issue #1099 - store hgvs converter used during matching process (on t…

…op of note)

classification/migrations/0145_importedalleleinfo_hgvs_converter_version.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.2.10 on 2024-07-04 08:06
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0144_one_off_populate_historical_resolved_variant_hgvsconverter_version'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='importedalleleinfo',
+            name='hgvs_converter_version',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, to='classification.hgvsconverterversion'),
+        ),
+    ]

classification/migrations/0146_hgvsconverterversion_used_converter_type.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.10 on 2024-07-05 03:02
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0145_importedalleleinfo_hgvs_converter_version'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='hgvsconverterversion',
+            name='used_converter_type',
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

classification/migrations/0147_one_off_populate_hgvsconverterversion_used_converter_type.py

@@ -0,0 +1,54 @@
+# Generated by Django 4.2.10 on 2024-07-05 03:02
+
+from django.db import migrations
+from django.db.models import F, Q, Min
+
+from genes.hgvs import HGVSConverterType
+
+
+def _one_off_populate_hgvsconverterversion_used_converter_type(apps, schema_editor):
+    HGVSConverterVersion = apps.get_model('classification', 'HGVSConverterVersion')
+    ResolvedVariantInfo = apps.get_model('classification', 'ResolvedVariantInfo')
+    ImportedAlleleInfo = apps.get_model('classification', 'ImportedAlleleInfo')
+
+    internal_qs = HGVSConverterVersion.objects.filter(method__startswith='Internally converted')
+    internal_qs.update(used_converter_type=F("hgvs_converter_type"))
+    clingen_qs = HGVSConverterVersion.objects.filter(method__startswith='ClinGen Allele Registry')
+    clingen_qs.update(used_converter_type=HGVSConverterType.CLINGEN_ALLELE_REGISTRY.name)
+
+    for converter_type in HGVSConverterType:
+        qs = HGVSConverterVersion.objects.filter(Q(method__startswith=str(converter_type)) | Q(method__startswith=converter_type.name))
+        qs.update(used_converter_type=converter_type.name)
+
+    # Legacy ones were 'unknown tool...' - ok to have these as NULL
+
+    # We should probably remove dupes too (not including method)
+    unique_fields = ("hgvs_converter_type", "version", "used_converter_type", "code_git_hash")
+    newest_hcvs = HGVSConverterVersion.objects.values(*unique_fields).annotate(first_id=Min('id'))
+    newest_ids = set(newest_hcvs.values_list("first_id", flat=True))
+
+    # The only object that should have it now is ResolvedVariantInfo
+    for hcvs in HGVSConverterVersion.objects.filter(pk__in=newest_ids):
+        kwargs = {
+            f"c_hgvs_converter_version__{field}": getattr(hcvs, field) for field in unique_fields
+        }
+        ResolvedVariantInfo.objects.filter(**kwargs).update(c_hgvs_converter_version=hcvs)
+
+    if num := HGVSConverterVersion.objects.exclude(pk__in=newest_ids).delete():
+        print(f"Deleted {num} dupe HGVSConverterVersion objects")
+
+    # Now we need to assign all AlleleInfo to hgvs_converter_version
+    if legacy := HGVSConverterVersion.objects.filter(version__startswith='Legacy').first():
+        ImportedAlleleInfo.objects.all().update(hgvs_converter_version=legacy)
+
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0146_hgvsconverterversion_used_converter_type'),
+    ]
+
+    operations = [
+        migrations.RunPython(_one_off_populate_hgvsconverterversion_used_converter_type)
+    ]

classification/migrations/0148_alter_hgvsconverterversion_unique_together_and_more.py

@@ -0,0 +1,21 @@
+# Generated by Django 4.2.10 on 2024-07-05 06:46
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0147_one_off_populate_hgvsconverterversion_used_converter_type'),
+    ]
+
+    operations = [
+        migrations.AlterUniqueTogether(
+            name='hgvsconverterversion',
+            unique_together={('hgvs_converter_type', 'version', 'used_converter_type', 'code_git_hash')},
+        ),
+        migrations.RemoveField(
+            model_name='hgvsconverterversion',
+            name='method',
+        ),
+    ]

classification/models/classification_variant_info_models.py

@@ -52,26 +52,29 @@
 class HGVSConverterVersion(TimeStampedModel):
     hgvs_converter_type = models.TextField()  # HGVSConverterType
     version = models.TextField()
-    method = models.TextField()  # Records e.g. fall back to ClinGen
+    used_converter_type = models.TextField(blank=True, null=True)  # HGVSConverterType
     code_git_hash = models.TextField()
 
+    class Meta:
+        unique_together = ("hgvs_converter_type", "version", "used_converter_type", "code_git_hash")
+
     @property
     def converted_using_library(self) -> bool:
-        return self.method.startswith("Internally converted using library")
+        return self.hgvs_converter_type == self.used_converter_type
 
     def __str__(self) -> str:
         desc = f"{self.hgvs_converter_type} version=\"{self.version}\""
-        if not self.converted_using_library:
-            desc += f" (method={self.method})"
+        if self.used_converter_type and not self.converted_using_library:
+            desc += f" (used_converter_type={self.used_converter_type})"
         if self.code_git_hash != "not-a-real-git-hash":
             desc += f" git@{self.code_git_hash}"
         return desc
 
     @staticmethod
-    def get(hgvs_converter_type: HGVSConverterType, version: str, method: str):
+    def get(hgvs_converter_type: HGVSConverterType, version: str, used_converter_type: HGVSConverterType):
         return HGVSConverterVersion.objects.get_or_create(hgvs_converter_type=hgvs_converter_type.name,
                                                           version=version,
-                                                          method=method,
+                                                          used_converter_type=used_converter_type.name,
                                                           code_git_hash=get_cached_project_git_hash())[0]
 
 
@@ -161,13 +164,14 @@ def set_variant_and_save(self, variant: Variant) -> 'ResolvedVariantInfo':
         version = hgvs_matcher.hgvs_converter.get_version()
 
         try:
-            hgvs_variant, method = hgvs_matcher.variant_to_hgvs_variant_and_method(variant, imported_transcript)
+            hgvs_variant, used_converter_type, method = hgvs_matcher.variant_to_hgvs_variant_used_converter_type_and_method(variant, imported_transcript)
             c_hgvs = hgvs_variant.format()
             c_hgvs_obj = CHGVS(c_hgvs)
             self.c_hgvs = c_hgvs
             self.c_hgvs_compat = hgvs_variant.format(use_compat=True,
                                                      max_ref_length=settings.CLASSIFICATION_MAX_REFERENCE_LENGTH)
-            self.c_hgvs_converter_version = HGVSConverterVersion.get(hgvs_converter_type, version=version, method=method)
+            self.c_hgvs_converter_version = HGVSConverterVersion.get(hgvs_converter_type, version=version,
+                                                                     used_converter_type=used_converter_type)
             self.transcript_version = c_hgvs_obj.transcript_version_model(genome_build=genome_build)
             self.gene_symbol = GeneSymbol.objects.filter(symbol=c_hgvs_obj.gene_symbol).first()
         except Exception as exception:
@@ -373,6 +377,7 @@ class CalculatedVariantCoordinate:
     variant_coordinate: Optional[VariantCoordinate]
     genome_build: GenomeBuild
     message: str
+    hgvs_converter_version: Optional[HGVSConverterVersion]
 
     @property
     def variant_coordinate_str(self) -> Optional[str]:
@@ -406,6 +411,9 @@ class ImportedAlleleInfo(TimeStampedModel):
 
     imported_g_hgvs = TextField(null=True, blank=True)
 
+    hgvs_converter_version = ForeignKey(HGVSConverterVersion, null=True, blank=True, on_delete=PROTECT)
+    """ Tool used to resolve hgvs  """
+
     imported_transcript = TextField(null=True, blank=True)
     """
     Only needed if we're using g.hgvs
@@ -680,17 +688,23 @@ def resolved_builds(self) -> list[ResolvedVariantInfo]:
     def calculate_variant_coordinate(self) -> CalculatedVariantCoordinate:
         vc: Optional[VariantCoordinate] = None
         genome_build: Optional[GenomeBuild] = None
-        message: str
+        hgvs_converter_version: Optional[HGVSConverterVersion] = None
         try:
             genome_build = self.imported_genome_build_patch_version.genome_build
             use_hgvs = self.imported_c_hgvs or self.imported_g_hgvs
             hgvs_matcher = HGVSMatcher(genome_build)
+            hgvs_converter_type = hgvs_matcher.hgvs_converter.get_hgvs_converter_type()
+            version = hgvs_matcher.hgvs_converter.get_version()
+
             vc_extra = hgvs_matcher.get_variant_coordinate_used_transcript_kind_method_and_matches_reference(use_hgvs)
             message = f"HGVS matched by \"{vc_extra.method}\""
+            hgvs_converter_version = HGVSConverterVersion.get(hgvs_converter_type, version=version,
+                                                              used_converter_type=vc_extra.used_converter_type)
             vc = vc_extra.variant_coordinate
         except Exception as ex:
             message = str(ex)
-        return CalculatedVariantCoordinate(variant_coordinate=vc, genome_build=genome_build, message=message)
+        return CalculatedVariantCoordinate(variant_coordinate=vc, genome_build=genome_build,
+                                           message=message, hgvs_converter_version=hgvs_converter_version)
 
     def update_variant_coordinate(self):
         """ returns if a valid variant_coordinate could be derived """
@@ -700,6 +714,7 @@ def update_variant_coordinate(self):
         # but it's better to do that in the validation step
         cvc = self.calculate_variant_coordinate()
         self.message = cvc.message
+        self.hgvs_converter_version = cvc.hgvs_converter_version
         self.variant_coordinate = cvc.variant_coordinate_str
         if not cvc.is_valid:
             self.status = ImportedAlleleInfoStatus.FAILED
@@ -779,6 +794,7 @@ def set_matching_failed(self, message: Optional[str] = None):
     def hard_reset_matching_info(self):
         self.status = ImportedAlleleInfoStatus.PROCESSING
         self.matched_variant = None
+        self.hgvs_converter_version = None
         self.allele = None
         for genome_build in [GenomeBuild.grch37(), GenomeBuild.grch38()]:
             self._update_variant(genome_build=genome_build, variant=None)

classification/templates/classification/imported_allele_info_detail.html

@@ -7,6 +7,9 @@
         <h4>Imported Allele Info ({{ allele_info.pk }})</h4>
     {% endif %}
 
+    {% labelled admin_only=True label="Created" value_css="text-monospace" %}{{ allele_info.created }}{% endlabelled %}
+    {% labelled admin_only=True label="Modified" value_css="text-monospace" %}{{ allele_info.modified }}{% endlabelled %}
+
     {% comment %}
     {% for diff_text in c_hgvses %}
         {% labelled label=diff_text.identifier value_css="text-monospace" %}{{ diff_text.html }}{% endlabelled %}
@@ -17,6 +20,7 @@ <h4>Imported Allele Info ({{ allele_info.pk }})</h4>
     {% else %}
         {% labelled label=c_hgvses.0.identifier value_css="text-monospace" %}{{ c_hgvses.0.html }}{% endlabelled %}
     {% endif %}
+    {% labelled admin_only=True label="HGVS matched by" value_css="text-monospace" %}{{ allele_info.hgvs_converter_version }}{% endlabelled %}
     {% if normalized_diff %}
         {% labelled label="Normalised Diffs" label_css="text-muted" value_css="text-muted" %}<i class="fa-solid fa-arrows-up-down"></i> {{ normalized_diff|separator:', ' }}{% endlabelled %}
     {% endif %}

genes/hgvs/hgvs_converter.py

@@ -11,6 +11,9 @@ class HGVSConverterType(Enum):
     COMBO = 3
     CLINGEN_ALLELE_REGISTRY = 4  # This is not a full implementation just enough for HGVS tester tool
 
+    def is_internal_type(self) -> bool:
+        return self in (HGVSConverterType.PYHGVS, HGVSConverterType.BIOCOMMONS_HGVS)
+
 
 class HgvsMatchRefAllele:
     def __init__(self, provided_ref: str, calculated_ref: str):