Test and update databases module

[yakutovicha]

fixes #457

[yakutovicha]

@unkcpz, @danielhollas - ok, I will remove atomic_tools extra. FYI, the reason for adding this was the pymysql dependency required for the CodQueryWidget. I will go ahead and add it as a direct dependency of AWB.

[codecov[bot]]

Codecov Report

Patch coverage: 100.00% and project coverage change: +2.52 :tada:

Comparison is base (02e0e33) 70.22% compared to head (b07dcb4) 72.75%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #458 +/- ## ========================================== + Coverage 70.22% 72.75% +2.52% ========================================== Files 22 23 +1 Lines 3490 3516 +26 ========================================== + Hits 2451 2558 +107 + Misses 1039 958 -81 ``` | Flag | Coverage Δ | | |---|---|---| | python-3.10 | `72.75% <100.00%> (+2.52%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aiidalab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/aiidalab/aiidalab-widgets-base/pull/458?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aiidalab) | Coverage Δ | | |---|---|---| | [aiidalab\_widgets\_base/databases.py](https://codecov.io/gh/aiidalab/aiidalab-widgets-base/pull/458?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aiidalab#diff-YWlpZGFsYWJfd2lkZ2V0c19iYXNlL2RhdGFiYXNlcy5weQ==) | `93.63% <100.00%> (+50.50%)` | :arrow_up: | | [tests/test\_databases.py](https://codecov.io/gh/aiidalab/aiidalab-widgets-base/pull/458?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aiidalab#diff-dGVzdHMvdGVzdF9kYXRhYmFzZXMucHk=) | `100.00% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aiidalab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aiidalab)

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