[Loris-dev] one-step insertion pipeline problem

[Cecile Madjar]

Hi Ali,

Note sure I understand completely why Perl cannot find the libraries as the
path to uploadNeuroDB seems to be added to the PERL5LIB variable.

Could you do a `ls -l /data/last/bin/mri/uploadNeuroDB` and send me the
result please? Maybe this is a permission issue?

A few other questions:

   - What is the OS you are using?
   - What version of Perl are you using?
   - Which user is used to run batch_upload_imageuploader?

Best,

On Mon, Nov 19, 2018 at 7:05 PM Ali Aarefi <aliaarefi1997 at gmail.com> wrote:

> 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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