From 3609a2d734bfc259ad29b865a9cb45d57124670a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 29 Oct 2021 06:59:57 +0300
Subject: Move `correlations_of_all_tissue_traits`

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* gn3/computations/partial_correlations.py: new
  function (`correlations_of_all_tissue_traits`).
* gn3/db/correlations.py: delete
  function (`correlations_of_all_tissue_traits`).

  Move the function to `gn3.computations.partial_correlations` module and
  comment out the db-access code.
  Rework it to receive, as arguments, the data it previously fetched from the
  database, and add comments on future rework to get the function working
  again.
---
 gn3/computations/partial_correlations.py | 27 +++++++++++++++++++++++++++
 gn3/db/correlations.py                   | 20 --------------------
 2 files changed, 27 insertions(+), 20 deletions(-)

(limited to 'gn3')

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index e73edfd..4ba2ba4 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -157,3 +157,30 @@ def batch_computed_tissue_correlation(
     `web.webqtl.correlation.correlationFunction.batchCalTissueCorr`"""
     raise Exception("Not implemented!")
     return ({}, {})
+
+def correlations_of_all_tissue_traits(
+        primary_trait_symbol_value_dict: dict, symbol_value_dict: dict,
+        method: str) -> Tuple[dict, dict]:
+    """
+    Computes and returns the correlation of all tissue traits.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait`
+    function in GeneNetwork1.
+    """
+    # The section below existed in the original function, but with the migration
+    # and the proposed rework (in the near future), the values from the database
+    # should be passed into this function, rather than have the function fetch
+    # the data for itself.
+    # ---------------------------------------------------
+    # primary_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
+    #     (trait_symbol,), probeset_freeze_id, conn)
+    # primary_trait_values = primary_trait_symbol_value_dict.vlaues()[0]
+    # symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
+    #     tuple(), probeset_freeze_id, conn)
+    # ---------------------------------------------------
+    # We might end up actually getting rid of this function all together as the
+    # rework is done.
+    primary_trait_values = primary_trait_symbol_value_dict.values()[0]
+    return batch_computed_tissue_correlation(
+        primary_trait_values, symbol_value_dict, method)
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index f43b8a5..39ed499 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -281,26 +281,6 @@ def fetch_gene_symbol_tissue_value_dict_for_trait(
         return fetch_gene_symbol_tissue_value_dict(xref_info[0], xref_info[2], conn)
     return {}
 
-def correlations_of_all_tissue_traits(
-        trait_symbol: str, probeset_freeze_id: int,
-        method: str, conn: Any) -> Tuple[dict, dict]:
-    """
-    Computes and returns the correlation of all tissue traits.
-
-    This is a migration of the
-    `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait`
-    function in GeneNetwork1.
-    """
-    primary_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
-        (trait_symbol,), probeset_freeze_id, conn)
-    primary_trait_value = primary_trait_symbol_value_dict.vlaues()[0]
-    symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
-        tuple(), probeset_freeze_id, conn)
-    if method == "1":
-        return batch_computed_tissue_correlation(
-            primaryTraitValue,SymbolValueDict,method='spearman')
-    return batch_computed_tissue_correlation(primaryTraitValue,SymbolValueDict)
-
 def build_temporary_tissue_correlations_table(
         trait_symbol: str, probeset_freeze_id: int, method: str,
         return_number: int, conn: Any) -> str:
-- 
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