search

tripal / t4d8

This is a temporary repository for Drupal 9 upgrade for Tripal v4. It is meant to house issues related to the upgrade.
GNU General Public License v2.0
1 stars 10 forks source link

Type Field Bug: Genome Assembly #311

Closed laceysanderson closed 1 year ago

laceysanderson commented 1 year ago

I came across this while testing PR #303. We will fix this after that PR is merged and after resolving issue #310.

Steps to reproduce

  1. Create a Genome Assembly (only required values are needed). This step works fine.
  2. Edit the same genome assembly you just created. Do not make any changes and click save. You should see the following errors on your entity page and see the following error in the logs:
Screen Shot 2022-12-19 at 10 36 08 AM 
PDOException: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "analysisprop_c1" DETAIL: Key (analysis_id, type_id, rank)=(1, 31, 0) already exists. in /var/www/drupal9/web/core/lib/Drupal/Core/Database/StatementWrapper.php:145 Stack trace: #0 /var/www/drupal9/web/core/lib/Drupal/Core/Database/StatementWrapper.php(145): PDOStatement->execute(NULL) #1 /var/www/drupal9/web/core/modules/pgsql/src/Driver/Database/pgsql/Insert.php(98): Drupal\Core\Database\StatementWrapper->execute(NULL, Array) #2 /var/www/drupal9/web/modules/contrib/tripal/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php(146): Drupal\pgsql\Driver\Database\pgsql\Insert->execute() #3 /var/www/drupal9/web/modules/contrib/tripal/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php(364): Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage->insertChadoRecord(Array, 'analysisprop', 0, Array) #4 /var/www/drupal9/web/modules/contrib/tripal/tripal/src/Entity/TripalEntity.php(559): Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage->updateValues(Array) #5 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityStorageBase.php(562): Drupal\tripal\Entity\TripalEntity->preSave(Object(Drupal\Core\Entity\Sql\SqlContentEntityStorage)) #6 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/ContentEntityStorageBase.php(756): Drupal\Core\Entity\EntityStorageBase->doPreSave(Object(Drupal\tripal\Entity\TripalEntity)) #7 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityStorageBase.php(517): Drupal\Core\Entity\ContentEntityStorageBase->doPreSave(Object(Drupal\tripal\Entity\TripalEntity)) #8 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php(804): Drupal\Core\Entity\EntityStorageBase->save(Object(Drupal\tripal\Entity\TripalEntity)) #9 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityBase.php(339): Drupal\Core\Entity\Sql\SqlContentEntityStorage->save(Object(Drupal\tripal\Entity\TripalEntity)) #10 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityForm.php(285): Drupal\Core\Entity\EntityBase->save() #11 /var/www/drupal9/web/modules/contrib/tripal/tripal/src/Form/TripalEntityForm.php(42): Drupal\Core\Entity\EntityForm->save(Array, Object(Drupal\Core\Form\FormState)) #12 [internal function]: Drupal\tripal\Form\TripalEntityForm->save(Array, Object(Drupal\Core\Form\FormState)) #13 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormSubmitter.php(114): call_user_func_array(Array, Array) #14 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormSubmitter.php(52): Drupal\Core\Form\FormSubmitter->executeSubmitHandlers(Array, Object(Drupal\Core\Form\FormState)) #15 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormBuilder.php(592): Drupal\Core\Form\FormSubmitter->doSubmitForm(Array, Object(Drupal\Core\Form\FormState)) #16 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormBuilder.php(320): Drupal\Core\Form\FormBuilder->processForm('tripal_entity_b...', Array, Object(Drupal\Core\Form\FormState)) #17 /var/www/drupal9/web/core/lib/Drupal/Core/Controller/FormController.php(73): Drupal\Core\Form\FormBuilder->buildForm(Object(Drupal\tripal\Form\TripalEntityForm), Object(Drupal\Core\Form\FormState)) #18 [internal function]: Drupal\Core\Controller\FormController->getContentResult(Object(Symfony\Component\HttpFoundation\Request), Object(Drupal\Core\Routing\RouteMatch)) #19 /var/www/drupal9/web/core/lib/Drupal/Core/EventSubscriber/EarlyRenderingControllerWrapperSubscriber.php(123): call_user_func_array(Array, Array) #20 /var/www/drupal9/web/core/lib/Drupal/Core/Render/Renderer.php(564): Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->Drupal\Core\EventSubscriber\@closure() #21 /var/www/drupal9/web/core/lib/Drupal/Core/EventSubscriber/EarlyRenderingControllerWrapperSubscriber.php(124): Drupal\Core\Render\Renderer->executeInRenderContext(Object(Drupal\Core\Render\RenderContext), Object(Closure)) #22 /var/www/drupal9/web/core/lib/Drupal/Core/EventSubscriber/EarlyRenderingControllerWrapperSubscriber.php(97): Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->wrapControllerExecutionInRenderContext(Array, Array) #23 /var/www/drupal9/vendor/symfony/http-kernel/HttpKernel.php(169): Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->Drupal\Core\EventSubscriber\@closure() #24 /var/www/drupal9/vendor/symfony/http-kernel/HttpKernel.php(81): Symfony\Component\HttpKernel\HttpKernel->handleRaw(Object(Symfony\Component\HttpFoundation\Request), 1) #25 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/Session.php(58): Symfony\Component\HttpKernel\HttpKernel->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #26 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/KernelPreHandle.php(48): Drupal\Core\StackMiddleware\Session->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #27 /var/www/drupal9/web/core/modules/page_cache/src/StackMiddleware/PageCache.php(106): Drupal\Core\StackMiddleware\KernelPreHandle->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #28 /var/www/drupal9/web/core/modules/page_cache/src/StackMiddleware/PageCache.php(85): Drupal\page_cache\StackMiddleware\PageCache->pass(Object(Symfony\Component\HttpFoundation\Request), 1, true) #29 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/ReverseProxyMiddleware.php(48): Drupal\page_cache\StackMiddleware\PageCache->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #30 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/NegotiationMiddleware.php(51): Drupal\Core\StackMiddleware\ReverseProxyMiddleware->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #31 /var/www/drupal9/vendor/stack/builder/src/Stack/StackedHttpKernel.php(23): Drupal\Core\StackMiddleware\NegotiationMiddleware->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #32 /var/www/drupal9/web/core/lib/Drupal/Core/DrupalKernel.php(709): Stack\StackedHttpKernel->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #33 /var/www/drupal9/web/index.php(19): Drupal\Core\DrupalKernel->handle(Object(Symfony\Component\HttpFoundation\Request)) #34 @main Next Drupal\Core\Database\IntegrityConstraintViolationException: SQLSTATE[23505]: Unique violation: 7 ERROR: duplicate key value violates unique constraint "analysisprop_c1" DETAIL: Key (analysis_id, type_id, rank)=(1, 31, 0) already exists.: INSERT INTO "chado"."analysisprop" ("type_id", "analysis_id") VALUES (:db_insert_placeholder_0, :db_insert_placeholder_1) RETURNING analysisprop_id; Array ( ) in /var/www/drupal9/web/core/lib/Drupal/Core/Database/ExceptionHandler.php:77 Stack trace: #0 /var/www/drupal9/web/core/modules/pgsql/src/Driver/Database/pgsql/Insert.php(106): Drupal\Core\Database\ExceptionHandler->handleExecutionException(Object(PDOException), Object(Drupal\Core\Database\StatementWrapper), Array, Array) #1 /var/www/drupal9/web/modules/contrib/tripal/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php(146): Drupal\pgsql\Driver\Database\pgsql\Insert->execute() #2 /var/www/drupal9/web/modules/contrib/tripal/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php(364): Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage->insertChadoRecord(Array, 'analysisprop', 0, Array) #3 /var/www/drupal9/web/modules/contrib/tripal/tripal/src/Entity/TripalEntity.php(559): Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage->updateValues(Array) #4 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityStorageBase.php(562): Drupal\tripal\Entity\TripalEntity->preSave(Object(Drupal\Core\Entity\Sql\SqlContentEntityStorage)) #5 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/ContentEntityStorageBase.php(756): Drupal\Core\Entity\EntityStorageBase->doPreSave(Object(Drupal\tripal\Entity\TripalEntity)) #6 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityStorageBase.php(517): Drupal\Core\Entity\ContentEntityStorageBase->doPreSave(Object(Drupal\tripal\Entity\TripalEntity)) #7 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php(804): Drupal\Core\Entity\EntityStorageBase->save(Object(Drupal\tripal\Entity\TripalEntity)) #8 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityBase.php(339): Drupal\Core\Entity\Sql\SqlContentEntityStorage->save(Object(Drupal\tripal\Entity\TripalEntity)) #9 /var/www/drupal9/web/core/lib/Drupal/Core/Entity/EntityForm.php(285): Drupal\Core\Entity\EntityBase->save() #10 /var/www/drupal9/web/modules/contrib/tripal/tripal/src/Form/TripalEntityForm.php(42): Drupal\Core\Entity\EntityForm->save(Array, Object(Drupal\Core\Form\FormState)) #11 [internal function]: Drupal\tripal\Form\TripalEntityForm->save(Array, Object(Drupal\Core\Form\FormState)) #12 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormSubmitter.php(114): call_user_func_array(Array, Array) #13 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormSubmitter.php(52): Drupal\Core\Form\FormSubmitter->executeSubmitHandlers(Array, Object(Drupal\Core\Form\FormState)) #14 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormBuilder.php(592): Drupal\Core\Form\FormSubmitter->doSubmitForm(Array, Object(Drupal\Core\Form\FormState)) #15 /var/www/drupal9/web/core/lib/Drupal/Core/Form/FormBuilder.php(320): Drupal\Core\Form\FormBuilder->processForm('tripal_entity_b...', Array, Object(Drupal\Core\Form\FormState)) #16 /var/www/drupal9/web/core/lib/Drupal/Core/Controller/FormController.php(73): Drupal\Core\Form\FormBuilder->buildForm(Object(Drupal\tripal\Form\TripalEntityForm), Object(Drupal\Core\Form\FormState)) #17 [internal function]: Drupal\Core\Controller\FormController->getContentResult(Object(Symfony\Component\HttpFoundation\Request), Object(Drupal\Core\Routing\RouteMatch)) #18 /var/www/drupal9/web/core/lib/Drupal/Core/EventSubscriber/EarlyRenderingControllerWrapperSubscriber.php(123): call_user_func_array(Array, Array) #19 /var/www/drupal9/web/core/lib/Drupal/Core/Render/Renderer.php(564): Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->Drupal\Core\EventSubscriber\@closure() #20 /var/www/drupal9/web/core/lib/Drupal/Core/EventSubscriber/EarlyRenderingControllerWrapperSubscriber.php(124): Drupal\Core\Render\Renderer->executeInRenderContext(Object(Drupal\Core\Render\RenderContext), Object(Closure)) #21 /var/www/drupal9/web/core/lib/Drupal/Core/EventSubscriber/EarlyRenderingControllerWrapperSubscriber.php(97): Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->wrapControllerExecutionInRenderContext(Array, Array) #22 /var/www/drupal9/vendor/symfony/http-kernel/HttpKernel.php(169): Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->Drupal\Core\EventSubscriber\@closure() #23 /var/www/drupal9/vendor/symfony/http-kernel/HttpKernel.php(81): Symfony\Component\HttpKernel\HttpKernel->handleRaw(Object(Symfony\Component\HttpFoundation\Request), 1) #24 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/Session.php(58): Symfony\Component\HttpKernel\HttpKernel->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #25 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/KernelPreHandle.php(48): Drupal\Core\StackMiddleware\Session->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #26 /var/www/drupal9/web/core/modules/page_cache/src/StackMiddleware/PageCache.php(106): Drupal\Core\StackMiddleware\KernelPreHandle->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #27 /var/www/drupal9/web/core/modules/page_cache/src/StackMiddleware/PageCache.php(85): Drupal\page_cache\StackMiddleware\PageCache->pass(Object(Symfony\Component\HttpFoundation\Request), 1, true) #28 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/ReverseProxyMiddleware.php(48): Drupal\page_cache\StackMiddleware\PageCache->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #29 /var/www/drupal9/web/core/lib/Drupal/Core/StackMiddleware/NegotiationMiddleware.php(51): Drupal\Core\StackMiddleware\ReverseProxyMiddleware->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #30 /var/www/drupal9/vendor/stack/builder/src/Stack/StackedHttpKernel.php(23): Drupal\Core\StackMiddleware\NegotiationMiddleware->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #31 /var/www/drupal9/web/core/lib/Drupal/Core/DrupalKernel.php(709): Stack\StackedHttpKernel->handle(Object(Symfony\Component\HttpFoundation\Request), 1, true) #32 /var/www/drupal9/web/index.php(19): Drupal\Core\DrupalKernel->handle(Object(Symfony\Component\HttpFoundation\Request)) #33 @main
  1. Edit the same genome assembly without changes again. You should get a WSOD/internal error with the following messages in the log:
InvalidArgumentException: Unable to remove item at non-existing index. in Drupal\Core\TypedData\Plugin\DataType\ItemList->removeItem() (line 138 of /var/www/drupal9/web/core/lib/Drupal/Core/TypedData/Plugin/DataType/ItemList.php).

Drupal\Core\Entity\EntityStorageException: Unable to remove item at non-existing index. in Drupal\Core\Entity\Sql\SqlContentEntityStorage->save() (line 815 of /var/www/drupal9/web/core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php).
spficklin commented 1 year ago

I believed this is fixed with PR #321

laceysanderson commented 1 year ago

Likely fixed in recent PR. Leaving open until it is specifically tested.

dsenalik commented 1 year ago

I just tested this with the current 9.x-4.x and there were no errors.

laceysanderson commented 1 year ago

Awesome! Thanks for the confirmation!