[Loris-dev] one-step insertion pipeline problem

Cecile Madjar cecile.madjar at mcin.ca
Tue Nov 20 14:15:37 EST 2018 

Hi Ali,

You should not be running the scripts as the root user but as ali (no need
to be the root user to run the LORIS imaging scripts).

Try out the following steps:
1) log to your VM as ali
2) source your environment file as ali
3) run "batch_upload_imageuploader -h" still as ali

Hopefully this will work. Let me know how it goes.

Best,

Cécile


On Tue, Nov 20, 2018 at 1:47 PM Ali Aarefi <aliaarefi1997 at gmail.com> wrote:

> Hi Cecile,
>
> Output of "ls -l /data/last/bin/mri/uploadNeuroDB" command :
> $ ls -l /data/last/bin/mri/uploadNeuroDB/
> total 180
> drwxrwx--- 2 ali www-data  4096 Sep 12 17:36 bin
> -rwxrwx--- 1 ali www-data  9797 Sep 12 17:36 cleanupTarchives.pl
> -rwxrwx--- 1 ali www-data  4275 Sep 12 17:36
> imaging_upload_file_cronjob.pl
> -rwxrwx--- 1 ali www-data 15606 Sep 12 17:36 imaging_upload_file.pl
> -rwxrwx--- 1 ali www-data  5590 Sep 12 17:36 mass_nii.pl
> -rwxrwx--- 1 ali www-data  5229 Sep 12 17:36 mass_pic.pl
> -rwxrwx--- 1 ali www-data 13867 Sep 12 17:36 minc_deletion.pl
> -rwxrwx--- 1 ali www-data 24990 Sep 12 17:36 minc_insertion.pl
> drwxrwx--- 2 ali www-data  4096 Sep 12 17:36 NeuroDB
> -rwxrwx--- 1 ali www-data 20987 Sep 12 17:36 register_processed_data.pl
> -rwxrwx--- 1 ali www-data 31065 Sep 12 17:36 tarchiveLoader
> -rwxrwx--- 1 ali www-data 16232 Sep 12 17:36 tarchive_validation.pl
> -rwxrwx--- 1 ali www-data  4055 Sep 12 17:36 undoUpload.pl
>
> About other questions:
> - Ubuntu 18.04
> - perl5 (revision 5 version 26 subversion 1)
> - root user
>
> Thanks.
>
> On Tue, Nov 20, 2018 at 6:25 PM Cecile Madjar <cecile.madjar at mcin.ca>
> wrote:
>
>> Hi Ali,
>>
>> Note sure I understand completely why Perl cannot find the libraries as
>> the path to uploadNeuroDB seems to be added to the PERL5LIB variable.
>>
>> Could you do a `ls -l /data/last/bin/mri/uploadNeuroDB` and send me the
>> result please? Maybe this is a permission issue?
>>
>> A few other questions:
>>
>>    - What is the OS you are using?
>>    - What version of Perl are you using?
>>    - Which user is used to run batch_upload_imageuploader?
>>
>> Best,
>>
>> On Mon, Nov 19, 2018 at 7:05 PM Ali Aarefi <aliaarefi1997 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Sorry about that.
>>>
>>> The output of that command (after sourcing the environment file)
>>> attached to this email as a text file.
>>> The only difference between two outputs of "perl -V" command (before and
>>> after sourcing environment file) attached to this email as an image.
>>> Please note that : In the attached image : left-side text is output of
>>> command after sourcing env. file and right-side text is output of command
>>> before sourcing env. file.
>>>
>>> Ali
>>>
>>>
>>> [image: Screenshot from 2018-11-19 17-00-32.png]
>>>
>>> On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar <cecile.madjar at mcin.ca>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I did not see any attachment to your email. Could you send it again?
>>>>
>>>> Thank you,
>>>>
>>>> Cécile
>>>>
>>>> On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi <aliaarefi1997 at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Cécile,
>>>>>
>>>>> Thank you for your help.
>>>>> The output of that command (after sourcing the environment file)
>>>>> attached to this email as a text file.
>>>>> The only difference between two outputs of "perl -V" command (before
>>>>> and after sourcing environment file) attached to this email as an image.
>>>>> Please note that : In the attached image : left-side text is output of
>>>>> command after sourcing env. file and right-side text is output of command
>>>>> before sourcing env. file.
>>>>>
>>>>> Best Regards.
>>>>> -Ali
>>>>>
>>>>> On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar <cecile.madjar at mcin.ca>
>>>>> wrote:
>>>>>
>>>>>> Hi Ali,
>>>>>>
>>>>>> That is strange, it should find the library then. Could you run perl
>>>>>> -V and send me the output of that command? (before and after sourcing the
>>>>>> environment file)
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Cécile
>>>>>>
>>>>>> On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi <aliaarefi1997 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *Hi,Yes, I've sourced the environment file before running
>>>>>>> batch_upload_imageuploader script, and there is no remained %PROJECT% in
>>>>>>> environment file.The environment file included the PERL5LIB setter line
>>>>>>> with correct replacement of %PROJECT%.*
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *The environment file content is attached to this
>>>>>>> email(Screenshot).But still the problem is unsolved.Thanks,- Ali*
>>>>>>>
>>>>>>> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>
>>>>>>>> Hi again,
>>>>>>>>
>>>>>>>> It seems you were able to run the script imaging_upload_file.pl
>>>>>>>> manually but still have problems running batch_upload_imageuploader.
>>>>>>>>
>>>>>>>> My guess is that the variable $PERL5LIB is not set properly in your
>>>>>>>> environment file so Perl cannot find the LORIS libraries that are under the
>>>>>>>> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can
>>>>>>>> since it is located directly in the uploadNeuroDB folder).
>>>>>>>>
>>>>>>>> Here is what you would need to do to fix this:
>>>>>>>> 1) open you environment file and add the following statement if it
>>>>>>>> is not already there (replace %PROJECT% by your project folder name):
>>>>>>>>
>>>>>>>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB
>>>>>>>> 2) source the environment file again
>>>>>>>> 3) rerun the pipeline
>>>>>>>>
>>>>>>>> From now on, all the scripts will be able to access all the LORIS
>>>>>>>> perl libraries under uploadNeuroDB (including NeuroDB:DBI)
>>>>>>>>
>>>>>>>> Hope this helps,
>>>>>>>>
>>>>>>>> Cécile
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> Have you sourced the environment file before trying to run the
>>>>>>>>> script? This file always need to be source before running the insertion
>>>>>>>>> pipeline.
>>>>>>>>>
>>>>>>>>> Also, make sure that in the environment file all instances of
>>>>>>>>> %PROJECT% have been replaced by your project's name (the one in the /data/
>>>>>>>>> directory).
>>>>>>>>>
>>>>>>>>> Let me know how it goes,
>>>>>>>>>
>>>>>>>>> Cécile
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi <
>>>>>>>>> aliaarefi1997 at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> *Hello,Dear LORIS dev. team,After running the one-step insertion
>>>>>>>>>> pipeline on my local LORIS, I've faced a problem. (Can't locate
>>>>>>>>>> NeuroDB/DBI.pm in @INC ...)*
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> *Could anyone help me in inserting a group of data into loris
>>>>>>>>>> based on following information?*
>>>>>>>>>> (executed command :
>>>>>>>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile
>>>>>>>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)*
>>>>>>>>>>
>>>>>>>>>> *In my local website > imaging menu tab > image uploader > upload
>>>>>>>>>> , the detailed log for those uploades shows :*
>>>>>>>>>> "MRI pipeline not yet executed for this upload."
>>>>>>>>>>
>>>>>>>>>> *And the log_batch_imageuploader.txt contains :*
>>>>>>>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the
>>>>>>>>>> NeuroDB::DBI module) (@INC contains: /etc/perl
>>>>>>>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1
>>>>>>>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5
>>>>>>>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26
>>>>>>>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
>>>>>>>>>> ./batch_uploads_imageuploader line 53.
>>>>>>>>>> BEGIN failed--compilation aborted at
>>>>>>>>>> ./batch_uploads_imageuploader line 53.
>>>>>>>>>>
>>>>>>>>>> *I couldn't find installation instruction for** NeuroDB::DBI*
>>>>>>>>>> * module.*
>>>>>>>>>>
>>>>>>>>>> *Best Regards.*
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>
>>>>>>>>>
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