[Loris-dev] upload_file.pl issue

[Ioannis Pappas]

Hi Nicolas.

Apologies for the late reply but I wanted to look into it more with the kind help of Julie (our sys admin). For your information the exact error is this:

Can't cd to (/tmp/ImagingUpload-15-8-Z8Hax5/) BR013_243782_V1: Permission denied
at /data/loris-mri/bin/mri/uploadNeuroDB/NeuroDB/ImagingUpload.pm line 202.

However, I can write in /tmp no problem e.g. 

[lorisadmin at loris ~]$ mkdir /tmp/ImagingUpload-15-8-Z8Hax5/
[lorisadmin at loris ~]$ ls -ld /tmp/ImagingUpload-15-8-Z8Hax5/
drwxrwxr-x 2 lorisadmin lorisadmin 4096 Sep 17 15:14 /tmp/ImagingUpload-15-8-Z8Hax5/

I think that the problem is that the perl script doesn’t make the temporary directory after unzipping in /tmp and then all of sudden it wants to cd there (that’s why I get “permission denied” it just doesn’t exist).
My .zip (BR013_243782_V1.zip) contains one folder (BR013_243782_V1) of .dcm files for simplicity. Should there be some internal structure there (or something else in terms of naming)?

Thank you very much. 

Best wishes,
Ioannis 





> On Sep 15, 2020, at 1:44 PM, Nicolas Brossard <nicolasbrossard.mni at gmail.com> wrote:
> 
> Hi Ioannis,
> 
> No worries, we're here to help!
> 
> On Unix systems, all users usually have permission to create directories in /tmp but just to be sure it'd be good idea to test that: just try
> 
> % mkdir /tmp/hello
> 
> and see if that works. If it does, then it means there's something more "sneaky" going on.
> 
> You can try specifying an alternate temporary directory in which the upload script will write files: just type the following line in your environment file (located in the LORIS-MRI root directory):
> 
> export TMPDIR=/my/alternate/temporary/dir
> 
> 
> Let me know if that helps.
> 
> 
> Cheers,
> Nicolas
> 
> 
> On Tue, Sep 15, 2020 at 4:23 PM Ioannis Pappas <ioannis at berkeley.edu <mailto:ioannis at berkeley.edu>> wrote:
> Hi Loris support.
> 
> Another quick question (hopefully I don’t occupy a lot of your time during this pandemic).
> 
> I am running the simple imaging upload pearl script like this:
> 
> sudo -i -u lorisadmin /data/loris-mri/bin/mri/uploadNeuroDB/imaging_upload_file.pl <http://imaging_upload_file.pl/> -profile prod -upload_id 2 /data/loris/incoming/BR013_243782_V1.zip -verbose
> 
> I think the script involves creating some directories because it leads to an error. The error is this:
> 
> mkdir /tmp/ImagingUpload-13-7-7Z_JFF/BR013_243782_V1/BIAS_12ch_22: Permission denied at /usr/local/share/perl5/Archive/Zip/DirectoryMember.pm 
> 
> Do you guys think it has to do with my permission at /tmp or there is something else more sneaky? The /tmp folder doesn’t seem to have anything related to ImagingUpload[..]
> 
> Thank you very much. Hopefully I don’t see more errors in the script.
> 
> Best wishes,
> Ioannis
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