Add Study accession to the target repository's assay

Author: kdp-cloud

mars-cli/mars_lib/isa_json.py

@@ -74,10 +74,10 @@ def detect_target_repo_comment(comments: List[Comment]) -> Comment:
 
 def is_assay_for_target_repo(assay: Assay, target_repo: str) -> bool:
     """
-    Defines whether the assays is meant for the target repository.
+    Defines whether the assays are meant for the target repository.
 
     Args:
-        assay_dict (Dict[str, str]): Dictionary representation of an assay.
+        assay (Assay): Assay model.
         target_repo (TargetRepository): Target repository as a constant.
 
     Returns:
@@ -484,6 +484,7 @@ def update_isa_json(isa_json: IsaJson, repo_response: RepositoryResponse) -> Isa
 
             add_accession_to_data_file_node(updated_node, accession.value)
         else:
+            # Add study accession to study comments
             updated_study = apply_filter(study_filter, investigation.studies)
 
             study_accession_comment: Comment = Comment(
@@ -492,6 +493,20 @@ def update_isa_json(isa_json: IsaJson, repo_response: RepositoryResponse) -> Isa
             )
             updated_study.comments.append(study_accession_comment)
 
+            # Add study accession to assay comments
+            updated_assay = next(
+                filter(
+                    lambda assay: is_assay_for_target_repo(assay, target_repository),
+                    updated_study.assays,
+                ),
+                None,
+            )
+            if updated_assay:
+                assay_accession_comment: Comment = Comment(
+                    name=f"{target_repository}_{target_level}_accession",
+                    value=accession.value,
+                )
+                updated_assay.comments.append(assay_accession_comment)
     isa_json.investigation = investigation
     return isa_json
 

mars-cli/tests/test_isa_json.py

@@ -6,6 +6,7 @@
     load_isa_json,
     update_isa_json,
     map_data_files_to_repositories,
+    is_assay_for_target_repo,
 )
 from mars_lib.target_repo import TargetRepository, TARGET_REPO_KEY
 import pytest
@@ -244,7 +245,7 @@ def test_update_study_materials_with_accession_categories():
     )
 
 
-def test_update_study_with_ena_study_accession_comment():
+def test_update_study_and_assay_with_ena_study_accession_comment():
     json_path = "tests/fixtures/isa_jsons/1_after_biosamples.json"
     isa_json = load_isa_json(json_path, False)
     response_file_path = "tests/fixtures/mars_receipts/ena_success_response.json"
@@ -258,6 +259,19 @@ def test_update_study_with_ena_study_accession_comment():
     )
     assert next(accession_comment).value == ena_study_accession_number
 
+    ena_assay = next(
+        filter(
+            lambda assay: is_assay_for_target_repo(assay, "ena"),
+            updated_isa_json.investigation.studies[0].assays,
+        ),
+        None,
+    )
+    assay_comments = ena_assay.comments
+    accession_comment = filter(
+        lambda x: x.name == "ena_study_accession", assay_comments
+    )
+    assert next(accession_comment).value == ena_study_accession_number
+
 
 def test_update_datafile_comment_with_accession_comment_present():
     json_path = "tests/fixtures/isa_jsons/1_after_biosamples.json"