formatting, linting and type checking

Author: kdp-cloud

mars-cli/mars_cli.py

@@ -376,11 +376,13 @@ def validate_isa_json(isa_json_file, investigation_is_root, validation_schema):
 @cli.command()
 @click.option(
     "--auth-provider",
-    type=click.Choice(['webin', 'metabolights_metadata', 'metabolights_data'], case_sensitive=False),
+    type=click.Choice(
+        ["webin", "metabolights_metadata", "metabolights_data"], case_sensitive=False
+    ),
     is_flag=False,
     flag_value="value",
     required=True,
-    help='',
+    help="",
 )
 @click.argument(
     "username",

mars-cli/mars_lib/authentication.py

@@ -38,10 +38,10 @@ def load_credentials(
     Returns:
     dict: The credentials.
     """
-    if type(credentials_file) == str:
+    if isinstance(credentials_file, str):
         with open(credentials_file, "r") as file:
             credentials = json.load(file)
-    elif type(credentials_file) == io.TextIOWrapper:
+    elif isinstance(credentials_file, io.TextIOWrapper):
         with open(credentials_file.name, "r") as file:
             credentials = json.load(file)
     else:

mars-cli/mars_lib/submit.py

@@ -114,7 +114,7 @@ def submission(
         # Submit to Biosamples
         biosamples_result = submit_to_biosamples(
             isa_json=isa_json,
-            biosamples_credentials=user_credentials,
+            biosamples_credentials=user_credentials[TargetRepository.BIOSAMPLES.value],
             biosamples_url=urls["BIOSAMPLES"]["SUBMISSION"],
             webin_token_url=urls["WEBIN"]["TOKEN"],
         )
@@ -137,7 +137,7 @@ def submission(
                 file_paths=[
                     Path(df) for df in data_file_map[TargetRepository.ENA.value]
                 ],
-                user_credentials=user_credentials,
+                user_credentials=user_credentials[TargetRepository.ENA.value],
                 submission_url=urls["ENA"]["DATA-SUBMISSION"],
                 file_transfer=file_transfer,
             )
@@ -148,7 +148,7 @@ def submission(
         # Step 2 : submit isa-json to ena
         ena_result = submit_to_ena(
             isa_json=isa_json,
-            user_credentials=user_credentials,
+            user_credentials=user_credentials[TargetRepository.ENA.value],
             submission_url=urls["ENA"]["SUBMISSION"],
         )
         print_and_log(
@@ -172,7 +172,9 @@ def submission(
             file_paths=data_file_map[TargetRepository.METABOLIGHTS.value],
             file_transfer=file_transfer,
             isa_json=isa_json,
-            metabolights_credentials=user_credentials,
+            metabolights_credentials=user_credentials[
+                TargetRepository.METABOLIGHTS.value
+            ],
             metabolights_url=urls["METABOLIGHTS"]["SUBMISSION"],
             metabolights_token_url=urls["METABOLIGHTS"]["TOKEN"],
         )