZFNsfFQLuLGGDYWboTxz9nHbcsbvAMzckiqpXM1GdojMFSMPV8sS7mjLRhmOs6bG6nrsygNu26O4wdyULoL dkocher@mellifera.local

@cyberduck
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@cyberduck cyberduck commented Feb 25, 2019

528c4d9 commented

Hi,
Thanks - please try now: tanzania-gwas@ftp.malariagen.net, accessed by sftp using the ssh key you've sent. The problem can be seen in:

/home/datarelease/data/callsets/genotyped/Tanzania_GWAS-2.5M_b37/master/

As reported the problems are

1: the list of files is incorrect (e.g. files with 'Tanzania_GWAS-2.5M_b37_chr19.vcf.gz' in appear twice in the list, including at the top after sorting by filename), while other files including the file 'Tanzania_GWAS-2.5M_b37_chr0X.vcf.gz' is missing.

2: There is equally a problem when downloading the whole folder of files - I think, but am not sure, that this has to do with trying to download Tanzania_GWAS-2.5M_b37_chr0X.vcf.gz but actually downloading Tanzania_GWAS-2.5M_b37_chr19.vcf.gz. (Sorry I realise this is vague, I can re-download to be more specific about this aspect of the problem, but maybe solving problem #1 will fix this.)

I am using Cyberduck 6.9.3 on a 2014 Macbook Pro running macOS High Sierra (10.13.6).

(Please note this data is restricted access - fine to download/access for testing purposes but please delete afterwards.)

Many thanks for your help with this,
Gavin.

@cyberduck
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@cyberduck cyberduck commented Feb 25, 2019

528c4d9 commented

FYI that should be:

tanzania-gwas AT ftp DOT malariagen DOT net .

Best wishes,
Gavin.

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@cyberduck cyberduck commented Feb 25, 2019

@dkocher commented

The list view (View → as List) is not affected by this bug.

@cyberduck
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@cyberduck cyberduck commented Feb 25, 2019

@dkocher commented

We can reproduce the issue which is caused by a hashing collision for 19 and 0X.

@cyberduck
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@cyberduck cyberduck commented Feb 25, 2019

@dkocher commented

Replying to [comment:14 gavinband]:

FYI that should be:

tanzania-gwas AT ftp DOT malariagen DOT net .

Best wishes,
Gavin.

Thanks for providing the test account which was very helpful to find the cause of this bug. We can reproduce the issue and you can revoke access.

@cyberduck
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@cyberduck cyberduck commented Feb 26, 2019

@ylangisc commented

In 6683fdf. Thanks for reporting this.

@cyberduck cyberduck closed this Feb 26, 2019
@cyberduck
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@cyberduck cyberduck commented Aug 22, 2019

@dkocher commented

Revised in 69de759.

@iterate-ch iterate-ch locked as resolved and limited conversation to collaborators Nov 26, 2021
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