Add output option

Author: kdp-cloud

mars-cli/mars_cli.py

@@ -206,6 +206,11 @@ def cli(ctx, development):
     type=click.BOOL,
     help="Boolean indicating if the investigation is the root of the ISA JSON. Set this to True if the ISA-JSON does not contain a 'investigation' field.",
 )
+@click.option(
+    "--output",
+    type=click.STRING,
+    default=f"output_{datetime.now().strftime('%Y-%m-%dT%H:%M:%S')}",
+)
 @click.pass_context
 def submit(
     ctx,
@@ -218,6 +223,7 @@ def submit(
     submit_to_metabolights,
     investigation_is_root,
     file_transfer,
+    output,
     data_files,
 ):
     """Start a submission to the target repositories."""
@@ -250,6 +256,7 @@ def submit(
             investigation_is_root,
             urls_dict,
             file_transfer,
+            output,
             data_file_paths,
         )
     except requests.RequestException as err:

mars-cli/mars_lib/submit.py

@@ -30,7 +30,7 @@
 
 
 def save_step_to_file(time_stamp: float, filename: str, isa_json: IsaJson):
-    dir_path = f"tmp/{str(time_stamp)}"
+    dir_path = f"tmp/{datetime.now().strftime('%Y-%m-%dT%H:%M:%S')}"
     os.makedirs(dir_path, exist_ok=True)
 
     with open(f"{dir_path}/{filename}.json", "w") as f:
@@ -49,8 +49,9 @@ def submission(
     investigation_is_root: bool,
     urls: dict[str, Any],
     file_transfer: str,
+    output: str,
     data_file_paths=None,
-):
+) -> None:
     # If credential manager info found:
     # Get password from the credential manager
     # Else:
@@ -150,8 +151,9 @@ def submission(
         )
         # TODO: Update `isa_json`, based on the receipt returned
 
-    # TODO: Return the updated ISA JSON
-    return isa_json
+    # Return the updated ISA JSON
+    with open(f"{output}.json", "w") as f:
+        f.write(isa_json.model_dump_json(by_alias=True, exclude_none=True))
 
 
 def submit_to_biosamples(

mars-cli/tests/test_ftp_upload.py

@@ -13,10 +13,17 @@ def test_upload_login_failure():
         uploader.upload([Path("./tests/fixtures/not_a_json_file.txt")])
 
 
-@pytest.mark.skip(reason="Relies on real ENA credentials in test_credentials_example.json")
+@pytest.mark.skip(
+    reason="Relies on real ENA credentials in test_credentials_example.json"
+)
 def test_upload_success():
     # For local testing, add ENA username/password to test_credentials_example.json
     with open("./tests/test_credentials_example.json") as f:
         creds = json.load(f)
     uploader = FTPUploader("webin2.ebi.ac.uk", creds["username"], creds["password"])
-    uploader.upload([Path("../test-data/ENA_TEST2.R1.fastq.gz"), Path("./tests/fixtures/not_a_json_file.txt")])
+    uploader.upload(
+        [
+            Path("../test-data/ENA_TEST2.R1.fastq.gz"),
+            Path("./tests/fixtures/not_a_json_file.txt"),
+        ]
+    )