[Loris-dev] MINC insertion

Fri Nov 26 14:34:08 EST 2021

Hi Cécile,

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 -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!

Cécile

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 Cécile,

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!

Cécile

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 Cécile,

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 . 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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