From 40f264876f2309fcccfcd3d04a2999bdf3fa5d98 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 24 Nov 2021 05:46:43 +0300
Subject: Retrieve the species name given the group

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

* Migrate the `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies`
  in GeneNetwork1 to `gn3.db.species.species_name` in GeneNetwork3 to enable
  the retrieval of the species name, given the group name (formerly RISet).
---
 gn3/db/species.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

(limited to 'gn3/db/species.py')

diff --git a/gn3/db/species.py b/gn3/db/species.py
index 702a9a8..20170ba 100644
--- a/gn3/db/species.py
+++ b/gn3/db/species.py
@@ -57,3 +57,20 @@ def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int:
             return translated_gene_id[0]
 
     return 0 # default if all else fails
+
+def species_name(conn: Any, group: str) -> str:
+    """
+    Retrieve the name of the species, given the group (RISet).
+
+    This is a migration of the
+    `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies` function in
+    GeneNetwork1.
+    """
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Species.Name FROM Species, InbredSet "
+             "WHERE InbredSet.Name = %(group_name)s "
+             "AND InbredSet.SpeciesId = Species.Id"),
+            group_name=group_name)
+        return cursor.fetchone()[0]
+    return None
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