Chado Prepare errors out when reinstalling chado instance
risharde opened this issue · 2 comments
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.
- Previous responses from the preparer have been trimmed -
[notice] Skipping content type, "Organism", as it already exists.
[error] 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) #0 /var/www/html/drupal/web/m
odules/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\ChadoPrepa
rer->createGeneralContentTypes()
#2 /var/www/html/drupal/web/modules/t4d8/tripal_chado/src/legacyFunctions.php(154): Drupal\tripal_chado\Task\ChadoPreparer
->performTask()
#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 /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.
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.
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 :-)