Merge pull request #65 from lbouri/fix_ena_pipeline

fix: process file upload before submitting isa-json to ena

mars-cli/mars_cli.py

@@ -188,12 +188,6 @@ def cli(ctx, development):
     multiple=True,
     help="Path of files to upload",
 )
-# @click.option(
-#     "--data-submit-to-ena",
-#     type=click.BOOL,
-#     default=False,
-#     help="Submit data files to ENA.",
-# )
 @click.option(
     "--submit-to-metabolights",
     type=click.BOOL,

mars-cli/mars_lib/submit.py

@@ -59,18 +59,16 @@ def submission(
         f"ISA JSON with investigation '{isa_json.investigation.title}' is valid."
     )
 
-    if (
-        TargetRepository.ENA in target_repositories
-        and data_file_paths
-        and file_transfer
-    ):
-        upload_to_ena(
-            file_paths=data_file_paths,
-            user_credentials=user_credentials,
-            submission_url=urls["ENA"]["DATA-SUBMISSION"],
-            file_transfer=file_transfer,
-        )
-    elif TargetRepository.ENA in target_repositories:
+    if TargetRepository.ENA in target_repositories:
+        # Step 1 : upload data if file paths are provided
+        if data_file_paths and file_transfer:
+            upload_to_ena(
+                file_paths=data_file_paths,
+                user_credentials=user_credentials,
+                submission_url=urls["ENA"]["DATA-SUBMISSION"],
+                file_transfer=file_transfer,
+            )
+        # Step 2 : submit isa-json to ena
         # TODO: Filter out other assays
         ena_result = submit_to_ena(
             isa_json=isa_json,