[Loris-dev] one-step insertion pipeline problem

[Cecile Madjar]

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 have been replaced by your project's name (the one in the /data/ directory).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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