[Loris-dev] one-step insertion pipeline problem

[Cecile Madjar]

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 have been replaced by your project's name (the one in the /data/ directory).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