ClinVarXMLRecord: Show SCV, more fixes to HGVS parsing

SACGF · Sep 1, 2023 · 1bc0e1b · 1bc0e1b
1 parent 3c66ae5
commit 1bc0e1b
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/annotation/clinvar_xml_parser.py b/annotation/clinvar_xml_parser.py
@@ -57,7 +57,7 @@ class ClinVarXmlParserOutput:
 class ClinVarXmlParser(XmlParser, ABC):
 
     RE_DATE_EXTRACTOR = re.compile("([0-9]+-[0-9]+-[0-9]+).*")
-    RE_GOOD_CHGVS = re.compile("^(N._(.+)?:c[.][0-9_a-zA-Z>]+)( .*)?$")
+    RE_GOOD_CHGVS = re.compile("^(N._(.+)?:c[.][^ ]+)( .*)?$")
     RE_ORPHA = re.compile("ORPHA([0-9]+)")
 
     @staticmethod

diff --git a/annotation/clinvar_xml_parser_via_vcv.py b/annotation/clinvar_xml_parser_via_vcv.py
@@ -7,7 +7,7 @@
 
 class ClinVarXmlParserViaVCV(ClinVarXmlParser):
 
-    PARSER_VERSION = 202  # change this whenever the parsing changes, so we know to ignore the old cache
+    PARSER_VERSION = 203  # change this whenever the parsing changes, so we know to ignore the old cache
 
     @classmethod
     def load_from_clinvar_id(cls, clinvar_variation_id: int) -> ClinVarXmlParserOutput:
@@ -115,7 +115,8 @@ def parse_variant_coordinate(self, elem):
         start = elem.get("start")
         ref = elem.get("referenceAllele")
         alt = elem.get("alternateAllele")
-        self.latest.variant_coordinate = f"{chr}:{start} {ref}>{alt} ({assembly})"
+        if chr and start and ref and alt:
+            self.latest.variant_coordinate = f"{chr}:{start} {ref}>{alt} ({assembly})"
 
 
     @parser_path(

diff --git a/annotation/templates/annotation/clinvar_records_detail.html b/annotation/templates/annotation/clinvar_records_detail.html
@@ -37,7 +37,9 @@
         <tbody>
             {% for record in records %}
                 <tr>
-                    <td>{% clinvar_stars record.stars record.review_status %} <a class="subtle-link" href="https://www.ncbi.nlm.nih.gov/clinvar/submitters/{{ record.org_id }}">{{ record.submitter }}</a></td>
+                    <td>{% clinvar_stars record.stars record.review_status %} <a class="subtle-link" href="https://www.ncbi.nlm.nih.gov/clinvar/submitters/{{ record.org_id }}">{{ record.submitter }}</a>
+                        <br/><span class="text-secondary">{{ record.record_id }}</span>
+                    </td>
                     <td>{% if record.c_hgvs %}{% c_hgvs record.c_hgvs %}{% elif record.variant_coordinate %}{{ record.variant_coordinate }}{% else %}<span class="no-value">-</span>{% endif %}</td>
                     <td class="cs-{{ record.clinical_significance|lower }} text-center">{{ record.clinical_significance | ekey:"clinical_significance" }}</td>
                     <td>{% if record.condition %}{% ontology_term record.condition %}{% else %}<span class="no-value">-</span>{% endif %}</td>