Revert "Revert "feat: including sample accessions in read sample endpoint response""

app/api/v1/endpoints/projects.py

@@ -52,12 +52,13 @@ def read_projects(
         if not project.project_accession:
             project_submission = (
                 db.query(ProjectSubmission)
-                .filter(ProjectSubmission.project_id == project.id)
+                .filter(
+                    ProjectSubmission.project_id == project.id,
+                    ProjectSubmission.status == "accepted",
+                )
                 .first()
             )
-            if not project_submission:
-                raise HTTPException(status_code=404, detail="Project submission record not found")
-            else:
+            if project_submission:
                 accession = _get_project_accession(project_submission)
                 project.project_accession = accession
 
@@ -116,11 +117,14 @@ def read_project(
     # If no project accession in the project table, injects accession from project_submission table into the endpoint response (does not change db content)
     if not project.project_accession:
         project_submission = (
-            db.query(ProjectSubmission).filter(ProjectSubmission.project_id == project_id).first()
+            db.query(ProjectSubmission)
+            .filter(
+                ProjectSubmission.project_id == project.id,
+                ProjectSubmission.status == "accepted",
+            )
+            .first()
         )
-        if not project_submission:
-            raise HTTPException(status_code=404, detail="Project submission record not found")
-        else:
+        if project_submission:
             accession = _get_project_accession(project_submission)
             project.project_accession = accession
 

app/api/v1/endpoints/samples.py

@@ -100,6 +100,11 @@ def _get_genomic_data_project_id(db: Session, taxon_id: int) -> UUID:
     return project.id
 
 
+def _get_sample_accession(sample_submission: SampleSubmission) -> str:
+    if hasattr(sample_submission, "accession"):  # returning ERS
+        return sample_submission.accession
+
+
 def _load_sample_mapping() -> Dict[str, Any]:
     with open(_SAMPLE_MAPPING_PATH, "r") as f:
         return json.load(f)
@@ -794,6 +799,20 @@ def read_sample(
     sample = db.query(Sample).filter(Sample.id == sample_id).first()
     if not sample:
         raise HTTPException(status_code=404, detail="Sample not found")
+
+    if not sample.biosample_accession:
+        sample_submission = (
+            db.query(SampleSubmission)
+            .filter(
+                SampleSubmission.sample_id == sample_id,
+                SampleSubmission.status == "accepted",
+            )
+            .first()
+        )
+        if sample_submission:
+            accession = _get_sample_accession(sample_submission)
+            sample.biosample_accession = accession
+
     return sample