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Provide the database cursor as an argument to the methods of the two
classes:
* wqflask.base.species.TheSpecies
* wqflask.base.species.Chromosomes
Also update dependent code to initialise and pass the cursor where
these classes are used.
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__init__.py
Previously it threw an error when it tried to use Markers/HumanMarkers
in datasetgroup.py; since Markers/HumanMarkers doesn't seem to be used
anywhere else, I think it's okay for the import to only be in
datasetgroup.py
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Pass the redis and database connection/cursors as arguments to the
class methods, and do not retain a copy of the connections/cursors.
This allows us to do the connection management in the context
managers elsewhere - ideally, at the top-level. For now the context
manager is within the `create_dataset` function, but this should be
moved out to a higher level once the lower levels are verified to be
working as expected.
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Since the `__post_init__` method in the 'DatasetType' class checks
whether data is in redis before hitting the database, it does not
matter whether there is a global object of the type, as long as we
make sure to call the object correctly.
This commit makes that happen.
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To ease future refactors on the code, decompose the file into a module
with multiple modules that can be refactored semi-independently.
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