[Loris-dev] one-step insertion pipeline problem

[zia mohades]

Hi Ali,

Before we start troubleshooting, Please let us know if you have followed
Mouna's instructions (detailed below - as per her last email to you).

Thank you


----------------------------------------------------------------------------------------------------------------------------------------
*From:* Mouna Safi-Harab
*Sent:* Tuesday, August 14, 2018 12:47 PM
*To:* Ali Aarefi
*Subject:* Re: [Loris-dev] Data insertion problem

Hi Ali,


I am going to propose a few steps you can look into to try to debug
further. Let me know what you get based on the recommendations below.


- Try running the command 'source environment' (without the single quotations),
BEFORE running the uploadNeuroDB/imaging_upload_file.plcommand. Then type
'echo $PATH' (without single quotations) and let me know what it gives you.
In parallel, can you please send me what is inside your 'environment' file
which is located in /data/%YOURProject/bin/mri/ directory?

- Make sure that the prod file is indeed present in the
dicom-archive/.loris_mri/ directory, and is accessible by lorisadmin (or
whichever user running the imaging_upload_file.pl). Then open it and make
sure there is a line in there like that:

@db = ('database_name','database_user', 'database_password',
'database_host');

and make sure all these database information on the line above the way you
have them in your prod file are correct (perhaps you can try to connect
directly to the mysql host from the command line to make sure this works
outside of the scripts).


Let me know!



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On Wed, Nov 14, 2018 at 7:25 AM 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.*
> (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*
>
>
> *Could anyone help me with this?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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