From 743a4623c53d30779cb884a69d0cf2c7ff411f0a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 9 Mar 2022 19:13:59 +0000
Subject: Add function for getting strain name from sample name

---
 wqflask/maintenance/gen_ind_genofiles.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py
index abca4a4a..6e818945 100644
--- a/wqflask/maintenance/gen_ind_genofiles.py
+++ b/wqflask/maintenance/gen_ind_genofiles.py
@@ -7,9 +7,7 @@ import MySQLdb
 
 from wqflask import app
 
-from gn3.db.datasets import retrieve_group_samples
-
-def db_conn():
+def conn():
     return MySQLdb.Connect(db=app.config.get("DB_NAME"),
                            user=app.config.get("DB_USER"),
                            passwd=app.config.get("DB_PASS"),
@@ -32,6 +30,17 @@ def main(args):
     # Generate the output .geno files
     generate_new_genofiles(strain_genotypes(source_genofile), target_groups)
 
+def get_strain_for_sample(sample):
+    query = (
+        "SELECT CaseAttributeXRefNew.Value "
+        "FROM CaseAttributeXRefNew, Strain "
+        "WHERE CaseAttributeXRefNew.CaseAttributeId=11 "
+        "AND CaseAttributeXRef.New.StrainId = Strain.Id "
+        "AND Strain.Name = %(name)s" )
+
+    with conn.cursor() as cursor:
+        return cursor.execute(query, {"name": name}).fetchone()[0]
+
 def group_samples(target_group: str) -> List:
     """
     Get the group samples from its "dummy" .geno file (which still contains the sample list)
@@ -115,3 +124,4 @@ def strain_genotypes(strain_genofile: str) -> List:
 if __name__ == "__main__":
     print("command line arguments:\n\t%s" % sys.argv)
     main(sys.argv)
+
-- 
cgit v1.2.3