[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Sep 20 09:37:37 EDT 2019
Hi,
I tried to create a new candidate using the API, is there something wrong
with the structure? why did i receive a 500 internal error? In the
loris-error log it state that there is something wrong with token, but i
verfied that the type of the token is a string.
[Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client
127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 passed to
SinglePointLogin::JWTAuthenticate() must be of the type string, null given,
called in /var/www/loris/php/libraries/SinglePointLogin.class.inc on line
169 and defined in
/var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
SinglePointLogin->JWTAuthenticate(NULL)\n#1
/var/www/loris/php/libraries/NDB_Client.class.inc(171):
SinglePointLogin->authenticate()\n#2
/var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
NDB_Client->initialize('/var/www/loris/...')\n#3
/var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
Loris\\API\\APIBase->__construct('POST')\n#4
/var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in
/var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
[image: image.png]
Στις Παρ, 20 Σεπ 2019 στις 2:39 μ.μ., ο/η Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> έγραψε:
> Hi,
>
> Is there a way also to delete candidates? Just to let you know what i did
> to clear candidates, because maybe i may have missed dependencies.
>
> First i deleted all their uploads
> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit the
> backup file ? )
>
> Afterwards i had some scanner candidates, so i deleted all the entries
> from mri_scanner except that i couldn't delete this entry with the 0 ID.
>
> [image: image.png]
>
>
> Lastly i deleted the session and then the candidate table.
>
> Thanks
>
> Στις Πέμ, 19 Σεπ 2019 στις 7:57 μ.μ., ο/η Christine Rogers, Ms. <
> christine.rogers at mcgill.ca> έγραψε:
>
>> Hi Sotirios,
>>
>> We recommend that you use our existing tools for creating new candidates
>> - either the LORIS API or if you are using a PHP script, by calling the Candidate
>> class's createNew()
>> <https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200>function.
>> These will create the necessary records for you. (It's not recommended to
>> make direct modifications to mysql database tables in your script, if I
>> understand you.)
>>
>> The CandID should be a randomized 6 digit randomized ID, and there are
>> multiple reasons for this.
>> You can use the PSCID for project-specific IDs and the External ID field
>> in the candidate table can also be used for any values you like.
>> Additionally, any number of custom IDs can be added in parallel - these
>> are entered/visible in the Candidate Information module and added in the
>> back-end as candidate parameters.
>>
>> Best,
>> Christine
>>
>>
>>
>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> We are building a script that will auto insert the candidates based on
>>> their ExternalID. We would like to know whethere when we are creating a new
>>> profile in the candidate table, if we also have to insert a new record at
>>> another table? Furthermore is there a problem that in our case CandID won't
>>> be a 6digit? ( should we start it from 100000?)
>>>
>>> Thanks
>>>
>>> [image: image.png]
>>>
>>>
>>> Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie Legault, Mrs <
>>> melanie.legault2 at mcgill.ca> έγραψε:
>>>
>>>> That would normally be the case but the numeric part of the PSCID get
>>>> paded with 0 on the left.
>>>>
>>>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char
>>>> with a min value of 1, the sequence would be:
>>>>
>>>> ABC0001
>>>> ABC0002
>>>> ...
>>>> ABC0010
>>>> ...
>>>>
>>>> thus sorting them ascending will always get the latest value generated
>>>> as the max value.
>>>>
>>>> Mélanie
>>>>
>>>> ------------------------------
>>>> *From:* Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>> *Sent:* September 13, 2019 10:15
>>>> *To:* Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
>>>> *Cc:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>;
>>>> loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>
>>>> I see, although the PSCID value is varchar(255), it must be stored
>>>> within a specific length of characters. Otherwise if we were to sort
>>>> strings with different lengths the result would not be sorted correctly (
>>>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).
>>>>
>>>> Thanks
>>>>
>>>> Στις Παρ, 13 Σεπ 2019 στις 4:52 μ.μ., ο/η Melanie Legault, Mrs <
>>>> melanie.legault2 at mcgill.ca> έγραψε:
>>>>
>>>> Hello Sotirios,
>>>>
>>>> There is no `last value` stored anywhere.
>>>> The code simply look for the PSCID with the max value and increase that
>>>> value by 1 in order to generate the next PSCID.
>>>>
>>>> Hope this info help.
>>>>
>>>> Mélanie Legault | Software developer | Faculty of Medicine | McGill
>>>> University
>>>> 3801 University, Montréal, QC H3A 2B4
>>>>
>>>> ------------------------------
>>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios
>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>> *Sent:* September 13, 2019 9:43
>>>> *To:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>
>>>> Hi,
>>>>
>>>> how does Loris determine the next available PSCID value for a new
>>>> candidate? https://github.com/aces/Loris/wiki/Project-Customization
>>>> e.x in the default case the PSCID is sequential, but where do we store the
>>>> last value for the sequential sequence?
>>>>
>>>> Thanks
>>>>
>>>> Στις Τρί, 10 Σεπ 2019 στις 4:00 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> έγραψε:
>>>>
>>>> Hi,
>>>>
>>>> the parameters in the mri_protocol you have assigned are global
>>>> standard? or were assigned after trial and error?
>>>>
>>>> Thanks
>>>>
>>>> Στις Κυρ, 8 Σεπ 2019 στις 10:11 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>> Hi Sotirios,
>>>>
>>>> Given you have done the initial setup of your tables to match your
>>>> intended protocol/parameters according to instructions --
>>>> the Troubleshooting guide documentation recommends
>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes>
>>>> re-running the pipeline (and first deleting prior uploads).
>>>>
>>>> Best,
>>>> Christine
>>>>
>>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>> *if i were to change their status to resolve what would happen?
>>>>
>>>> Στις Κυρ, 8 Σεπ 2019 στις 5:12 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> έγραψε:
>>>>
>>>> I noticed that i can view the mnics at the brainbrowser from the
>>>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/
>>>> if i were to click their issue to resolve what would happend? would they
>>>> appear in the dicom_archive view too? ).
>>>>
>>>>
>>>>
>>>> Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> έγραψε:
>>>>
>>>> Hi,
>>>>
>>>> The defaut values of the schema exists in my local database. If i
>>>> adjust the default values of TR_min and TE_min the mincs will be uploaded?
>>>>
>>>> [image: image.png]
>>>>
>>>>
>>>> [image: image.png]
>>>>
>>>> Thanks
>>>>
>>>> Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>> Hi Sotirios,
>>>>
>>>> Is it possible that you haven't set up your mri_protocol table ? (and
>>>> mri_scan_type table too, for additional types of scans)
>>>>
>>>> Like the psc table, this is a pre-requisite for the Imaging insertion
>>>> setup : See the install/setup documentation :
>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>
>>>> To add new rows, just use MySQL insert statements. You can adapt the
>>>> insert statements which load the default table values --> e.g. Here on
>>>> GitHub :
>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>> (see also the mri_scan_type table)
>>>>
>>>> Best,
>>>> Christine
>>>>
>>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>> I see that i can edit the values but not how to insert new rows.
>>>>
>>>> [image: image.png]
>>>>
>>>> If i choose Inserted with flag then will the minc be inserted?
>>>>
>>>> [image: image.png]
>>>>
>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>> Hi Sotirios,
>>>>
>>>> Glad to hear that *dcmodify* worked correctly.
>>>>
>>>> For the MRI Violations module, the screenshot is enough.
>>>>
>>>> It says "could not identify scan type", which we knew already. Did you
>>>> click on the link on those words?
>>>>
>>>> It will take you to the next page of the module, showing for each scan
>>>> what the scan parameters were, and will also show for comparison what's
>>>> stored in your *mri_protocol* table.
>>>> Compare these values to find which parameter was not correct according
>>>> to your *mri_protocol* table scan type definitions.
>>>>
>>>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE)
>>>> for scans.
>>>> This can be done in the front-end, by editing the database table
>>>> directly in the same subpage of the MRI Violations module.
>>>>
>>>> The MRI Violations module features are explained in more detail in the
>>>> Help text for this module inside LORIS (click the ["?"] icon in the menu
>>>> bar.)
>>>>
>>>> See also: Loris-MRI troubleshooting guide
>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md>
>>>> : no MINCs inserted- violated scans
>>>>
>>>> Best,
>>>> Christine
>>>>
>>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> looks like my previous email's attachment wasn't delivered due to
>>>> security reasons, i uploaded my file at google drive
>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>
>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:02 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> έγραψε:
>>>>
>>>> Hi,
>>>>
>>>> From Dicat's view seems that dcmodify worked in both cases
>>>>
>>>> [image: image.png]
>>>>
>>>> [image: image.png]
>>>>
>>>> For the mri_violations i attached the .html output from webbrowser, so
>>>> that you can check the filelds easier.
>>>>
>>>> [image: image.png]
>>>>
>>>> Thanks
>>>>
>>>>
>>>>
>>>> Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>> Hi Sotirios --
>>>> Great, sounds like more progress.
>>>>
>>>> About the dcmodify command -- I'm not sure why you're getting an Endian
>>>> warning. (it's a warning not an error, correct?)
>>>> To clarify -- Were the DICOM headers (PatientName) all successfully
>>>> relabelled, after the command ran?
>>>>
>>>> You can use also our DICAT tool (https://github.com/aces/DICAT) to
>>>> verify and/or update local DICOM headers -- though your dcmodify command is
>>>> a great and fast solution for bulk header updates.
>>>>
>>>> If you're concerned about fields being changed (e.g. "(2001,105f)" from
>>>> the warning message) - you can also dcmdump a DICOM slice before and look
>>>> at these fields specifically.
>>>> It's also not a bad "sanity check" to backup your DICOMS before/after
>>>> running dcmodify, and use dcmdump on each version to diff the outputs --
>>>> this will pinpoint what changed.
>>>>
>>>> Re the protocol violation -- AcquisitionProtocol not recognized or
>>>> unknown : this means your scans did not match what is stored in your
>>>> mri_protocol table.
>>>> Check the MRI Violations front-end module -- can you see why they
>>>> didn't match?
>>>> Send us an example, in addition to the contents of the mri_protocol
>>>> table, if you can't find the source of the mismatch.
>>>>
>>>> Best,
>>>> Christine
>>>>
>>>>
>>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>> Here is the psc table
>>>> [image: image.png]
>>>>
>>>> I created 2 candidates profiles through the interface
>>>>
>>>> [image: image.png]
>>>>
>>>> then runned dcmodify command to a dicom file
>>>>
>>>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>
>>>> and got those warning: is this okay?
>>>> W: Found element (2001,105f) with VR UN and undefined length, reading a
>>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>> W: Found element (2005,1083) with VR UN and undefined length, reading a
>>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>> W: Found element (2005,1402) with VR UN and undefined length, reading a
>>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>> W: Found element (2005,140f) with VR UN and undefined length, reading a
>>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>> W: Found element (2001,105f) with VR UN and undefined length, reading a
>>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>> W: Found element (2005,1083) with VR UN and undefined length, reading a
>>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>
>>>> dcmodify at another Dicom didn't show warnings. Below you can see the
>>>> execution for the second dicom. Mnics could not be inserted due to
>>>> AcquisitionProtocol being unknown.
>>>>
>>>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/
>>>> imaging_upload_file.pl -profile prod -upload_id 12
>>>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>
>>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>> -delete
>>>>
>>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>> Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>> Target: /data/loris/data/tarchive
>>>>
>>>> Testing for database connectivity.
>>>> Database is available.
>>>>
>>>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>>
>>>> You are creating a tar with the following command:
>>>>
>>>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>> ImagingUpload-18-36-mTrxXs
>>>>
>>>>
>>>> getting md5sums and gzipping!!
>>>>
>>>> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs
>>>> * Archive target location :
>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>> * Name of creating host : 127.0.1.1
>>>> * Name of host OS : Linux
>>>> * Created by user : lorisadmin
>>>> * Archived on : 2019-09-06 18:36:50
>>>> * dicomSummary version : 1
>>>> * dicomTar version : 1
>>>> * md5sum for DICOM tarball :
>>>> b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar
>>>> * md5sum for DICOM tarball gzipped :
>>>> aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz
>>>> * md5sum for complete archive :
>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>
>>>> Adding archive info into database
>>>>
>>>> Removing temporary files from target location
>>>>
>>>>
>>>> Done adding archive info into database
>>>>
>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>> -profile prod
>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>> -uploadID 12 -verbose
>>>> md5sum
>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> candidate id 602102
>>>> Set centerID = 1
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>>
>>>> Number of MINC files that will be considered for inserting into the
>>>> database: 2
>>>>
>>>> log dir is /data/loris/data//logs and log file is
>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> candidate id 602102
>>>>
>>>> log dir is /data/loris/data//logs and log file is
>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> PSCID is: DCC0001
>>>> CandID id: 602102
>>>> visit_label is: V1
>>>> candidate id 602102
>>>>
>>>> Cleaning up temp files: rm -rf
>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>
>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>> cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>
>>>> ==> Loading file from disk
>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>
>>>> --> mapping DICOM parameter for
>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>
>>>> ==> computing md5 hash for MINC body.
>>>>
>>>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>
>>>> ==> verifying acquisition protocol
>>>>
>>>> Acquisition protocol is unknown
>>>>
>>>> --> The minc file cannot be registered since the AcquisitionProtocol
>>>> is unknown
>>>>
>>>> Στις Τετ, 4 Σεπ 2019 στις 10:46 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>> Hi Sotirios:
>>>>
>>>> Sure -- you can delete imaging datasets with the
>>>> *delete_imaging_upload* script --
>>>> details here:
>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>
>>>> What's in your *psc* table? (Is it properly populated? This is a
>>>> pre-requisite to loading imaging data.
>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>> )
>>>> The foreign key constraint error on the candidate record is curious.
>>>>
>>>> There are also a few options for creating candidates when inserting
>>>> imaging data:
>>>>
>>>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline
>>>>
>>>> a. via the LORIS API -- Create the candidates (and visits, optionally I
>>>> think)
>>>> How to:
>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>
>>>> Then as a second step:
>>>> b. Use the imaging insertion pipeline
>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets>
>>>> to load your DICOMs.
>>>> You will want to first ensure that the PatientName header in the DICOMs
>>>> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel
>>>>
>>>> -- Method 2: for BIDS-format datasets:
>>>> How to :
>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>
>>>> Be sure to use the *-c* and *-s* options when running the bids_import script,
>>>> to automatically create your candidates and sessions.
>>>>
>>>> Best,
>>>> Christine
>>>>
>>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> 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
>>>>
>>>> _______________________________________________
>>>> 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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