[Loris-dev] one-step insertion pipeline problem

Ali Aarefi aliaarefi1997 at gmail.com
Thu Nov 29 05:38:01 EST 2018 

Hi Cécile,

I modified that and finally it's done, the script ran successfuly.
Thank you so much for your time and consideration.

Best Regards,
Ali

On Wed, Nov 21, 2018 at 6:05 PM Cecile Madjar <cecile.madjar at mcin.ca> wrote:

> Hi Ali,
>
> We are making progress. Now the scripts can find NeuroDB::DBI. Always use
> the first two steps before running any script in the imaging pipeline and
> stay as user ali.
>
> For the error message, it looks like you don't have qsub installed so you
> need to modify the following in the Config module:
>
>    - Under the "Imaging Pipeline" section of the Config module of the
>    LORIS front-end, there is a configuration setting called "Project batch
>    management used". Set this config to "No", Save it and then try rerunning
>    batch_upload_imageuploader.
>
> Let me know how it goes!
>
> Cécile
>
> On Wed, Nov 21, 2018 at 6:00 AM Ali Aarefi <aliaarefi1997 at gmail.com>
> wrote:
>
>> Hi,
>>
>> I tried those three steps and attached the output of step 3 to this email
>> as "step3".
>>
>> And also the errors of executing the following command attached as
>> "log_batch_imageuploader.txt":
>> "/data/last/bin/mri/batch_uploads_imageuploader -profile prod <
>> /home/ali/Documents/imageUploader.txt >log_batch_imageuploader.txt 2>&1"
>>
>> Thanks,
>> Ali
>>
>> On Tue, Nov 20, 2018 at 10:45 PM Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>>> Hi Ali,
>>>
>>> You should not be running the scripts as the root user but as ali (no
>>> need to be the root user to run the LORIS imaging scripts).
>>>
>>> Try out the following steps:
>>> 1) log to your VM as ali
>>> 2) source your environment file as ali
>>> 3) run "batch_upload_imageuploader -h" still as ali
>>>
>>> Hopefully this will work. Let me know how it goes.
>>>
>>> Best,
>>>
>>> Cécile
>>>
>>>
>>> On Tue, Nov 20, 2018 at 1:47 PM Ali Aarefi <aliaarefi1997 at gmail.com>
>>> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> Output of "ls -l /data/last/bin/mri/uploadNeuroDB" command :
>>>> $ ls -l /data/last/bin/mri/uploadNeuroDB/
>>>> total 180
>>>> drwxrwx--- 2 ali www-data  4096 Sep 12 17:36 bin
>>>> -rwxrwx--- 1 ali www-data  9797 Sep 12 17:36 cleanupTarchives.pl
>>>> -rwxrwx--- 1 ali www-data  4275 Sep 12 17:36
>>>> imaging_upload_file_cronjob.pl
>>>> -rwxrwx--- 1 ali www-data 15606 Sep 12 17:36 imaging_upload_file.pl
>>>> -rwxrwx--- 1 ali www-data  5590 Sep 12 17:36 mass_nii.pl
>>>> -rwxrwx--- 1 ali www-data  5229 Sep 12 17:36 mass_pic.pl
>>>> -rwxrwx--- 1 ali www-data 13867 Sep 12 17:36 minc_deletion.pl
>>>> -rwxrwx--- 1 ali www-data 24990 Sep 12 17:36 minc_insertion.pl
>>>> drwxrwx--- 2 ali www-data  4096 Sep 12 17:36 NeuroDB
>>>> -rwxrwx--- 1 ali www-data 20987 Sep 12 17:36 register_processed_data.pl
>>>> -rwxrwx--- 1 ali www-data 31065 Sep 12 17:36 tarchiveLoader
>>>> -rwxrwx--- 1 ali www-data 16232 Sep 12 17:36 tarchive_validation.pl
>>>> -rwxrwx--- 1 ali www-data  4055 Sep 12 17:36 undoUpload.pl
>>>>
>>>> About other questions:
>>>> - Ubuntu 18.04
>>>> - perl5 (revision 5 version 26 subversion 1)
>>>> - root user
>>>>
>>>> Thanks.
>>>>
>>>> On Tue, Nov 20, 2018 at 6:25 PM Cecile Madjar <cecile.madjar at mcin.ca>
>>>> wrote:
>>>>
>>>>> 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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