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* Pass the URI string to parse into `gn3.db_utils.parse_db_url` rather than
relying on a global variable.
* Pass the URI string to use to generate the database connection to the
`gn3.db_utils.database_connector` function rather than depending on a global
variable. Use the global `SQL_URI` variable as a default value if one is not
provided when calling the function.
The changes above make the creation of the database connection more flexible,
since the database URI passed into the function can be changed at the site
where the call is made.
The port is also parsed, and used where present, to allow for either a socket
connection or one based on a port.
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Fix some issues caught by tests due to changes introducing the hand-off of the
partial correlations computations to an external process
Fix some issues due to the changes that introduce context managers for
database connections
Update some tests to take the above two changes into consideration
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* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
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Use pytest's `mark` feature to explicitly categorise the tests and run them
per category
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- add new api for gn2-gn3 sample r integration
- delete map for sample list to values
- add db util file
- add python msql-client dependency
- add db for fetching lit correlation results
- add unittests for db utils
- add tests for db_utils
- modify api for fetching lit correlation results
- refactor Mock Database Connector and unittests
- add sql url parser
- add SQL URI env variable
- refactor code for db utils
- modify return data for lit correlation
- refactor tissue correlation endpoint
- replace db_instance with conn
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