From b6ecd0888ccf51b1dd2bfcbbbc4e03b1c5a92699 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 1 Mar 2022 15:41:56 +0300
Subject: Extract a strain name given a csv string and it's header

* gn3/csvcmp.py (extract_strain_name): New function.
* gn3/db/sample_data (delete_sample_data): Use the aforementioned function.
(insert_sample_data): Ditto.
* tests/unit/test_csvcmp: Test cases for above.
---
 gn3/csvcmp.py         | 7 +++++++
 gn3/db/sample_data.py | 5 +++--
 2 files changed, 10 insertions(+), 2 deletions(-)

(limited to 'gn3')

diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py
index ebd323e..360a101 100644
--- a/gn3/csvcmp.py
+++ b/gn3/csvcmp.py
@@ -4,6 +4,13 @@ import uuid
 from gn3.commands import run_cmd
 
 
+def extract_strain_name(csv_header, data, seek="Strain Name"):
+    for column, value in zip(csv_header.split(","), data.split(",")):
+        if seek in column:
+            return value
+    return ""
+
+
 def create_dirs_if_not_exists(dirs: list):
     for dir_ in dirs:
         if not os.path.exists(dir_):
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index 06b5767..a410978 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -1,3 +1,4 @@
+from gn3.csvcmp import extract_strain_name
 from typing import Any, Tuple, Union
 
 import MySQLdb
@@ -200,7 +201,7 @@ def delete_sample_data(conn: Any,
     strain_id, data_id, inbredset_id = get_sample_data_ids(
         conn=conn, publishxref_id=trait_name,
         phenotype_id=phenotype_id,
-        strain_name=strain_name)
+        strain_name=extract_strain_name(csv_header, data))
 
     none_case_attrs = {
         "Strain Name": lambda: 0,
@@ -273,7 +274,7 @@ def insert_sample_data(conn: Any,  # pylint: disable=[R0913]
     strain_id, data_id, inbredset_id = get_sample_data_ids(
         conn=conn, publishxref_id=trait_name,
         phenotype_id=phenotype_id,
-        strain_name=strain_name)
+        strain_name=extract_strain_name(csv_header, data))
 
     none_case_attrs = {
         "Strain Name": lambda _: 0,
-- 
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