[Loris-dev] one-step insertion pipeline problem

[Ali Aarefi]

*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 have been replaced by your project's name (the one in the /data/ directory).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
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20181115/b6d60f30/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2018-11-15 17-01-31.png
Type: image/png
Size: 181761 bytes
Desc: not available
URL: <http://www.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20181115/b6d60f30/attachment-0001.png>