[Loris-dev] one-step insertion pipeline problem

[Ali Aarefi]

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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