[Loris-dev] one-step insertion pipeline problem
Ali Aarefi
aliaarefi1997 at gmail.com
Tue Nov 20 13:47:42 EST 2018
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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