From c150b5e87d7124538ba0ae8b7419725ce20e9b66 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Tue, 20 Sep 2022 10:57:33 +0200
Subject: [PATCH] Fixing ClinVar submission XML generation (#677)

Closes: #677
Related-Issue: #677
Projected-Results-Impact: none
---
 HISTORY.rst                   |  2 ++
 clinvar_export/clinvar_xml.py |  3 ++-
 clinvar_export/views_ajax.py  | 18 ++++++++++++++----
 3 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/HISTORY.rst b/HISTORY.rst
index d5d1021e5..0d817d305 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -16,6 +16,7 @@ End-User Summary
   **This will require an import of the updated Clinvar ``20210728c`` data (#296).**
 - Warning in the case of truncated displayed results (#641).
 - Improving Clinvar record aggregation (#640).
+- Fixing ClinVar submission XML generation (#677).
 
 Full Change List
 ================
@@ -28,6 +29,7 @@ Full Change List
   **This will require an import of the updated Clinvar ``20210728c`` data (#296).**
 - Improving Clinvar record aggregation (#640).
 - Fixing Docker builds (#660).
+- Fixing ClinVar submission XML generation (#677).
 
 -----------------
 v1.2.2 (anthenea)
diff --git a/clinvar_export/clinvar_xml.py b/clinvar_export/clinvar_xml.py
index 7fd07ec9d..183356095 100644
--- a/clinvar_export/clinvar_xml.py
+++ b/clinvar_export/clinvar_xml.py
@@ -223,7 +223,8 @@ def build_xref(term_id):
                                 self.em("ElementValueType", "Preferred", **{"val_type": "name"}),
                                 self.em("ElementValue", phenotype["term_name"]),
                             ),
-                            self.em("XRef", **{"db": "HP", "id": phenotype["term_id"],}),
+                            self.em("XRef", **{"db": "HP", "id": phenotype["term_id"],},),
+                            **{"ClinicalFeaturesAffectedStatus": "present",},
                         )
                         for phenotype in submission_individual.phenotypes
                     ],
diff --git a/clinvar_export/views_ajax.py b/clinvar_export/views_ajax.py
index 210291b7a..e11a5e601 100644
--- a/clinvar_export/views_ajax.py
+++ b/clinvar_export/views_ajax.py
@@ -258,10 +258,20 @@ def get(self, request, *args, **kwargs):
                 "valid": True,
             }
         else:
-            result = {
-                "valid": False,
-                "details": "\n".join(e.message for e in schema.error_log),
-            }
+            ignored_message = (
+                "Element 'Trait', attribute 'ClinicalFeaturesAffectedStatus': The attribute "
+                "'ClinicalFeaturesAffectedStatus' is not allowed."
+            )
+            filtered_es = [e for e in schema.error_log if e.message != ignored_message]
+            if filtered_es:
+                result = {
+                    "valid": False,
+                    "details": "\n".join(e.message for e in filtered_es),
+                }
+            else:
+                result = {
+                    "valid": True,
+                }
         return JsonResponse(result)
 
     def _get_schema(self, root):