We recently upgraded a journal from 22.214.171.124 to 126.96.36.199, migrating it from an outdated RHEL to Ubuntu 18.04 running latest Apache and PHP 7.2 and using MySQL on a separate database server. The upgrade went well and the “php tools/upgrade.php check” confirms the code and database are on 188.8.131.52.
However, the editor began to upload their production-ready files and noticed that in the Workflow > Production step of a submission that once the file is selected and he presses “continue” it takes a looooong time (i.e. 1-2 minutes) for the process to complete. The files in question are small (<1MB) and it used to be instantaneous.
I have ensured the stacktrace and other debugging options are turned off in config.inc.php so as not to introduce extra processing.
I have reviewed patches that people have mentioned on the forums, and our code base already has the suggested code.
We have turned on “slow query” logging for the site in MySQL. The following appears in the slow query log when attempting an upload.
[03-Mar-2021 11:47:00] [pool cjds] pid 25017 script_filename = //var/www/cjds/index.php [0x00007f293b41dd10] mysqli_query() /var/www/cjds/lib/pkp/lib/vendor/adodb/adodb-php/drivers/adodb-mysqli.inc.php:788 [0x00007f293b41dbf0] _query() /var/www/cjds/lib/pkp/lib/vendor/adodb/adodb-php/adodb.inc.php:1263 [0x00007f293b41db00] _Execute() /var/www/cjds/lib/pkp/lib/vendor/adodb/adodb-php/adodb.inc.php:1217 [0x00007f293b41d990] Execute() /var/www/cjds/lib/pkp/classes/db/DAO.inc.php:229 [0x00007f293b41d890] update() /var/www/cjds/lib/pkp/classes/search/SubmissionSearchDAO.inc.php:125 [0x00007f293b41d7e0] insertObjectKeyword() /var/www/cjds/classes/search/ArticleSearchIndex.inc.php:311 [0x00007f293b41d700] _indexObjectKeywords() /var/www/cjds/classes/search/ArticleSearchIndex.inc.php:115 [0x00007f293b41d5e0] submissionFileChanged() /var/www/cjds/classes/search/ArticleSearchIndex.inc.php:158 [0x00007f293b41d4f0] submissionFilesChanged() /var/www/cjds/lib/pkp/controllers/api/file/PKPManageFileApiHandler.inc.php:225 [0x00007f293b41d380] saveMetadata() /var/www/cjds/lib/pkp/classes/core/PKPRouter.inc.php:391 [0x00007f293b41d2a0] _authorizeInitializeAndCallRequest() /var/www/cjds/lib/pkp/classes/core/PKPComponentRouter.inc.php:257 [0x00007f293b41d200] route() /var/www/cjds/lib/pkp/classes/core/Dispatcher.inc.php:143 [0x00007f293b41d110] dispatch() /var/www/cjds/lib/pkp/classes/core/PKPApplication.inc.php:281 [0x00007f293b41d0a0] execute() /var/www/cjds/index.php:68
At this point we are considering upgrading to 184.108.40.206 on dev to see if the issue still persists. However, this would mean upgrading our PHP to at least 7.3.
Are any others seeing this problem on their 220.127.116.11 journals?
As always, any guidance is appreciated.
[Edit: I also ran the rebuild of the Search Index in the hopes it might help things, to no avail, and also verified that all tables are the expected collation.]
University of Waterloo Library, Digital Initiatives