[Loris-dev] one-step insertion pipeline problem

[zia mohades]

Hi Ali,

My pleasure. I am glad to hear that your issue is now resolved.

Best regards,

ᐧ

On Wed, Nov 14, 2018 at 11:37 AM Ali Aarefi <aliaarefi1997 at gmail.com> wrote:

>
>
>
>
> *Hi Zia,Thanks for your quick response.I should note that the problem was
> solved and I could insert a scan to database manually(with
> imaging_uplaod_file.pl <http://imaging_uplaod_file.pl>), but now I'm
> writing a script to use APIs to automate candidate/VisitLabel creation and
> data insertion.And also I was answered that mail. The results of Mouna's
> instructions are :*
> *$ echo $PATH*
>
> /opt/minc/1.9.16/bin:/opt/minc/1.9.16/pipeline:/opt/minc/1.9.16/bin:/data/last/bin/mri:/data/last/bin/mri/uploadNeuroDB:/data/last/bin/mri/uploadNeuroDB/bin:/data/last/bin/mri/dicom-archive:/opt/minc/1.9.16/bin:/opt/minc/1.9.16/pipeline:/opt/minc/1.9.16/bin:/data/last/bin/mri:/data/last/bin/mri/uploadNeuroDB:/data/last/bin/mri/uploadNeuroDB/bin:/data/last/bin/mri/dicom-archive:/home/ali/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/JetBrains/clion-2018.1.5/bin/:/opt/JetBrains/GoLand-2018.1.5/bin/:/opt/JetBrains/idea-IU-181.5281.24/bin/:/opt/JetBrains/pycharm-2018.1.4/bin/:/opt/JetBrains/WebStorm-181.5281.31/bin/
>
> *$ cat environment ( I've added "source /data/last/bin/mri/environment" to
> the .bashrc file)*
> export
> PATH=/opt/minc/1.9.16/bin:/data/last/bin/mri:/data/last/bin/mri/uploadNeuroDB:/data/last/bin/mri/uploadNeuroDB/bin:/data/last/bin/mri/dicom-archive:$PATH
> export PERL5LIB=/data/last/bin/mri/uploadNeuroDB:$PERL5LIB
> export TMPDIR=/tmp
> export LORIS_CONFIG=/data/last/bin/mri/dicom-archive
> source /opt/minc/1.9.16/minc-toolkit-config.sh
> umask 0002
>
> *The prod file is present and has the following file permission(readable
> for all users) :* "-rw-r--r-- 1 ali www-data 5.4K Sep 12 18:50 prod"
> *and there is a line in my prod file like "*@db =
> ('database_name','database_user', 'database_password', 'database_host');" *that
> the variables replaced with proper values and I accessed directly to
> database with those correct values.*
>
>
> *Thank you.- Ali*
>
> On Wed, Nov 14, 2018 at 7:01 PM zia mohades <zia.mohades at gmail.com> wrote:
>
>> Hi Ali,
>>
>> Before we start troubleshooting, Please let us know if you have followed
>> Mouna's instructions (detailed below - as per her last email to you).
>>
>> Thank you
>>
>>
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------
>> *From:* Mouna Safi-Harab
>> *Sent:* Tuesday, August 14, 2018 12:47 PM
>> *To:* Ali Aarefi
>> *Subject:* Re: [Loris-dev] Data insertion problem
>>
>> Hi Ali,
>>
>>
>> I am going to propose a few steps you can look into to try to debug
>> further. Let me know what you get based on the recommendations below.
>>
>>
>> - Try running the command 'source environment' (without the single quotations),
>> BEFORE running the uploadNeuroDB/imaging_upload_file.plcommand. Then
>> type 'echo $PATH' (without single quotations) and let me know what it gives
>> you. In parallel, can you please send me what is inside your
>> 'environment' file which is located in /data/%YOURProject/bin/mri/
>> directory?
>>
>> - Make sure that the prod file is indeed present in the
>> dicom-archive/.loris_mri/ directory, and is accessible by lorisadmin (or
>> whichever user running the imaging_upload_file.pl). Then open it and
>> make sure there is a line in there like that:
>>
>> @db = ('database_name','database_user', 'database_password',
>> 'database_host');
>>
>> and make sure all these database information on the line above the way
>> you have them in your prod file are correct (perhaps you can try to connect
>> directly to the mysql host from the command line to make sure this works
>> outside of the scripts).
>>
>>
>> Let me know!
>>
>>
>>
>> ᐧ
>> ᐧ
>> ᐧ
>>
>> On Wed, Nov 14, 2018 at 7:25 AM Ali Aarefi <aliaarefi1997 at gmail.com>
>> wrote:
>>
>>>
>>>
>>>
>>>
>>> *Hello,Dear LORIS dev. team,After running the one-step insertion
>>> pipeline on my local LORIS, I've faced a problem.*
>>> (executed command :
>>> * cd /data/$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*
>>>
>>>
>>> *Could anyone help me with this?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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