biocore / biocore/LabControl

Make a more generalized 'upstream' connector in composition objects/tables?

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code refactor scope:large
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Description

Yesterday, @mortonjt and I were working together on issue #77 and running into a challenge that @ElDeveloper and I also encountered in issue #195: different composition types have differently named tables or methods names necessary to access the constituent samples.

In issue #195, this led to the following code:

https://github.com/jdereus/labman/blob/0dd5afef6a980ff25d6b420618828a2bddae383c/labman/gui/handlers/process_handlers/quantification_process.py#L57-L67

In issue #77, we're trying to follow compositions 'upstream', but this requires us to have a lookup table that references the current composition type so that we can know the appropriate column name to query for the upstream composition:

screenshot

https://github.com/mortonjt/labman/blob/33277e138dde41a5789759df20e3c08c01ddfad2/labman/db/plate.py#L580-L607

Would it be possible to generalize this somehow? @AmandaBirmingham, do you have any thoughts on this? Is it possible, for example, to add a column name alias to the composition type tables so that one could `SELECT upstream_composition_id FROM qiita.gdna_composition` instead of `SELECT sample_composition_id FROM qiita.gdna_composition`?

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