From f3f05970ea4dfaf84fea52d8f4212e72ff21b3d0 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 24 Feb 2021 10:32:57 +0300
Subject: Check if phenotype exists before creating one

---
 gn3/computations/gemma.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

(limited to 'gn3')

diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index ea0f86a..42b4b36 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -1,9 +1,11 @@
 """Procedures related gemma computations"""
+import os
 import random
 import string
 
 from base64 import b64encode
 from hashlib import md5
+from typing import List
 
 def generate_random_n_string(n_length: int) -> str:
     """Generate a random string that is N chars long"""
@@ -16,11 +18,22 @@ def generate_hash_of_string(unhashed_str: str) -> str:
 the end"""
     hashed_str = md5(unhashed_str.encode("utf-8")).digest()
     return b64encode(hashed_str).decode("utf-8").replace("==", "")
+
+
 def generate_pheno_txt_file(trait_filename: str,
-                            values: str,
+                            values: List,
                             tmpdir: str = "/tmp") -> str:
-    """Given VALUES, and TMPDIR, generate a valide traits file"""
-    trait_filename += f"_{generate_random_n_string(6)}"
+    """Given VALUES, and TMPDIR, generate a valid traits file"""
+    if not os.path.isdir(f"{tmpdir}/gn2/"):
+        os.mkdir(f"{tmpdir}/gn2/")
+    ext = trait_filename.partition(".")[-1]
+    if ext:
+        trait_filename = trait_filename.replace(f".{ext}", "")
+        ext = f".{ext}"
+    trait_filename += f"_{generate_hash_of_string(''.join(values))}{ext}"
+    # Early return if this already exists!
+    if os.path.isfile(f"{tmpdir}/gn2/{trait_filename}"):
+        return f"{tmpdir}/gn2/{trait_filename}"
     with open(f"{tmpdir}/gn2/{trait_filename}", "w") as _file:
         for value in values:
             if value == "x":
-- 
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