2 files changed, 41 insertions, 16 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index 87ab082..f43b8a5 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -265,14 +265,41 @@ def fetch_tissue_probeset_xref_info(
         results or tuple(),
         (tuple(), {}, {}, {}, {}, {}, {}))
 
-def correlations_of_all_tissue_traits() -> Tuple[dict, dict]:
+def fetch_gene_symbol_tissue_value_dict_for_trait(
+        gene_name_list: Tuple[str, ...], probeset_freeze_id: int,
+        conn: Any) -> dict:
     """
+    Fetches a map of the gene symbols to the tissue values.
+
     This is a migration of the
-    `web.webqtl.correlation.CorrelationPage.calculateCorrOfAllTissueTrait`
+    `web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait`
     function in GeneNetwork1.
     """
-    raise Exception("Unimplemented!!!")
-    return ({}, {})
+    xref_info = fetch_tissue_probeset_xref_info(
+        gene_name_list, probeset_freeze_id, conn)
+    if xref_info[0]:
+        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,
@@ -283,6 +310,8 @@ def build_temporary_tissue_correlations_table(
     This is a migration of the
     `web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in
     GeneNetwork1."""
+    symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits(
+        trait_symbol, probeset_freeze_id, method, conn)
     raise Exception("Unimplemented!!!")
     return ""
 
diff --git a/gn3/db/species.py b/gn3/db/species.py
index 1e5015f..702a9a8 100644
--- a/gn3/db/species.py
+++ b/gn3/db/species.py
@@ -47,17 +47,13 @@ def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int:
         return geneid
 
     with conn.cursor as cursor:
-        if species == "rat":
-            cursor.execute(
-                "SELECT mouse FROM GeneIDXRef WHERE rat = %s", geneid)
-            rat_geneid = cursor.fetchone()
-            if rat_geneid:
-                return rat_geneid[0]
-
-        cursor.execute(
-            "SELECT mouse FROM GeneIDXRef WHERE human = %s", geneid)
-        human_geneid = cursor.fetchone()
-        if human_geneid:
-            return human_geneid[0]
+        query = {
+            "rat": "SELECT mouse FROM GeneIDXRef WHERE rat = %s",
+            "human": "SELECT mouse FROM GeneIDXRef WHERE human = %s"
+        }
+        cursor.execute(query[species], geneid)
+        translated_gene_id = cursor.fetchone()
+        if translated_gene_id:
+            return translated_gene_id[0]
 
     return 0 # default if all else fails