Make mysqlnd.net_read_timeout configurable from environment var (#1320)

`mysqlnd.net_read_timeout` should determine how long the API waits on a
connection with the database for incoming packets. It should be long
enough to accommodate database queries executing, but short enough to
not halt forever on a connection issue.

Surpress warning if file is not found in `get_csv` (#1307)

This avoids a PHP warning being raised due to `fopen` being called with
an inaccessible location.
Instead, we log a more meaningful message on failure so we can
investigate these cases. I also added some logging for other failure
modes since they likely point to bad data.

If the PHP API is running in `production` mode (in `index.php`) then the
observable behavior is the same: a 404 response with a 404 HTML webpage.
The only change is the logged message. If it is running in
`development`, then the API used to return the PHP warning to the client
but now no longer does so.

Add individual index creation, and allow continue on error (#1303)

The build_es_indices was deliberately kept in this way since that is
used in some scripts and I did not want to change their behavior.

Merge pull request #1295 from openml/default-log-level

Set default log threshold and path

Merge pull request #1290

Change policies around modifying certain assets

Merge pull request #1281 from openml/increase-upload-size

Increase the maximum limit for POST requests and uploaded files

Merge pull request #1277 from openml/feature/do_not_index_es_during_s…

…tartup

Optionally do not index es during startup

Refactor status check logic in study listing

Commented-out code enforcing active status by default.

Merge pull request #1237 from openml/release/v1.2.0

Added the correct jar now, with dependencies

Merge pull request #1236 from openml/release/v1.2.0

Release/v1.2.0 to develop