fips #205

ACEnglish · Apr 3, 2024 · a8dbd30 · a8dbd30
1 parent d862e76
commit a8dbd30
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/repo_utils/test_files/external/fake_mafft/mafft b/repo_utils/test_files/external/fake_mafft/mafft
@@ -11,7 +11,7 @@ sys.stderr.write(f"Running fake MAFFT\n")
 m_dir = os.path.dirname(os.path.realpath(__file__))
 
 stdin = sys.stdin.read()
-md5sum = hashlib.md5(stdin.encode()).hexdigest()
+md5sum = hashlib.md5(stdin.encode(), usedforsecurity=False).hexdigest()
 fn = os.path.join(m_dir, f"lookup/fm_{md5sum}.msa")
 
 #if not os.path.exists(fn):

diff --git a/repo_utils/test_files/external/fake_mafft/make_fake_mafft_results.py b/repo_utils/test_files/external/fake_mafft/make_fake_mafft_results.py
@@ -16,7 +16,7 @@
     # For every haps.fa, read it in, get a hash key, save hash key to file's msa.fa
     with open(haps, 'r') as fh:
         data = fh.read()
-        m_key = hashlib.md5(data.encode('utf-8')).hexdigest()
+        m_key = hashlib.md5(data.encode('utf-8'), usedforsecurity=False).hexdigest()
         if m_key in lookup:
             sys.stderr.write("!!WARN!! Conflicting key %s on %s with %s\n" % (m_key, haps, lookup[m_key]))
         lookup[m_key] = os.path.join(os.path.dirname(haps), 'msa.fa')

diff --git a/truvari/phab.py b/truvari/phab.py
@@ -285,7 +285,7 @@ def run_mafft(seq_bytes, params=DEFAULT_MAFFT_PARAM):
     dev_name = None
     if "PHAB_WRITE_MAFFT" in os.environ and os.environ["PHAB_WRITE_MAFFT"] == "1":
         import hashlib  # pylint: disable=import-outside-toplevel
-        dev_name = hashlib.md5(seq_bytes).hexdigest()
+        dev_name = hashlib.md5(seq_bytes, usedforsecurity=False).hexdigest()
 
     ret = truvari.cmd_exe(f"mafft {params} -", stdin=seq_bytes)
     if ret.ret_code != 0: