[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Wed Sep 4 11:42:48 EDT 2019
How do i delete a Study? And everytime do i have to create a new candidate
to get DCCID and a PSCID?
*First execution:*
(loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./
batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./
batch_uploads_imageuploader.pl line 144.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN
KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
/data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner
(CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
SET @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
Medical Systems';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint
fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY
(`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
ERROR: The validation has failed. Either re-run the validation again and
fix the problem. Or re-run tarchiveLoader.pl using -force to force the
execution.
The tarchiveLoader.pl insertion script has failed.
Can't exec "mail": No such file or directory at ./
batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line
250.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line
251.
*And second execution:*
(loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./
batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./
batch_uploads_imageuploader.pl line 144.
PROBLEM:
The user 'lorisadmin' has already inserted this study.
The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
This is the information retained from the first time the study was inserted:
* Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy
* Archive target location :
/data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-04 18:33:05
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d
ImagingUpload-18-33-Qq7HGy.tar
* md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec
ImagingUpload-18-33-Qq7HGy.tar.gz
* md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053
DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
Last update of record:
The dicomTar.pl execution has failed.
Can't exec "mail": No such file or directory at ./
batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line
250.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line
251.
Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine Rogers, Ms. <
christine.rogers at mcgill.ca> έγραψε:
> Hi Sotirios,
>
> Ok, this sounds like good progress. Let us know when you next encounter
> issues as you progress through the Imaging Install/Setup docs
> <https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>.
> I'll look into how we can better handle the incoming/ directory next time.
> Best,
> Christine
>
> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>> populated correctly except its port is 'port' : ''. Also i have tested
>> that i can connect to MySQL with lorisuser.
>>
>> I executed the script again, because the only error i had previously was
>> that the /data/incoming folder didn't exist and there are no errors
>> reported back except of warnings <<mysql: [Warning] Using a password on the
>> command line interface can be insecure>>.
>>
>>
>> Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine Rogers, Ms. <
>> christine.rogers at mcgill.ca> έγραψε:
>>
>>> Hi Sotirios,
>>>
>>> It's possible -- if the script was unable to connect to the database
>>> during its execution (e.g. typo in the password), that would explain the
>>> underpopulated Image path and Loris-MRI code path you saw in the Config
>>> module.
>>> It's hard to tell without seeing the output from your script run -- Did
>>> you see a sign of any such error?
>>> The Config fields are populated by the imaging_install.sh script (starting
>>> at line 222
>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222>
>>> )
>>>
>>> For example, check if the database connection information was populated
>>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py
>>>
>>> Best,
>>> Christine
>>>
>>>
>>>
>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Christine,
>>>>
>>>> If you are referring to the imaging_install.sh here is an image with
>>>> the configurations i typed. Maybe the problem is somewhere at the last part
>>>> which asks to configure as much as possible automatically?
>>>>
>>>> Thanks
>>>>
>>>>
>>>> Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> Glad to hear your LORIS core install is up and working and all the
>>>>> front-end pages are loading.
>>>>>
>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project
>>>>> > and the web interface worked.
>>>>>
>>>>> Yes, it's important that project/ have 775 permissions and that
>>>>> lorisadmin be part of the sudoers group, per step 1 in the install
>>>>> Readme <https://github.com/aces/Loris#install-steps>.
>>>>>
>>>>> > As for the Paths, LORIS-MRI code and Image should change LORIS to
>>>>> loris, right?
>>>>>
>>>>> These imaging paths will be updated during your imaging installation
>>>>> <https://github.com/aces/Loris/wiki/Setup> by an automated script --
>>>>> you do not need to set them manually via the Config module.
>>>>> Please continue to follow the Setup Guide
>>>>> <https://github.com/aces/Loris/wiki/Setup> for detailed steps to
>>>>> follow.
>>>>>
>>>>> Best,
>>>>> Christine
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> As for the Paths, LORIS-MRI code and Image should change LORIS to
>>>>>> loris, right?
>>>>>>
>>>>>> [image: image.png]
>>>>>>
>>>>>>
>>>>>> Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> i used
>>>>>>>
>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>>>>>> sudo apt-get install -y nodejs
>>>>>>>
>>>>>>>
>>>>>>> you had suggested in the past, make worked and now i can see all the
>>>>>>> contents in the web-interface, but i don't need make install?
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Loris-dev mailing list
>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> christine.rogers at mcgill.ca
>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>> Montreal Neurological Institute
>>>>> McGill University | Montreal | Canada
>>>>>
>>>> _______________________________________________
>>>> Loris-dev mailing list
>>>> Loris-dev at bic.mni.mcgill.ca
>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
>
> --
>
> christine.rogers at mcgill.ca
> McGill Centre for Integrative Neuroscience | MCIN.ca
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>
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