Imaging Preprocessing Scripts: Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893

[MounaSafiHarab]

• Imaging insertion scripts configuration options can now be set from the Configuration module and/or Config table in the database, instead of the $profile ("prod") file in the Loris-MRI repo.

• Please check the Loris-MRI pull request (Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 Loris-MRI#182) for existing projects on how to migrate existing $profile values to the database.

• These settings can not be overwritten in the config.xml (because they are used by Loris-MRI perl scripts)

Related to:
aces/Loris-MRI#182
and
aces/dicom-archive-tools#45

[MounaSafiHarab]

@driusan
default values are set as if it is a new install (so I took the current default values in $profileTemplate);
is it Ok to assume that projects will import the values from their prod file? (since I assume I have no way of reading their "prod" file)

[driusan]

@MounaSafiHarab Interesting question. I think you're right that we don't have any way to extract them from the prod file (unless you write a script on the Loris-MRI side), so I don't think there's really anything else you could do than just use the defaults.

Is there anything in them that's going to affect the data validity if people forget to manually change them in the config module?

[gluneau]

Data truncated for column 'Description'

INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'converter', 'If converter is set to dcm2mnc, the c-version of dcm2mnc will be used. If however you want to use any of the various versions of the perl converter dicom_to_minc of mydcm2mnc you will have to specify what it is called and the uploader will try to invoke it', 1, 0, 'text', ID, 'dcm2mnc binary to use when converting', 1 FROM ConfigSettings WHERE Name="imaging_pipeline"

1 row(s) affected, 1 warning(s): 1265 Data truncated for column 'Description' at row 1 Records: 1  Duplicates: 0  Warnings: 1

[MounaSafiHarab]

@driusan
I added the script to read the values from the $profile to change those "default" values on the Loris-MRI side. It is added to my Loris-MRI pull request, and it is placed in the tools/ directory of the Loris-MRI codebase.

@gluneau
I addressed the truncated value.

[driusan]

@MounaSafiHarab this has conflicts that need to be resolved.

[driusan]

I assume that the default value's that it's using are the same as what's currently in the default pofileTemplate, in which case it looks fine.. but it needs to be merged alongside the script in Loris-MRI that populates it for existing projects, and the PR that updates the code to use the config setting for the imaging pipeline..

[driusan]

also, when this is eventually merged it needs to be squashed to ensure that the unnecessary merge commit doesn't get committed into the history.

[MounaSafiHarab]

@driusan
yes the default values in the Loris-MRI installer were used here as well.
I agree, this should NOT be merged before the Loris-MRI one is approved and about to be merged!

[ridz1208]

@MounaSafiHarab does this still need testing or is it ready to merge after the related PR has been merged ?

[MounaSafiHarab]

@ridz1208

This needs testing mostly on the Loris-MRI side (main changes are there not in this patch) which is why I believe @driusan added the Blocked label. @gluneau was supposed to test it when he is back.

[driusan]

Yeah, I added the blocked tag because of the 3 interrelated pull requests.

Maybe they can be discussed/merged at an imaging meeting to make sure they go in in the right order and all works together?

[MounaSafiHarab]

@cmadjar
as discussed in the imaging meeting today, assigned to you, along with the Loris-MRI ones (specifically to test the DTI pipeline), while @gluneau is focusing on the /data/ being on a different VM (mounted) as is the case for IBIS

[MounaSafiHarab]

@cmadjar
@gluneau

please test at your earliest convenience (i.e. ASAP:)) so I can incorporate your feedback!

[gluneau]

cs.Name should be: "dataDirBasepath"

[MounaSafiHarab]

@gluneau

thanks!

[gluneau]

@MounaSafiHarab @driusan tested with IBIS data, and with insertion of a zip.