Debugging session biosamples ena

mars-cli/mars_cli.py

@@ -246,39 +246,18 @@ def submit(
 
     data_file_paths = [f.name for f in data_files] if file_transfer else []
 
-    try:
-        submission(
-            credential_service_name,
-            username_credentials,
-            credentials_file,
-            isa_json_file.name,
-            target_repositories,
-            investigation_is_root,
-            urls_dict,
-            file_transfer,
-            output,
-            data_file_paths,
-        )
-    except requests.RequestException as err:
-        tb = sys.exc_info()[2]  # Traceback value
-        print_and_log(
-            f"Request to repository could not be made.\n{err.with_traceback(tb)}",
-            level="error",
-        )
-
-    except ValidationError as err:
-        tb = sys.exc_info()[2]  # Traceback value
-        print_and_log(
-            f"A validation error occurred while reading the ISA JSON. Please correct the following mistakes:\n{err.with_traceback(tb)}",
-            level="error",
-        )
-
-    except Exception as err:
-        tb = sys.exc_info()[2]  # Traceback value
-        print_and_log(
-            f"Unexpected error occurred during submission.\n{err.with_traceback(tb)}",
-            level="error",
-        )
+    submission(
+        credential_service_name,
+        username_credentials,
+        credentials_file,
+        isa_json_file.name,
+        target_repositories,
+        investigation_is_root,
+        urls_dict,
+        file_transfer,
+        output,
+        data_file_paths,
+    )
 
 
 @cli.command()

mars-cli/mars_lib/isa_json.py

@@ -365,44 +365,58 @@ def update_isa_json(isa_json: IsaJson, repo_response: RepositoryResponse) -> Isa
     investigation = isa_json.investigation
     for accession in repo_response.accessions:
 
-        has_assay_in_path = [p for p in accession.path if p.key == "assays"]
-        target_level = "assay" if len(has_assay_in_path) > 0 else "study"
-        material_type_path = next(
-            p
-            for p in accession.path
-            if p.key in ["sources", "samples", "otherMaterials"]
+        has_assay_in_path = len([p for p in accession.path if p.key == "assays"]) > 0
+        has_materials_in_path = (
+            len([p for p in accession.path if p.key == "materials"]) > 0
         )
+        target_level = "assay" if has_assay_in_path else "study"
 
         study_filter = get_filter_for_accession_key(accession, "studies")
         if not study_filter:
             raise ValueError(f"Study filter is not present in {accession.path}.")
 
-        updated_node = apply_filter(study_filter, investigation.studies)
+        if has_materials_in_path:
+            material_type_path = next(
+                p
+                for p in accession.path
+                if p.key in ["sources", "samples", "otherMaterials"]
+            )
 
-        if target_level == "assay":
-            assay_filter = get_filter_for_accession_key(accession, "assays")
-            if not assay_filter:
-                raise ValueError(f"Assay filter is not present in {accession.path}.")
+            updated_node = apply_filter(study_filter, investigation.studies)
 
-            updated_node = apply_filter(assay_filter, updated_node.assays)
+            if target_level == "assay":
+                assay_filter = get_filter_for_accession_key(accession, "assays")
+                if not assay_filter:
+                    raise ValueError(
+                        f"Assay filter is not present in {accession.path}."
+                    )
 
-        if not updated_node:
-            raise ValueError(f"Node not found for {accession.value}.")
-        if not accession_characteristic_category_present(updated_node):
-            (accession_id, category) = create_accession_characteristic_category(
-                updated_node
-            )
+                updated_node = apply_filter(assay_filter, updated_node.assays)
+
+            if not updated_node:
+                raise ValueError(f"Node not found for {accession.value}.")
+            if not accession_characteristic_category_present(updated_node):
+                (accession_id, category) = create_accession_characteristic_category(
+                    updated_node
+                )
+            else:
+                (accession_id, category) = fetch_existing_characteristic_category(
+                    updated_node
+                )
+
+            if not accession_characteristic_present(updated_node, material_type_path):
+                create_accession_characteristic(
+                    updated_node, material_type_path, category, accession_id
+                )
+
+            add_accession_to_node(updated_node, accession.value, material_type_path)
         else:
-            (accession_id, category) = fetch_existing_characteristic_category(
-                updated_node
-            )
+            updated_study = apply_filter(study_filter, investigation.studies)
 
-        if not accession_characteristic_present(updated_node, material_type_path):
-            create_accession_characteristic(
-                updated_node, material_type_path, category, accession_id
+            study_accession_comment: Comment = Comment(
+                name="accession", value=accession.value
             )
-
-        add_accession_to_node(updated_node, accession.value, material_type_path)
+            updated_study.comments.append(study_accession_comment)
 
     isa_json.investigation = investigation
     return isa_json

mars-cli/mars_lib/submit.py

@@ -118,6 +118,7 @@ def submission(
                 submission_url=urls["ENA"]["DATA-SUBMISSION"],
                 file_transfer=file_transfer,
             )
+        print_and_log(f"Start submitting to {TargetRepository.ENA}.", level="debug")
 
         # Step 2 : submit isa-json to ena
         ena_result = submit_to_ena(
@@ -128,8 +129,14 @@ def submission(
         print_and_log(
             f"Submission to {TargetRepository.ENA} was successful. Result:\n{ena_result.json()}"
         )
-        # Update `isa_json`, based on the receipt returned
-        ena_mars_receipt = RepositoryResponse.from_json(str(ena_result.content))
+
+        print_and_log(
+            f"Update ISA-JSON based on receipt from {TargetRepository.ENA}.",
+            level="debug",
+        )
+        ena_mars_receipt = RepositoryResponse.model_validate(
+            json.loads(ena_result.content)
+        )
         isa_json = update_isa_json(isa_json, ena_mars_receipt)
         if DEBUG:
             save_step_to_file(time_stamp, "2_after_ena", isa_json)

test-data/biosamples-input-isa.json

@@ -152,7 +152,7 @@
           {
             "@id": "#characteristic_category/collection_date_323",
             "characteristicType": {
-              "annotationValue": "collection_date",
+              "annotationValue": "collection date",
               "termAccession": "",
               "termSource": ""
             }
@@ -853,7 +853,7 @@
             "dataFiles": [
               {
                 "@id": "#data/334",
-                "name": "RD file 1b",
+                "name": "ENA_TEST2.R2.fastq.gz",
                 "type": "Raw Data File",
                 "comments": [
                   {