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tripal / t4d8

This is a temporary repository for Drupal 9 upgrade for Tripal v4. It is meant to house issues related to the upgrade.
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Chado Prepare errors out when reinstalling chado instance #326

Closed risharde closed 1 year ago

risharde commented 1 year ago

This error happens when Drupal is already installed and I try to reinstall 'chado'. In the meanwhile I'll attempt to do a fresh Drupal install since it's possible core things may have changed.

Error: Call to a member function getIdSpace() on null in /var/www/html/drupal/web/modules/t4d8/tripal_chado/src/Task/ChadoPreparer.php on line 1446 #0 /var/www/html/drupal/web/modules/t4d8/tripal_chado/src/Task/ChadoPreparer.php(1482): Drupal\tripal_chado\Task\ChadoPreparer->addTypeField()

1 /var/www/html/drupal/web/modules/t4d8/tripal_chado/src/Task/ChadoPreparer.php(180): Drupal\tripal_chado\Task\ChadoPreparer->createGeneralContentTypes()

2 /var/www/html/drupal/web/modules/t4d8/tripal_chado/src/legacyFunctions.php(154): Drupal\tripal_chado\Task\ChadoPreparer->performTask()

3 [internal function]: tripal_chado_prepare_chado()

4 /var/www/html/drupal/web/modules/t4d8/tripal/src/Services/TripalJob.php(359): call_user_func_array()

5 /var/www/html/drupal/web/modules/t4d8/tripal/src/api/tripal.jobs.api.php(443): Drupal\tripal\Services\TripalJob->run()

6 /var/www/html/drupal/web/modules/t4d8/tripal/src/Commands/TripalCommands.php(76): tripal_launch_job()

7 [internal function]: Drupal\tripal\Commands\TripalCommands->runJobs()

8 /var/www/html/drupal/vendor/consolidation/annotated-command/src/CommandProcessor.php(257): call_user_func_array()

9 /var/www/html/drupal/vendor/consolidation/annotated-command/src/CommandProcessor.php(212): Consolidation\AnnotatedCommand\CommandProcessor->runCommandCallback()

10 /var/www/html/drupal/vendor/consolidation/annotated-command/src/CommandProcessor.php(176): Consolidation\AnnotatedCommand\CommandProcessor->validateRunAndAlter()

11 /var/www/html/drupal/vendor/consolidation/annotated-command/src/AnnotatedCommand.php(350): Consolidation\AnnotatedCommand\CommandProcessor->process()

12 /var/www/html/drupal/vendor/symfony/console/Command/Command.php(255): Consolidation\AnnotatedCommand\AnnotatedCommand->execute()

13 /var/www/html/drupal/vendor/symfony/console/Application.php(1027): Symfony\Component\Console\Command\Command->run()

14 /var/www/html/drupal/vendor/symfony/console/Application.php(273): Symfony\Component\Console\Application->doRunCommand()

15 /var/www/html/drupal/vendor/symfony/console/Application.php(149): Symfony\Component\Console\Application->doRun()

16 /var/www/html/drupal/vendor/drush/drush/src/Runtime/Runtime.php(118): Symfony\Component\Console\Application->run()

17 /var/www/html/drupal/vendor/drush/drush/src/Runtime/Runtime.php(48): Drush\Runtime\Runtime->doRun()

18 /var/www/html/drupal/vendor/drush/drush/drush.php(72): Drush\Runtime\Runtime->run()

19 /var/www/html/drupal/vendor/drush/drush/drush(4): require('/var/www/html/d...')

20 {main}

Error: Call to a member function getIdSpace() on null in Drupal\tripal_chado\Task\ChadoPreparer->addTypeField() (line 1446 of /var/www/html/drupal/web/modules/t4d8/tripal_chado/src/Task/ChadoPreparer.php). [warning] Drush command terminated abnormally.

risharde commented 1 year ago

Reinstalling from afresh seems to resolve this issue. Removed chado and reinstalled it as well and did not receive the error. One caveat untested was that I didn't create an organism while doing the reinstall of chado during testing. I may follow up on this as I test in relation to getting the loaders to work.

laceysanderson commented 1 year ago

Thanks @risharde. Since using a fresh install of the new codebase resolved this issue and I have also tested on the docker and not had any problems, I'm going to close this. If you do find it causes a problem once content already exists, please create a new issue in the tripal/tripal repository and tag it tripal4, potential bug :-)