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John Coquitlam
Dec 22, 2020, 1:23:35 PM12/22/20
to AtoM Users
Hi,
Our installation of version 2.6 ended with a 500 Internal Server Error after the 'Config search' page.
Re-loading the browser, we were able to get to the Welcome page.
Is there a way to do the 'Config search' again so it completes properly?
As the setup did not complete, how can we setup administrator access?
Re-loading the browser, we were able to get to the Welcome page.
Is there a way to do the 'Config search' again so it completes properly?
As the setup did not complete, how can we setup administrator access?
We are using ubuntu 18.04 and following every step of the installation.
Thank you,
John
Dan Gillean
Dec 22, 2020, 3:44:16 PM12/22/20
to ICA-AtoM Users
Hi John,
Yes, you can try adding /index.php/sfInstallPlugin/configureSearch to your base URL to return to the search configuration page.
If the error repeats, start by taking a look at the web server error logs so we can learn more about the actual issue causing the error. See:
I've also found an older thread with a number of suggestions that might help identify and resolve Elasticsearch issues. See:
he / him
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Dan Gillean
Dec 22, 2020, 3:47:45 PM12/22/20
to ICA-AtoM Users
PS: In terms of setting up administrator access, there are two ways you can try this.
First, if you haven't loaded any data yet, then you can use the tools:purge command. This will flush ALL DATA from the site, and then walk you through adding the site title, description, and an admin user account. Don't use this if you're loading a SQL dump from a previous version of AtoM and upgrading, or you'll have to repeat the data load, as this will wipe everything! For a new installation, this will work well, however.
If you just want to create an admin user so you can log in, we have a command-line task that can do that, here:
Other details, such as the site title and description and the base URL, can be configured through the user interface, via Admin > Settings. See:
Cheers,
he / him
John Coquitlam
Dec 22, 2020, 4:37:31 PM12/22/20
to AtoM Users
Hi Dan,
I checked the nginx log and found Integrity constraint violation on an insert statement.
I don't really understand this since I am still trying to install and there should be no data inserted yet.
Here is a few lines from the error.log
Thank you for you help.
2020/12/22 16:44:34 [crit] 7378#7378: *6 connect() to unix:/run/php7.2-fpm.atom.sock failed (2: No such file or directory) while connecting to upstream, client: 142.219.72.65, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "142.219.44.9"2020/12/22 17:09:59 [error] 1577#1577: *2 FastCGI sent in stderr: "PHP message: No connection information in your runtime configuration file for datasource [propel]" while reading response header from upstream, client: 142.219.72.65, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "142.219.44.9"
2020/12/22 17:14:51 [error] 1577#1577: *11 upstream timed out (110: Connection timed out) while reading response header from upstream, client: 142.219.72.65, server: _, request: "GET /index.php/sfInstallPlugin/loadData HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock", host: "142.219.44.9", referrer: "http://142.219.44.9/index.php/sfInstallPlugin/configureSearch"
2020/12/22 17:15:05 [error] 1577#1577: *11 FastCGI sent in stderr: "PHP message: Unable to execute INSERT statement. [wrapped: SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '1' for key 'object.PRIMARY']" while reading response header from upstream, client: 142.219.72.65, server: _, request: "GET /index.php/sfInstallPlugin/loadData HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "142.219.44.9", referrer: "http://142.219.44.9/index.php/sfInstallPlugin/configureSearch"
2020/12/22 17:14:51 [error] 1577#1577: *11 upstream timed out (110: Connection timed out) while reading response header from upstream, client: 142.219.72.65, server: _, request: "GET /index.php/sfInstallPlugin/loadData HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock", host: "142.219.44.9", referrer: "http://142.219.44.9/index.php/sfInstallPlugin/configureSearch"
2020/12/22 17:15:05 [error] 1577#1577: *11 FastCGI sent in stderr: "PHP message: Unable to execute INSERT statement. [wrapped: SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '1' for key 'object.PRIMARY']" while reading response header from upstream, client: 142.219.72.65, server: _, request: "GET /index.php/sfInstallPlugin/loadData HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "142.219.44.9", referrer: "http://142.219.44.9/index.php/sfInstallPlugin/configureSearch"
Dan Gillean
Dec 22, 2020, 4:52:35 PM12/22/20
to ICA-AtoM Users
Hi John,
Strange. One thing to check would be the SQL modes - I think with MySQL 8, STRICT_TRANS_TABLES might be on by default, but we've found that this has caused some strange errors in AtoM similar to this, so for now we recommend disabling it. There's a section in the installation docs where we set the SQL modes here:
Additionally, we have some SQL queries on how you can check and change them here:
If you're new to using the MySQL command prompt, we have basic instructions on how to access it, and how to find out your MySQL credentials if you don't know them, here:
If everything looks fine there, then another thing you could try is purging the database, then dropping and recreating it.
First, we'll use the purge command - remember, this is the command that deletes ALL DATA, so back up now if there's anything you want to keep (though in your case it sounds like this isn't an issue). Note as well that this command - and any task that begins with php symfony - should be run from AtoM's root installation directory, which is typically /usr/share/nginx/atom if you've followed our recommended installation instructions.
- php symfony tools:purge
Now, let's try dropping and recreating the AtoM database. This is typically done from the MySQL command prompt. The example command below, taken from the Upgrading docs, assumes your database name is atom - if not, make sure to modify the command:
- mysql -u username -p -e "DROP DATABASE IF EXISTS atom;"
- mysql -u username -p -e "CREATE DATABASE atom CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci;"
Finally, it can often help to restart services - and we can also try populating the search index, to see if Elasticsearch is running as expected. Exit the MySQL command prompt and return to AtoM's root directory, if you're not already there.
Clear the application cache:
- php symfony cc
Restart PHP-FPM:
- sudo systemctl restart php7.2-fpm
Now try to populate the search index:
- php symfony search:populate
Hopefully the above should help! If not, let us know and I'll follow up with the developers for further suggestions.
Cheers,
he / him
To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/85af07fa-fc56-46be-bead-693327e5cdfcn%40googlegroups.com.
Dan Gillean
Dec 22, 2020, 4:56:35 PM12/22/20
to ICA-AtoM Users
Hi again!
One of our developers has just suggested that you should actually REVERSE the first 2 steps - do the drop and recreation of the database first, and THEN run the tools:purge command. Sorry about that!
he / him
John Coquitlam
Dec 23, 2020, 12:45:38 PM12/23/20
to AtoM Users
Hi Dan,
I followed you instructions above but got the following errors:
The purge instruction ended with a 'You must create a schema.yml or schema.xml file.'
After completing all the steps and going to main page, got the 500 internal server error still.
In the error.log we got
2020/12/22 23:00:42 [error] 1577#1577: *69 FastCGI sent in stderr: "PHP message: [wrapped: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'atom.object' doesn't exist]" while reading response header from upstream, client: 142.219.72.65, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "142.219.44.9"
Thanks,
John
José Raddaoui
Dec 23, 2020, 1:16:49 PM12/23/20
to AtoM Users
Hi John,
The error running the purge task could be a permissions issue, depending on the permissions configuration, you may need to run that task with the Nginx user, e.g.:
sudo -u www-data php symfony tools:purge
Make sure you're located on the AtoM folder or that you indicate the path to the Symfony executable in that command (/usr/share/nginx/atom/symfony). If that doesn't work, could you share the entire output of the task? To check if there is anything else before the error. For example, I see the following lines before the confirmation question (ignore the different paths from my environment) ...
>> schema converting "/atom/src/config/schema.yml" to XML
>> schema putting /atom/src/config/generated-schema.xml
>> schema converting "/atom/src/plugins/qbAclPlugin/config/schema.yml" to XML
>> schema putting /atom/src/plugins/qbAclPlugin/config/generated-qbAclPlugin-schema.xml
>> schema converting "/atom/src/plugins/qtAccessionPlugin/config/schema.yml" to XML
>> schema putting /atom/src/plugins/qtAccessionPlugin/config/generated-qtAccessionPlugin-schema.xml
>> file+ config/generated-qbAclPlugin-schema.xml
>> file- /atom/src/plugins/qbAclPlugin/config/generated-qbAclPlugin-schema.xml
>> file+ config/generated-qtAccessionPlugin-schema.xml
>> file- /atom/src/plugins/qtAccessionPlugin/config/generated-qtAccessionPlugin-schema.xml
Best regards.
John Coquitlam
Dec 23, 2020, 2:09:07 PM12/23/20
to AtoM Users
Thank you Jose,
That purge statement worked great.
Now the welcome page can be displayed.
Should also note that I need to add sudo to 'php symfony search:populate' otherwise I get error cannot open qubit_cli.log
Thank you to you and Dan.
John
José Raddaoui
Dec 23, 2020, 2:53:27 PM12/23/20
to AtoM Users
Anytime John,
Good point about the search populate task. However, the "cannot open qubit_cli.log" error may be due to permission issues too. I'd suggest that you double check the AtoM folder permissions:
Best regards,
Radda.
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