vanderbilt-redcap / advanced_import Goto Github PK

Hi @bi0nd0,

When setting up an import job within the module, upon running it I get this error:

Error processing the CSV file - SplFileObject::__construct(/var/app/current/redcap/edocs/advanced_import/uploads/fbef449bc5d42d29039385492a2c8e71.csv): failed to open stream: No such file or directory - (code 0)

My institution runs REDCap on cloud infrastructure within AWS so I've passed this to our DevOps engineer who believes that this module has an issue with recognising the local storage due to the infrastructure setup. Would you be able to take a look at this?

Curious what part of the EM is dependent on v11
thanks!

Hi @bi0nd0

We have received this error in our emails this morning - is this an issue that you need to be aware of?

[This message was automatically generated by REDCap]

Cron job 'advanced_import_process_jobs' failed for External Module 'advanced_import'.

Exception: Exception: The 'advanced_import' module MUST specify a 'namespace' in it's config.json file. in /var/app/current/redcap/redcap_v13.3.3/ExternalModules/classes/ExternalModules.php:3641
Stack trace:
#0 /var/app/current/redcap/redcap_v13.3.3/ExternalModules/classes/ExternalModules.php(6262): ExternalModules\ExternalModules::getFrameworkInstance('advanced_import')
#1 /var/app/current/redcap/redcap_v13.3.3/Classes/Cron.php(319): ExternalModules\ExternalModules::callCronMethod('6', 'advanced_import...')
#2 /var/app/current/redcap/redcap_v13.3.3/cron.php(23): Cron->execute()
#3 /var/app/current/redcap/cron.php(9): include('/var/app/curren...')
#4 {main}

Server: ***
User: SYSTEM
Module Name: (advanced_import)
Module Author(s):
Run Time: 0 seconds

I see in my log the following after trying to import from a csv file.

I can send you further project details if you wish as there is no personal/sensitive data.

Cheers,

John

REDCap 13.8.1 · PHP 8.2.7 (Windows OS) · MySQL 8.0.33

14:23:15 | Error message: Uncaught Error: Object of class stdClass could not be converted to string in modules\advanced_import_v1.9.5\AdvancedImport.php:561 Stack trace: #0 modules\advanced_import_v1.9.5\app\Models\Logs.php(60): Vanderbilt\AdvancedImport\AdvancedImport::escape(Object(stdClass)) #1 modules\advanced_import_v1.9.5\app\Controllers\LogsController.php(33): Vanderbilt\AdvancedImport\App\Models\Logs->getList(0, '...') #2 [internal function]: Vanderbilt\AdvancedImport\App\Controllers\LogsController->index() #3 modules\advanced_import_v1.9.5\app\Helpers\Router.php(91): call_user_func_array(Array, Array) #4 modules\advanced_import_v1.9.5\app\router.php(34): Vanderbilt\AdvancedImport\App\Helpers\Router->dispatch('...') #5 modules\advanced_import_v1.9.5\api.php(4): require_once('...') #6 redcap_v13.8.1\ExternalModules\index.php(139): require('...') #7 redcap_v13.8.1\API\index.php(67): require_once('...') #8 {main} thrownFile: modules\advanced_import_v1.9.5\AdvancedImport.phpLine: 561

We've just been upgrading the infrastructure for one of our test instances of REDCap and it seems that this external module is not compatible with PHP 8.0 or PHP 8.1 (PHP 7 went EOL Monday 28th Nov 2022). I've tried different versions of REDCap and consistently get this issue from 12.5.9 (the earliest version I've tried it with) through to 13.0.1.

[This message was automatically generated by REDCap]

Cron job 'advanced_import_check_jobs' failed for External Module 'advanced_import'.

Exception: TypeError: count(): Argument #1 ($value) must be of type Countable|array, null given in /var/app/current/redcap/modules/advanced_import_v1.9.3/AdvancedImport.php:291
Stack trace:
#0 /var/app/current/redcap/modules/advanced_import_v1.9.3/AdvancedImport.php(291): count(NULL)
#1 /var/app/current/redcap/redcap_v13.0.1/ExternalModules/classes/ExternalModules.php(6289): Vanderbilt\AdvancedImport\AdvancedImport->cron_checkJobs(Array)
#2 /var/app/current/redcap/redcap_v13.0.1/Classes/Cron.php(319): ExternalModules\ExternalModules::callCronMethod('5', 'advanced_import...')
#3 /var/app/current/redcap/redcap_v13.0.1/cron.php(23): Cron->execute()
#4 /var/app/current/redcap/cron.php(9): include('/var/app/curren...')
#5 {main}

Server: removed
User: SYSTEM
Module Name: Advanced Import/Export (advanced_import)
Module Author(s): [email protected]
Run Time: 0 seconds

The error refers to line 291 of AdvancedImport.php https://github.com/vanderbilt-redcap/advanced_import/blob/master/AdvancedImport.php#L291

288: function cron_checkJobs($cronInfo)
289: {
290:        $stuckJobs = $this->stopStuckJobs();
291:        $totalStuck = count($stuckJobs);
292:        $messages = ['All jobs have been checked.'];
293:        if($totalStuck>=1) {

Line 290 $stuckJobs = $this->stopStuckJobs(); is always null as the stopStuckJobs(); method does not have a return statement.

https://github.com/vanderbilt-redcap/advanced_import/blob/master/AdvancedImport.php#L264

252:    private function stopStuckJobs() {
253:        $queue = new Queue();
         ...
263:        }
264:        $stuckJobs;
265:    }

Line 264, the last line of stopStuckJobs doesn't return anything. I've manually added the return keyword to this line and no longer get the error. It also doesn't look like $stuckJobs is actually being set apart from it being set to an empty array.

I don't know if there are any other compatibility issues as I do not know enough about this external module to test it.