SACGF/variantgrid_shariant#167 changes to wording, include plain text…

… conditions
SACGF · Jul 12, 2024 · cd8038a · cd8038a
1 parent 132d6c4
commit cd8038a
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Showing 2 changed files with 16 additions and 12 deletions.
diff --git a/classification/templates/classification/classification_export.html b/classification/templates/classification/classification_export.html
@@ -509,9 +509,9 @@
                 <div class="form-check">
                     <label class="form-check-label">
                         <input id="vcf_target_system_emedgene" type="radio" name="vcf_target_system" value="emedgene" class="form-check-input" />
-                        Illumina
+                        Emedgene
                     </label>
-                    <div class="text-info">For Illumina's Emedgene system. In case of conflicting classification values the most pathogenic will be provided.<br/>Risk Factor &amp; Drug Response will be given the same priority as VUS.</div>
+                    <div class="text-info">For Illumina's Emedgene system. In case of conflicting classification values, the most pathogenic will be provided.<br/>Risk Factor &amp; Drug Response will be given the same priority as VUS.</div>
                 </div>
                 <div class="form-check">
                     <label class="form-check-label">
@@ -525,7 +525,7 @@
                         <input checked="checked" id="vcf_target_system_generic" type="radio" name="vcf_target_system" value="generic" class="form-check-input" />
                         Generic
                     </label>
-                    <div class="text-info">Generic provides the most information, but not formatted for any specific system.</div>
+                    <div class="text-info">VCF not formatted for any specific system.</div>
                 </div>
             {% endlabelled %}
         </div>

diff --git a/classification/views/exports/classification_export_formatter_vcf.py b/classification/views/exports/classification_export_formatter_vcf.py
@@ -43,7 +43,7 @@ def from_request(request: HttpRequest) -> 'FormatDetailsVCF':
         return FormatDetailsVCF(target_system=target_system)
 
 
-ALLELE_ORIGIN_BUCKET_TO_LABEL = {
+EMEDGENE_ALLELE_ORIGIN_BUCKET_TO_LABEL = {
     AlleleOriginBucket.SOMATIC: "somatic",
     AlleleOriginBucket.GERMLINE: "germline",
     AlleleOriginBucket.UNKNOWN: "allele_origin_unknown"
@@ -109,7 +109,7 @@ def link(self):
     @export_vcf_info_cell(
         header_id="labs",
         header_type=VCFHeaderType.String,
-        description="Allele origin bucket, values will be 1 or more of: somatic, germline, allele_origin_unknown",
+        description="Allele origin bucket, values will be 1 or more of: somatic, germline, unknown",
         categories={"system": {VCFTargetSystem.GENERIC, VCFTargetSystem.VARSEQ}})
     def lab_names(self):
         all_labs = sorted({cm.classification.lab for cm in self.allele_data.cms})
@@ -164,17 +164,21 @@ def unique_values(self, evidence_key: str, raw: bool = False):
         header_id="condition_terms",
         number=VCFHeaderNumberSpecial.UNBOUND,
         header_type=VCFHeaderType.String,
-        description="All unique conditions this variant is being curated against, only provides values that could be matched to exact ontology terms",
+        description="All unique conditions this variant is being curated against, provides standard terms where possible, otherwise plain text",
         categories={"system": {VCFTargetSystem.GENERIC, VCFTargetSystem.VARSEQ}}
     )
     def condition_terms(self):
         all_terms: set[OntologyTerm] = set()
+        all_plain_text: set[str] = set()
         for cm in self.allele_data.cms:
             if cr := cm.classification.condition_resolution_obj:
-                all_terms.update(cr.terms)
-        if all_terms:
-            sorted_terms = sorted(all_terms)
-            return [f"{t.id} {t.name}" for t in sorted_terms]
+                if terms := cr.terms:
+                    all_terms.update(terms)
+                elif plain := cr.plain_text:
+                    all_plain_text.add(plain)
+            elif condition := cm.get(SpecialEKeys.CONDITION):
+                all_plain_text.add(condition)
+        return [f"{t.id} {t.name}" for t in sorted(all_terms)] + list(sorted(all_plain_text))
 
     @export_vcf_info_cell(
         header_id="classification",
@@ -236,7 +240,7 @@ def lab_count(self):
         header_id="discordance_status",
         number=VCFHeaderNumberSpecial.UNBOUND,
         header_type=VCFHeaderType.String,
-        description="If present, describes the discordance status of allele ongoing (yet to be resolved), continued (parties could not resolve), pending (parties have agreed to change classifications, waiting on data updates), if absent, the allele is not in discordance",
+        description="If present, describes the discordance status of allele. Possible values are: ongoing (yet to be resolved), continued (parties could not resolve), pending (parties have agreed to change classifications, waiting on data updates), if absent, the allele is not in discordance",
         categories={"system": {VCFTargetSystem.GENERIC, VCFTargetSystem.VARSEQ}}
     )
     def discordance_status(self):
@@ -259,7 +263,7 @@ def category(self):
         parts.append(f"labs:{self.lab_count()}")
 
         if allele_origins := self.allele_data.cms_allele_origins:
-            for allele_origin in sorted(ALLELE_ORIGIN_BUCKET_TO_LABEL.get(ao) for ao in allele_origins):
+            for allele_origin in sorted(EMEDGENE_ALLELE_ORIGIN_BUCKET_TO_LABEL.get(ao) for ao in allele_origins):
                 parts.append(allele_origin)
         parts += self.unique_values(SpecialEKeys.CLINICAL_SIGNIFICANCE)
         parts += self.unique_values(SpecialEKeys.SOMATIC_CLINICAL_SIGNIFICANCE)