Merge pull request #102 from elixir-europe/101-cli-should-handle-errors-in-any-case

Raises an error if the MARS receipt contains errors

Author: kdp-cloud

mars-cli/mars_lib/authentication.py

@@ -24,7 +24,7 @@ def is_valid_provider(cls, provider: str):
 
 
 def load_credentials(
-    credentials_file: Union[io.TextIOWrapper, str]
+    credentials_file: Union[io.TextIOWrapper, str],
 ) -> dict[str, dict[str, str]]:
     """
     Validate the credentials.

mars-cli/mars_lib/isa_json.py

@@ -304,7 +304,7 @@ def add_accession_to_data_file_node(node: DataFile, accession_number: str) -> No
 
 
 def create_accession_characteristic_category(
-    node: Union[Study, Assay]
+    node: Union[Study, Assay],
 ) -> Tuple[str, MaterialAttribute]:
     """
     creates a new characteristic category for the accession number.
@@ -348,7 +348,7 @@ def fetch_existing_accession_data_file_comment(node: DataFile) -> Comment:
 
 
 def fetch_existing_characteristic_category(
-    node: Union[Study, Assay]
+    node: Union[Study, Assay],
 ) -> Tuple[str, MaterialAttribute]:
     """
     Fetches the existing characteristic category for the accession number.

mars-cli/mars_lib/submit.py

@@ -230,17 +230,17 @@ def submit_to_biosamples(
         ).model_dump(by_alias=True, exclude_none=True),
     )
 
-    if result.status_code != 200:
-        body = (
-            result.request.body.decode()
-            if isinstance(result.request.body, bytes)
-            else result.request.body or ""
-        )
-        raise requests.HTTPError(
-            f"Request towards BioSamples failed!\nRequest:\nMethod:{result.request.method}\nStatus:{result.status_code}\nURL:{result.request.url}\nHeaders:{result.request.headers}\nBody:{body}"
-        )
+    if result.status_code == 200 and not result.json().get("errors", []):
+        return result
 
-    return result
+    body = (
+        result.request.body.decode()
+        if isinstance(result.request.body, bytes)
+        else result.request.body or ""
+    )
+    raise requests.HTTPError(
+        f"Request towards BioSamples failed!\nRequest:\nMethod:{result.request.method}\nStatus:{result.status_code}\nURL:{result.request.url}\nHeaders:{result.request.headers}\nBody:{body}"
+    )
 
 
 def upload_to_metabolights(
@@ -282,6 +282,14 @@ def upload_to_metabolights(
             timeout=120,
         )
         submission_response.raise_for_status()
+        if submission_response.json().get("errors", []):
+            response_body = submission_response.request.body
+            if isinstance(response_body, bytes):
+                response_body = response_body.decode("utf-8")
+            raise requests.HTTPError(
+                f"Request towards MetaboLights failed!\nRequest:\nMethod:{submission_response.request.method}\nStatus:{submission_response.status_code}\nURL:{submission_response.request.url}\nHeaders:{submission_response.request.headers}\nBody:{response_body}"
+            )
+
         result = submission_response.json()
     except Exception as exc:
         raise exc
@@ -368,17 +376,17 @@ def submit_to_ena(
         ).model_dump(by_alias=True, exclude_none=True),
     )
 
-    if result.status_code != 200:
-        body = (
-            result.request.body.decode()
-            if isinstance(result.request.body, bytes)
-            else result.request.body or ""
-        )
-        raise requests.HTTPError(
-            f"Request towards ENA failed!\nRequest:\nMethod:{result.request.method}\nStatus:{result.status_code}\nURL:{submission_url}\nParams: ['webinUserName': {params.get('webinUserName')}, 'webinPassword': ****]\nHeaders:{result.request.headers}\nBody:{body}"
-        )
+    if result.status_code == 200 and not result.json().get("errors", []):
+        return result
 
-    return result
+    body = (
+        result.request.body.decode()
+        if isinstance(result.request.body, bytes)
+        else result.request.body or ""
+    )
+    raise requests.HTTPError(
+        f"Request towards ENA failed!\nRequest:\nMethod:{result.request.method}\nStatus:{result.status_code}\nURL:{submission_url}\nParams: ['webinUserName': {params.get('webinUserName')}, 'webinPassword': ****]\nHeaders:{result.request.headers}\nBody:{body}"
+    )
 
 
 def upload_to_ena(

mars-cli/setup.py

@@ -38,7 +38,7 @@ def run(self):
     extras_require={
         "test": [
             # Dependencies for testing only
-            "black",
+            "black == 25.1.*",
             "ruff",
             "pytest",
             "pytest-cov",