Add ability to reset the database

[nicholasray]

The ability to reset the database before a test group runs can be necessary when
using previous branch (e.g. when using the -b flag) as that code may assume an
older database schema structure that the database may not have.

Resetting the db will also become critical when tests are introduced that make
changes to the database (e.g. tests that edit an article ). Providing this flag
enables the ability for each test group to be completely isolated from the side
effects that another test group may cause.

Additionally:

• Update database seed file to database_2022-06-13_12-27-44-0600(MDT).tar.gz
  to fix crash messages appearing in the mysql logs.

• Revise db:save npm script to enable "slow shutdown" of mysql prior to taking a physical backup. Mysql states this is needed in their docs [1]

• Revise healthcheck logic in docker compose after noticing the healthcheck
  reporting that the db was healthy when it wasn't accepting any connections yet.
  Relying on a status query for the my_wiki should be more reliable.

[1] https://dev.mysql.com/doc/refman/8.0/en/innodb-backup.html

[jdlrobson]

I went to http://localhost:3000/wiki/Main_Page and edited the page. After running npm run db:save I'm still seeing the edited main page. Is that intentional?

[nicholasray]

I went to http://localhost:3000/wiki/Main_Page and edited the page. After running npm run db:save I'm still seeing the edited main page. Is that intentional?

Yes. This commit's main focus was adding a --reset-db flag that you can use with the reference (e.g. ./pixel.js reference --reset-db) or the test command (e.g. ./pixel.js test --reset-db) to reset any database changes you've made or a test has made.

For example, if a test group were to edit the Test page but you didn't want those database changes to bleed into the next test group, you could run ./pixel.js reference --reset-db -g ... and it should reset the database to the original seed data.

It also adds a reset-db command that you can use to reset the database yourself (e.g. ./pixel.js reset-db). If you edit a page, and then run that command, it should reset the database to the original seed data.

[jdlrobson]

Now getting:

rsync: change_dir "/var/lib/mysql_backup" failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1207) [sender=3.1.3]
(node:24963) UnhandledPromiseRejectionWarning: Error: Exit with error code 23
    at ChildProcess.<anonymous> (/Users/jrobson/git/pixel/src/BatchSpawn.js:70:13)
    at ChildProcess.emit (events.js:400:28)
    at Process.ChildProcess._handle.onexit (internal/child_process.js:277:12)
(Use `node --trace-warnings ...` to show where the warning was created)
(node:24963) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag `--unhandled-rejections=strict` (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 1)
(node:24963) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.

[nicholasray]

Now getting:

rsync: change_dir "/var/lib/mysql_backup" failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1207) [sender=3.1.3]
(node:24963) UnhandledPromiseRejectionWarning: Error: Exit with error code 23
    at ChildProcess.<anonymous> (/Users/jrobson/git/pixel/src/BatchSpawn.js:70:13)
    at ChildProcess.emit (events.js:400:28)
    at Process.ChildProcess._handle.onexit (internal/child_process.js:277:12)
(Use `node --trace-warnings ...` to show where the warning was created)
(node:24963) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). To terminate the node process on unhandled promise rejection, use the CLI flag `--unhandled-rejections=strict` (see https://nodejs.org/api/cli.html#cli_unhandled_rejections_mode). (rejection id: 1)
(node:24963) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.

Since this patch changes the database docker image, you'll need to run./pixel.js clean so that the database image can be rebuilt. Please note that running this command will destroy any data you currently have in the database