Access enum's value field

elixir-europe · Nov 8, 2024 · 9ee367d · 9ee367d
1 parent 5ea2bd8
commit 9ee367d
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Showing 4 changed files with 30 additions and 26 deletions.
diff --git a/mars-cli/mars_cli.py b/mars-cli/mars_cli.py
@@ -263,13 +263,13 @@ def submit(
     target_repositories = []
 
     if submit_to_biosamples:
-        target_repositories.append(TargetRepository.BIOSAMPLES)
+        target_repositories.append(TargetRepository.BIOSAMPLES.value)
 
     if submit_to_ena:
-        target_repositories.append(TargetRepository.ENA)
+        target_repositories.append(TargetRepository.ENA.value)
 
     if submit_to_metabolights:
-        target_repositories.append(TargetRepository.METABOLIGHTS)
+        target_repositories.append(TargetRepository.METABOLIGHTS.value)
 
     print_and_log(
         f"Starting submission of the ISA JSON to the target repositories: {', '.join(target_repositories)}."

diff --git a/mars-cli/mars_lib/isa_json.py b/mars-cli/mars_lib/isa_json.py
@@ -40,7 +40,7 @@ def reduce_isa_json_for_target_repo(
     new_studies = []
     studies = filtered_isa_json.investigation.studies
     for study in studies:
-        if target_repo == TargetRepository.BIOSAMPLES:
+        if target_repo == TargetRepository.BIOSAMPLES.value:
             filtered_assays = []
         else:
             assays = study.assays

diff --git a/mars-cli/mars_lib/submit.py b/mars-cli/mars_lib/submit.py
@@ -97,7 +97,7 @@ def submission(
     ):
         raise ValueError("No target repository selected.")
 
-    if TargetRepository.BIOSAMPLES in target_repositories:
+    if TargetRepository.BIOSAMPLES.value in target_repositories:
         # Submit to Biosamples
         biosamples_result = submit_to_biosamples(
             isa_json=isa_json,
@@ -106,7 +106,7 @@ def submission(
             webin_token_url=urls["WEBIN"]["TOKEN"],
         )
         print_and_log(
-            f"Submission to {TargetRepository.BIOSAMPLES} was successful. Result:\n{biosamples_result.json()}",
+            f"Submission to {TargetRepository.BIOSAMPLES.value} was successful. Result:\n{biosamples_result.json()}",
             level="info",
         )
         # Update `isa_json`, based on the receipt returned
@@ -117,16 +117,20 @@ def submission(
         if DEBUG:
             save_step_to_file(time_stamp, "1_after_biosamples", isa_json)
 
-    if TargetRepository.ENA in target_repositories:
+    if TargetRepository.ENA.value in target_repositories:
         # Step 1 : upload data if file paths are provided
         if data_file_paths and file_transfer:
             upload_to_ena(
-                file_paths=[Path(df) for df in data_file_map[TargetRepository.ENA]],
+                file_paths=[
+                    Path(df) for df in data_file_map[TargetRepository.ENA.value]
+                ],
                 user_credentials=user_credentials,
                 submission_url=urls["ENA"]["DATA-SUBMISSION"],
                 file_transfer=file_transfer,
             )
-        print_and_log(f"Start submitting to {TargetRepository.ENA}.", level="debug")
+        print_and_log(
+            f"Start submitting to {TargetRepository.ENA.value}.", level="debug"
+        )
 
         # Step 2 : submit isa-json to ena
         ena_result = submit_to_ena(
@@ -135,11 +139,11 @@ def submission(
             submission_url=urls["ENA"]["SUBMISSION"],
         )
         print_and_log(
-            f"Submission to {TargetRepository.ENA} was successful. Result:\n{ena_result.json()}"
+            f"Submission to {TargetRepository.ENA.value} was successful. Result:\n{ena_result.json()}"
         )
 
         print_and_log(
-            f"Update ISA-JSON based on receipt from {TargetRepository.ENA}.",
+            f"Update ISA-JSON based on receipt from {TargetRepository.ENA.value}.",
             level="debug",
         )
         ena_mars_receipt = RepositoryResponse.model_validate(
@@ -149,10 +153,10 @@ def submission(
         if DEBUG:
             save_step_to_file(time_stamp, "2_after_ena", isa_json)
 
-    if TargetRepository.METABOLIGHTS in target_repositories:
+    if TargetRepository.METABOLIGHTS.value in target_repositories:
         # Submit to MetaboLights
         metabolights_result = upload_to_metabolights(
-            file_paths=data_file_map[TargetRepository.ENA],
+            file_paths=data_file_map[TargetRepository.METABOLIGHTS.value],
             file_transfer=file_transfer,
             isa_json=isa_json,
             metabolights_credentials=user_credentials,
@@ -161,7 +165,7 @@ def submission(
         )
         metabolights_receipt_obj = metabolights_result.json()
         print_and_log(
-            f"Submission to {TargetRepository.METABOLIGHTS} was successful. Result:\n{metabolights_receipt_obj}",
+            f"Submission to {TargetRepository.METABOLIGHTS.value} was successful. Result:\n{metabolights_receipt_obj}",
             level="info",
         )
         metabolights_receipt = RepositoryResponse.model_validate(
@@ -177,11 +181,11 @@ def submission(
         if DEBUG:
             save_step_to_file(time_stamp, "3_after_metabolights", isa_json)
 
-    if TargetRepository.EVA in target_repositories:
+    if TargetRepository.EVA.value in target_repositories:
         # Submit to EVA
         # TODO: Filter out other assays
         print_and_log(
-            f"Submission to {TargetRepository.EVA} was successful.", level="info"
+            f"Submission to {TargetRepository.EVA.value} was successful.", level="info"
         )
         # TODO: Update `isa_json`, based on the receipt returned
 
@@ -207,7 +211,7 @@ def submit_to_biosamples(
         headers=headers,
         params=params,
         json=reduce_isa_json_for_target_repo(
-            isa_json, TargetRepository.BIOSAMPLES
+            isa_json, TargetRepository.BIOSAMPLES.value
         ).model_dump(by_alias=True, exclude_none=True),
     )
 
@@ -344,9 +348,9 @@ def submit_to_ena(
         submission_url,
         headers=headers,
         params=params,
-        json=reduce_isa_json_for_target_repo(isa_json, TargetRepository.ENA).model_dump(
-            by_alias=True, exclude_none=True
-        ),
+        json=reduce_isa_json_for_target_repo(
+            isa_json, TargetRepository.ENA.value
+        ).model_dump(by_alias=True, exclude_none=True),
     )
 
     if result.status_code != 200:

diff --git a/mars-cli/tests/test_isa_json.py b/mars-cli/tests/test_isa_json.py
@@ -46,7 +46,7 @@ def test_reduce_isa_json_for_target_repo():
     )
 
     filtered_isa_json = reduce_isa_json_for_target_repo(
-        good_isa_json, TargetRepository.ENA
+        good_isa_json, TargetRepository.ENA.value
     )
 
     good_isa_json_study = good_isa_json.investigation.studies[0]
@@ -63,7 +63,7 @@ def test_reduce_isa_json_for_biosamples():
     )
 
     filtered_isa_json = reduce_isa_json_for_target_repo(
-        good_isa_json, TargetRepository.BIOSAMPLES
+        good_isa_json, TargetRepository.BIOSAMPLES.value
     )
 
     assert len(filtered_isa_json.investigation.studies[0].assays) == 0
@@ -110,7 +110,7 @@ def test_target_repo_comment_validator():
             {
                 "@id": "comment_001",
                 "name": f"{TARGET_REPO_KEY}",
-                "value": TargetRepository.ENA,
+                "value": TargetRepository.ENA.value,
             }
         ],
     }
@@ -134,12 +134,12 @@ def test_target_repo_comment_validator():
             {
                 "@id": "comment_003",
                 "name": f"{TARGET_REPO_KEY}",
-                "value": TargetRepository.ENA,
+                "value": TargetRepository.ENA.value,
             },
             {
                 "@id": "comment_004",
                 "name": f"{TARGET_REPO_KEY}",
-                "value": TargetRepository.METABOLIGHTS,
+                "value": TargetRepository.METABOLIGHTS.value,
             },
         ],
     }
@@ -308,7 +308,7 @@ def test_map_data_files_to_repositories():
 
     with pytest.raises(
         ValueError,
-        match=rf"Assay for repository '{TargetRepository.ARRAYEXPRESS}' has encountered",
+        match=rf"Assay for repository '{TargetRepository.ARRAYEXPRESS.value}' has encountered",
     ):
         map_data_files_to_repositories(not_enough_files, isa_json)