Updated run.sh to pass in the mysql key & trust stores.

[kshakir]

Also updated jenkins with file that appears in the dev /etc/cromwell.conf.

[kshakir]

Tex-- assuming liquibase has been successfully run in the past, this run.sh, combined with the latest jenkins config file, should start up the server cleanly. If you could sanity check run for me, I'd appreciate it.

[mcovarr]

So... what exactly was not working before?

[mcovarr]

why would we expect one or the other?

[kshakir]

When using HikariCP, the default Slick 3.0.0 connection pool, with the newer javax.sql.DataSource, the urlKey is properties.url. For other combinations, the key is url.

The following additional keys are supported for HikariCP only:
• dataSourceClass (String, optional): ... Note that url is ignored when this key is set (You have to use properties to configure the database connection instead).
…

-- Database.forConfig

[kshakir]

Not 100% sure what wasn't working at what point.

I suspect that based on the order of the original commits¹, the RunMysql and server should have both worked at "4.". At that point I believe the config url still contained useSSL=true, the application config was being passed on the command line, and the mysql jdbc code should have been in the main assembly.

By the time I was running "11." earlier today, the configuration url no longer contained useSSL=true, and connections within SlickDataAccess were returning the error combo:

java.sql.SQLTimeoutException: Timeout after 1000ms of waiting for a connection.
...
Caused by: java.sql.SQLException: Access denied for user '…'@'…' (using password: YES)

I did add another variable in "11." by always testing with useSSL=true&requireSSL=true, but according to the logs of the latest 'RunMysql', jdbcMain and jdbcRequireSsl passed. So that shouldn't have changed the results.

Meanwhile, all test combinations of setting ssl worked for both slick and raw datasource connections, in tests via the url (Ssl), or via the dataSource properties (*Prop). So I think just setting back the useSSL=true is the minimum required fix, but I'd prefer to see requiredSSL=true added as well, as was successfully run in slickSslDriver.

¹ What I believe is the previous order of the commits:

1. Updated run.sh to pass in the mysql key & trust stores.
2. log database config
3. make mysql not test-only
4. Add config file option in run.sh to make container use custom configuration
5. debugging "script"
6. log actual uniquified config
7. Test at JDBC level.
8. hardcode use of SSL
9. count rows in WORKFLOW_EXECUTION
10. Logging the just the URL in SlickDataAccess, not the entire config.
11. Added a suite of mysql ssl test.

[kshakir]

Received a verbal tentative 👍 from @mcovarr (I will follow up with more inline docs regarding conversation above) and 👍 from @coreone with his latest JAVA_OPTS commit.

This jenkins build may break in develop due to server-conf-file logic required from #102, but we believe it should all work once that's merged in too.

Merging.