[Loris-dev] MINC insertion

Fri Nov 26 15:31:20 EST 2021

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?

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://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L503>
function of MRIProcessingUtility.pm (called by minc_insertion.pl in line 454
<https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/minc_insertion.pl#L454>).
I would be curious to see what the $center_name and $centerID values
returned are.

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

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?

Thank you!

Cécile

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

> 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> 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> 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> 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> 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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>>
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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
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