From 6b1db4eeaff75bd46c43945f6eeb7599747fc9f2 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, 19 insertions(+), 4 deletions(-)

diff --git a/HISTORY.rst b/HISTORY.rst
index 96b20f6ab..b2510d862 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -57,6 +57,7 @@ End-User Summary
 - Improving Clinvar filter performance (#635).
 - Warning in the case of truncated displayed results (#641).
 - Improving Clinvar record aggregation (#640).
+- Fixing ClinVar submission XML generation (#677).
 
 Full Change List
 ================
@@ -112,6 +113,7 @@ Full Change List
 - Warning in the case of truncated displayed results (#641).
 - Improving Clinvar record aggregation (#640).
 - Fixing Docker builds (#660).
+- Fixing ClinVar submission XML generation (#677).
 
 ------
 v1.2.0
diff --git a/clinvar_export/clinvar_xml.py b/clinvar_export/clinvar_xml.py
index edf8aa146..f965ebbaa 100644
--- a/clinvar_export/clinvar_xml.py
+++ b/clinvar_export/clinvar_xml.py
@@ -260,6 +260,9 @@ def build_xref(term_id):
                                     "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 7da164a38..1b915d1ac 100644
--- a/clinvar_export/views_ajax.py
+++ b/clinvar_export/views_ajax.py
@@ -254,10 +254,20 @@ 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):