Fix bugs uncovered by flake8 and a typo

Clinical-Genomics · Jul 4, 2024 · fd6fbcc · fd6fbcc
1 parent 940bb26
commit fd6fbcc
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/microSALT/cli.py b/microSALT/cli.py
@@ -43,7 +43,8 @@
     sys.exit(-1)
 
 
-def set_cli_config(config):
+@click.pass_context
+def set_cli_config(ctx, config):
     if config != "":
         if os.path.exists(config):
             try:

diff --git a/tests/test_commands.py b/tests/test_commands.py
@@ -38,8 +38,8 @@ def dbm():
   dbm = DB_Manipulator(config=preset_config,log=logger)
   dbm.create_tables()
 
-  for antry in unpack_db_json('sampleinfo_projects.json'):
-    dbm.add_rec(antry, 'Projects')
+  for entry in unpack_db_json('sampleinfo_projects.json'):
+    dbm.add_rec(entry, 'Projects')
   for entry in unpack_db_json('sampleinfo_mlst.json'):
     dbm.add_rec(entry, 'Seq_types')
   for bentry in unpack_db_json('sampleinfo_resistance.json'):

diff --git a/tests/test_config.py b/tests/test_config.py
@@ -70,7 +70,7 @@ def test_paths(exp_config):
   for entry in preset_config.keys():
     if entry != '_comment':
       if isinstance(preset_config[entry], str) and '/' in preset_config[entry] and entry not in ['database', 'genologics']:
-        unmade_fldr = preset_config[entry][thing]
+        unmade_fldr = preset_config[entry]
         assert (pathlib.Path(unmade_fldr).exists())
 
       #level two