
<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Nicolas.<div class=""><br class=""><div class="">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:</div><div class=""><br class=""></div><div class="">Can't cd to (/tmp/ImagingUpload-15-8-Z8Hax5/) BR013_243782_V1: Permission denied<br class="">at /data/loris-mri/bin/mri/uploadNeuroDB/NeuroDB/ImagingUpload.pm line 202.</div><div class=""><br class=""></div><div class="">However, I can write in /tmp no problem e.g. </div><div class=""><br class=""></div><div class="">[lorisadmin@loris ~]$ mkdir /tmp/ImagingUpload-15-8-Z8Hax5/<br class="">[lorisadmin@loris ~]$ ls -ld /tmp/ImagingUpload-15-8-Z8Hax5/<br class="">drwxrwxr-x 2 lorisadmin lorisadmin 4096 Sep 17 15:14 /tmp/ImagingUpload-15-8-Z8Hax5/<br class=""></div><div class=""><br class=""></div><div class="">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).</div><div class="">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)?</div><div class=""><br class=""></div><div class="">Thank you very much. </div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Ioannis </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 15, 2020, at 1:44 PM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" class="">nicolasbrossard.mni@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Ioannis,<div class=""><br class=""></div><div class="">No worries, we're here to help!</div><div class=""><br class=""></div><div class="">On Unix systems, all users usually have permission to create directories in <font face="monospace" class="">/tmp</font> but just to be sure it'd be good idea to test that: just try</div><div class=""><br class=""></div><div class=""><font face="monospace" class="">% mkdir /tmp/hello</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="arial, sans-serif" class="">and see if that works. If it does, then it means there's something more "sneaky" going on.</font></div><div class=""><font face="arial, sans-serif" class=""><br class=""></font></div><div class=""><font face="arial, sans-serif" class="">You can try specifying an alternate temporary directory in which the upload script will write files: just type the following line in your </font><font face="monospace" class="">environment</font><font face="arial, sans-serif" class=""> file (located in the LORIS-MRI root directory):</font></div><div class=""><font face="arial, sans-serif" class=""><br class=""></font></div><div class=""><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">export TMPDIR=/my/alternate/temporary/dir</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><br class=""></span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class="">Let me know if that helps.</font></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><br class=""></font></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><br class=""></font></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class="">Cheers,</font></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class="">Nicolas</font></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><br class=""></font></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 15, 2020 at 4:23 PM Ioannis Pappas <<a href="mailto:ioannis@berkeley.edu" class="">ioannis@berkeley.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class=""><div class="">Hi Loris support.</div><div class=""><br class=""></div><div class="">Another quick question (hopefully I don’t occupy a lot of your time during this pandemic).</div><div class=""><br class=""></div><div class="">I am running the simple imaging upload pearl script like this:</div><div class=""><br class=""></div><div class=""><i class="">sudo -i -u lorisadmin /data/loris-mri/bin/mri/uploadNeuroDB/<a href="http://imaging_upload_file.pl/" target="_blank" class="">imaging_upload_file.pl</a> -profile prod -upload_id 2 /data/loris/incoming/BR013_243782_V1.zip -verbose</i></div><div class=""><br class=""></div><div class="">I think the script involves creating some directories because it leads to an error. The error is this:</div><div class=""><br class=""></div><div class=""><i class="">mkdir /tmp/ImagingUpload-13-7-7Z_JFF/BR013_243782_V1/BIAS_12ch_22: Permission denied at /usr/local/share/perl5/Archive/Zip/DirectoryMember.pm </i></div><div class=""><br class=""></div><div class="">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 <i class="">ImagingUpload</i>[..]</div><div class=""><br class=""></div><div class="">Thank you very much. Hopefully I don’t see more errors in the script.</div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Ioannis</div></div>_______________________________________________<br class="">

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