add links to pagetab of original study in study attributes (#251)

BioImage-Archive · Nov 28, 2024 · 1f37588 · 1f37588
1 parent b71aa74
commit 1f37588
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Showing 2 changed files with 19 additions and 1 deletion.
diff --git a/bia-ingest/bia_ingest/biostudies/v4/study.py b/bia-ingest/bia_ingest/biostudies/v4/study.py
@@ -73,6 +73,16 @@ def get_study(
         }
         for key, value in study_attributes.items()
     ]
+    attribute.append(
+        {
+            "provenance": semantic_models.AttributeProvenance("bia_ingest"),
+            "name": "biostudies json/pagetab entry",
+            "value": {
+                "json": f"https://www.ebi.ac.uk/biostudies/files/{submission.accno}/{submission.accno}.json",
+                "pagetab": f"https://www.ebi.ac.uk/biostudies/files/{submission.accno}/{submission.accno}.tsv",
+            },
+        }
+    )
 
     study_dict = {
         "uuid": get_study_uuid(submission),
@@ -249,7 +259,7 @@ def get_affiliation(
             for k, v, default in key_mapping
         }
 
-        result_summary_for_accession_if =  result_summary[submission.accno]
+        result_summary_for_accession_if = result_summary[submission.accno]
 
         affiliation = dict_to_api_model(
             model_dict, semantic_models.Affiliation, result_summary[submission.accno]

diff --git a/bia-ingest/test/mock_objects/mock_study.py b/bia-ingest/test/mock_objects/mock_study.py
@@ -171,6 +171,14 @@ def get_study() -> bia_data_model.Study:
                     "Extra attribute 2": "Extra attribute 2 to test semantic_model.study.attribute",
                 },
             },
+            {
+                "provenance": semantic_models.AttributeProvenance("bia_ingest"),
+                "name": "biostudies json/pagetab entry",
+                "value": {
+                    "json": f"https://www.ebi.ac.uk/biostudies/files/{accession_id}/{accession_id}.json",
+                    "pagetab": f"https://www.ebi.ac.uk/biostudies/files/{accession_id}/{accession_id}.tsv",
+                },
+            },
         ],
         "related_publication": [],
         "author": [c.model_dump() for c in contributor],