Add the option to read credentials from env variables

README.md

@@ -78,7 +78,7 @@ All supported arguments:
                         specify the version of the tool this submission is done with
   --no_data_upload      indicate if no upload should be performed and you like to submit a RUN object (e.g. if uploaded was done separately).
   --draft               indicate if no submission should be performed
-  --secret SECRET       .secret.yml file containing the password and Webin ID of your ENA account
+  --secret SECRET       .secret.yml file containing the password and Webin ID of your ENA account OR set ENA_USER and ENA_PASS env variables
   -d, --dev             flag to use the dev/sandbox endpoint of ENA
 ```
 
@@ -88,10 +88,17 @@ Mandatory arguments: --action, --center and --secret.
 
 A Webin can be made [here](https://www.ebi.ac.uk/ena/submit/sra/#home) if you don't have one already. The Webin ID makes use of the full username looking like: `Webin-XXXXX`. Visit [Webin online](https://www.ebi.ac.uk/ena/submit/webin) to check on your submissions or [dev Webin](https://wwwdev.ebi.ac.uk/ena/submit/webin) to check on test submissions.
 
-### The .secret.yml file
+### Credentials
+There are two supported ways to provide your ENA credentials.
+
+#### The .secret.yml file
 
 To avoid exposing your credentials through the terminal history, it is recommended to make use of a `.secret.yml` file, containing your password and username keywords. An example is given in the root of this directory.
 
+#### Environment variables
+
+Alternatively, credentials can be provided via environment variables. Set the variables ENA_USER and ENA_PASS in your environment and run the tool without the --secret option.
+
 ### ENA sample checklists
 
 You can specify ENA sample checklist using the `--checklist` parameter. By default the ENA default sample checklist is used supporting the minimum information required for the sample (ERC000011). The supported checklists are listed on our [template repo](https://github.com/ELIXIR-Belgium/ENA-metadata-templates).  

ena_upload/ena_upload.py

@@ -779,8 +779,8 @@ def process_args():
                         help='indicate if no submission should be performed')
 
     parser.add_argument('--secret',
-                        required=True,
-                        help='.secret.yml file containing the password and Webin ID of your ENA account')
+                        required=False,
+                        help='.secret.yml file containing the password and Webin ID of your ENA account OR set ENA_USER and ENA_PASS env variables')
 
     parser.add_argument(
         '-d', '--dev', help="flag to use the dev/sandbox endpoint of ENA", action="store_true")
@@ -792,8 +792,14 @@ def process_args():
     if tables == {None} and not args.xlsx and not args.isa_json:
         parser.error('Requires at least one table for submission')
 
-    # check if .secret file exists
-    if args.secret:
+    # check credentials source
+    if not args.secret:
+        if not (os.environ.get('ENA_USER') and os.environ.get('ENA_PASS')):
+            parser.error(
+                f"Credentials required: provide --secret or set "
+                f"ENA_USER and ENA_PASS environment variables"
+            )
+    else:
         if not os.path.isfile(args.secret):
             msg = f"Oops, the file {args.secret} does not exist"
             parser.error(msg)
@@ -868,16 +874,22 @@ def main():
     isa_assay_stream = args.isa_assay_stream
     auto_action = args.auto_action
 
-    with open(secret, 'r') as secret_file:
-        credentials = yaml.load(secret_file, Loader=yaml.FullLoader)
+    if secret:
+        with open(secret, 'r') as secret_file:
+            credentials = yaml.load(secret_file, Loader=yaml.FullLoader)
+        password = credentials.get('password', '').strip()
+        webin_id = credentials.get('username', '').strip()
+    else:
+        webin_id = os.environ.get('ENA_USER', '').strip()
+        password = os.environ.get('ENA_PASS', '').strip()
 
-    password = credentials['password'].strip()
-    webin_id = credentials['username'].strip()
 
     if not password or not webin_id:
-        print(
-            f"Oops, file {args.secret} does not contain a password or username")
-    secret_file.close()
+        sys.exit(
+            "Oops, missing ENA credentials (username or password). "
+            "Provide --secret or set ENA_USER and ENA_PASS."
+        )
+
 
     if xlsx:
         # create dataframe from xlsx table