Implement in submission function

elixir-europe · Nov 21, 2024 · 21a481c · 21a481c
1 parent 3313b52
commit 21a481c
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Showing 2 changed files with 24 additions and 9 deletions.
diff --git a/mars-cli/mars_cli.py b/mars-cli/mars_cli.py
@@ -197,17 +197,22 @@ def cli(ctx, development):
 
 @cli.command()
 @click.option(
-    "--webin-username", type=click.STRING, help="Username for webin authentication"
+    "--webin-username",
+    type=click.STRING,
+    help="Username for webin authentication",
+    envvar="WEBIN_USERNAME",
 )
 @click.option(
     "--metabolights-username",
     type=click.STRING,
     help="Username for MetaboLights metadata submission",
+    envvar="METABOLIGHTS_USERNAME",
 )
 @click.option(
     "--metabolights-ftp-username",
     type=click.STRING,
     help="Username for MetaboLights data submission",
+    envvar="METABOLIGHTS_FTP_USERNAME",
 )
 @click.option(
     "--credentials-file",
@@ -288,8 +293,9 @@ def submit(
     data_file_paths = [f.name for f in data_files] if file_transfer else []
 
     submission(
-        credential_service_name,
-        username_credentials,
+        webin_username,
+        metabolights_username,
+        metabolights_ftp_username,
         credentials_file,
         isa_json_file.name,
         target_repositories,

diff --git a/mars-cli/mars_lib/submit.py b/mars-cli/mars_lib/submit.py
@@ -10,6 +10,7 @@
     get_metabolights_auth_token,
     get_webin_auth_token,
     load_credentials,
+    AuthProvider,
 )
 from mars_lib.biosamples_external_references import (
     get_header,
@@ -48,8 +49,9 @@ def save_step_to_file(time_stamp: float, filename: str, isa_json: IsaJson):
 
 
 def submission(
-    credential_service_name: str,
-    username_credentials: str,
+    webin_username: str,
+    metabolights_username: str,
+    metabolights_ftp_username: str,
     credentials_file: TextIOWrapper,
     isa_json_file: str,
     target_repositories: list[str],
@@ -63,11 +65,18 @@ def submission(
     # Get password from the credential manager
     # Else:
     # read credentials from file
-    if not (credential_service_name is None or username_credentials is None):
-        cm = CredentialManager(credential_service_name)
+    if all([webin_username, metabolights_username, metabolights_ftp_username]):
         user_credentials = {
-            "username": username_credentials,
-            "password": cm.get_password_keyring(username_credentials),
+            cred_pair[0]: {
+                "username": cred_pair[1],
+                "password": CredentialManager(cred_pair[0]).get_password_keyring(
+                    cred_pair[1]
+                ),
+            }
+            for cred_pair in zip(
+                AuthProvider.available_providers(),
+                [webin_username, metabolights_username, metabolights_ftp_username],
+            )
         }
     else:
         if credentials_file == "":