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Add CenterID class to LORIS #7359

Merged
merged 33 commits into from
May 10, 2021
Merged

Add CenterID class to LORIS #7359

merged 33 commits into from
May 10, 2021

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driusan
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@driusan driusan commented Feb 26, 2021

This adds a new CenterID class and updates it throughout LORIS.

I updated SiteHaver and MultiSiteHaver interfaces, user->hasCenterID, and then followed through all the numerous phan errors that were introduced.

@driusan driusan mentioned this pull request Mar 18, 2021
Merged
@driusan driusan added the "Help! I don't understand Travis!" PR is having a beef with TRAVIS. Someone needs to help label Mar 22, 2021
@driusan driusan force-pushed the CenterIDClass branch 4 times, most recently from 29be378 to 526a4c9 Compare March 24, 2021 17:52
@driusan driusan added Cleanup PR or issue introducing/requiring at least one clean-up operation and removed "Help! I don't understand Travis!" PR is having a beef with TRAVIS. Someone needs to help labels Mar 24, 2021
@kongtiaowang
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Can't create a new new_profile.
Fatal error: Uncaught TypeError: Candidate::createNew(): Argument #1 ($centerID) must be of type CenterID, string given, called in /var/www/html/modules/new_profile/php/new_profile.class.inc on line 81 and defined in /var/www/html/php/libraries/Candidate.class.inc:216
Stack trace:
#0 /var/www/html/modules/new_profile/php/new_profile.class.inc(81): Candidate::createNew('2', '2021-04-12', NULL, Object(LORIS\StudyEntities\Candidate\Sex), NULL, Object(ProjectID))
#1 /var/www/html/php/libraries/NDB_Form.class.inc(104): LORIS\new_profile\New_Profile->_process(Array)
#2 /var/www/html/php/libraries/LorisForm.class.inc(1453): NDB_Form->_save(Array)
#3 /var/www/html/php/libraries/NDB_Form.class.inc(75): LorisForm->process(Array)
#4 /var/www/html/modules/new_profile/php/new_profile.class.inc(106): NDB_Form->save()
#5 /var/www/html/src/Middleware/UserPageDecorationMiddleware.php(240): LORIS\new_profile\New_Profile->handle(Object(Laminas\Diactoros\ServerRequest))
#6 /var/www/html/src/Middleware/PageDecorationMiddleware.php(56): LORIS\Middleware\UserPageDecorationMiddleware->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\new_profile\New_Profile))
#7 /var/www/html/php/libraries/NDB_Page.class.inc(708): LORIS\Middleware\PageDecorationMiddleware->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\new_profile\New_Profile))
#8 /var/www/html/php/libraries/Module.class.inc(411): NDB_Page->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\new_profile\New_Profile))
#9 /var/www/html/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\Diactoros\ServerRequest))
#10 /var/www/html/src/Middleware/AuthMiddleware.php(63): LORIS\Middleware\ResponseGenerator->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\new_profile\Module))
#11 /var/www/html/src/Router/ModuleRouter.php(74): LORIS\Middleware\AuthMiddleware->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\new_profile\Module))
#12 /var/www/html/src/Middleware/ExceptionHandlingMiddleware.php(35): LORIS\Router\ModuleRouter->handle(Object(Laminas\Diactoros\ServerRequest))
#13 /var/www/html/src/Router/BaseRouter.php(112): LORIS\Middleware\ExceptionHandlingMiddleware->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\Router\ModuleRouter))
#14 /var/www/html/src/Middleware/ResponseGenerator.php(50): LORIS\Router\BaseRouter->handle(Object(Laminas\Diactoros\ServerRequest))
#15 /var/www/html/src/Middleware/ContentLength.php(52): LORIS\Middleware\ResponseGenerator->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\Router\BaseRouter))
#16 /var/www/html/htdocs/index.php(48): LORIS\Middleware\ContentLength->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\Router\BaseRouter))
#17 {main}
thrown in /var/www/html/php/libraries/Candidate.class.inc on line 216

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driusan commented Apr 26, 2021

@kongtiaowang should be fixed (assuming it still passes GitHub actions after a rebase..)

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@driusan last issue.
dicom_archive can't load.
http://localhost:8081/dicom_archive/?format=json

Fatal error: Uncaught TypeError: ValidatableIdentifier::__construct(): Argument #1 ($value) must be of type string, null given, called in /var/www/html/modules/dicom_archive/php/dicomarchiverowprovisioner.class.inc on line 75 and defined in /var/www/html/php/libraries/ValidatableIdentifier.php:57 Stack trace: #0 /var/www/html/modules/dicom_archive/php/dicomarchiverowprovisioner.class.inc(75): ValidatableIdentifier->__construct(NULL) #1 /var/www/html/src/Data/Provisioners/DBRowProvisioner.php(118): LORIS\dicom_archive\DicomArchiveRowProvisioner->getInstance(Array) #2 [internal function]: IteratorIterator@anonymous->current() #3 [internal function]: IteratorIterator->next() #4 /var/www/html/src/Data/Table.php(83): FilterIterator->next() #5 /var/www/html/src/Data/Table.php(98): LORIS\Data\Table->toArray(Object(User)) #6 /var/www/html/php/libraries/DataFrameworkMenu.class.inc(144): LORIS\Data\Table->toJSON(Object(User)) #7 /var/www/html/php/libraries/NDB_Menu_Filter.class.inc(648): DataFrameworkMenu->toJSON() #8 /var/www/html/php/libraries/NDB_Page.class.inc(728): NDB_Menu_Filter->display() #9 /var/www/html/php/libraries/DataFrameworkMenu.class.inc(169): NDB_Page->handle(Object(Laminas\Diactoros\ServerRequest)) #10 /var/www/html/php/libraries/NDB_Page.class.inc(707): DataFrameworkMenu->handle(Object(Laminas\Diactoros\ServerRequest)) #11 /var/www/html/php/libraries/Module.class.inc(414): NDB_Page->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\dicom_archive\Dicom_Archive)) #12 /var/www/html/modules/dicom_archive/php/module.class.inc(72): Module->handle(Object(Laminas\Diactoros\ServerRequest)) #13 /var/www/html/src/Middleware/ResponseGenerator.php(50): LORIS\dicom_archive\Module->handle(Object(Laminas\Diactoros\ServerRequest)) #14 /var/www/html/src/Middleware/AuthMiddleware.php(63): LORIS\Middleware\ResponseGenerator->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\dicom_archive\Module)) #15 /var/www/html/src/Router/ModuleRouter.php(74): LORIS\Middleware\AuthMiddleware->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\dicom_archive\Module)) #16 /var/www/html/src/Middleware/ExceptionHandlingMiddleware.php(35): LORIS\Router\ModuleRouter->handle(Object(Laminas\Diactoros\ServerRequest)) #17 /var/www/html/src/Router/BaseRouter.php(112): LORIS\Middleware\ExceptionHandlingMiddleware->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\Router\ModuleRouter)) #18 /var/www/html/src/Middleware/ResponseGenerator.php(50): LORIS\Router\BaseRouter->handle(Object(Laminas\Diactoros\ServerRequest)) #19 /var/www/html/src/Middleware/ContentLength.php(52): LORIS\Middleware\ResponseGenerator->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\Router\BaseRouter)) #20 /var/www/html/htdocs/index.php(48): LORIS\Middleware\ContentLength->process(Object(Laminas\Diactoros\ServerRequest), Object(LORIS\Router\BaseRouter)) #21 {main} thrown in /var/www/html/php/libraries/ValidatableIdentifier.php on line 57

driusan added 20 commits April 28, 2021 10:51
@driusan
more test fixing
2c825e3
@driusan
Maybe fix?
f7c9aa1
@driusan
Fix typo in comment
f651a01
@driusan
Try interpolating instead of casting string
198d704
@driusan
dump some info for debugging
6e80dd9
@driusan
Add RegistrationCenterID case
a72fe10
@driusan
Unused variable and remove debugging var_dumps
c7c1bed
@driusan
Fix double construction of CenterID object
95a6ac5
@driusan
Add debugging statements to failing test
4563876
@driusan
Dump function call output
cce14da
@driusan
output the booleans too
0ac4e12
@driusan
add onlyMethods
5ebda59
@driusan
Remove extra debugging calls
4e434c6
@driusan
Fix an API endpoint
8db1449
@driusan
Fix timepoint accessibility check
7fa8318 
Objects should not be compared with strict equality
@driusan
Fix more API integration tests
d7b8072
@driusan
phpcs
4a4ac28
@driusan
Fix candidate creation when user has multiple sites
1e4d42f
@driusan
Handle both tarchive rows that have a session and that do not
645367b 
We do not have a CenterID to associate with tarchive rows that
have no session (ie. an invalid patient name), so need a DataInstance
type that doesn't implement SiteHaver for those rows.
@driusan
phpcs
f6f512d
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driusan commented Apr 28, 2021

@kongtiaowang need to see if it still passes the tests but it should be fixed.

kongtiaowang
kongtiaowang approved these changes May 8, 2021
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LGTM

@kongtiaowang kongtiaowang added the Passed manual tests PR has been successfully tested by at least one peer label May 8, 2021
@driusan driusan merged commit c38f1c1 into aces:main May 10, 2021
AlexandraLivadas pushed a commit to AlexandraLivadas/Loris that referenced this pull request Jun 29, 2021
@driusan @AlexandraLivadas
Add CenterID class to LORIS (aces#7359)
1cfdaa4 
This adds a new CenterID class and updates it throughout LORIS.
@ridz1208 ridz1208 added this to the 24.0.0 milestone Aug 24, 2021
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