Where to Start

Find the symptom in the table, run its command on the InteLIS machine, and follow the page it points to. Each command reports what it found and prints the next command to run.

Symptom	Run first	Then read
The site will not open in the browser	sudo intelis doctor	Browser Shows PHP Code
The browser shows PHP code instead of InteLIS	sudo intelis doctor	Browser Shows PHP Code
MySQL is stopped, or the site reports a database error	sudo intelis fix-database	MySQL Will Not Start
An update stops at Running database migrations...	Nothing yet. Read the page first.	Update Stuck at Database Migrations
InteLIS fails to start after an update or a server change	sudo intelis check	The fix it prints for each failure
Permission denied in the browser or a log	sudo intelis check	Permission Denied Issue
Illegal mix of collations in the browser or a log	sudo intelis check	Fix Collation Mismatch
The lab was never connected to the STS, or the STS address changed	sudo intelis sts-setup	Connect a Lab to the STS
Results or requests are not reaching the STS	sudo intelis check	Results Not Reaching the STS
Analyzer results are not arriving in InteLIS	sudo intelis interface	Analyzer Results Not Arriving
The site is slow, or the disk is nearly full	sudo intelis health	Free disk space
Backups are not running, or are old	sudo intelis backup status	Setting Up Off-Machine Backups
Scheduled work stopped: no imports, no sync, no backups	sudo crontab -l \| grep cron.sh	Check the scheduled tasks are running

Do not reinstall or reformat the machine

The data is almost always intact. A reinstall is the one step that can turn a fixable fault into lost data.

What each command checks

The four diagnostic commands change nothing unless they ask first.

Command	What it checks	When to use it
sudo intelis check	PHP, the web server's PHP settings, vendor/, the configuration file, writable paths, the database, and pending migrations. Prints the command that fixes each failure.	InteLIS will not start, or after any change to the server.
sudo intelis health	Disk usage, MySQL response time, writable paths, and off-machine backups.	InteLIS runs, but something seems wrong.
sudo intelis doctor	Why the site will not open: the web server, PHP, and the files it serves and who may read them. Offers each safe repair. Runs fix-database itself when MySQL is at fault.	The site will not open.
sudo intelis fix-database	Why MySQL will not start: disk space, memory, edited configuration files, the data folder owner, and damaged data files. Offers each safe repair.	MySQL is stopped.

doctor and fix-database accept --check to report without repairing. Maintenance scripts lists every intelis command.

Before asking for help

Collect these and send them together:

1. The output of sudo intelis check.
2. The output of sudo intelis health.
3. The report the doctor saved, if it ran. It is site-report.txt or mysql-report.txt on the Desktop, or in the home folder when there is no Desktop. Passwords are removed from it.
4. The newest file in /var/www/intelis/var/logs.