Staging area validator incorrectly fails on supplementary LungMAP file

[hannes-ucsc]

… thinking it's a supplementary CGM, just because it has a submitter ID.

There should be an additional condition on the content description as per the DCP/2 specification. Azul currently uses "matrix" in content_description but that's not strictly compliant with the specification.

[dsotirho-ucsc]

Index: hca/staging_area_validator.py
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/hca/staging_area_validator.py b/hca/staging_area_validator.py
--- a/hca/staging_area_validator.py	(revision a431f127ab30280f7b935b6c65d9ca452b3b43eb)
+++ b/hca/staging_area_validator.py	(revision bef07f6f008c1a42ea09246017c8aa37f3023d32)
@@ -218,17 +218,19 @@
             if metadata_type.endswith("_file"):
                 metadata_file["data_file_name"] = file_json["file_core"]["file_name"]
                 metadata_file["found_data_file"] = False
-            if metadata_type == "supplementary_file" and file_json.get(
-                "provenance", {}
-            ).get("submitter_id"):
-                try:
-                    self.validate_file_description(file_json.get("file_description"))
-                except Exception as e:
-                    self.file_errors[blob.name] = e
-                    metadata_file["valid_stratification"] = False
-                    log.error("Invalid file_description in %s.", blob.name)
-                else:
-                    metadata_file["valid_stratification"] = True
+            if metadata_type == "supplementary_file":
+                submitter_id = file_json.get("provenance", {}).get("submitter_id")
+                content_description = file_json["file_core"].get('content_description', {})
+                ontology_label = content_description.get("ontology_label")
+                if submitter_id is not None and ontology_label == 'Matrix':
+                    try:
+                        self.validate_file_description(file_json.get("file_description"))
+                    except Exception as e:
+                        self.file_errors[blob.name] = e
+                        metadata_file["valid_stratification"] = False
+                        log.error("Invalid file_description in %s.", blob.name)
+                    else:
+                        metadata_file["valid_stratification"] = True
         else:
             self.extra_files.append(blob.name)
 

[hannes-ucsc]

More or less, but please file a PR.

[achave11-ucsc]

@hannes-ucsc: "The PR has been created. I consider our work done."