From rogers at bic.mni.mcgill.ca  Tue Nov  8 15:00:20 2022
From: rogers at bic.mni.mcgill.ca (Christine Rogers)
Date: Tue, 8 Nov 2022 15:00:20 -0500
Subject: [Loris-dev] (no subject)
Message-ID: <CALbt7NDWudKdjjnRRezBcJ4OeBjy+BHCC6BgQ95JPrmQLA5N+g@mail.gmail.com>

Hi LORIS-dev community,

This is a periodic reminder that we offer support to the community both on
this listserv and via Discussions on our LORIS GitHub (
https://github.com/aces/Loris/discussions) - check it out if you haven't
yet and let us know what you think.

best,
Christine Rogers
the LORIS team
--
christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute-Hospital
McGill University | Montreal | Canada
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From julianpitney at gmail.com  Sun Nov 13 14:46:49 2022
From: julianpitney at gmail.com (Julian Pitney)
Date: Sun, 13 Nov 2022 14:46:49 -0500
Subject: [Loris-dev] Loris Docs 2022
Message-ID: <CAP_nU5eu0Gx3OCCX=SMUU-3aVaSF3grdAxSo3dPSkBg8sauPwg@mail.gmail.com>

Hi Guys,

My team and I are working on deploying our own instance of Loris for use
inside our lab. We have an instance of loris running already. Now we're
trying to learn how to set up our study using the web interface.

Currently I'm leaning on this documentation ->
https://acesloris.readthedocs.io/en/latest/index.html

It's helping a bit but it's not comprehensive and many pages are missing or
just have something like a "to do" message. I'm wondering if you guys are
maintaining any public documentation elsewhere that I missed or if you have
internal docs that are more complete. I guess in general just wondering
what you recommend for teaching oneself how to use Loris. Any assistance
would be greatly appreciated.

Thank you and hope to hear from you,
Julian
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From rida.abou-haidar at mcin.ca  Sun Nov 13 15:26:03 2022
From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar)
Date: Sun, 13 Nov 2022 15:26:03 -0500
Subject: [Loris-dev] Loris Docs 2022
In-Reply-To: <CAP_nU5eu0Gx3OCCX=SMUU-3aVaSF3grdAxSo3dPSkBg8sauPwg@mail.gmail.com>
References: <CAP_nU5eu0Gx3OCCX=SMUU-3aVaSF3grdAxSo3dPSkBg8sauPwg@mail.gmail.com>
Message-ID: <CABbkjAhHFh57j04G29gsUN6MsXj5YJV7=Bjbh5Q8kcrSDJSsFw@mail.gmail.com>

Hi Julian,

We are slowly going through a documentation shift towards Read the Docs
but, as you have noticed, the move is not nearly complete. We do have other
public documentation directly on the loris repository WIKI
<https://github.com/aces/Loris/wiki> and in some instances you might find
some docs directly in the code (such as the docs/ directory). The Wiki
documentation might however be out of date in some instances because the
info was moved or being moved to the Read the Docs site.

We are sorry for the confusion and if you have some specific questions you
want to ask, please feel free to ask them here and we will make sure to get
you an answer.

Best,
Rida Abou-Haidar
Software Developer
Montreal Neurological Institute
McGill University
rida.abou-haidar at mcin.ca


On Sun, Nov 13, 2022 at 2:47 PM Julian Pitney <julianpitney at gmail.com>
wrote:

> Hi Guys,
>
> My team and I are working on deploying our own instance of Loris for use
> inside our lab. We have an instance of loris running already. Now we're
> trying to learn how to set up our study using the web interface.
>
> Currently I'm leaning on this documentation ->
> https://acesloris.readthedocs.io/en/latest/index.html
>
> It's helping a bit but it's not comprehensive and many pages are missing
> or just have something like a "to do" message. I'm wondering if you guys
> are maintaining any public documentation elsewhere that I missed or if you
> have internal docs that are more complete. I guess in general just
> wondering what you recommend for teaching oneself how to use Loris. Any
> assistance would be greatly appreciated.
>
> Thank you and hope to hear from you,
> Julian
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From molano at ext.cnio.es  Wed Nov 16 08:10:53 2022
From: molano at ext.cnio.es (=?iso-8859-1?Q?Olano=2EMar=EDa?=)
Date: Wed, 16 Nov 2022 13:10:53 +0000
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52EC9E9@DONAR.cnio.es>

Good afternoon,

Hope this email finds you well. We are having problems using the imaging_non_minc_insertion.pl as when we execute the command this what pops up in the terminal.

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space native -reckless -verbose

This script inserts a file in the files and parameter_file tables.

Usage: perl imaging_non_minc_insertion.pl [options]

-help for options


                ERROR: missing -scanner_id argument

As you can see, scanner_id is included in the options accompanying the command, but when changing the ID from 0 to 10 it does recognize scanner_id, shown as followed:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-49-8uubDY.log.

                ERROR: Invalid ScannerID 10.

Both IDs are in the MYSQL table "mri_scanner" so we don't know what the problem could be.

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+-------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+-------+---------------+----------+--------+
|  0 | NULL         | NULL  | NULL          | NULL     |   NULL |
| 10 | NULL         | NULL  | NULL          | NULL     |   NULL |
+----+--------------+-------+---------------+----------+--------+

Any help would be much appreciated.

Best regards,

Mar?a




[Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] <https://www.cnio.es/es/colaborar/comocolaborar.asp>

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De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
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From molano at ext.cnio.es  Thu Nov 17 10:24:22 2022
From: molano at ext.cnio.es (=?iso-8859-1?Q?Olano=2EMar=EDa?=)
Date: Thu, 17 Nov 2022 15:24:22 +0000
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52ECA91@DONAR.cnio.es>

Good afternoon!

We managed to solve the issue with the scanner_id by linking the CandID to the scanner

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+---------+---------------+----------+--------+
| ID | Manufacturer | Model   | Serial_number | Software | CandID |
+----+--------------+---------+---------------+----------+--------+
|  0 | NULL         | NULL    | NULL          | NULL     |   NULL |
|  1 | SIEMENS      | TrioTim | 35008         | Python   | 359572 |
| 10 | NULL         | NULL    | NULL          | NULL     |   NULL |
+----+--------------+---------+---------------+----------+--------+

And later got the upload_id error:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.

                ERROR: Invalid UploadID 1.

Managed to side step this error by using the front end Imaging Uploader which filled out the mri_upload table with the UploadID 1

mysql> SELECT * FROM `mri_upload`;
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| UploadID | UploadedBy | UploadDate          | UploadLocation                                  | DecompressedLocation | InsertionComplete | Inserting | PatientName       | number_of_mincInserted | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated | IsTarchiveValidated | IsPhantom |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
|        1 | lorisadmin | 2022-11-17 14:40:58 | /data/incoming/lorisadmin/DCC0000_359572_V3.zip |                      |                 0 |      NULL | DCC0000_359572_V3 |                   NULL |                  NULL |       NULL |         1 |                     NULL |                   0 | N         |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+

However! It didn't manage to upload correctly so we tried to use the back end again with imaging_non_minc_insertion.pl (as this isn't a DICOM file) and we are presented with our last error:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip

=> No Visit label

                ERROR: Candidate IDs mismatch for /data/incoming/lorisadmin/DCC0000_359572_V3.zip.

This Visit label has been populated in the MySQL visit table, so we don't know what mismatch it is referring to.

Any help would be much appreciated.

Mar?a

De: Olano.Mar?a
Enviado el: mi?rcoles, 16 de noviembre de 2022 14:11
Para: 'loris-dev at bic.mni.mcgill.ca' <loris-dev at bic.mni.mcgill.ca>
Asunto: imaging_non_minc_insertion.pl issue with scanner_id

Good afternoon,

Hope this email finds you well. We are having problems using the imaging_non_minc_insertion.pl as when we execute the command this what pops up in the terminal.

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space native -reckless -verbose

This script inserts a file in the files and parameter_file tables.

Usage: perl imaging_non_minc_insertion.pl [options]

-help for options


                ERROR: missing -scanner_id argument

As you can see, scanner_id is included in the options accompanying the command, but when changing the ID from 0 to 10 it does recognize scanner_id, shown as followed:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-49-8uubDY.log.

                ERROR: Invalid ScannerID 10.

Both IDs are in the MYSQL table "mri_scanner" so we don't know what the problem could be.

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+-------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+-------+---------------+----------+--------+
|  0 | NULL         | NULL  | NULL          | NULL     |   NULL |
| 10 | NULL         | NULL  | NULL          | NULL     |   NULL |
+----+--------------+-------+---------------+----------+--------+

Any help would be much appreciated.

Best regards,

Mar?a


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
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From cecile.madjar at mcin.ca  Tue Nov 22 11:35:24 2022
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Tue, 22 Nov 2022 11:35:24 -0500
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
Message-ID: <CAMkiY3ep8AWFkzfFEf09ENF9yuWDq+y8Hh2YqeAwQfUk1r-R4g@mail.gmail.com>

Dear Maria,

Sorry for the late reply. For some reason I never received your email.
Luckily, someone else from the LORIS team just flagged it and sent it to me.

It looks like the latest issue you are encountering is that the visit label
is not properly parsed by the getSubjectIDs function in your prod file.
Instead of returning V3, it returns V3.zip which is most likely not a valid
visit label for your project.

The other possibility could be that DCC0000 and 359572 do not refer to the
same candidate.

In any case, I think for both situations, an entry has been added to the
MRICandidateErrors table and you could see the file in the MRI violations
module where the file would be logged there.

Let me know if that helps. Best,

C?cile

---------- Forwarded message ---------
From: Olano.Mar?a <molano at ext.cnio.es>
Date: Thu, Nov 17, 2022 at 10:24 AM
Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>


Good afternoon!



We managed to solve the issue with the scanner_id by linking the CandID to
the scanner



mysql> SELECT * FROM `mri_scanner`;

+----+--------------+---------+---------------+----------+--------+

| ID | Manufacturer | Model   | Serial_number | Software | CandID |

+----+--------------+---------+---------------+----------+--------+

|  0 | NULL         | NULL    | NULL          | NULL     |   NULL |

|  1 | SIEMENS      | TrioTim | 35008         | Python   | 359572 |

| 10 | NULL         | NULL    | NULL          | NULL     |   NULL |

+----+--------------+---------+---------------+----------+--------+



And later got the upload_id error:



(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
-file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
native -reckless -verbose



log dir is /data/loris/data/logs and log file is
/data/loris/data/logs/FileLoad-11-48-F5qW5R.log.



                ERROR: Invalid UploadID 1.



Managed to side step this error by using the front end Imaging Uploader
which filled out the mri_upload table with the UploadID 1



mysql> SELECT * FROM `mri_upload`;

+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+

| UploadID | UploadedBy | UploadDate          |
UploadLocation                                  | DecompressedLocation |
InsertionComplete | Inserting | PatientName       | number_of_mincInserted
| number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated
| IsTarchiveValidated | IsPhantom |

+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+

|        1 | lorisadmin | 2022-11-17 14:40:58 |
/data/incoming/lorisadmin/DCC0000_359572_V3.zip |
|                 0 |      NULL | DCC0000_359572_V3 |
NULL |                  NULL |       NULL |         1 |
                NULL |                   0 | N         |

+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+



However! It didn?t manage to upload correctly so we tried to use the back
end again with imaging_non_minc_insertion.pl (as this isn?t a DICOM file)
and we are presented with our last error:



(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
-file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type
native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
native -reckless -verbose



log dir is /data/loris/data/logs and log file is
/data/loris/data/logs/FileLoad-16-0-_g35H2.log.

PSCID is: DCC0000

CandID id: 359572

visit_label is: V3.zip

PSCID is: DCC0000

CandID id: 359572

visit_label is: V3.zip



=> No Visit label



                ERROR: Candidate IDs mismatch for
/data/incoming/lorisadmin/DCC0000_359572_V3.zip.



This Visit label has been populated in the MySQL visit table, so we don?t
know what mismatch it is referring to.



Any help would be much appreciated.



Mar?a



*De:* Olano.Mar?a
*Enviado el:* mi?rcoles, 16 de noviembre de 2022 14:11
*Para:* 'loris-dev at bic.mni.mcgill.ca' <loris-dev at bic.mni.mcgill.ca>
*Asunto:* imaging_non_minc_insertion.pl issue with scanner_id



Good afternoon,



Hope this email finds you well. We are having problems using the
imaging_non_minc_insertion.pl as when we execute the command this what pops
up in the terminal.



(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
-file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space
native -reckless -verbose



This script inserts a file in the files and parameter_file tables.



Usage: perl imaging_non_minc_insertion.pl [options]



-help for options





                ERROR: missing -scanner_id argument



As you can see, scanner_id is included in the options accompanying the
command, but when changing the ID from 0 to 10 it does recognize
scanner_id, shown as followed:



(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
-file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10
-coordin_space native -reckless -verbose



log dir is /data/loris/data/logs and log file is
/data/loris/data/logs/FileLoad-12-49-8uubDY.log.



                ERROR: Invalid ScannerID 10.



Both IDs are in the MYSQL table ?mri_scanner? so we don?t know what the
problem could be.



mysql> SELECT * FROM `mri_scanner`;

+----+--------------+-------+---------------+----------+--------+

| ID | Manufacturer | Model | Serial_number | Software | CandID |

+----+--------------+-------+---------------+----------+--------+

|  0 | NULL         | NULL  | NULL          | NULL     |   NULL |

| 10 | NULL         | NULL  | NULL          | NULL     |   NULL |

+----+--------------+-------+---------------+----------+--------+



Any help would be much appreciated.



Best regards,



Mar?a


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From kchen339 at wisc.edu  Tue Nov 22 11:47:43 2022
From: kchen339 at wisc.edu (Aaron Chen)
Date: Tue, 22 Nov 2022 16:47:43 +0000
Subject: [Loris-dev] Unable to Access the Front-end
Message-ID: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>

Good morning,

Hope this email finds you well. Our team is trying to set up the LORIS system for research. It was working before but somehow, we aren't able to access the front-end. Below are some snips of errors from the loris-error.log under the /var/log/apache2/ directory.

    [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741] PHP Warning:  simplexml_load_file(): /var/www/loris/php/libraries/../../project/config.xml:69: parser error : Opening and ending tag mismatch: item line 69 and tem in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741] PHP Warning:  simplexml_load_file():             &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741] PHP Warning:  simplexml_load_file():                                                        ^ in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client 128.105.29.144:61741] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/loris/php/libraries/../../project/config.xml in /var/www/loris/php/libraries/NDB_Config.class.inc:100
    Stack trace:
    #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load()
    #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104): NDB_Config::singleton()
    #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config()
    #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
    #4 {main}
      thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 100
It seems like the path to the config.xml isn't correct. It should be /var/www/loris/php/libraries/project/config.xml, not /var/www/loris/php/libraries/../../project/config.xml. Where could I change the path?

Any help would be much appreciated.

Best,
Aaron Chen

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From laetitia.fesselier at mcin.ca  Tue Nov 22 12:16:10 2022
From: laetitia.fesselier at mcin.ca (Laetitia Fesselier)
Date: Tue, 22 Nov 2022 12:16:10 -0500
Subject: [Loris-dev] Unable to Access the Front-end
In-Reply-To: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
References: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
Message-ID: <CAArLUV_=ytEUVTamVP7LMYnjFFK23BM8zdXbJ7n0fp0RU0ipNA@mail.gmail.com>

Hello Aaron,

Thanks for reaching out. It appears that your config.xml is at the correct
place, but that its syntax is wrong.
You can try this tool to check if there is any syntax problem in your
config.xml: https://www.liquid-technologies.com/online-xml-validator
Also, here is a config.xml template you can use for comparison:
https://github.com/aces/Loris/blob/main/raisinbread/config/config.xml
Let us know if that solves your issue.

The Loris Team




On Tue, Nov 22, 2022 at 11:48 AM Aaron Chen <kchen339 at wisc.edu> wrote:

> Good morning,
>
> Hope this email finds you well. Our team is trying to set up the LORIS
> system for research. It was working before but somehow, we aren't able to
> access the front-end. Below are some snips of errors from the
> loris-error.log under the /var/log/apache2/ directory.
>
>     [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
> /var/www/loris/php/libraries/../../project/config.xml:69: parser error :
> Opening and ending tag mismatch: item line 69 and tem in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
> &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
>                                          ^ in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client
> 128.105.29.144:61741] PHP Fatal error:  Uncaught Exception: Could not
> load Loris config file
> /var/www/loris/php/libraries/../../project/config.xml in
> /var/www/loris/php/libraries/NDB_Config.class.inc:100
>     Stack trace:
>     #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
> NDB_Config->load()
>     #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104):
> NDB_Config::singleton()
>     #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
> NDB_Factory->config()
>     #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
>     #4 {main}
>       thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line
> 100
>
> It seems like the path to the config.xml isn't correct. It should be
> /var/www/loris/php/libraries/project/config.xml, not
> /var/www/loris/php/libraries/../../project/config.xml. Where could I change
> the path?
>
> Any help would be much appreciated.
>
> Best,
> Aaron Chen
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>


-- 
Laetitia Fesselier
LORIS Software Developer
Montreal Neurological Institute
McGill University
laetitia.fesselier at mcin.ca
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From dave.macfarlane at mcin.ca  Tue Nov 22 12:44:23 2022
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Tue, 22 Nov 2022 12:44:23 -0500
Subject: [Loris-dev] Unable to Access the Front-end
In-Reply-To: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
References: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
Message-ID: <CAN9cDwFadOywreGzh8p8uLVPyXtrQBALP7N0LnV9ppmpnFg3fg@mail.gmail.com>

Hi Aaron,

After resolving the ../ references the path looks like it's correctly
looking at /var/www/loris/project.xml but the errors suggest that the file
isn't valid xml.

It looks like from the second line &lt;item value=&quot;V2&quot;&gt;V2
label description&lt;/tem&gt; that you made a typo in the V2 and missed the
"i" in the closing tag for the "item" tag.

- Dave

On Tue, Nov 22, 2022 at 11:48 AM Aaron Chen <kchen339 at wisc.edu> wrote:

> Good morning,
>
> Hope this email finds you well. Our team is trying to set up the LORIS
> system for research. It was working before but somehow, we aren't able to
> access the front-end. Below are some snips of errors from the
> loris-error.log under the /var/log/apache2/ directory.
>
>     [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
> /var/www/loris/php/libraries/../../project/config.xml:69: parser error :
> Opening and ending tag mismatch: item line 69 and tem in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
> &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
>                                          ^ in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client
> 128.105.29.144:61741] PHP Fatal error:  Uncaught Exception: Could not
> load Loris config file
> /var/www/loris/php/libraries/../../project/config.xml in
> /var/www/loris/php/libraries/NDB_Config.class.inc:100
>     Stack trace:
>     #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
> NDB_Config->load()
>     #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104):
> NDB_Config::singleton()
>     #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
> NDB_Factory->config()
>     #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
>     #4 {main}
>       thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line
> 100
>
> It seems like the path to the config.xml isn't correct. It should be
> /var/www/loris/php/libraries/project/config.xml, not
> /var/www/loris/php/libraries/../../project/config.xml. Where could I change
> the path?
>
> Any help would be much appreciated.
>
> Best,
> Aaron Chen
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From molano at ext.cnio.es  Wed Nov 23 06:53:16 2022
From: molano at ext.cnio.es (=?utf-8?B?T2xhbm8uTWFyw61h?=)
Date: Wed, 23 Nov 2022 11:53:16 +0000
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
In-Reply-To: <CAMkiY3ep8AWFkzfFEf09ENF9yuWDq+y8Hh2YqeAwQfUk1r-R4g@mail.gmail.com>
References: <CAMkiY3ep8AWFkzfFEf09ENF9yuWDq+y8Hh2YqeAwQfUk1r-R4g@mail.gmail.com>
Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52F5079@DONAR.cnio.es>

Hello Cecile!

Thank you for your kind response. You were completely correct, the problem was the visit label not being read correctly, but we managed to solve this by adding an optional parameter: patient_name as seen below

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose -patient_name DCC0000_359572_V3

However, this proved to come with its fair share of errors, it seems the file Is read well and moved to another location (/data/loris/data/assembly/359572/V3/mri/native/) but the console output reads as follows:

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-20-gEsQPj.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3
    -> ScannerID was set to 1

    -> SessionID was set to 1

    -> Acquisition date was set to 2012-04-20

    -> Output type was set to native

Acquisition date: 2012-04-20
DBD::mysql::db do failed: Unknown column 'PhaseEncodingDirection' in 'field list' at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 793.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 818.

We had the idea of adding another parameter indicating there was a json file with said Phase encoding direction inside ((loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1 -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose -patient_name DCC0000_359572_V3 -metadata_file /home/lorisadmin/Downloads/patient.json) , but it was of no use, the console sent us the same message.

Inside the log file FileLoad-12-20-gEsQPj.log here is what is written:

==> computing md5 hash for MINC body.

--> md5: aab815082fbf91e7e3e26b7f6b899e2d

File /home/lorisadmin/Downloads/DCC0000_359572_V3.zip
moved to:
/data/loris/data/assembly/359572/V3/mri/native/loris_359572_V3_t1_001.zip
ative

And the MRICandidateErrors has an empty set.

Any help would be much appreciated, best regards!

Mar?a

De: Cecile Madjar <cecile.madjar at mcin.ca>
Enviado el: martes, 22 de noviembre de 2022 17:35
Para: Olano.Mar?a <molano at ext.cnio.es>; loris-dev <loris-dev at bic.mni.mcgill.ca>
Asunto: imaging_non_minc_insertion.pl issue with scanner_id

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

Dear Maria,

Sorry for the late reply. For some reason I never received your email. Luckily, someone else from the LORIS team just flagged it and sent it to me.

It looks like the latest issue you are encountering is that the visit label is not properly parsed by the getSubjectIDs function in your prod file. Instead of returning V3, it returns V3.zip which is most likely not a valid visit label for your project.

The other possibility could be that DCC0000 and 359572 do not refer to the same candidate.

In any case, I think for both situations, an entry has been added to the MRICandidateErrors table and you could see the file in the MRI violations module where the file would be logged there.

Let me know if that helps. Best,

C?cile

---------- Forwarded message ---------
From: Olano.Mar?a <molano at ext.cnio.es<mailto:molano at ext.cnio.es>>
Date: Thu, Nov 17, 2022 at 10:24 AM
Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> issue with scanner_id
To: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>

Good afternoon!

We managed to solve the issue with the scanner_id by linking the CandID to the scanner

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+---------+---------------+----------+--------+
| ID | Manufacturer | Model   | Serial_number | Software | CandID |
+----+--------------+---------+---------------+----------+--------+
|  0 | NULL         | NULL    | NULL          | NULL     |   NULL |
|  1 | SIEMENS      | TrioTim | 35008         | Python   | 359572 |
| 10 | NULL         | NULL    | NULL          | NULL     |   NULL |
+----+--------------+---------+---------------+----------+--------+

And later got the upload_id error:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.

                ERROR: Invalid UploadID 1.

Managed to side step this error by using the front end Imaging Uploader which filled out the mri_upload table with the UploadID 1

mysql> SELECT * FROM `mri_upload`;
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| UploadID | UploadedBy | UploadDate          | UploadLocation                                  | DecompressedLocation | InsertionComplete | Inserting | PatientName       | number_of_mincInserted | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated | IsTarchiveValidated | IsPhantom |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
|        1 | lorisadmin | 2022-11-17 14:40:58 | /data/incoming/lorisadmin/DCC0000_359572_V3.zip |                      |                 0 |      NULL | DCC0000_359572_V3 |                   NULL |                  NULL |       NULL |         1 |                     NULL |                   0 | N         |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+

However! It didn?t manage to upload correctly so we tried to use the back end again with imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> (as this isn?t a DICOM file) and we are presented with our last error:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip

=> No Visit label

                ERROR: Candidate IDs mismatch for /data/incoming/lorisadmin/DCC0000_359572_V3.zip.

This Visit label has been populated in the MySQL visit table, so we don?t know what mismatch it is referring to.

Any help would be much appreciated.

Mar?a

De: Olano.Mar?a
Enviado el: mi?rcoles, 16 de noviembre de 2022 14:11
Para: 'loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>' <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Asunto: imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> issue with scanner_id

Good afternoon,

Hope this email finds you well. We are having problems using the imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> as when we execute the command this what pops up in the terminal.

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space native -reckless -verbose

This script inserts a file in the files and parameter_file tables.

Usage: perl imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> [options]

-help for options


                ERROR: missing -scanner_id argument

As you can see, scanner_id is included in the options accompanying the command, but when changing the ID from 0 to 10 it does recognize scanner_id, shown as followed:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-49-8uubDY.log.

                ERROR: Invalid ScannerID 10.

Both IDs are in the MYSQL table ?mri_scanner? so we don?t know what the problem could be.

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+-------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+-------+---------------+----------+--------+
|  0 | NULL         | NULL  | NULL          | NULL     |   NULL |
| 10 | NULL         | NULL  | NULL          | NULL     |   NULL |
+----+--------------+-------+---------------+----------+--------+

Any help would be much appreciated.

Best regards,

Mar?a


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De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es<mailto:delegado_lopd at cnio.es>. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es<mailto:delegado_lopd at cnio.es>. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
_______________________________________________
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Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
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From kchen339 at wisc.edu  Wed Nov 23 04:02:03 2022
From: kchen339 at wisc.edu (Aaron Chen)
Date: Wed, 23 Nov 2022 09:02:03 +0000
Subject: [Loris-dev] Unable to Access the Front-end
In-Reply-To: <CAN9cDwFadOywreGzh8p8uLVPyXtrQBALP7N0LnV9ppmpnFg3fg@mail.gmail.com>
References: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
 <CAN9cDwFadOywreGzh8p8uLVPyXtrQBALP7N0LnV9ppmpnFg3fg@mail.gmail.com>
Message-ID: <DS7PR06MB69364472BAA7D4712F2D066EFC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>

Hi,

Thank you very much for the help. I did see there was a typo in my config.xml file. However, the front end is still inaccessible after I corrected the typo. I also throw our XML file into the XML validator but there is no syntax error. Below is the new error log I got after fixing the typo.
[Tue Nov 22 16:40:55.155037 2022] [php7:notice] [pid 500127] [client 10.138.220.162:62703] [ERROR] Unable to load template 'file:404.tpl'#0 /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(232): Smarty_Internal_Template->render()
#1 /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(116): Smarty_Internal_TemplateBase->_execute()
#2 /var/www/loris/src/Http/Error.php(86): Smarty_Internal_TemplateBase->fetch()
#3 /var/www/loris/src/Router/PrefixRouter.php(102): LORIS\\Http\\Error->__construct()
#4 /var/www/loris/php/libraries/Module.class.inc(340): LORIS\\Router\\PrefixRouter->handle()
#5 /var/www/loris/src/Router/ModuleRouter.php(77): Module->handle()
#6 /var/www/loris/src/Middleware/ExceptionHandlingMiddleware.php(54): LORIS\\Router\\ModuleRouter->handle()
#7 /var/www/loris/src/Router/BaseRouter.php(126): LORIS\\Middleware\\ExceptionHandlingMiddleware->process()
#8 /var/www/loris/src/Middleware/ResponseGenerator.php(50): LORIS\\Router\\BaseRouter->handle()
#9 /var/www/loris/src/Middleware/ContentLength.php(52): LORIS\\Middleware\\ResponseGenerator->process()
#10 /var/www/loris/htdocs/index.php(55): LORIS\\Middleware\\ContentLength->process()
#11 {main}

[Tue Nov 22 16:40:55.159740 2022] [php7:error] [pid 500127] [client 10.138.220.162:62703] PHP Fatal error:  Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown in /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php on line 195
[Tue Nov 22 16:40:55.159776 2022] [php7:notice] [pid 500127] [client 10.138.220.162:62703] [CRITICAL] /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php:195: Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown

It seems like there are some other errors that LORIS is trying to display via frontend but can't find the template in the system. Though, I did find 404.tpl and 500.tpl under /var/www/loris/smarty/templates/ directory. Also, the path to load the config.xml somehow was fixed by itself as I didn't see the error message again in the log file.[cid:2260ab22-b5a5-46c8-9828-84261b9d78c6]

Thank you in advance!


Best,

Aaron

________________________________
From: Dave MacFarlane <dave.macfarlane at mcin.ca>
Sent: Tuesday, November 22, 2022 11:44 AM
To: Aaron Chen <kchen339 at wisc.edu>
Cc: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Unable to Access the Front-end

Hi Aaron,

After resolving the ../ references the path looks like it's correctly looking at /var/www/loris/project.xml but the errors suggest that the file isn't valid xml.

It looks like from the second line &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; that you made a typo in the V2 and missed the "i" in the closing tag for the "item" tag.

- Dave

On Tue, Nov 22, 2022 at 11:48 AM Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>> wrote:
Good morning,

Hope this email finds you well. Our team is trying to set up the LORIS system for research. It was working before but somehow, we aren't able to access the front-end. Below are some snips of errors from the loris-error.log under the /var/log/apache2/ directory.

    [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file(): /var/www/loris/php/libraries/../../project/config.xml:69: parser error : Opening and ending tag mismatch: item line 69 and tem in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file():             &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file():                                                        ^ in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/loris/php/libraries/../../project/config.xml in /var/www/loris/php/libraries/NDB_Config.class.inc:100
    Stack trace:
    #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load()
    #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104): NDB_Config::singleton()
    #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config()
    #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
    #4 {main}
      thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 100
It seems like the path to the config.xml isn't correct. It should be /var/www/loris/php/libraries/project/config.xml, not /var/www/loris/php/libraries/../../project/config.xml. Where could I change the path?

Any help would be much appreciated.

Best,
Aaron Chen

_______________________________________________
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Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
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From cecile.madjar at mcin.ca  Wed Nov 23 09:11:12 2022
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Wed, 23 Nov 2022 09:11:12 -0500
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
In-Reply-To: <1AAB0BC03205B240B7809934CFCF8DF52F5079@DONAR.cnio.es>
References: <CAMkiY3ep8AWFkzfFEf09ENF9yuWDq+y8Hh2YqeAwQfUk1r-R4g@mail.gmail.com>
 <1AAB0BC03205B240B7809934CFCF8DF52F5079@DONAR.cnio.es>
Message-ID: <CAMkiY3cd_yLi4HnnnsOqjzAK6QgsPK9Jm7Y8-Yx8NknV94L4wg@mail.gmail.com>

Hi Maria,

It looks like the following SQL patch has not been run to update the MRI
tables. Try sourcing this upgrade patch
<https://github.com/aces/Loris/blob/v24.1.1/SQL/Release_patches/24.0_To_24.1_upgrade.sql>
and
the script should work.

Let me know how it goes,

C?cile

On Wed, Nov 23, 2022 at 6:53 AM Olano.Mar?a <molano at ext.cnio.es> wrote:

> Hello Cecile!
>
>
>
> Thank you for your kind response. You were completely correct, the problem
> was the visit label not being read correctly, but we managed to solve this
> by adding an optional parameter: patient_name as seen below
>
>
>
> *(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl
> <http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1
> -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose -patient_name DCC0000_359572_V3 *
>
>
>
> However, this proved to come with its fair share of errors, it seems the
> file Is read well and moved to another location
> (/data/loris/data/assembly/359572/V3/mri/native/) but the console output
> reads as follows:
>
>
>
> *log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-12-20-gEsQPj.log.*
>
> *PSCID is: DCC0000*
>
> *CandID id: 359572*
>
> *visit_label is: V3*
>
> *PSCID is: DCC0000*
>
> *CandID id: 359572*
>
> *visit_label is: V3*
>
> *    -> ScannerID was set to 1*
>
>
>
> *    -> SessionID was set to 1*
>
>
>
> *    -> Acquisition date was set to 2012-04-20*
>
>
>
> *    -> Output type was set to native*
>
>
>
> *Acquisition date: 2012-04-20*
>
> *DBD::mysql::db do failed: Unknown column 'PhaseEncodingDirection' in
> 'field list' at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 793.*
>
> *DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`LORIS`.`parameter_file`, CONSTRAINT
> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`))
> at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 818.*
>
>
>
> We had the idea of adding another parameter indicating there was a json
> file with said Phase encoding direction inside ((*loris-mri-python)
> lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl
> <http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1
> -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose -patient_name DCC0000_359572_V3 -metadata_file
> /home/lorisadmin/Downloads/patient.json*) , but it was of no use, the
> console sent us the same message.
>
>
>
> Inside the log file *FileLoad-12-20-gEsQPj.log* here is what is written*:*
>
>
>
> *==> computing md5 hash for MINC body.*
>
>
>
> *--> md5: aab815082fbf91e7e3e26b7f6b899e2d*
>
>
>
> *File /home/lorisadmin/Downloads/DCC0000_359572_V3.zip *
>
> *moved to:*
>
> */data/loris/data/assembly/359572/V3/mri/native/loris_359572_V3_t1_001.zip*
>
> *ative*
>
>
>
> And the MRICandidateErrors has an empty set.
>
>
>
> Any help would be much appreciated, best regards!
>
>
>
> Mar?a
>
>
>
> *De:* Cecile Madjar <cecile.madjar at mcin.ca>
> *Enviado el:* martes, 22 de noviembre de 2022 17:35
> *Para:* Olano.Mar?a <molano at ext.cnio.es>; loris-dev <
> loris-dev at bic.mni.mcgill.ca>
> *Asunto:* imaging_non_minc_insertion.pl issue with scanner_id
>
>
>
> *CAUTION: This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe*
>
>
>
> Dear Maria,
>
>
>
> Sorry for the late reply. For some reason I never received your email.
> Luckily, someone else from the LORIS team just flagged it and sent it to me.
>
>
>
> It looks like the latest issue you are encountering is that the visit
> label is not properly parsed by the getSubjectIDs function in your prod
> file. Instead of returning V3, it returns V3.zip which is most likely not a
> valid visit label for your project.
>
>
>
> The other possibility could be that DCC0000 and 359572 do not refer to the
> same candidate.
>
>
>
> In any case, I think for both situations, an entry has been added to the
> MRICandidateErrors table and you could see the file in the MRI violations
> module where the file would be logged there.
>
>
>
> Let me know if that helps. Best,
>
>
>
> C?cile
>
>
>
> ---------- Forwarded message ---------
> From: *Olano.Mar?a* <molano at ext.cnio.es>
> Date: Thu, Nov 17, 2022 at 10:24 AM
> Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl issue with
> scanner_id
> To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>
>
>
> Good afternoon!
>
>
>
> We managed to solve the issue with the scanner_id by linking the CandID to
> the scanner
>
>
>
> mysql> SELECT * FROM `mri_scanner`;
>
> +----+--------------+---------+---------------+----------+--------+
>
> | ID | Manufacturer | Model   | Serial_number | Software | CandID |
>
> +----+--------------+---------+---------------+----------+--------+
>
> |  0 | NULL         | NULL    | NULL          | NULL     |   NULL |
>
> |  1 | SIEMENS      | TrioTim | 35008         | Python   | 359572 |
>
> | 10 | NULL         | NULL    | NULL          | NULL     |   NULL |
>
> +----+--------------+---------+---------------+----------+--------+
>
>
>
> And later got the upload_id error:
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose
>
>
>
> log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.
>
>
>
>                 ERROR: Invalid UploadID 1.
>
>
>
> Managed to side step this error by using the front end Imaging Uploader
> which filled out the mri_upload table with the UploadID 1
>
>
>
> mysql> SELECT * FROM `mri_upload`;
>
>
> +----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
>
> | UploadID | UploadedBy | UploadDate          |
> UploadLocation                                  | DecompressedLocation |
> InsertionComplete | Inserting | PatientName       | number_of_mincInserted
> | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated
> | IsTarchiveValidated | IsPhantom |
>
>
> +----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
>
> |        1 | lorisadmin | 2022-11-17 14:40:58 |
> /data/incoming/lorisadmin/DCC0000_359572_V3.zip |
> |                 0 |      NULL | DCC0000_359572_V3 |
> NULL |                  NULL |       NULL |         1 |
>                 NULL |                   0 | N         |
>
>
> +----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
>
>
>
> However! It didn?t manage to upload correctly so we tried to use the back
> end again with imaging_non_minc_insertion.pl (as this isn?t a DICOM file)
> and we are presented with our last error:
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose
>
>
>
> log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
>
> PSCID is: DCC0000
>
> CandID id: 359572
>
> visit_label is: V3.zip
>
> PSCID is: DCC0000
>
> CandID id: 359572
>
> visit_label is: V3.zip
>
>
>
> => No Visit label
>
>
>
>                 ERROR: Candidate IDs mismatch for
> /data/incoming/lorisadmin/DCC0000_359572_V3.zip.
>
>
>
> This Visit label has been populated in the MySQL visit table, so we don?t
> know what mismatch it is referring to.
>
>
>
> Any help would be much appreciated.
>
>
>
> Mar?a
>
>
>
> *De:* Olano.Mar?a
> *Enviado el:* mi?rcoles, 16 de noviembre de 2022 14:11
> *Para:* 'loris-dev at bic.mni.mcgill.ca' <loris-dev at bic.mni.mcgill.ca>
> *Asunto:* imaging_non_minc_insertion.pl issue with scanner_id
>
>
>
> Good afternoon,
>
>
>
> Hope this email finds you well. We are having problems using the
> imaging_non_minc_insertion.pl as when we execute the command this what
> pops up in the terminal.
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space
> native -reckless -verbose
>
>
>
> This script inserts a file in the files and parameter_file tables.
>
>
>
> Usage: perl imaging_non_minc_insertion.pl [options]
>
>
>
> -help for options
>
>
>
>
>
>                 ERROR: missing -scanner_id argument
>
>
>
> As you can see, scanner_id is included in the options accompanying the
> command, but when changing the ID from 0 to 10 it does recognize
> scanner_id, shown as followed:
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10
> -coordin_space native -reckless -verbose
>
>
>
> log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-12-49-8uubDY.log.
>
>
>
>                 ERROR: Invalid ScannerID 10.
>
>
>
> Both IDs are in the MYSQL table ?mri_scanner? so we don?t know what the
> problem could be.
>
>
>
> mysql> SELECT * FROM `mri_scanner`;
>
> +----+--------------+-------+---------------+----------+--------+
>
> | ID | Manufacturer | Model | Serial_number | Software | CandID |
>
> +----+--------------+-------+---------------+----------+--------+
>
> |  0 | NULL         | NULL  | NULL          | NULL     |   NULL |
>
> | 10 | NULL         | NULL  | NULL          | NULL     |   NULL |
>
> +----+--------------+-------+---------------+----------+--------+
>
>
>
> Any help would be much appreciated.
>
>
>
> Best regards,
>
>
>
> Mar?a
>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
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> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
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> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
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> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
>
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From molano at ext.cnio.es  Wed Nov 23 09:39:23 2022
From: molano at ext.cnio.es (=?utf-8?B?T2xhbm8uTWFyw61h?=)
Date: Wed, 23 Nov 2022 14:39:23 +0000
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
In-Reply-To: <CAMkiY3cd_yLi4HnnnsOqjzAK6QgsPK9Jm7Y8-Yx8NknV94L4wg@mail.gmail.com>
References: <CAMkiY3ep8AWFkzfFEf09ENF9yuWDq+y8Hh2YqeAwQfUk1r-R4g@mail.gmail.com>
 <1AAB0BC03205B240B7809934CFCF8DF52F5079@DONAR.cnio.es>
 <CAMkiY3cd_yLi4HnnnsOqjzAK6QgsPK9Jm7Y8-Yx8NknV94L4wg@mail.gmail.com>
Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52F50BE@DONAR.cnio.es>

Hi Cecile,

Can?t thank you enough, that was exactly what we needed for it to work!

De: Cecile Madjar <cecile.madjar at mcin.ca>
Enviado el: mi?rcoles, 23 de noviembre de 2022 15:11
Para: Olano.Mar?a <molano at ext.cnio.es>
CC: loris-dev <loris-dev at bic.mni.mcgill.ca>
Asunto: Re: imaging_non_minc_insertion.pl issue with scanner_id

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

Hi Maria,

It looks like the following SQL patch has not been run to update the MRI tables. Try sourcing this upgrade patch<https://github.com/aces/Loris/blob/v24.1.1/SQL/Release_patches/24.0_To_24.1_upgrade.sql> and the script should work.

Let me know how it goes,

C?cile

On Wed, Nov 23, 2022 at 6:53 AM Olano.Mar?a <molano at ext.cnio.es<mailto:molano at ext.cnio.es>> wrote:
Hello Cecile!

Thank you for your kind response. You were completely correct, the problem was the visit label not being read correctly, but we managed to solve this by adding an optional parameter: patient_name as seen below

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1 -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose -patient_name DCC0000_359572_V3

However, this proved to come with its fair share of errors, it seems the file Is read well and moved to another location (/data/loris/data/assembly/359572/V3/mri/native/) but the console output reads as follows:

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-20-gEsQPj.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3
    -> ScannerID was set to 1

    -> SessionID was set to 1

    -> Acquisition date was set to 2012-04-20

    -> Output type was set to native

Acquisition date: 2012-04-20
DBD::mysql::db do failed: Unknown column 'PhaseEncodingDirection' in 'field list' at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 793.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 818.

We had the idea of adding another parameter indicating there was a json file with said Phase encoding direction inside ((loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1 -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose -patient_name DCC0000_359572_V3 -metadata_file /home/lorisadmin/Downloads/patient.json) , but it was of no use, the console sent us the same message.

Inside the log file FileLoad-12-20-gEsQPj.log here is what is written:

==> computing md5 hash for MINC body.

--> md5: aab815082fbf91e7e3e26b7f6b899e2d

File /home/lorisadmin/Downloads/DCC0000_359572_V3.zip
moved to:
/data/loris/data/assembly/359572/V3/mri/native/loris_359572_V3_t1_001.zip
ative

And the MRICandidateErrors has an empty set.

Any help would be much appreciated, best regards!

Mar?a

De: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Enviado el: martes, 22 de noviembre de 2022 17:35
Para: Olano.Mar?a <molano at ext.cnio.es<mailto:molano at ext.cnio.es>>; loris-dev <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Asunto: imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> issue with scanner_id

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

Dear Maria,

Sorry for the late reply. For some reason I never received your email. Luckily, someone else from the LORIS team just flagged it and sent it to me.

It looks like the latest issue you are encountering is that the visit label is not properly parsed by the getSubjectIDs function in your prod file. Instead of returning V3, it returns V3.zip which is most likely not a valid visit label for your project.

The other possibility could be that DCC0000 and 359572 do not refer to the same candidate.

In any case, I think for both situations, an entry has been added to the MRICandidateErrors table and you could see the file in the MRI violations module where the file would be logged there.

Let me know if that helps. Best,

C?cile

---------- Forwarded message ---------
From: Olano.Mar?a <molano at ext.cnio.es<mailto:molano at ext.cnio.es>>
Date: Thu, Nov 17, 2022 at 10:24 AM
Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> issue with scanner_id
To: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>

Good afternoon!

We managed to solve the issue with the scanner_id by linking the CandID to the scanner

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+---------+---------------+----------+--------+
| ID | Manufacturer | Model   | Serial_number | Software | CandID |
+----+--------------+---------+---------------+----------+--------+
|  0 | NULL         | NULL    | NULL          | NULL     |   NULL |
|  1 | SIEMENS      | TrioTim | 35008         | Python   | 359572 |
| 10 | NULL         | NULL    | NULL          | NULL     |   NULL |
+----+--------------+---------+---------------+----------+--------+

And later got the upload_id error:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.

                ERROR: Invalid UploadID 1.

Managed to side step this error by using the front end Imaging Uploader which filled out the mri_upload table with the UploadID 1

mysql> SELECT * FROM `mri_upload`;
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
| UploadID | UploadedBy | UploadDate          | UploadLocation                                  | DecompressedLocation | InsertionComplete | Inserting | PatientName       | number_of_mincInserted | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated | IsTarchiveValidated | IsPhantom |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
|        1 | lorisadmin | 2022-11-17 14:40:58 | /data/incoming/lorisadmin/DCC0000_359572_V3.zip |                      |                 0 |      NULL | DCC0000_359572_V3 |                   NULL |                  NULL |       NULL |         1 |                     NULL |                   0 | N         |
+----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+

However! It didn?t manage to upload correctly so we tried to use the back end again with imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> (as this isn?t a DICOM file) and we are presented with our last error:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip
PSCID is: DCC0000
CandID id: 359572
visit_label is: V3.zip

=> No Visit label

                ERROR: Candidate IDs mismatch for /data/incoming/lorisadmin/DCC0000_359572_V3.zip.

This Visit label has been populated in the MySQL visit table, so we don?t know what mismatch it is referring to.

Any help would be much appreciated.

Mar?a

De: Olano.Mar?a
Enviado el: mi?rcoles, 16 de noviembre de 2022 14:11
Para: 'loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>' <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Asunto: imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> issue with scanner_id

Good afternoon,

Hope this email finds you well. We are having problems using the imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> as when we execute the command this what pops up in the terminal.

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space native -reckless -verbose

This script inserts a file in the files and parameter_file tables.

Usage: perl imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> [options]

-help for options


                ERROR: missing -scanner_id argument

As you can see, scanner_id is included in the options accompanying the command, but when changing the ID from 0 to 10 it does recognize scanner_id, shown as followed:

(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$ uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> -profile prod -upload_id 1 -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10 -coordin_space native -reckless -verbose

log dir is /data/loris/data/logs and log file is /data/loris/data/logs/FileLoad-12-49-8uubDY.log.

                ERROR: Invalid ScannerID 10.

Both IDs are in the MYSQL table ?mri_scanner? so we don?t know what the problem could be.

mysql> SELECT * FROM `mri_scanner`;
+----+--------------+-------+---------------+----------+--------+
| ID | Manufacturer | Model | Serial_number | Software | CandID |
+----+--------------+-------+---------------+----------+--------+
|  0 | NULL         | NULL  | NULL          | NULL     |   NULL |
| 10 | NULL         | NULL  | NULL          | NULL     |   NULL |
+----+--------------+-------+---------------+----------+--------+

Any help would be much appreciated.

Best regards,

Mar?a


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es<mailto:delegado_lopd at cnio.es>. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es<mailto:delegado_lopd at cnio.es>. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
_______________________________________________
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**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
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From cecile.madjar at mcin.ca  Wed Nov 23 09:42:35 2022
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Wed, 23 Nov 2022 09:42:35 -0500
Subject: [Loris-dev] imaging_non_minc_insertion.pl issue with scanner_id
In-Reply-To: <1AAB0BC03205B240B7809934CFCF8DF52F50BE@DONAR.cnio.es>
References: <CAMkiY3ep8AWFkzfFEf09ENF9yuWDq+y8Hh2YqeAwQfUk1r-R4g@mail.gmail.com>
 <1AAB0BC03205B240B7809934CFCF8DF52F5079@DONAR.cnio.es>
 <CAMkiY3cd_yLi4HnnnsOqjzAK6QgsPK9Jm7Y8-Yx8NknV94L4wg@mail.gmail.com>
 <1AAB0BC03205B240B7809934CFCF8DF52F50BE@DONAR.cnio.es>
Message-ID: <CAMkiY3e9gSj6Top3KvLoCKJz-DAa0ETzYWK2F1bM-8M0eB+ckQ@mail.gmail.com>

Great! Glad it works!!

On Wed, Nov 23, 2022 at 9:39 AM Olano.Mar?a <molano at ext.cnio.es> wrote:

> Hi Cecile,
>
>
>
> Can?t thank you enough, that was exactly what we needed for it to work!
>
>
>
> *De:* Cecile Madjar <cecile.madjar at mcin.ca>
> *Enviado el:* mi?rcoles, 23 de noviembre de 2022 15:11
> *Para:* Olano.Mar?a <molano at ext.cnio.es>
> *CC:* loris-dev <loris-dev at bic.mni.mcgill.ca>
> *Asunto:* Re: imaging_non_minc_insertion.pl issue with scanner_id
>
>
>
> *CAUTION: This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe*
>
>
>
> Hi Maria,
>
>
>
> It looks like the following SQL patch has not been run to update the MRI
> tables. Try sourcing this upgrade patch
> <https://github.com/aces/Loris/blob/v24.1.1/SQL/Release_patches/24.0_To_24.1_upgrade.sql> and
> the script should work.
>
>
>
> Let me know how it goes,
>
>
>
> C?cile
>
>
>
> On Wed, Nov 23, 2022 at 6:53 AM Olano.Mar?a <molano at ext.cnio.es> wrote:
>
> Hello Cecile!
>
>
>
> Thank you for your kind response. You were completely correct, the problem
> was the visit label not being read correctly, but we managed to solve this
> by adding an optional parameter: patient_name as seen below
>
>
>
> *(loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl
> <http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1
> -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose -patient_name DCC0000_359572_V3 *
>
>
>
> However, this proved to come with its fair share of errors, it seems the
> file Is read well and moved to another location
> (/data/loris/data/assembly/359572/V3/mri/native/) but the console output
> reads as follows:
>
>
>
> *log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-12-20-gEsQPj.log.*
>
> *PSCID is: DCC0000*
>
> *CandID id: 359572*
>
> *visit_label is: V3*
>
> *PSCID is: DCC0000*
>
> *CandID id: 359572*
>
> *visit_label is: V3*
>
> *    -> ScannerID was set to 1*
>
>
>
> *    -> SessionID was set to 1*
>
>
>
> *    -> Acquisition date was set to 2012-04-20*
>
>
>
> *    -> Output type was set to native*
>
>
>
> *Acquisition date: 2012-04-20*
>
> *DBD::mysql::db do failed: Unknown column 'PhaseEncodingDirection' in
> 'field list' at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 793.*
>
> *DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`LORIS`.`parameter_file`, CONSTRAINT
> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`))
> at /opt/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 818.*
>
>
>
> We had the idea of adding another parameter indicating there was a json
> file with said Phase encoding direction inside ((*loris-mri-python)
> lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl
> <http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1
> -file_path /home/lorisadmin/Downloads/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose -patient_name DCC0000_359572_V3 -metadata_file
> /home/lorisadmin/Downloads/patient.json*) , but it was of no use, the
> console sent us the same message.
>
>
>
> Inside the log file *FileLoad-12-20-gEsQPj.log* here is what is written*:*
>
>
>
> *==> computing md5 hash for MINC body.*
>
>
>
> *--> md5: aab815082fbf91e7e3e26b7f6b899e2d*
>
>
>
> *File /home/lorisadmin/Downloads/DCC0000_359572_V3.zip *
>
> *moved to:*
>
> */data/loris/data/assembly/359572/V3/mri/native/loris_359572_V3_t1_001.zip*
>
> *ative*
>
>
>
> And the MRICandidateErrors has an empty set.
>
>
>
> Any help would be much appreciated, best regards!
>
>
>
> Mar?a
>
>
>
> *De:* Cecile Madjar <cecile.madjar at mcin.ca>
> *Enviado el:* martes, 22 de noviembre de 2022 17:35
> *Para:* Olano.Mar?a <molano at ext.cnio.es>; loris-dev <
> loris-dev at bic.mni.mcgill.ca>
> *Asunto:* imaging_non_minc_insertion.pl issue with scanner_id
>
>
>
> *CAUTION: This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe*
>
>
>
> Dear Maria,
>
>
>
> Sorry for the late reply. For some reason I never received your email.
> Luckily, someone else from the LORIS team just flagged it and sent it to me.
>
>
>
> It looks like the latest issue you are encountering is that the visit
> label is not properly parsed by the getSubjectIDs function in your prod
> file. Instead of returning V3, it returns V3.zip which is most likely not a
> valid visit label for your project.
>
>
>
> The other possibility could be that DCC0000 and 359572 do not refer to the
> same candidate.
>
>
>
> In any case, I think for both situations, an entry has been added to the
> MRICandidateErrors table and you could see the file in the MRI violations
> module where the file would be logged there.
>
>
>
> Let me know if that helps. Best,
>
>
>
> C?cile
>
>
>
> ---------- Forwarded message ---------
> From: *Olano.Mar?a* <molano at ext.cnio.es>
> Date: Thu, Nov 17, 2022 at 10:24 AM
> Subject: Re: [Loris-dev] imaging_non_minc_insertion.pl issue with
> scanner_id
> To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>
>
>
> Good afternoon!
>
>
>
> We managed to solve the issue with the scanner_id by linking the CandID to
> the scanner
>
>
>
> mysql> SELECT * FROM `mri_scanner`;
>
> +----+--------------+---------+---------------+----------+--------+
>
> | ID | Manufacturer | Model   | Serial_number | Software | CandID |
>
> +----+--------------+---------+---------------+----------+--------+
>
> |  0 | NULL         | NULL    | NULL          | NULL     |   NULL |
>
> |  1 | SIEMENS      | TrioTim | 35008         | Python   | 359572 |
>
> | 10 | NULL         | NULL    | NULL          | NULL     |   NULL |
>
> +----+--------------+---------+---------------+----------+--------+
>
>
>
> And later got the upload_id error:
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose
>
>
>
> log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-11-48-F5qW5R.log.
>
>
>
>                 ERROR: Invalid UploadID 1.
>
>
>
> Managed to side step this error by using the front end Imaging Uploader
> which filled out the mri_upload table with the UploadID 1
>
>
>
> mysql> SELECT * FROM `mri_upload`;
>
>
> +----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
>
> | UploadID | UploadedBy | UploadDate          |
> UploadLocation                                  | DecompressedLocation |
> InsertionComplete | Inserting | PatientName       | number_of_mincInserted
> | number_of_mincCreated | TarchiveID | SessionID | IsCandidateInfoValidated
> | IsTarchiveValidated | IsPhantom |
>
>
> +----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
>
> |        1 | lorisadmin | 2022-11-17 14:40:58 |
> /data/incoming/lorisadmin/DCC0000_359572_V3.zip |
> |                 0 |      NULL | DCC0000_359572_V3 |
> NULL |                  NULL |       NULL |         1 |
>                 NULL |                   0 | N         |
>
>
> +----------+------------+---------------------+-------------------------------------------------+----------------------+-------------------+-----------+-------------------+------------------------+-----------------------+------------+-----------+--------------------------+---------------------+-----------+
>
>
>
> However! It didn?t manage to upload correctly so we tried to use the back
> end again with imaging_non_minc_insertion.pl (as this isn?t a DICOM file)
> and we are presented with our last error:
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /data/incoming/lorisadmin/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 1 -coordin_space
> native -reckless -verbose
>
>
>
> log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-16-0-_g35H2.log.
>
> PSCID is: DCC0000
>
> CandID id: 359572
>
> visit_label is: V3.zip
>
> PSCID is: DCC0000
>
> CandID id: 359572
>
> visit_label is: V3.zip
>
>
>
> => No Visit label
>
>
>
>                 ERROR: Candidate IDs mismatch for
> /data/incoming/lorisadmin/DCC0000_359572_V3.zip.
>
>
>
> This Visit label has been populated in the MySQL visit table, so we don?t
> know what mismatch it is referring to.
>
>
>
> Any help would be much appreciated.
>
>
>
> Mar?a
>
>
>
> *De:* Olano.Mar?a
> *Enviado el:* mi?rcoles, 16 de noviembre de 2022 14:11
> *Para:* 'loris-dev at bic.mni.mcgill.ca' <loris-dev at bic.mni.mcgill.ca>
> *Asunto:* imaging_non_minc_insertion.pl issue with scanner_id
>
>
>
> Good afternoon,
>
>
>
> Hope this email finds you well. We are having problems using the
> imaging_non_minc_insertion.pl as when we execute the command this what
> pops up in the terminal.
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 0 -coordin_space
> native -reckless -verbose
>
>
>
> This script inserts a file in the files and parameter_file tables.
>
>
>
> Usage: perl imaging_non_minc_insertion.pl [options]
>
>
>
> -help for options
>
>
>
>
>
>                 ERROR: missing -scanner_id argument
>
>
>
> As you can see, scanner_id is included in the options accompanying the
> command, but when changing the ID from 0 to 10 it does recognize
> scanner_id, shown as followed:
>
>
>
> (loris-mri-python) lorisadmin at maria-HP-ProBook-650-G2:/opt/loris/bin/mri$
> uploadNeuroDB/imaging_non_minc_insertion.pl -profile prod -upload_id 1
> -file_path /home/lorisadmin/Documents/DCC0000_359572_V3.zip -output_type
> native -scan_type t1 -date_acquired 2012-04-20 -scanner_id 10
> -coordin_space native -reckless -verbose
>
>
>
> log dir is /data/loris/data/logs and log file is
> /data/loris/data/logs/FileLoad-12-49-8uubDY.log.
>
>
>
>                 ERROR: Invalid ScannerID 10.
>
>
>
> Both IDs are in the MYSQL table ?mri_scanner? so we don?t know what the
> problem could be.
>
>
>
> mysql> SELECT * FROM `mri_scanner`;
>
> +----+--------------+-------+---------------+----------+--------+
>
> | ID | Manufacturer | Model | Serial_number | Software | CandID |
>
> +----+--------------+-------+---------------+----------+--------+
>
> |  0 | NULL         | NULL  | NULL          | NULL     |   NULL |
>
> | 10 | NULL         | NULL  | NULL          | NULL     |   NULL |
>
> +----+--------------+-------+---------------+----------+--------+
>
>
>
> Any help would be much appreciated.
>
>
>
> Best regards,
>
>
>
> Mar?a
>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
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> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
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> **LEGAL NOTICE**: This email and any attached files may contain protected
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> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
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From dave.macfarlane at mcin.ca  Wed Nov 23 10:08:11 2022
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Wed, 23 Nov 2022 10:08:11 -0500
Subject: [Loris-dev] Unable to Access the Front-end
In-Reply-To: <DS7PR06MB69364472BAA7D4712F2D066EFC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
References: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
 <CAN9cDwFadOywreGzh8p8uLVPyXtrQBALP7N0LnV9ppmpnFg3fg@mail.gmail.com>
 <DS7PR06MB69364472BAA7D4712F2D066EFC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
Message-ID: <CAN9cDwFpF4tjE1g4d273X+W-aDOe-esfPNrgurejdkja2BEKAg@mail.gmail.com>

This sometimes happens if the base path config setting isn't set correctly.

Can you run the SQL: SELECT * from Config WHERE ConfigID=(SELECT ID FROM
ConfigSettings WHERE Name='base');
and see what the result is? Also check if there's a xml tag named <base> in
the config.xml (which would override the database value)

The value should be the directory where you installed LORIS including the
trailing slash. ie `/var/www/loris/` (errors like this sometimes happen if
it's set to `/var/www/loris`)

If that config value is correct, it could also be a filesystem permission
issue. Make sure the files' unix permissions are readable by apache and the
directory permissions leading up to it are all executable by apache
(including the /var and /var/www).

- Dave


On Wed, Nov 23, 2022 at 9:04 AM Aaron Chen <kchen339 at wisc.edu> wrote:

> Hi,
>
> Thank you very much for the help. I did see there was a typo in my
> config.xml file. However, the front end is still inaccessible after I
> corrected the typo. I also throw our XML file into the XML validator but
> there is no syntax error. Below is the new error log I got after fixing the
> typo.
>
> [Tue Nov 22 16:40:55.155037 2022] [php7:notice] [pid 500127] [client
> 10.138.220.162:62703] [ERROR] Unable to load template 'file:404.tpl'#0
> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(232):
> Smarty_Internal_Template->render()
> #1
> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(116):
> Smarty_Internal_TemplateBase->_execute()
> #2 /var/www/loris/src/Http/Error.php(86):
> Smarty_Internal_TemplateBase->fetch()
> #3 /var/www/loris/src/Router/PrefixRouter.php(102):
> LORIS\\Http\\Error->__construct()
> #4 /var/www/loris/php/libraries/Module.class.inc(340):
> LORIS\\Router\\PrefixRouter->handle()
> #5 /var/www/loris/src/Router/ModuleRouter.php(77): Module->handle()
> #6 /var/www/loris/src/Middleware/ExceptionHandlingMiddleware.php(54):
> LORIS\\Router\\ModuleRouter->handle()
> #7 /var/www/loris/src/Router/BaseRouter.php(126):
> LORIS\\Middleware\\ExceptionHandlingMiddleware->process()
> #8 /var/www/loris/src/Middleware/ResponseGenerator.php(50):
> LORIS\\Router\\BaseRouter->handle()
> #9 /var/www/loris/src/Middleware/ContentLength.php(52):
> LORIS\\Middleware\\ResponseGenerator->process()
> #10 /var/www/loris/htdocs/index.php(55):
> LORIS\\Middleware\\ContentLength->process()
> #11 {main}
>
> [Tue Nov 22 16:40:55.159740 2022] [php7:error] [pid 500127] [client
> 10.138.220.162:62703] PHP Fatal error:  Uncaught  --> Smarty: Unable to
> load template 'file:500.tpl' <-- \n  thrown in
> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php
> on line 195
>
> [Tue Nov 22 16:40:55.159776 2022] [php7:notice] [pid 500127] [client
> 10.138.220.162:62703] [CRITICAL]
> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php:195:
> Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown
>
> It seems like there are some other errors that LORIS is trying to display
> via frontend but can't find the template in the system. Though, I did find
> 404.tpl and 500.tpl under /var/www/loris/smarty/templates/ directory. Also,
> the path to load the config.xml somehow was fixed by itself as I didn't see
> the error message again in the log file.
>
> Thank you in advance!
>
>
> Best,
>
> Aaron
>
> ------------------------------
> *From:* Dave MacFarlane <dave.macfarlane at mcin.ca>
> *Sent:* Tuesday, November 22, 2022 11:44 AM
> *To:* Aaron Chen <kchen339 at wisc.edu>
> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
> *Subject:* Re: [Loris-dev] Unable to Access the Front-end
>
> Hi Aaron,
>
> After resolving the ../ references the path looks like it's correctly
> looking at /var/www/loris/project.xml but the errors suggest that the file
> isn't valid xml.
>
> It looks like from the second line &lt;item value=&quot;V2&quot;&gt;V2
> label description&lt;/tem&gt; that you made a typo in the V2 and missed the
> "i" in the closing tag for the "item" tag.
>
> - Dave
>
> On Tue, Nov 22, 2022 at 11:48 AM Aaron Chen <kchen339 at wisc.edu> wrote:
>
> Good morning,
>
> Hope this email finds you well. Our team is trying to set up the LORIS
> system for research. It was working before but somehow, we aren't able to
> access the front-end. Below are some snips of errors from the
> loris-error.log under the /var/log/apache2/ directory.
>
>     [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
> /var/www/loris/php/libraries/../../project/config.xml:69: parser error :
> Opening and ending tag mismatch: item line 69 and tem in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
> &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client
> 128.105.29.144:61741] PHP Warning:  simplexml_load_file():
>                                          ^ in
> /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
>     [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client
> 128.105.29.144:61741] PHP Fatal error:  Uncaught Exception: Could not
> load Loris config file
> /var/www/loris/php/libraries/../../project/config.xml in
> /var/www/loris/php/libraries/NDB_Config.class.inc:100
>     Stack trace:
>     #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70):
> NDB_Config->load()
>     #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104):
> NDB_Config::singleton()
>     #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54):
> NDB_Factory->config()
>     #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
>     #4 {main}
>       thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line
> 100
>
> It seems like the path to the config.xml isn't correct. It should be
> /var/www/loris/php/libraries/project/config.xml, not
> /var/www/loris/php/libraries/../../project/config.xml. Where could I change
> the path?
>
> Any help would be much appreciated.
>
> Best,
> Aaron Chen
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
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From kchen339 at wisc.edu  Wed Nov 23 14:27:58 2022
From: kchen339 at wisc.edu (Aaron Chen)
Date: Wed, 23 Nov 2022 19:27:58 +0000
Subject: [Loris-dev] Unable to Access the Front-end
In-Reply-To: <CAN9cDwFpF4tjE1g4d273X+W-aDOe-esfPNrgurejdkja2BEKAg@mail.gmail.com>
References: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
 <CAN9cDwFadOywreGzh8p8uLVPyXtrQBALP7N0LnV9ppmpnFg3fg@mail.gmail.com>
 <DS7PR06MB69364472BAA7D4712F2D066EFC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
 <CAN9cDwFpF4tjE1g4d273X+W-aDOe-esfPNrgurejdkja2BEKAg@mail.gmail.com>
Message-ID: <DS7PR06MB6936ACBF76E4B06AEFC83C52FC0C9@DS7PR06MB6936.namprd06.prod.outlook.com>

Hi Dave,

It is working! Seems like it is because the path wasn't correct. We forgot to add the forward slash at the end of the path. Very much appreciated your help.

There is also one question I will like to ask which might be an error too. I was trying to debug it by myself before knowing the missing forward slash. I got an error log like this.
[Sat Nov 19 23:30:15.205931 2022] [php7:error] [pid 485530] [client 10.138.220.162:59913] PHP Fatal error:  Uncaught LorisNoSuchModuleException: No such module: acknowledgements in /var/www/loris/php/libraries/Module.class.inc:123
Stack trace:
#0 /var/www/loris/src/LorisInstance.php(79): Module::factory()
#1 /var/www/loris/src/LorisInstance.php(111): LORIS\\LorisInstance->getActiveModules()
#2 /var/www/loris/src/Router/BaseRouter.php(111): LORIS\\LorisInstance->hasModule()
#3 /var/www/loris/src/Middleware/ResponseGenerator.php(50): LORIS\\Router\\BaseRouter->handle()
#4 /var/www/loris/src/Middleware/ContentLength.php(52): LORIS\\Middleware\\ResponseGenerator->process()
#5 /var/www/loris/htdocs/index.php(55): LORIS\\Middleware\\ContentLength->process()
#6 {main}
 thrown in /var/www/loris/php/libraries/Module.class.inc on line 123

I found out that the path to find the module in the Module.class.inc file wasn't correct. I added a forward slash before project and modules and the error was gone.[cid:6f4d8945-b5a6-4ac0-9c29-ba9d544cb59b]

Should there be a forward slash before project and modules? Thank you in advance and Happy Thanksgiving!


Best,

Aaron

________________________________
From: Dave MacFarlane <dave.macfarlane at mcin.ca>
Sent: Wednesday, November 23, 2022 9:08 AM
To: Aaron Chen <kchen339 at wisc.edu>
Cc: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Unable to Access the Front-end

This sometimes happens if the base path config setting isn't set correctly.

Can you run the SQL: SELECT * from Config WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');
and see what the result is? Also check if there's a xml tag named <base> in the config.xml (which would override the database value)

The value should be the directory where you installed LORIS including the trailing slash. ie `/var/www/loris/` (errors like this sometimes happen if it's set to `/var/www/loris`)

If that config value is correct, it could also be a filesystem permission issue. Make sure the files' unix permissions are readable by apache and the directory permissions leading up to it are all executable by apache (including the /var and /var/www).

- Dave


On Wed, Nov 23, 2022 at 9:04 AM Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>> wrote:
Hi,

Thank you very much for the help. I did see there was a typo in my config.xml file. However, the front end is still inaccessible after I corrected the typo. I also throw our XML file into the XML validator but there is no syntax error. Below is the new error log I got after fixing the typo.
[Tue Nov 22 16:40:55.155037 2022] [php7:notice] [pid 500127] [client 10.138.220.162:62703<http://10.138.220.162:62703>] [ERROR] Unable to load template 'file:404.tpl'#0 /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(232): Smarty_Internal_Template->render()
#1 /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(116): Smarty_Internal_TemplateBase->_execute()
#2 /var/www/loris/src/Http/Error.php(86): Smarty_Internal_TemplateBase->fetch()
#3 /var/www/loris/src/Router/PrefixRouter.php(102): LORIS\\Http\\Error->__construct()
#4 /var/www/loris/php/libraries/Module.class.inc(340): LORIS\\Router\\PrefixRouter->handle()
#5 /var/www/loris/src/Router/ModuleRouter.php(77): Module->handle()
#6 /var/www/loris/src/Middleware/ExceptionHandlingMiddleware.php(54): LORIS\\Router\\ModuleRouter->handle()
#7 /var/www/loris/src/Router/BaseRouter.php(126): LORIS\\Middleware\\ExceptionHandlingMiddleware->process()
#8 /var/www/loris/src/Middleware/ResponseGenerator.php(50): LORIS\\Router\\BaseRouter->handle()
#9 /var/www/loris/src/Middleware/ContentLength.php(52): LORIS\\Middleware\\ResponseGenerator->process()
#10 /var/www/loris/htdocs/index.php(55): LORIS\\Middleware\\ContentLength->process()
#11 {main}

[Tue Nov 22 16:40:55.159740 2022] [php7:error] [pid 500127] [client 10.138.220.162:62703<http://10.138.220.162:62703>] PHP Fatal error:  Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown in /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php on line 195
[Tue Nov 22 16:40:55.159776 2022] [php7:notice] [pid 500127] [client 10.138.220.162:62703<http://10.138.220.162:62703>] [CRITICAL] /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php:195: Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown

It seems like there are some other errors that LORIS is trying to display via frontend but can't find the template in the system. Though, I did find 404.tpl and 500.tpl under /var/www/loris/smarty/templates/ directory. Also, the path to load the config.xml somehow was fixed by itself as I didn't see the error message again in the log file.[cid:184a5021f97cb971f161]

Thank you in advance!


Best,

Aaron

________________________________
From: Dave MacFarlane <dave.macfarlane at mcin.ca<mailto:dave.macfarlane at mcin.ca>>
Sent: Tuesday, November 22, 2022 11:44 AM
To: Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>>
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Subject: Re: [Loris-dev] Unable to Access the Front-end

Hi Aaron,

After resolving the ../ references the path looks like it's correctly looking at /var/www/loris/project.xml but the errors suggest that the file isn't valid xml.

It looks like from the second line &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; that you made a typo in the V2 and missed the "i" in the closing tag for the "item" tag.

- Dave

On Tue, Nov 22, 2022 at 11:48 AM Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>> wrote:
Good morning,

Hope this email finds you well. Our team is trying to set up the LORIS system for research. It was working before but somehow, we aren't able to access the front-end. Below are some snips of errors from the loris-error.log under the /var/log/apache2/ directory.

    [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file(): /var/www/loris/php/libraries/../../project/config.xml:69: parser error : Opening and ending tag mismatch: item line 69 and tem in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file():             &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file():                                                        ^ in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/loris/php/libraries/../../project/config.xml in /var/www/loris/php/libraries/NDB_Config.class.inc:100
    Stack trace:
    #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load()
    #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104): NDB_Config::singleton()
    #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config()
    #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
    #4 {main}
      thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 100
It seems like the path to the config.xml isn't correct. It should be /var/www/loris/php/libraries/project/config.xml, not /var/www/loris/php/libraries/../../project/config.xml. Where could I change the path?

Any help would be much appreciated.

Best,
Aaron Chen

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
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From kchen339 at wisc.edu  Fri Nov 25 19:04:45 2022
From: kchen339 at wisc.edu (Aaron Chen)
Date: Sat, 26 Nov 2022 00:04:45 +0000
Subject: [Loris-dev] Unable to Access the Front-end
In-Reply-To: <DS7PR06MB6936ACBF76E4B06AEFC83C52FC0C9@DS7PR06MB6936.namprd06.prod.outlook.com>
References: <DS7PR06MB6936777D533F61213C689EB9FC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
 <CAN9cDwFadOywreGzh8p8uLVPyXtrQBALP7N0LnV9ppmpnFg3fg@mail.gmail.com>
 <DS7PR06MB69364472BAA7D4712F2D066EFC0D9@DS7PR06MB6936.namprd06.prod.outlook.com>
 <CAN9cDwFpF4tjE1g4d273X+W-aDOe-esfPNrgurejdkja2BEKAg@mail.gmail.com>
 <DS7PR06MB6936ACBF76E4B06AEFC83C52FC0C9@DS7PR06MB6936.namprd06.prod.outlook.com>
Message-ID: <DS7PR06MB693626A379F328B481D9B23CFC0F9@DS7PR06MB6936.namprd06.prod.outlook.com>

Hi Dave,

I just realized that there should be no forward slash before it since there is a forward slash at the end of the base path which I forgot to add at the beginning. Sorry for bothering you and thank you very much for your help!


Best,

Aaron

________________________________
From: Aaron Chen <kchen339 at wisc.edu>
Sent: Wednesday, November 23, 2022 1:27 PM
To: Dave MacFarlane <dave.macfarlane at mcin.ca>
Cc: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Unable to Access the Front-end

Hi Dave,

It is working! Seems like it is because the path wasn't correct. We forgot to add the forward slash at the end of the path. Very much appreciated your help.

There is also one question I will like to ask which might be an error too. I was trying to debug it by myself before knowing the missing forward slash. I got an error log like this.
[Sat Nov 19 23:30:15.205931 2022] [php7:error] [pid 485530] [client 10.138.220.162:59913] PHP Fatal error:  Uncaught LorisNoSuchModuleException: No such module: acknowledgements in /var/www/loris/php/libraries/Module.class.inc:123
Stack trace:
#0 /var/www/loris/src/LorisInstance.php(79): Module::factory()
#1 /var/www/loris/src/LorisInstance.php(111): LORIS\\LorisInstance->getActiveModules()
#2 /var/www/loris/src/Router/BaseRouter.php(111): LORIS\\LorisInstance->hasModule()
#3 /var/www/loris/src/Middleware/ResponseGenerator.php(50): LORIS\\Router\\BaseRouter->handle()
#4 /var/www/loris/src/Middleware/ContentLength.php(52): LORIS\\Middleware\\ResponseGenerator->process()
#5 /var/www/loris/htdocs/index.php(55): LORIS\\Middleware\\ContentLength->process()
#6 {main}
 thrown in /var/www/loris/php/libraries/Module.class.inc on line 123

I found out that the path to find the module in the Module.class.inc file wasn't correct. I added a forward slash before project and modules and the error was gone.[cid:6f4d8945-b5a6-4ac0-9c29-ba9d544cb59b]

Should there be a forward slash before project and modules? Thank you in advance and Happy Thanksgiving!


Best,

Aaron

________________________________
From: Dave MacFarlane <dave.macfarlane at mcin.ca>
Sent: Wednesday, November 23, 2022 9:08 AM
To: Aaron Chen <kchen339 at wisc.edu>
Cc: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: Re: [Loris-dev] Unable to Access the Front-end

This sometimes happens if the base path config setting isn't set correctly.

Can you run the SQL: SELECT * from Config WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');
and see what the result is? Also check if there's a xml tag named <base> in the config.xml (which would override the database value)

The value should be the directory where you installed LORIS including the trailing slash. ie `/var/www/loris/` (errors like this sometimes happen if it's set to `/var/www/loris`)

If that config value is correct, it could also be a filesystem permission issue. Make sure the files' unix permissions are readable by apache and the directory permissions leading up to it are all executable by apache (including the /var and /var/www).

- Dave


On Wed, Nov 23, 2022 at 9:04 AM Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>> wrote:
Hi,

Thank you very much for the help. I did see there was a typo in my config.xml file. However, the front end is still inaccessible after I corrected the typo. I also throw our XML file into the XML validator but there is no syntax error. Below is the new error log I got after fixing the typo.
[Tue Nov 22 16:40:55.155037 2022] [php7:notice] [pid 500127] [client 10.138.220.162:62703<http://10.138.220.162:62703>] [ERROR] Unable to load template 'file:404.tpl'#0 /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(232): Smarty_Internal_Template->render()
#1 /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(116): Smarty_Internal_TemplateBase->_execute()
#2 /var/www/loris/src/Http/Error.php(86): Smarty_Internal_TemplateBase->fetch()
#3 /var/www/loris/src/Router/PrefixRouter.php(102): LORIS\\Http\\Error->__construct()
#4 /var/www/loris/php/libraries/Module.class.inc(340): LORIS\\Router\\PrefixRouter->handle()
#5 /var/www/loris/src/Router/ModuleRouter.php(77): Module->handle()
#6 /var/www/loris/src/Middleware/ExceptionHandlingMiddleware.php(54): LORIS\\Router\\ModuleRouter->handle()
#7 /var/www/loris/src/Router/BaseRouter.php(126): LORIS\\Middleware\\ExceptionHandlingMiddleware->process()
#8 /var/www/loris/src/Middleware/ResponseGenerator.php(50): LORIS\\Router\\BaseRouter->handle()
#9 /var/www/loris/src/Middleware/ContentLength.php(52): LORIS\\Middleware\\ResponseGenerator->process()
#10 /var/www/loris/htdocs/index.php(55): LORIS\\Middleware\\ContentLength->process()
#11 {main}

[Tue Nov 22 16:40:55.159740 2022] [php7:error] [pid 500127] [client 10.138.220.162:62703<http://10.138.220.162:62703>] PHP Fatal error:  Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown in /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php on line 195
[Tue Nov 22 16:40:55.159776 2022] [php7:notice] [pid 500127] [client 10.138.220.162:62703<http://10.138.220.162:62703>] [CRITICAL] /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php:195: Uncaught  --> Smarty: Unable to load template 'file:500.tpl' <-- \n  thrown

It seems like there are some other errors that LORIS is trying to display via frontend but can't find the template in the system. Though, I did find 404.tpl and 500.tpl under /var/www/loris/smarty/templates/ directory. Also, the path to load the config.xml somehow was fixed by itself as I didn't see the error message again in the log file.[cid:184a5021f97cb971f161]

Thank you in advance!


Best,

Aaron

________________________________
From: Dave MacFarlane <dave.macfarlane at mcin.ca<mailto:dave.macfarlane at mcin.ca>>
Sent: Tuesday, November 22, 2022 11:44 AM
To: Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>>
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Subject: Re: [Loris-dev] Unable to Access the Front-end

Hi Aaron,

After resolving the ../ references the path looks like it's correctly looking at /var/www/loris/project.xml but the errors suggest that the file isn't valid xml.

It looks like from the second line &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; that you made a typo in the V2 and missed the "i" in the closing tag for the "item" tag.

- Dave

On Tue, Nov 22, 2022 at 11:48 AM Aaron Chen <kchen339 at wisc.edu<mailto:kchen339 at wisc.edu>> wrote:
Good morning,

Hope this email finds you well. Our team is trying to set up the LORIS system for research. It was working before but somehow, we aren't able to access the front-end. Below are some snips of errors from the loris-error.log under the /var/log/apache2/ directory.

    [Mon Nov 21 22:05:36.946133 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file(): /var/www/loris/php/libraries/../../project/config.xml:69: parser error : Opening and ending tag mismatch: item line 69 and tem in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946178 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file():             &lt;item value=&quot;V2&quot;&gt;V2 label description&lt;/tem&gt; in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946190 2022] [php7:warn] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Warning:  simplexml_load_file():                                                        ^ in /var/www/loris/php/libraries/NDB_Config.class.inc on line 97
    [Mon Nov 21 22:05:36.946239 2022] [php7:error] [pid 495460] [client 128.105.29.144:61741<http://128.105.29.144:61741>] PHP Fatal error:  Uncaught Exception: Could not load Loris config file /var/www/loris/php/libraries/../../project/config.xml in /var/www/loris/php/libraries/NDB_Config.class.inc:100
    Stack trace:
    #0 /var/www/loris/php/libraries/NDB_Config.class.inc(70): NDB_Config->load()
    #1 /var/www/loris/php/libraries/NDB_Factory.class.inc(104): NDB_Config::singleton()
    #2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config()
    #3 /var/www/loris/htdocs/index.php(34): NDB_Client->initialize()
    #4 {main}
      thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 100
It seems like the path to the config.xml isn't correct. It should be /var/www/loris/php/libraries/project/config.xml, not /var/www/loris/php/libraries/../../project/config.xml. Where could I change the path?

Any help would be much appreciated.

Best,
Aaron Chen

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
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From AMORALESPINZON at BWH.HARVARD.EDU  Mon Nov 28 08:53:07 2022
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 28 Nov 2022 13:53:07 +0000
Subject: [Loris-dev] LORIS - Change visit label
Message-ID: <260179D8-16F7-4CFA-B132-BD6A9AE04CE0@bwh.harvard.edu>

Dear LorisDev Team,

By mistake we have mislabeled a visit label for some scans. For instance instead of using ?w24? we used ?et1?, and have uploaded some images to the ?et1? visit. What would you suggest to change the label of the visit? In the example that would be changing the visit label from ?et1? to ?w24?.

Thank you for your help.

Best regards,
Alfredo.
The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 


From cecile.madjar at mcin.ca  Mon Nov 28 16:52:39 2022
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 28 Nov 2022 16:52:39 -0500
Subject: [Loris-dev] LORIS - Change visit label
In-Reply-To: <260179D8-16F7-4CFA-B132-BD6A9AE04CE0@bwh.harvard.edu>
References: <260179D8-16F7-4CFA-B132-BD6A9AE04CE0@bwh.harvard.edu>
Message-ID: <CAMkiY3eAAO00WQxX90zOhOFpHzO6D89FuEcH2PU=45rB+B2tJQ@mail.gmail.com>

Hi Alfredo,

I guess that would depend on the imaging data that was uploaded into LORIS.

Are they DICOM images converted to MINC images etc... If so, then the visit
label is going to be in all the headers. In that case, we usually remove
the imaging files, change the visit label on the DB, rename PatientName in
the DICOM images and reupload the data.

For files uploaded directly as BIDS datasets, I don't think the visit label
ends up in the JSON file or any header, so in that case, I guess you could
rename the files and then update the DB with the correct file paths and
visit label.

Let me know which situation corresponds to yours or if you have questions
on how to do those changes,

C?cile

On Mon, Nov 28, 2022 at 8:53 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear LorisDev Team,
>
> By mistake we have mislabeled a visit label for some scans. For instance
> instead of using ?w24? we used ?et1?, and have uploaded some images to the
> ?et1? visit. What would you suggest to change the label of the visit? In
> the example that would be changing the visit label from ?et1? to ?w24?.
>
> Thank you for your help.
>
> Best regards,
> Alfredo.
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> https://www.massgeneralbrigham.org/complianceline <
> https://www.massgeneralbrigham.org/complianceline> .
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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