[Loris-dev] Fw: Data insertion problem

Tue Aug 14 12:49:10 EDT 2018

cc'ing the loris-dev mailing list on my reply to you, Ali

________________________________
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.pl command. 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!

- Mouna

________________________________
From: Ali Aarefi <aliaarefi1997 at gmail.com>
Sent: Wednesday, August 8, 2018 9:22:50 AM
To: Mouna Safi-Harab
Subject: Re: [Loris-dev] Data insertion problem

Dear Mouna,

Hello,

First of all thank you very much for your help,

Regarding your previous response, Yes, the scans are uploaded into /tmp directory and the MRI-Upload Directory in the Configuration module was set and the permissions of /data/incoming directory has been changed, so the scan .zip file successfully moved into /data/incoming directory.
So, in the browser of imaging uploader module, for our last try, the uploadLocation changed from /tmp directory to /data/incoming directory.[screenshot 1]

The missing dependencies installed and error of executing  uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl>  file has changed to:

[command]$ ./imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -verbose -upload_id 6 /data/incoming/MTL0000_336898_V1.zip

STDERR:

Use of uninitialized value $ENV{"LORIS_CONFIG"} in concatenation (.) or string at ./imaging_upload_file.pl<http://imaging_upload_file.pl> line 108.
Use of uninitialized value $ENV{"LORIS_CONFIG"} in concatenation (.) or string at ./imaging_upload_file.pl<http://imaging_upload_file.pl> line 110.

ERROR: You don't have a @db setting in the file /.loris_mri/prod

Also, I have attached related screenshots. Thanks again for your time and consideration.

Best Regards,
Ali

On Mon, Jul 23, 2018 at 9:42 PM Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca<mailto:mouna.safi-harb at mail.mcgill.ca>> wrote:

Hi Ali,

Based on your screenshots,

1) it looks like your scans are being uploaded into the `/tmp/` directory. So if you want them to go to `/data/incoming`/, can you please configure the MRI-Upload Directory in the Configuration module, under the Path submenu, to read /data/incoming/, and ensure this path is accessible and writable by the front end user

2) it looks like some dependencies are missing in your install; can you please refer to Installation Troubleshooting Notes in: https://github.com/aces/Loris/wiki/Imaging-Database (there is a section on missing dependencies, and the ones in the example on the Wiki seem to be the ones you are missing as well)

3) Setting/Not setting up the instruments should not impact your scan insertion workflow

Let me know if this answers your questions!

- Mouna

________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca> <loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca>> on behalf of Ali Aarefi <aliaarefi1997 at gmail.com<mailto:aliaarefi1997 at gmail.com>>
Sent: Sunday, July 22, 2018 11:54:34 AM
To: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Subject: [Loris-dev] Data insertion problem

Dear LORIS support team,
I'm a research assistant at NIAG (Neuro Imaging and Analysis Group) at NeuroImaging Center, Imam Khomeini Hospital, Tehran, Iran as a part of TUMS (Tehran University of Medical Science).

We've been trying to upload DICOM files using imaging uploader on our already installed LORIS server but we faced some problems.

All of following sections were done successfully with respect to github wiki page:
1. Installing loris
2. Project customization

Third section (Behavioural database) ignored (does it matter?)

And in the fourth section (imaging database) the subsections mentioned below was done successfully:
1. Install the imaging pipeline codebase
2. Setup imaging insertion scripts
3. Loading a scan into loris

In this subsection, while executing post-upload script (pre-processing and insertion into loris) an error has occurred in line 19 in imaging_upload_file.pl<http://imaging_upload_file.pl> with this following message:

command : uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -verbose -upload_id 1 ~/Desktop/MTL0000_336898_V1.zip # we know that the .zip file should be in /data/incoming , but after loading the scan into loris, this directory kept empty !

```
Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /data/project-name/bin/mri/uploadNeuroDB /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /data/project-name/bin/mri/uploadNeuroDB/NeuroDB/DBI.pm line 19.
BEGIN failed--compilation aborted at /data/project-name/bin/mri/uploadNeuroDB/NeuroDB/DBI.pm line 19.
Compilation failed in require at uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> line 19.
BEGIN failed--compilation aborted at uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> line 19.
```

And also the /data/incoming directory is empty (the uploaded file that was assigned an upload_id, doesn't exist in this directory)

Some other information that might be useful:
- The upload successful pop-up message was shown in imaging uploader module.
- upload_id was assigned to our upload tries.
- In the imaging uploader, there is no progress status.
- In the server processes manager module, some columns are meaningless like error codes with respect to loris documents.

Some screenshots attacked to this email for more information.

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