[Loris-dev] one-step insertion pipeline problem

[Ali Aarefi]

Hi,

Sorry about that.

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.

Ali


[image: Screenshot from 2018-11-19 17-00-32.png]

On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar <cecile.madjar at mcin.ca>
wrote:

> Hi,
>
> I did not see any attachment to your email. Could you send it again?
>
> Thank you,
>
> Cécile
>
> On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi <aliaarefi1997 at gmail.com>
> wrote:
>
>> 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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