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| -rw-r--r-- | issues/simplify_data_set_py_in_gn2.gmi | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/issues/simplify_data_set_py_in_gn2.gmi b/issues/simplify_data_set_py_in_gn2.gmi new file mode 100644 index 0000000..404cf85 --- /dev/null +++ b/issues/simplify_data_set_py_in_gn2.gmi @@ -0,0 +1,27 @@ +# Simplify `dataset.py` in GeneNetwork2 + +## Tags + +* assigned: +* priority: medium +* type: bug +* status: pending +* keywords: technical debt + +## Description + +The entire file +=>https://github.com/genenetwork/genenetwork2/blob/9cd9b91412734f8f084439690082f9e699ebd89e/wqflask/base/data_set.py +is a mess, and we need to chunk it out into smaller logic. + +As part of this, the idea is to begin with the +=> get_trait_data https://github.com/genenetwork/genenetwork2/blob/9cd9b91412734f8f084439690082f9e699ebd89e/wqflask/base/data_set.py#L740-L832 +and split it into various chunks, that +* compute the `self.sample_list` +* retrieve `sample_ids` values from the database using the `self.sample_list` values computed above +* retrieve `trait_sample_data` from `sample_ids` retrieved above. This can have a number of helper function to compute the appropriate queries for each of the `dataset_type` values ("Publish", "Geno", "ProbeSet", "Temp") +* compute the `self.trait_data` from the `trait_sample_data` above + +We can split each of the steps above into one or more methods. + +To help with moving away from using classes, we can ensure that each of these methods returns the values computed/retrieved (in addition to setting the class member variables). |