From AMORALESPINZON at BWH.HARVARD.EDU  Fri Dec 10 14:01:44 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 10 Dec 2021 19:01:44 +0000
Subject: [Loris-dev] MINC insertion
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Hi C?cile, (sorry if receive this email multiple times, I'm having issues with my email client)

We managed to import some MINC files with the proper thumbnails in LORIS. The files seem to be properly stored in the hard-drive (LORIS data folder) but we are facing the following issues:

1. When loading them in the front-end the MINC images cannot be visualized
2. When getting the headers using the API we are getting {"error":"not found"}
3. When downloading them using the API we get the error code "404"

Any ideas?

On a side note, how can I change the acquisition label of an acquisition that I uploaded with an improper label?

Thank you for your help.

Best,
Alfredo.
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca>
Sent: Tuesday, November 30, 2021 4:15 PM
To: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU>
Cc: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>; Sridar Narayanan <sridar.narayanan at mcgill.ca>; Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu>; Istvan Akos Imre Morocz, Dr <istvan.morocz at mcgill.ca>; Samir Das <samirdas99 at gmail.com>
Subject: Re: [Loris-dev] MINC insertion


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Hi Alfredo,

Sorry for the delay. Time flies quickly this week.

How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?

Let me know if one of those times works for you.
Thanks!

C?cile

On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Here is the results of the query:

===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
  CenterID: 843
      Name: inf_0102
   PSCArea: NULL
   Address: NULL
      City: NULL
   StateID: NULL
       ZIP: NULL
    Phone1: NULL
    Phone2: NULL
  Contact1: NULL
  Contact2: NULL
     Alias: BGI
 MRI_alias: BGI
   Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===

Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.

Best,
Alfredo.

On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


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Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


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Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


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Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


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Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;

Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

Best,
Alfredo.

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From AMORALESPINZON at BWH.HARVARD.EDU  Fri Dec 10 14:02:55 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 10 Dec 2021 19:02:55 +0000
Subject: [Loris-dev] MINC insertion
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Message-ID: <D6A8D890-1308-42A9-854F-196525F58A3B@bwh.harvard.edu>

Hi C?cile,

We managed to import some MINC files with the proper thumbnails in LORIS. The files seem to be properly stored in the hard drive but we are facing the following issues:

1. When loading them in the front-end the MINC images cannot be visualized
2. When getting the headers usign the API we are getting {"error":"not found"}
3. When downloading them using the API we get the error code "404"

Any ideas?

On a side question, how can I change the acquisition label of an acquisition that I uploaded with an improper label?

Thank you for your help.

Best,
Alfredo.

On Nov 30, 2021, at 11:19 PM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>> wrote:


        External Email - Use Caution

Hi C?cile,

Thank you. 4pm works. I?ll send a send in a separate email.

Best,
Alfredo.



Get Outlook for iOS<https://secure-web.cisco.com/1PNz5U6EhZ9bpIT12Ja8UKYftUkpn_Raq5yJAq5UlUVrzASfWdBGB_NTKH4r4SdXViI-uWyNsITpiECc6lxGRXh1u3HE4UmK6DiIO4pPwbV1b24od2Cv8ptLxRGkuzK6CSy10s58NjPqm5Ffi1QeTzQouRc_9aAMW3D-5patrAXX3y0Hjmx8e_SoiiVUKcweg2W7TnPI0rqDenpUUoAsZPjYbr5o3UUykL385AC-_2dv9lxhFXEgV6pey6erqBaWmS3sbqwA3-jsSkIjQDLK5nUtz1EeRnH3NsrT4jFbU5iCV2LtY8B8G19ot6upbSxA7oBDZbHJQ6XX_V2LtFjJlvw/https%3A%2F%2Faka.ms%2Fo0ukef>
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Sent: Tuesday, November 30, 2021 4:15:28 PM
To: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.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>>; Sridar Narayanan <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>; Istvan Akos Imre Morocz, Dr <istvan.morocz at mcgill.ca<mailto:istvan.morocz at mcgill.ca>>; Samir Das <samirdas99 at gmail.com<mailto:samirdas99 at gmail.com>>
Subject: Re: [Loris-dev] MINC insertion


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay. Time flies quickly this week.

How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?

Let me know if one of those times works for you.
Thanks!

C?cile

On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Here is the results of the query:

===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
  CenterID: 843
      Name: inf_0102
   PSCArea: NULL
   Address: NULL
      City: NULL
   StateID: NULL
       ZIP: NULL
    Phone1: NULL
    Phone2: NULL
  Contact1: NULL
  Contact2: NULL
     Alias: BGI
 MRI_alias: BGI
   Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===

Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.

Best,
Alfredo.

On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;

Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

Best,
Alfredo.

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From AMORALESPINZON at BWH.HARVARD.EDU  Fri Dec 10 14:12:12 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 10 Dec 2021 19:12:12 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <MN2PR04MB616084F0AB13FA4BC5B23C988F689@MN2PR04MB6160.namprd04.prod.outlook.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
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Message-ID: <0F4435F9-C745-469E-8152-D60CFC0A2594@bwh.harvard.edu>

Hi C?cile,

We managed to import some MINC files with the proper thumbnails in LORIS. The files seem to be properly stored in the hard drive but we are facing the following issues:

1. When loading them in the front-end the MINC images cannot be visualized
2. When getting the headers usign the API we are getting {"error":"not found"}
3. When downloading them using the API we get the error code "404"

Any ideas?

On a side note, how can I change the acquistion label of an acquisition that I uploaded with an improper label?

Thank you for your help.

Best,
Alfredo.

On Nov 30, 2021, at 11:19 PM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>> wrote:


        External Email - Use Caution

Hi C?cile,

Thank you. 4pm works. I?ll send a send in a separate email.

Best,
Alfredo.



Get Outlook for iOS<https://secure-web.cisco.com/1PNz5U6EhZ9bpIT12Ja8UKYftUkpn_Raq5yJAq5UlUVrzASfWdBGB_NTKH4r4SdXViI-uWyNsITpiECc6lxGRXh1u3HE4UmK6DiIO4pPwbV1b24od2Cv8ptLxRGkuzK6CSy10s58NjPqm5Ffi1QeTzQouRc_9aAMW3D-5patrAXX3y0Hjmx8e_SoiiVUKcweg2W7TnPI0rqDenpUUoAsZPjYbr5o3UUykL385AC-_2dv9lxhFXEgV6pey6erqBaWmS3sbqwA3-jsSkIjQDLK5nUtz1EeRnH3NsrT4jFbU5iCV2LtY8B8G19ot6upbSxA7oBDZbHJQ6XX_V2LtFjJlvw/https%3A%2F%2Faka.ms%2Fo0ukef>
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Sent: Tuesday, November 30, 2021 4:15:28 PM
To: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.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>>; Sridar Narayanan <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>; Istvan Akos Imre Morocz, Dr <istvan.morocz at mcgill.ca<mailto:istvan.morocz at mcgill.ca>>; Samir Das <samirdas99 at gmail.com<mailto:samirdas99 at gmail.com>>
Subject: Re: [Loris-dev] MINC insertion


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay. Time flies quickly this week.

How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?

Let me know if one of those times works for you.
Thanks!

C?cile

On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Here is the results of the query:

===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
  CenterID: 843
      Name: inf_0102
   PSCArea: NULL
   Address: NULL
      City: NULL
   StateID: NULL
       ZIP: NULL
    Phone1: NULL
    Phone2: NULL
  Contact1: NULL
  Contact2: NULL
     Alias: BGI
 MRI_alias: BGI
   Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===

Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.

Best,
Alfredo.

On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;

Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

Best,
Alfredo.

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From cecile.madjar at mcin.ca  Fri Dec 10 14:20:28 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 10 Dec 2021 14:20:28 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <MN2PR04MB6160DE1F60810D12069D7DED8F719@MN2PR04MB6160.namprd04.prod.outlook.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
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Message-ID: <CAMkiY3fbT8E7ZaOMNUyJ7DrWqRrn98WD=jkCuXBxWZAGQ0i=og@mail.gmail.com>

Hi Alfredo,

Glad to hear you were able to import the MINC files. It seems the issue you
are having might be due to file permissions. Can you make sure the apache
user can see the directories/files that were created by the import?

To change the label, the least risky route would be to remove the
mislabelled file from the files and parameter_file tables and reimport with
the correct label for scan type.

Hope this helps,

C?cile


On Fri, Dec 10, 2021 at 2:01 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile, (sorry if receive this email multiple times, I'm having issues
> with my email client)
>
> We managed to import some MINC files with the proper thumbnails in LORIS.
> The files seem to be properly stored in the hard-drive (LORIS data folder)
> but we are facing the following issues:
>
> 1. When loading them in the front-end the MINC images cannot be visualized
> 2. When getting the headers using the API we are getting {"error":"not
> found"}
> 3. When downloading them using the API we get the error code "404"
>
> Any ideas?
>
> On a side note, how can I change the acquisition label of an acquisition
> that I uploaded with an improper label?
>
> Thank you for your help.
>
> Best,
> Alfredo.
> ------------------------------
> *From:* Cecile Madjar <cecile.madjar at mcin.ca>
> *Sent:* Tuesday, November 30, 2021 4:15 PM
> *To:* Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU>
> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>; Sridar
> Narayanan <sridar.narayanan at mcgill.ca>; Rozie Arnaoutelis <
> rozie.arnaoutelis at mcgill.ca>; Douglas Arnold, Dr. <
> douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. <
> guttmann at bwh.harvard.edu>; Istvan Akos Imre Morocz, Dr <
> istvan.morocz at mcgill.ca>; Samir Das <samirdas99 at gmail.com>
> *Subject:* Re: [Loris-dev] MINC insertion
>
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Sorry for the delay. Time flies quickly this week.
>
> How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?
>
> Let me know if one of those times works for you.
> Thanks!
>
> C?cile
>
> On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> Here is the results of the query:
>
> ===
> mysql> SELECT * FROM psc WHERE CenterID=843 \G;
> *************************** 1. row ***************************
>   CenterID: 843
>       Name: inf_0102
>    PSCArea: NULL
>    Address: NULL
>       City: NULL
>    StateID: NULL
>        ZIP: NULL
>     Phone1: NULL
>     Phone2: NULL
>   Contact1: NULL
>   Contact2: NULL
>      Alias: BGI
>  MRI_alias: BGI
>    Account: NULL
> Study_site: Y
> 1 row in set (0.00 sec)
> ===
>
> Alias and MRI_alias look fine. What should we look into now? We can debug
> over Zoom if that works for you.
>
> Best,
> Alfredo.
>
> On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> I think we are indeed narrowing where the error happens. It looks like for
> some reason this getPSC
> <https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm>
> function is returning "UNKN", 0. It might be related to the Alias or
> MRI_alias content of the psc table for CenterID 843.
>
> What do you get when you run the following query?
> SELECT * FROM psc WHERE CenterID=843;
>
> In the Alias or MRI_alias column, you should be able to see BGI so that
> the scanner candidate can be identified with the proper site.
>
> Let me know,
>
> C?cile
>
> On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> Thank you, it looks like we?re getting closer to find a solution. Find the
> answers to your questions inline below.
>
> Happy to debug over Zoom if it?s easier for you.
>
> Best,
> Alfredo.
>
>
> On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> I notice that the CenterID for the site is 0. Do you have an entry in the
> psc table for a CenterID=0?
>
> No, we don?t have it. The CenterID starts at 1.
> ===
> select * from psc where CenterID=0;
> Empty set (0.00 sec)
> ===
>
>
> The problem here is that the data comes from a new scanner and the
> pipeline tries to first register a new candidate for the scanner (scanner
> candidate) before adding an entry in the mri_scanner table. To determine
> the site of the scanner, the pipeline uses the determinePSC
> <https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503>
> function of MRIProcessingUtility.pm (called by minc_insertion.pl
> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
> in line 454
> <https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>).
> I would be curious to see what the $center_name and $centerID values
> returned are.
>
> These are the returned values. Maybe we need to look deeper into this.
> ===
> determinePSC->Center name: UNKN
> determinePSC->Center ID: 0
> ===
>
>
> Could you also copy the code you have in your prod file for the function
> getSubjectIDs?
>
>
> You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the
> function enclosed.
>
>
> Finally, could you check that the candidate BGI102001_207019 does have a
> RegistrationCenterID set and if there is already a screening session
> created in the session table, that the CenterID of that session has
> properly been set?
>
>
> The candidate has a RegistrationCenterID (843):
> ===
> select * from candidate where CandID=207019 \G;
> *************************** 1. row ***************************
>                   ID: 8974
>               CandID: 207019
>                PSCID: BGI102001
>           ExternalID: NULL
>                  DoB: 1969-05-15
>                  EDC: NULL
>                  Sex: Female
> RegistrationCenterID: 843
> RegistrationProjectID: 12
>            Ethnicity: NULL
>               Active: Y
>          Date_active: 2021-05-27
>         RegisteredBy: dataman
>               UserID: dataman
>      Date_registered: 2021-05-27
> flagged_caveatemptor: false
>       flagged_reason: NULL
>        flagged_other: NULL
> flagged_other_status: NULL
>             Testdate: 2021-06-09 10:55:35
>          Entity_type: Human
>           ProbandSex: NULL
>           ProbandDoB: NULL
>                  DoD: NULL
> 1 row in set (0.00 sec)
> ===
>
> The session with the proper values already exists:
> ===
> mysql> select * from session where CandID=207019 and
> Visit_label="screening" \G;
> *************************** 1. row ***************************
>                  ID: 127260
>              CandID: 207019
>            CenterID: 843
>             VisitNo: 1
>         Visit_label: screening
>        SubprojectID: 2
>           Submitted: N
>       Current_stage: Not Started
>   Date_stage_change: NULL
>           Screening: NULL
>      Date_screening: NULL
>               Visit: NULL
>          Date_visit: NULL
>            Approval: NULL
>       Date_approval: NULL
>              Active: Y
>         Date_active: 2021-05-27
>        RegisteredBy: dataman
>              UserID: dataman
>     Date_registered: 2021-05-27
>            Testdate: 2021-06-10 18:35:41
>    Hardcopy_request: -
>         BVLQCStatus: NULL
>           BVLQCType: NULL
>      BVLQCExclusion: NULL
>                 QCd: NULL
>           Scan_done: Y
>         MRIQCStatus:
>        MRIQCPending: N
> MRIQCFirstChangeTime: NULL
> MRIQCLastChangeTime: NULL
>           MRICaveat: false
>           ProjectID: 12
>          languageID: 1
> 1 row in set (0.00 sec)
> ===
>
> Thank you!
>
> C?cile
>
> On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> Thank you for answer.
>
> I included the following lines:
>
> ===
>                   . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
> +        print "\nCenter ID: " . $centerID . "\n\n";
> +        print "\nQuery:" . $query . "\n\n";
>          $dbh->do($query);
>      }
> ===
>
> And I got the following output:
>
> ===
> perl minc_insertion.pl
> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
> -verbose -acquisition_protocol t1c -create_minc_pics
>
> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is
> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
>     SELECT       ArchiveLocation     FROM       tarchive     WHERE
> TarchiveID = (                      SELECT TarchiveID
> FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?
>                   )
> Center ID: 0
>
>
> Query:INSERT INTO candidate (CandID,          PSCID,
> RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type
>                     ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),
>   'NeuroDB::MRI', 'Scanner'          )
>
> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
> 1020.
> ERROR: Failed to insert record in table mri_scanner:
> The following database commands failed:
>         PREPARE s FROM 'INSERT INTO mri_scanner
> (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
>         SET
> @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
>         EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
> Error obtained:Cannot add or update a child row: a foreign key constraint
> fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
> ===
>
> I think it?s important to mention that this candidate was created by the
> bids importing script. Maybe there is center associated with the candidates
> when using the bids script?
>
> Let me know your thoughts.
>
> Best,
> Alfredo.
>
> On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Thank you Alfredo.
>
> I wonder whether the variable $centerID is null when provided to the query
> here
> <https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012>
> in your case.
>
> Could you add in MRI.pm line 1018 the following print statements and let
> me know what you get? (Right before the $dbh->do($query);
> print($centerID);
> print($query);
>
> Thank you!
>
> C?cile
>
> On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> This is the branch that we are using in the IPMSA project:
>
> https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA
> <https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>
>
> Best,
> Alfredo.
>
> On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Could you point me to the version of the code you are using on GitHub so I
> can take a look at the correct MRI.pm file.
>
> Thank you!
>
> C?cile
>
> On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
> I?m getting the following error when inserting a minc file using the
> minc_insertion.pl
> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
> script:
>
> ===
> $ perl minc_insertion.pl
> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
> -verbose -acquisition_protocol t1c -create_minc_pics
>
> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
> 1018.
>
> ERROR: Failed to insert record in table mri_scanner:
>
> The following database commands failed:
> PREPARE s FROM 'INSERT INTO mri_scanner
> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>
> Error obtained:Cannot add or update a child row: a foreign key constraint
> fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
> ===
>
> Could you help me figuring out what is happening? Is there something I
> should add to the minc headers?
>
> Best,
> Alfredo.
>
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From AMORALESPINZON at BWH.HARVARD.EDU  Fri Dec 10 14:51:30 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 10 Dec 2021 19:51:30 +0000
Subject: [Loris-dev] MINC insertion
In-Reply-To: <CAMkiY3fbT8E7ZaOMNUyJ7DrWqRrn98WD=jkCuXBxWZAGQ0i=og@mail.gmail.com>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
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 <CAMkiY3cKpqDwbpSxQKKtUir1Jvx9-ZwRn+PQ5DUp3kjZ0YLuxg@mail.gmail.com>
 <MN2PR04MB6160DE1F60810D12069D7DED8F719@MN2PR04MB6160.namprd04.prod.outlook.com>
 <CAMkiY3fbT8E7ZaOMNUyJ7DrWqRrn98WD=jkCuXBxWZAGQ0i=og@mail.gmail.com>
Message-ID: <005CC558-3055-489E-AD9E-55BE109BE467@bwh.harvard.edu>

Hi C?cile,

Thank you, it was indeed an issue with file permissions.

Regarding removing the mislabelled files, should I also remove the file itself from the LORIS data folder before reuploading?

Best,
Alfredo.

On Dec 10, 2021, at 2:20 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Glad to hear you were able to import the MINC files. It seems the issue you are having might be due to file permissions. Can you make sure the apache user can see the directories/files that were created by the import?

To change the label, the least risky route would be to remove the mislabelled file from the files and parameter_file tables and reimport with the correct label for scan type.

Hope this helps,

C?cile


On Fri, Dec 10, 2021 at 2:01 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile, (sorry if receive this email multiple times, I'm having issues with my email client)

We managed to import some MINC files with the proper thumbnails in LORIS. The files seem to be properly stored in the hard-drive (LORIS data folder) but we are facing the following issues:

1. When loading them in the front-end the MINC images cannot be visualized
2. When getting the headers using the API we are getting {"error":"not found"}
3. When downloading them using the API we get the error code "404"

Any ideas?

On a side note, how can I change the acquisition label of an acquisition that I uploaded with an improper label?

Thank you for your help.

Best,
Alfredo.
________________________________
From: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Sent: Tuesday, November 30, 2021 4:15 PM
To: Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.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>>; Sridar Narayanan <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>; Douglas Arnold, Dr. <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>; Guttmann, Charles,M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>; Istvan Akos Imre Morocz, Dr <istvan.morocz at mcgill.ca<mailto:istvan.morocz at mcgill.ca>>; Samir Das <samirdas99 at gmail.com<mailto:samirdas99 at gmail.com>>
Subject: Re: [Loris-dev] MINC insertion


        External Email - Use Caution

Hi Alfredo,

Sorry for the delay. Time flies quickly this week.

How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?

Let me know if one of those times works for you.
Thanks!

C?cile

On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Here is the results of the query:

===
mysql> SELECT * FROM psc WHERE CenterID=843 \G;
*************************** 1. row ***************************
  CenterID: 843
      Name: inf_0102
   PSCArea: NULL
   Address: NULL
      City: NULL
   StateID: NULL
       ZIP: NULL
    Phone1: NULL
    Phone2: NULL
  Contact1: NULL
  Contact2: NULL
     Alias: BGI
 MRI_alias: BGI
   Account: NULL
Study_site: Y
1 row in set (0.00 sec)
===

Alias and MRI_alias look fine. What should we look into now? We can debug over Zoom if that works for you.

Best,
Alfredo.

On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I think we are indeed narrowing where the error happens. It looks like for some reason this getPSC<https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm> function is returning "UNKN", 0. It might be related to the Alias or MRI_alias content of the psc table for CenterID 843.

What do you get when you run the following query?
SELECT * FROM psc WHERE CenterID=843;

In the Alias or MRI_alias column, you should be able to see BGI so that the scanner candidate can be identified with the proper site.

Let me know,

C?cile

On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you, it looks like we?re getting closer to find a solution. Find the answers to your questions inline below.

Happy to debug over Zoom if it?s easier for you.

Best,
Alfredo.


On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I notice that the CenterID for the site is 0. Do you have an entry in the psc table for a CenterID=0?
No, we don?t have it. The CenterID starts at 1.
===
select * from psc where CenterID=0;
Empty set (0.00 sec)
===

The problem here is that the data comes from a new scanner and the pipeline tries to first register a new candidate for the scanner (scanner candidate) before adding an entry in the mri_scanner table. To determine the site of the scanner, the pipeline uses the determinePSC<https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503> function of MRIProcessingUtility.pm (called by minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> in line 454<https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>). I would be curious to see what the $center_name and $centerID values returned are.
These are the returned values. Maybe we need to look deeper into this.
===
determinePSC->Center name: UNKN
determinePSC->Center ID: 0
===


Could you also copy the code you have in your prod file for the function getSubjectIDs?

You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the function enclosed.


Finally, could you check that the candidate BGI102001_207019 does have a RegistrationCenterID set and if there is already a screening session created in the session table, that the CenterID of that session has properly been set?


The candidate has a RegistrationCenterID (843):
===
select * from candidate where CandID=207019 \G;
*************************** 1. row ***************************
                  ID: 8974
              CandID: 207019
               PSCID: BGI102001
          ExternalID: NULL
                 DoB: 1969-05-15
                 EDC: NULL
                 Sex: Female
RegistrationCenterID: 843
RegistrationProjectID: 12
           Ethnicity: NULL
              Active: Y
         Date_active: 2021-05-27
        RegisteredBy: dataman
              UserID: dataman
     Date_registered: 2021-05-27
flagged_caveatemptor: false
      flagged_reason: NULL
       flagged_other: NULL
flagged_other_status: NULL
            Testdate: 2021-06-09 10:55:35
         Entity_type: Human
          ProbandSex: NULL
          ProbandDoB: NULL
                 DoD: NULL
1 row in set (0.00 sec)
===

The session with the proper values already exists:
===
mysql> select * from session where CandID=207019 and Visit_label="screening" \G;
*************************** 1. row ***************************
                 ID: 127260
             CandID: 207019
           CenterID: 843
            VisitNo: 1
        Visit_label: screening
       SubprojectID: 2
          Submitted: N
      Current_stage: Not Started
  Date_stage_change: NULL
          Screening: NULL
     Date_screening: NULL
              Visit: NULL
         Date_visit: NULL
           Approval: NULL
      Date_approval: NULL
             Active: Y
        Date_active: 2021-05-27
       RegisteredBy: dataman
             UserID: dataman
    Date_registered: 2021-05-27
           Testdate: 2021-06-10 18:35:41
   Hardcopy_request: -
        BVLQCStatus: NULL
          BVLQCType: NULL
     BVLQCExclusion: NULL
                QCd: NULL
          Scan_done: Y
        MRIQCStatus:
       MRIQCPending: N
MRIQCFirstChangeTime: NULL
MRIQCLastChangeTime: NULL
          MRICaveat: false
          ProjectID: 12
         languageID: 1
1 row in set (0.00 sec)
===

Thank you!

C?cile

On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

Thank you for answer.

I included the following lines:

===
                  . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
+        print "\nCenter ID: " . $centerID . "\n\n";
+        print "\nQuery:" . $query . "\n\n";
         $dbh->do($query);
     }
===

And I got the following output:

===
perl minc_insertion.pl<http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc -verbose -acquisition_protocol t1c -create_minc_pics

log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
    SELECT       ArchiveLocation     FROM       tarchive     WHERE       TarchiveID = (                      SELECT TarchiveID                      FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?                    )
Center ID: 0


Query:INSERT INTO candidate (CandID,          PSCID,  RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type                       ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),   'NeuroDB::MRI', 'Scanner'          )

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1020.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
        PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
        SET @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
        EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

I think it?s important to mention that this candidate was created by the bids importing script. Maybe there is center associated with the candidates when using the bids script?

Let me know your thoughts.

Best,
Alfredo.

On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Thank you Alfredo.

I wonder whether the variable $centerID is null when provided to the query here<https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012> in your case.

Could you add in MRI.pm line 1018 the following print statements and let me know what you get? (Right before the $dbh->do($query);
print($centerID);
print($query);

Thank you!

C?cile

On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

This is the branch that we are using in the IPMSA project:

https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA<https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>

Best,
Alfredo.

On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Could you point me to the version of the code you are using on GitHub so I can take a look at the correct MRI.pm file.

Thank you!

C?cile

On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi C?cile,

I?m getting the following error when inserting a minc file using the minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> script:

===
$ perl minc_insertion.pl<http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc  -verbose -acquisition_protocol t1c -create_minc_pics

DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1018.

ERROR: Failed to insert record in table mri_scanner:

The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;

Error obtained:Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
===

Could you help me figuring out what is happening? Is there something I should add to the minc headers?

Best,
Alfredo.

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From cecile.madjar at mcin.ca  Fri Dec 10 14:54:13 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 10 Dec 2021 14:54:13 -0500
Subject: [Loris-dev] MINC insertion
In-Reply-To: <005CC558-3055-489E-AD9E-55BE109BE467@bwh.harvard.edu>
References: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>
 <CAMkiY3fKNoN1U=t3mjM2VnOgWU56=0-YadQwLkc6xZOGUc-mvA@mail.gmail.com>
 <ED989A0A-3A12-4161-AF6A-8F7586F7DDFE@bwh.harvard.edu>
 <CAMkiY3eHjFAd1-bKdCx_5_k1nf2Mx_GCKDs2htAaTxxFoPqKhQ@mail.gmail.com>
 <63278E0B-C75D-467E-9A2C-579BC947EBC3@bwh.harvard.edu>
 <CAMkiY3fJcP0O=j++Rjjmymh9QqMofBY0NaTw0YH8GYTco7ZxSg@mail.gmail.com>
 <53B91CC9-99CE-4E76-A080-9E902115673A@bwh.harvard.edu>
 <CAMkiY3fUqgyP-BoFb71aOjBLfnPNRqt1UyQSEq6Q2TtObsNFoA@mail.gmail.com>
 <79E009D1-6AA8-4090-812A-F7405AE257C9@bwh.harvard.edu>
 <CAMkiY3eFwZbaCZXdBc-eS6Skp9-bSz5mHH6A2WwwS83_2WNmhg@mail.gmail.com>
 <94B44F39-0E17-4C7B-AE35-490F8BF95ABD@bwh.harvard.edu>
 <CAMkiY3erKTvEXScZofQeP-u2jFh4GK4gPEJnD7TgFuqsPYqSiQ@mail.gmail.com>
 <E92E7EDA-FF77-41B1-82CD-1ABF0F0DFCCA@bwh.harvard.edu>
 <CAMkiY3cKpqDwbpSxQKKtUir1Jvx9-ZwRn+PQ5DUp3kjZ0YLuxg@mail.gmail.com>
 <MN2PR04MB6160DE1F60810D12069D7DED8F719@MN2PR04MB6160.namprd04.prod.outlook.com>
 <CAMkiY3fbT8E7ZaOMNUyJ7DrWqRrn98WD=jkCuXBxWZAGQ0i=og@mail.gmail.com>
 <005CC558-3055-489E-AD9E-55BE109BE467@bwh.harvard.edu>
Message-ID: <CAMkiY3eiRsa8OLArF7-O9wRvBz-eTndJ6J99iDXrMbFXB_LGXw@mail.gmail.com>

Yes, it would be good to remove the file from the data folder as well as
the pic generated for the file.

On Fri, Dec 10, 2021 at 2:51 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Thank you, it was indeed an issue with file permissions.
>
> Regarding removing the mislabelled files, should I also remove the file
> itself from the LORIS data folder before reuploading?
>
> Best,
> Alfredo.
>
> On Dec 10, 2021, at 2:20 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Glad to hear you were able to import the MINC files. It seems the issue
> you are having might be due to file permissions. Can you make sure the
> apache user can see the directories/files that were created by the import?
>
> To change the label, the least risky route would be to remove the
> mislabelled file from the files and parameter_file tables and reimport with
> the correct label for scan type.
>
> Hope this helps,
>
> C?cile
>
>
> On Fri, Dec 10, 2021 at 2:01 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile, (sorry if receive this email multiple times, I'm having issues
>> with my email client)
>>
>> We managed to import some MINC files with the proper thumbnails in LORIS.
>> The files seem to be properly stored in the hard-drive (LORIS data folder)
>> but we are facing the following issues:
>>
>> 1. When loading them in the front-end the MINC images cannot be visualized
>> 2. When getting the headers using the API we are getting {"error":"not
>> found"}
>> 3. When downloading them using the API we get the error code "404"
>>
>> Any ideas?
>>
>> On a side note, how can I change the acquisition label of an acquisition
>> that I uploaded with an improper label?
>>
>> Thank you for your help.
>>
>> Best,
>> Alfredo.
>> ------------------------------
>> *From:* Cecile Madjar <cecile.madjar at mcin.ca>
>> *Sent:* Tuesday, November 30, 2021 4:15 PM
>> *To:* Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU>
>> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>; Sridar
>> Narayanan <sridar.narayanan at mcgill.ca>; Rozie Arnaoutelis <
>> rozie.arnaoutelis at mcgill.ca>; Douglas Arnold, Dr. <
>> douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. <
>> guttmann at bwh.harvard.edu>; Istvan Akos Imre Morocz, Dr <
>> istvan.morocz at mcgill.ca>; Samir Das <samirdas99 at gmail.com>
>> *Subject:* Re: [Loris-dev] MINC insertion
>>
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Sorry for the delay. Time flies quickly this week.
>>
>> How about a Zoom call tomorrow (Wednesday) at 10:30AM or at 4PM?
>>
>> Let me know if one of those times works for you.
>> Thanks!
>>
>> C?cile
>>
>> On Mon, Nov 29, 2021 at 1:30 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> Here is the results of the query:
>>
>> ===
>> mysql> SELECT * FROM psc WHERE CenterID=843 \G;
>> *************************** 1. row ***************************
>>   CenterID: 843
>>       Name: inf_0102
>>    PSCArea: NULL
>>    Address: NULL
>>       City: NULL
>>    StateID: NULL
>>        ZIP: NULL
>>     Phone1: NULL
>>     Phone2: NULL
>>   Contact1: NULL
>>   Contact2: NULL
>>      Alias: BGI
>>  MRI_alias: BGI
>>    Account: NULL
>> Study_site: Y
>> 1 row in set (0.00 sec)
>> ===
>>
>> Alias and MRI_alias look fine. What should we look into now? We can debug
>> over Zoom if that works for you.
>>
>> Best,
>> Alfredo.
>>
>> On Nov 29, 2021, at 8:40 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> I think we are indeed narrowing where the error happens. It looks like
>> for some reason this getPSC
>> <https://secure-web.cisco.com/1WKyW2D76xw9mcH7c3mrbUADimOSPIUAeml9rWivk7bItei0PlVHDbuGfrRpzeITWbL6b0Rr61uaOfjR-rrMpspUFVDp6AC5wXTy-v_mpx-SO9Fro3_O7WqkuAEbxZTWwVIvoAIdW5_K9PSX2xdI8_T64tIgsBc859NyIdKSuS4vJjdvc2VsaapiuHVAY8oaJ0x4ikpKSaiQocNEm2yqtX0tRI26lOCf1qGK5nam_R1310B5bXRHQRMJEmJ3EE9nx5WgxcJcOt078poMQe4krTe5X1yOWE9G3LauCi0VwvI_qoqKmqtkbU_6q0PES2OKttGDvMWpti_tEMV67ieEFVQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2Fv23.0.3_IPMSA%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm>
>> function is returning "UNKN", 0. It might be related to the Alias or
>> MRI_alias content of the psc table for CenterID 843.
>>
>> What do you get when you run the following query?
>> SELECT * FROM psc WHERE CenterID=843;
>>
>> In the Alias or MRI_alias column, you should be able to see BGI so that
>> the scanner candidate can be identified with the proper site.
>>
>> Let me know,
>>
>> C?cile
>>
>> On Sun, Nov 28, 2021 at 12:42 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> Thank you, it looks like we?re getting closer to find a solution. Find
>> the answers to your questions inline below.
>>
>> Happy to debug over Zoom if it?s easier for you.
>>
>> Best,
>> Alfredo.
>>
>>
>> On Nov 26, 2021, at 3:31 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> I notice that the CenterID for the site is 0. Do you have an entry in the
>> psc table for a CenterID=0?
>>
>> No, we don?t have it. The CenterID starts at 1.
>> ===
>> select * from psc where CenterID=0;
>> Empty set (0.00 sec)
>> ===
>>
>>
>> The problem here is that the data comes from a new scanner and the
>> pipeline tries to first register a new candidate for the scanner (scanner
>> candidate) before adding an entry in the mri_scanner table. To determine
>> the site of the scanner, the pipeline uses the determinePSC
>> <https://secure-web.cisco.com/1Dc-fajrB7Ud53q9lvqwcvWI66c8Sjd_VWPzsGJnI1xtsFo2tce71aRhvXOFAeXFyiXWHCRtrsuOUxz9FTymBxjmkO9QVm92NieBTkPQt3sHgPQQUT2j2bpLa-AQKrAp6CJLMFA3SshUHX9tSHCkDZl4-687CTtyUYa8o_QDxRn0UEiy6yqufe-DTaVIJxY2bFtGERf0kTxBUy4JaS_ZiEHYQ3uGUjy9x3F25dMV0RZ_8hv74gXSGJW3t7AJ2zm-stvAEvizinmIQrzN-OP0L0FTHPAmoHzn0NFzDCrYvCDnMCfBNCexzjhZ9JcsQSpQS_LK_oW8UEy8ObHNoEsbzKA/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRIProcessingUtility.pm%23L503>
>> function of MRIProcessingUtility.pm (called by minc_insertion.pl
>> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
>> in line 454
>> <https://secure-web.cisco.com/1UWbEiJQk9qeievujOxfe9vFYw_u8x2SaJKAYzS6WrKuX-cWcA62bpRkJ-fOL-6hCS2oSzF8ye-G99zRPL7lv-ggMi48rbGxbcOhqRu-S7FGWEZpc-vb_j_YA73XsG7Od4qBB98i5AMLyLXi5SZAwP5E_nbdjI626BeW24SmnD6Hd_MocuW8oOqNs4mTZSGh8EkMpO-BOuH4bMikoRDLakpW-VmFznZ130h0pg4vTAAfwsjwTvbjqHgFlzExIBUHDqgaeYpD5aWuC1jjiXxEy182es4Wv0VMpe5btqKR8f0VjaB-rl2G6tC0A8q5fHAfkY5fNxpYViSFAv6jJO-8F8w/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2Fminc_insertion.pl%23L454>).
>> I would be curious to see what the $center_name and $centerID values
>> returned are.
>>
>> These are the returned values. Maybe we need to look deeper into this.
>> ===
>> determinePSC->Center name: UNKN
>> determinePSC->Center ID: 0
>> ===
>>
>>
>> Could you also copy the code you have in your prod file for the function
>> getSubjectIDs?
>>
>>
>> You mean this file ?mri/dicom-archive/.loris_mri/prod?, right? Find the
>> function enclosed.
>>
>>
>> Finally, could you check that the candidate BGI102001_207019 does have a
>> RegistrationCenterID set and if there is already a screening session
>> created in the session table, that the CenterID of that session has
>> properly been set?
>>
>>
>> The candidate has a RegistrationCenterID (843):
>> ===
>> select * from candidate where CandID=207019 \G;
>> *************************** 1. row ***************************
>>                   ID: 8974
>>               CandID: 207019
>>                PSCID: BGI102001
>>           ExternalID: NULL
>>                  DoB: 1969-05-15
>>                  EDC: NULL
>>                  Sex: Female
>> RegistrationCenterID: 843
>> RegistrationProjectID: 12
>>            Ethnicity: NULL
>>               Active: Y
>>          Date_active: 2021-05-27
>>         RegisteredBy: dataman
>>               UserID: dataman
>>      Date_registered: 2021-05-27
>> flagged_caveatemptor: false
>>       flagged_reason: NULL
>>        flagged_other: NULL
>> flagged_other_status: NULL
>>             Testdate: 2021-06-09 10:55:35
>>          Entity_type: Human
>>           ProbandSex: NULL
>>           ProbandDoB: NULL
>>                  DoD: NULL
>> 1 row in set (0.00 sec)
>> ===
>>
>> The session with the proper values already exists:
>> ===
>> mysql> select * from session where CandID=207019 and
>> Visit_label="screening" \G;
>> *************************** 1. row ***************************
>>                  ID: 127260
>>              CandID: 207019
>>            CenterID: 843
>>             VisitNo: 1
>>         Visit_label: screening
>>        SubprojectID: 2
>>           Submitted: N
>>       Current_stage: Not Started
>>   Date_stage_change: NULL
>>           Screening: NULL
>>      Date_screening: NULL
>>               Visit: NULL
>>          Date_visit: NULL
>>            Approval: NULL
>>       Date_approval: NULL
>>              Active: Y
>>         Date_active: 2021-05-27
>>        RegisteredBy: dataman
>>              UserID: dataman
>>     Date_registered: 2021-05-27
>>            Testdate: 2021-06-10 18:35:41
>>    Hardcopy_request: -
>>         BVLQCStatus: NULL
>>           BVLQCType: NULL
>>      BVLQCExclusion: NULL
>>                 QCd: NULL
>>           Scan_done: Y
>>         MRIQCStatus:
>>        MRIQCPending: N
>> MRIQCFirstChangeTime: NULL
>> MRIQCLastChangeTime: NULL
>>           MRICaveat: false
>>           ProjectID: 12
>>          languageID: 1
>> 1 row in set (0.00 sec)
>> ===
>>
>> Thank you!
>>
>> C?cile
>>
>> On Fri, Nov 26, 2021 at 2:34 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> Thank you for answer.
>>
>> I included the following lines:
>>
>> ===
>>                   . " NOW(),   'NeuroDB::MRI', 'Scanner'          ) ";
>> +        print "\nCenter ID: " . $centerID . "\n\n";
>> +        print "\nQuery:" . $query . "\n\n";
>>          $dbh->do($query);
>>      }
>> ===
>>
>> And I got the following output:
>>
>> ===
>> perl minc_insertion.pl
>> <http://secure-web.cisco.com/1AcpksGPD0fcXlGw-72nF5bIorKsi2a9cDq7Wv-13LsJ3nMgtSqaBUK52_TDPgdnaR31cAXitmHZBROzlbUzVSLt7NNfNUEoLAzoVzQxbeMcKgKRPZKB5buA54ELuCzLsaxCmaICUrqPr9kBNY64H9sQ07LVj_j4VK-Nhmk1d8H6bVa4T3fXZ2LnHlBqWGLRwsp6j2TPPyxS2PtujnfjzbAbVIaLJuxAOYmjNJPE15dPo8Mfm_XBeAuFgKDQBx78EgSHLn5oS5e9hHqPLghSbr_gClpiauYIGe2TzPPrTwRO-bQh8hPTQ2rcHfkITL3as/http%3A%2F%2Fminc_insertion.pl>
>> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
>> -verbose -acquisition_protocol t1c -create_minc_pics
>>
>> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is
>> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-14-31-d7FH_S.log
>>     SELECT       ArchiveLocation     FROM       tarchive     WHERE
>> TarchiveID = (                      SELECT TarchiveID
>> FROM tarchive_series                      WHERE SeriesUID=? AND EchoTime=?
>>                   )
>> Center ID: 0
>>
>>
>> Query:INSERT INTO candidate (CandID,          PSCID,
>> RegistrationCenterID, Date_active,   Date_registered, UserID, Entity_type
>>                     ) VALUES (442627, 'scanner',      0,  NOW(),    NOW(),
>>   'NeuroDB::MRI', 'Scanner'          )
>>
>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
>> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>> 1020.
>> ERROR: Failed to insert record in table mri_scanner:
>> The following database commands failed:
>>         PREPARE s FROM 'INSERT INTO mri_scanner
>> (CandID,Model,Manufacturer,Serial_number,Software) VALUES (?,?,?,?,?)';
>>         SET
>> @x1='442627', at x2='Sonata', at x3='Siemens', at x4='syngo_MR_2004A_4VA25A';
>>         EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>> Error obtained:Cannot add or update a child row: a foreign key constraint
>> fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
>> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>> ===
>>
>> I think it?s important to mention that this candidate was created by the
>> bids importing script. Maybe there is center associated with the candidates
>> when using the bids script?
>>
>> Let me know your thoughts.
>>
>> Best,
>> Alfredo.
>>
>> On Nov 26, 2021, at 11:13 AM, Cecile Madjar <cecile.madjar at mcin.ca>
>> wrote:
>>
>>         External Email - Use Caution
>>
>> Thank you Alfredo.
>>
>> I wonder whether the variable $centerID is null when provided to the
>> query here
>> <https://secure-web.cisco.com/1BZxp6fiw85BciAlo2QCPeT44gOAdEJUbAAAM3VJsTVYkl_27h-GCDhXtVO-8fh2ghdX3L0808bpAkrN-4-dTSIuf12yvdTBrdZ5Wl5YcKE3s4BTaFeJPBISOXE6-2TppWqpX8R4fldLsB6dpee4WAltjKy3u6ZJa01r-_Up1j5vB6cy_vbAyEgWl_Ft7ACUJ4VwQkwh01nnF8cpg5ePrLbF5bQw28VLFdg3Uo7dO81Ow5-zFCp5KKdHX0KX7vdIPmPuijtNDX9V5jT_YKMml5cX_tM2IVASxDa-wmo0JijRQ7k6oCTwK52FO0yRmVVeFj4108ZlyK2avqXijVKYreQ/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Fblob%2F19f469cce904ebe93ba5f641533e4c0ef39fadab%2FuploadNeuroDB%2FNeuroDB%2FMRI.pm%23L1012>
>> in your case.
>>
>> Could you add in MRI.pm line 1018 the following print statements and let
>> me know what you get? (Right before the $dbh->do($query);
>> print($centerID);
>> print($query);
>>
>> Thank you!
>>
>> C?cile
>>
>> On Fri, Nov 26, 2021 at 10:55 AM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> This is the branch that we are using in the IPMSA project:
>>
>> https://github.com/SPINEProject/Loris-MRI/tree/v23.0.3_IPMSA
>> <https://secure-web.cisco.com/1_p5UjMqREHagXmmz7NxbZe91yrcn34HNneKcFN4qKhR9mT7798DmL7TgbLwjpDr1U0bQaX2Rdqcdu3-l5R95gEJ5AzIbYu4-psDEz9Gw3fmrcgxEel3V6rugNzEisR_jZbIG2f2KPrVumnb1MY-TJCYuPQqzVuM_3KHLYTzVKha7RbWAHq6GLefQmer8auU6BALsWue7RBcrrbG9kbGC-S-e1DZ-WP4gVNTDegrcGaghwyxclA9m6SZqs-OljIR6E7IViTaySgZuDnOp5meeyJlKdlksyj5cGVErq4YprL6I9uHWuLjB-06KBUFTBK6C1E38yyToTkJVVH-8LKRPKg/https%3A%2F%2Fgithub.com%2FSPINEProject%2FLoris-MRI%2Ftree%2Fv23.0.3_IPMSA>
>>
>> Best,
>> Alfredo.
>>
>> On Nov 26, 2021, at 9:55 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Could you point me to the version of the code you are using on GitHub so
>> I can take a look at the correct MRI.pm file.
>>
>> Thank you!
>>
>> C?cile
>>
>> On Thu, Nov 25, 2021 at 8:09 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>> Hi C?cile,
>>
>> I?m getting the following error when inserting a minc file using the
>> minc_insertion.pl
>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>> script:
>>
>> ===
>> $ perl minc_insertion.pl
>> <http://secure-web.cisco.com/1TzLj0luctz8Wb38Vv2psbWhbcU-f__EKvLSSaDYgEXmz5b0aqjDuEoOYgCDeNvO_wd_jY7vbVfBPyzukTp8u3bszcvl9RlzkffyCB96NEJ6ldbRDtpB5Dm1t3H6zAKfXwb47TCFKN4jo2cTx22wsEoMCjd40dMRoMr5y7-MMPE_rF9MBpp5uEB4y849W6nkPHoaERmNpP67XVRUarntyB3RrW-aH-TPtdYKd6qDPGkllZKISL3hlhs7AG4CCOQdZEVjiW6N9fr5aaSxBevb9TptNEJgPfB3dj-0XRNXWAt9bp6fvmGUwjIXEdKZVASmz/http%3A%2F%2Fminc_insertion.pl>
>> -profile prod -force -mincPath /data/BGI102001_207019_screening.mnc
>> -verbose -acquisition_protocol t1c -create_minc_pics
>>
>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
>> constraint fails (`IPMSA_LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>> 1018.
>>
>> ERROR: Failed to insert record in table mri_scanner:
>>
>> The following database commands failed:
>> PREPARE s FROM 'INSERT INTO mri_scanner
>> (Serial_number,Software,Manufacturer,Model,CandID) VALUES (?,?,?,?,?)';
>> SET @x1='syngo_MR_2004A_4VA25A', at x2='Siemens', at x3='Sonata', at x4='247660';
>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>
>> Error obtained:Cannot add or update a child row: a foreign key constraint
>> fails (`IPMSA_LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN
>> KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>> ===
>>
>> Could you help me figuring out what is happening? Is there something I
>> should add to the minc headers?
>>
>> Best,
>> Alfredo.
>>
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>> 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
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/14m8jq3YFX-kL4WHSOD3NyklDH3_1jO6LrSN9gvfM5CyvUtE7cihaLOo51ulZdVQKgs5rOFUrgJxphRC2W3gjEcYsYyqJP3GlMV3sJHwLGLwsGvslUlp9df_5QkEDbk0OiO4v-SgA4uMhT6od0larJxEIegxbPKpy9GmlloLw6cDlPw0voUhi7Y0kxA_zjwDvxaVMhZ7RIpojsrcwl2crdOHamo_wQI9pz9cAU_qxwUGkhiSfwtcCe8i-UtBjbSEY9dM0SpejAYJqhqEpOK_aCqQ4_wOl8FxQWWNK2nOsD7QawkuH5liIxDIL5XojDqICa2oljEN17RtZIEy425vItA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . If the e-mail was sent to you in error but does not contain patient
>> information, please contact the sender and properly dispose of the e-mail.
>>
>> 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.
>>
>>
>> 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
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/1fFVWywiC_KI2wX-iM-iipSCRfAdgcr8caPgwKQ4dp_E6amXdXGc7f5R2bEhT0ZmPeCy6AXOIj0LWU8x0g9SAwx5xHb4GLCF-WQaSnrmTYPMha1wCzNZjbbBFCQIWFh-5N5ZGDPDOldyduZuC8MKXnKD0Q-W-6m3qAJrKOYtCur2SJ-tEq_MUeMO32jd104Mmv3FTkOUPxaDqSzIyJdrDtb-wImxqqblDaBhzm4JjA7RYkdtxpS9SlOO_KlPpmstVVrRotFCLSgjsT4iejspAR2jzTrd7Q6rQFUDBKugqnSW_Tn0i3OURMIorUsRwMg8dE6slT8k7I3iv88FTtVp8cA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . If the e-mail was sent to you in error but does not contain patient
>> information, please contact the sender and properly dispose of the e-mail.
>>
>> 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.
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>>
>> 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
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/14gGcX-ZD6Amc10oWq9YHUYDZwfI3Ra0YaIetGnqyBxDXjW2fkG07-SpnWf6ZWiMMuWxnSoLULOR9NMLOcJiMgBuZCcIt0RYXiMw3EibvjtSF-QMJ3sGSOAMIROOiVMwlt5nrV2O7wLJlh3xOKBlVMU7fcJsx9UxZkRIrvXGY3If6E2iTE4UQ5ZI1j6xGWgdYq5ff8qBRME2FK0lFmNWaFYVTYkmphxy8dXKWJMPtlpfY2km6XVTFG28sO33tQBCVVJ-jGy9f7bMO8sAj6sP8h9mT1Mrv2oq5fwVO8Zx6Ec1j9vTarLT6L_MOVQWPA1YvjGshE6gRajrWQAAwcQfw-w/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . If the e-mail was sent to you in error but does not contain patient
>> information, please contact the sender and properly dispose of the e-mail.
>>
>> 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.
>>
>> 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
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/1_8K3dzuoAmF45eq9RLiv9ckB8WCwnJbX_kgvkm40UZMPSepY09Rg3le0gcHoMWOCHCiJt4wJPQEp0P2JR7KbzbgzFCP32YGiMGsX3PUj0sgx2Jxh5o65IMe2hc__auFkKo4SqF0YMvG-h4uI5EInRzykbrGj23VibyzKCitjPcoh8F81YhUC8WkiL21KemQOJ_Nhon2xzvxfay6_ReByRZzXX2ZCqnrNB_sj5DpZo9j2pVPjYznfu05RsE2lTTiU9SnTG6GHLzAC0-ppLhkZ_POrX7KgTlM3EgdrUuAeo29iEHIqGTztaAhDmGIaeL5-p9l2vw__dLA6GKowt-eOnQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . If the e-mail was sent to you in error but does not contain patient
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>> 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.
>>
>
> 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
> http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
>
> 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.
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From oricod at ext.cnio.es  Thu Dec 16 08:50:07 2021
From: oricod at ext.cnio.es (=?utf-8?B?Umljb19Ew61lei5PbGdh?=)
Date: Thu, 16 Dec 2021 13:50:07 +0000
Subject: [Loris-dev] installation difficulties
In-Reply-To: <CADM4SCz9JnDAAX7ivK-eeWFV6zkQzUGF4g6S4M4j-tXDHo31oQ@mail.gmail.com>
References: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32A5E9D@DONAR.cnio.es>
 <CADM4SCz9JnDAAX7ivK-eeWFV6zkQzUGF4g6S4M4j-tXDHo31oQ@mail.gmail.com>
Message-ID: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32B9888@DONAR.cnio.es>

Hello again,

I have installed the version 16.13.0 of node. But it says that the nodejs version is 10.19.0, why?


I have this errors bellow now:

make
npm install

> loris at 1.0.0<mailto:loris at 1.0.0> postinstall
> cd modules/electrophysiology_browser/jsx/react-series-data-viewer && npm install

audited 94 packages in 2.038s
found 0 vulnerabilities


up to date, audited 2222 packages in 15s

306 packages are looking for funding
  run `npm fund` for details

27 vulnerabilities (16 moderate, 11 high)

To address all issues, run:
  npm audit fix

Run `npm audit` for details.
npm run compile

> loris at 1.0.0<mailto:loris at 1.0.0> compile
> webpack

[webpack-cli] Failed to load '/var/www/loris/webpack.config.js' config
[webpack-cli] Invalid options object. Terser Plugin has been initialized using an options object that does not match the API schema.
 - options has an unknown property 'sourceMap'. These properties are valid:
   object { test?, include?, exclude?, terserOptions?, extractComments?, parallel?, minify? }


Olga Rico.

De: Shen Wang <wangshen.mcin at gmail.com>
Enviado el: lunes, 29 de noviembre de 2021 14:59
Para: Rico_D?ez.Olga <oricod at ext.cnio.es>
CC: loris-dev at bic.mni.mcgill.ca
Asunto: Re: [Loris-dev] installation difficulties

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 Rico,
Please update your node js version  [NodeJS 16.10.0 (or higher)] ,  then run "make" again.
I hope this will solve the problem.
Good luck
Best
Shen


On Mon, 29 Nov 2021 at 08:52, Rico_D?ez.Olga <oricod at ext.cnio.es<mailto:oricod at ext.cnio.es>> wrote:
Hello,

I am having some difficulties installing Loris.

The page that I have follow to install Loris is https://github.com/aces/Loris/blob/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/Ubuntu/README.md

and also https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth

I have installed the versions on 0ubuntu0.20.04.1 for Linux on x86_64 ((Ubuntu)):
PHP 7.4.3
mysql  Ver 8.0.27
Composer version 2.1.11
Server version: Apache/2.4.41
npm 8.1.4
nodejs v10.19.0
But an error keep showing when i do the "make" (Posted bellow):

make
tools/gen-version.sh
npm install

> loris at 1.0.0<mailto:loris at 1.0.0> postinstall
> cd modules/electrophysiology_browser/jsx/react-series-data-viewer && npm install

up to date in 2.438s

up to date in 1m

314 packages are looking for funding
  run `npm fund` for details
npm run compile

> loris at 1.0.0<mailto:loris at 1.0.0> compile
> webpack

[webpack-cli] Invalid configuration object. Webpack has been initialized using a configuration object that does not match the API schema.
 - configuration[0].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[1].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[2].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[3].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[4].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[5].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[6].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[7].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[8].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[9].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[10].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[11].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[12].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[13].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[14].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[15].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[16].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[17].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[18].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[19].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[20].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[21].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[22].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[23].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[24].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[25].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[26].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[27].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[28].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[29].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[30].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[31].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[32].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[33].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[34].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[35].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[36].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[37].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[38].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
 - configuration[39].node has an unknown property 'fs'. These properties are valid:
   object { __dirname?, __filename?, global? }
   -> Options object for node compatibility features.
make: *** [Makefile:15: javascript] Error 2
What is going on?

Thanks in advance,
Olga




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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
_______________________________________________
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


--
Shen Wang
Loris<https://github.com/aces/Loris>  Developer
Montreal Neurological Institute
McGill University



**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 wangshen.mcin at gmail.com  Fri Dec 17 09:10:16 2021
From: wangshen.mcin at gmail.com (Shen Wang)
Date: Fri, 17 Dec 2021 09:10:16 -0500
Subject: [Loris-dev] installation difficulties
In-Reply-To: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32B9888@DONAR.cnio.es>
References: <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32A5E9D@DONAR.cnio.es>
 <CADM4SCz9JnDAAX7ivK-eeWFV6zkQzUGF4g6S4M4j-tXDHo31oQ@mail.gmail.com>
 <99B67BC1EEE7BC4E8F6D4B2EEC1F75A32B9888@DONAR.cnio.es>
Message-ID: <CADM4SCzhXJp3hmZoTUNX69-MZxb2+Lnp3c7KYn0-HeKJk2jUnQ@mail.gmail.com>

Hello,
Sorry for the late reply.
try this
"
curl -sL https://deb.nodesource.com/setup_16.x | sudo -E bash -
sudo apt-get install -y nodejs
"
Please restart your terminal to check the node version.

If it still doesn't work, purge node and install node 16 again.

"
https://dev.to/mdmarufsarker/how-to-update-nodejs-to-the-latest-version-on-ubuntu-3md6
"

 Good luck


On Thu, 16 Dec 2021 at 08:50, Rico_D?ez.Olga <oricod at ext.cnio.es> wrote:

> Hello again,
>
>
>
> I have installed the version 16.13.0 of node. But it says that the nodejs
> version is 10.19.0, why?
>
>
>
>
>
> I have this errors bellow now:
>
>
>
> make
> npm install
>
> > loris at 1.0.0 postinstall
> > cd modules/electrophysiology_browser/jsx/react-series-data-viewer && npm
> install
>
> audited 94 packages in 2.038s
> found 0 vulnerabilities
>
>
> up to date, audited 2222 packages in 15s
>
> 306 packages are looking for funding
>   run `npm fund` for details
>
> 27 vulnerabilities (16 moderate, 11 high)
>
> To address all issues, run:
>   npm audit fix
>
> Run `npm audit` for details.
> npm run compile
>
> > loris at 1.0.0 compile
> > webpack
>
> [webpack-cli] Failed to load '/var/www/loris/webpack.config.js' config
> [webpack-cli] Invalid options object. Terser Plugin has been initialized
> using an options object that does not match the API schema.
>  - options has an unknown property 'sourceMap'. These properties are valid:
>    object { test?, include?, exclude?, terserOptions?, extractComments?,
> parallel?, minify? }
>
>
>
>
>
> Olga Rico.
>
>
>
> *De:* Shen Wang <wangshen.mcin at gmail.com>
> *Enviado el:* lunes, 29 de noviembre de 2021 14:59
> *Para:* Rico_D?ez.Olga <oricod at ext.cnio.es>
> *CC:* loris-dev at bic.mni.mcgill.ca
> *Asunto:* Re: [Loris-dev] installation difficulties
>
>
>
> *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 Rico,
>
> Please update your node js version  [NodeJS 16.10.0 (or higher)] ,  then
> run "make" again.
>
> I hope this will solve the problem.
>
> Good luck
>
> Best
>
> Shen
>
>
>
>
>
> On Mon, 29 Nov 2021 at 08:52, Rico_D?ez.Olga <oricod at ext.cnio.es> wrote:
>
> Hello,
>
>
>
> I am having some difficulties installing Loris.
>
>
>
> The page that I have follow to install Loris is
> https://github.com/aces/Loris/blob/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/Ubuntu/README.md
>
>
>
> and also https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth
>
>
>
> I have installed the versions on 0ubuntu0.20.04.1 for Linux on x86_64
> ((Ubuntu)):
>
> PHP 7.4.3
>
> mysql  Ver 8.0.27
> Composer version 2.1.11
> Server version: Apache/2.4.41
> npm 8.1.4
> nodejs v10.19.0
>
> But an error keep showing when i do the "make" (Posted bellow):
>
>
>
>
>
>
>
> *make tools/gen-version.sh npm install > **loris at 1.0.0* <loris at 1.0.0>
>
>
>
>
>
>
>
>
>
>
> * postinstall > cd
> modules/electrophysiology_browser/jsx/react-series-data-viewer && npm
> install up to date in 2.438s up to date in 1m 314 packages are looking for
> funding   run `npm fund` for details npm run compile > **loris at 1.0.0*
> <loris at 1.0.0>
>
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>
> * compile > webpack [webpack-cli] Invalid configuration object. Webpack
> has been initialized using a configuration object that does not match the
> API schema.  - configuration[0].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[1].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[2].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[3].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[4].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[5].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[6].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[7].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[8].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[9].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[10].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[11].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[12].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[13].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[14].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[15].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[16].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[17].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[18].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[19].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[20].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[21].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[22].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[23].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[24].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[25].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[26].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[27].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[28].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[29].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[30].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[31].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[32].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[33].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[34].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features.  - configuration[35].node has an unknown property 'fs'. These
> properties are valid:    object { __dirname?, __filename?, global? }    ->
> Options object for node compatibility features.  - configuration[36].node
> has an unknown property 'fs'. These properties are valid:    object {
> __dirname?, __filename?, global? }    -> Options object for node
> compatibility features.  - configuration[37].node has an unknown property
> 'fs'. These properties are valid:    object { __dirname?, __filename?,
> global? }    -> Options object for node compatibility features.  -
> configuration[38].node has an unknown property 'fs'. These properties are
> valid:    object { __dirname?, __filename?, global? }    -> Options object
> for node compatibility features.  - configuration[39].node has an unknown
> property 'fs'. These properties are valid:    object { __dirname?,
> __filename?, global? }    -> Options object for node compatibility
> features. make: *** [Makefile:15: javascript] Error 2*
>
> What is going on?
>
>
>
> Thanks in advance,
>
> Olga
>
>
>
>
>
> [image: Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer]
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> **LEGAL NOTICE**: This email and any attached files may contain protected
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> Pursuant to the provisions of EU Regulation 2016/679 regarding the
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>
>
> --
>
> Shen Wang
>
> Loris <https://github.com/aces/Loris>  Developer
>
> Montreal Neurological Institute
>
> McGill University
>
>
>
>
> **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
>


-- 
Shen Wang
Loris <https://github.com/aces/Loris>  Developer
Montreal Neurological Institute
McGill University
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