HGVS Resolution Tool: include version numbers, format message vs error

SACGF · Aug 22, 2023 · 1f69195 · 1f69195
1 parent d25d8ea
commit 1f69195
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 7 deletions.
diff --git a/classification/templates/classification/hgvs_resolution_tool.html b/classification/templates/classification/hgvs_resolution_tool.html
@@ -3,6 +3,7 @@
 {% load static %}
 {% load classification_tags %}
 {% load js_tags %}
+{% load ui_utils %}
 {% load compress %}
 {% load ui_help %}
 {% load ui_menu_bars %}
@@ -49,7 +50,13 @@ <h3>HGVS Resolution Tool</h3>
                             <td>{{ output.variant_coordinate|dash_if_empty }}</td>
                             <td>{{ output.transcript_version|dash_if_empty }}</td>
                             <td>{% c_hgvs output.hgvs %}</td>
-                            <td>{{ output.error|default_if_none:"" }}</td>
+                            <td>
+                                {% if output.is_error %}
+                                    {{ 'E' | severity_icon }} {{ output.message }}
+                                {% elif output.message %}
+                                    <span class="text-secondary">{{ output.message }}</span>
+                                {% endif %}
+                            </td>
                         </tr>
                     {% endfor %}
                 </tbody>

diff --git a/classification/views/views_hgvs_resolution_tool.py b/classification/views/views_hgvs_resolution_tool.py
@@ -29,13 +29,17 @@ class MatcherOutput:
     variant_coordinate: Optional[VariantCoordinate] = None
     transcript_version: Optional[TranscriptParts] = None
     hgvs: Optional[str] = None
-    error: Optional[str] = None
+    message: Optional[str] = None
 
     @property
     def explicit_variant_coordinate(self):
         if vc := self.variant_coordinate:
             return vc.explicit_reference()
 
+    @property
+    def is_error(self):
+        return not self.hgvs
+
 
 class MatcherOutputs:
 
@@ -91,13 +95,12 @@ def hgvs_resolution_tool(request: HttpRequest):
                     output.transcript_version = tv.as_parts
                 if v := resolved_variant.variant:
                     output.variant_coordinate = v.coordinate
-            output.error = iai.message
+            output.message = iai.message
 
-        use_matchers = [(HGVSConverterType.PYHGVS, "pyhgvs"), (HGVSConverterType.BIOCOMMONS_HGVS, "biocommons")]
-        for matcher_id, matcher_name in use_matchers:
+        for matcher_id in [HGVSConverterType.PYHGVS, HGVSConverterType.BIOCOMMONS_HGVS]:
             matcher = HGVSMatcher(genome_build, hgvs_converter_type=matcher_id)
 
-            output = MatcherOutput(matcher_name=matcher_name)
+            output = MatcherOutput(matcher_name=matcher.hgvs_converter.description())
             all_output.append(output)
 
             stage = "Basic Parsing"
@@ -118,7 +121,7 @@ def hgvs_resolution_tool(request: HttpRequest):
                         output.hgvs = variant_details.format()
 
             except Exception as ex:
-                output.error = stage + ": " + str(ex)
+                output.message = stage + ": " + str(ex)
 
     return render(request, "classification/hgvs_resolution_tool.html", context)