Workflow status stuck on Submitted

[NicHerndon]

Workflow invoked with Tripal Galaxy API gets its status stuck in "Submitted" (i.e., it doesn't update to "Completed" when Galaxy finishes executing the workflow).

URL: %Tripal_instance%/user/user_id/galaxy-jobs?status=All&workflow_name=

[shawnawsu]

Is your cron configured to run the galaxy status check?

https://tripal-galaxy.readthedocs.io/en/latest/automating_tasks.html#automatic-job-status-checking

[NicHerndon]

@Sean?

[Ferrisx4]

The Galaxy checking is being handled by the built-in Drupal cron (as opposed to setting it up with a regular crontab):

For some reason, jobs are not being queued up in the Tripal Job queue on this server (they are being queued and run successfully on the production server) - looking into configuration differences now.

Running the command from the linked documentation manually: drush trp-galaxy-status --uri=http://my.tripal.site/ --root=/var/www/html results in an error:

<h1>Additional uncaught exception thrown while handling exception.</h1><h2>Original</h2>

<p>TypeError: Argument 2 passed to tripal_galaxy_get_history() must be of the type string, null given, called in /var/www/Drupal/sites/all/modules/tripal_galaxy/api/tripal_galaxy.api.inc on line 555 in tripal_galaxy_get_history() (line 1014 of /var/www/Drupal/sites/all/modules/tripal_galaxy/api/tripal_galaxy.api.inc).</p>

<h2>Additional</h2>

<p>TYPO3\PharStreamWrapper\Exception: Unexpected file extension in &amp;quot;phar:///usr/bin/drush/commands/core/drupal&amp;quot; in Drupal\Core\Security\PharExtensionInterceptor-&gt;assert() (line 38 of /var/www/Drupal/misc/typo3/drupal-security/PharExtensionInterceptor.php).</p><hr />Drush command terminated abnormally due to an unrecoverable error.

[shawnawsu]

Hi @Ferrisx4 ,

Just following up, did you figure out what the problem was? If you setup a proper crontab for Tripal Galaxy does the job run?

Thanks, Shawna

[Ferrisx4]

Hi @shawnawsu

Setting up a crontab with the command from the linked documentation does not work. The error that that command returns points at the tripal_galaxy_drush_command() function, which calls the tripal_galaxy_check_submission() function. From there, the active submissions are fetched from the database.

I suspect a database state issue on our end because this line returns null, which inspires the error:

TypeError: Argument 2 passed to tripal_galaxy_get_history() must be of the type string, null given, called in /var/www/Drupal/sites/all/modules/tripal_galaxy/api/tripal_galaxy.api.inc on line 555 in tripal_galaxy_get_history() (line 1014 of /var/www/Drupal/sites/all/modules/tripal_galaxy/api/tripal_galaxy.api.inc).

I'm comparing the contents of a database that seems to be working and the one on our dev server (the one in question now). Perhaps tripal_galaxy's database schema changed at one point and there are rows that have no data in a specific column which this function is looking for.

[spficklin]

I believe PR #144 fixes this. The PR is merged. Please comment if the problem persists.