issue #1054 - misc liftover issues

snpdb/bcftools_liftover.py

@@ -24,7 +24,8 @@ def bcftools_liftover(source_vcf: str, source_genome_build: GenomeBuild,
     source_fasta_filename = source_vep_config["fasta"]
     dest_fasta_filename = dest_vep_config["fasta"]
 
-    chain_filename = source_vep_config["liftover"].get(out_genome_build.name)
+    annotation_build_config = settings.ANNOTATION[source_genome_build.name]
+    chain_filename = annotation_build_config["liftover"].get(out_genome_build.name)
     required_files = {
         "source_fasta_filename": source_fasta_filename,
         "dest_fasta_filename": dest_fasta_filename,

snpdb/grids.py

@@ -559,6 +559,21 @@ def get_initial_queryset(self) -> QuerySet[AlleleLiftover]:
 
 
 class AlleleLiftoverFailureColumns(AbstractAlleleLiftoverColumns):
+    def __init__(self, request):
+        super().__init__(request)
+        ct_column = RichColumn(key="liftover__conversion_tool",
+                               label="Conversion Tool", renderer=self.render_conversion_tool,
+                               orderable=True)
+        self.rich_columns.insert(1, ct_column)
+
+    def render_conversion_tool(self, row: dict[str, Any]) -> JsonDataType:
+        label = ""
+        if status := row['liftover__conversion_tool']:
+            conversion_tool = AlleleConversionTool(status)
+            label = conversion_tool.label
+        return label
+
+
     def get_initial_queryset(self) -> QuerySet[AlleleLiftover]:
         genome_build_name = self.get_query_param("genome_build_name")
         if genome_build_name is None:

snpdb/liftover.py

@@ -8,7 +8,6 @@
 from functools import reduce
 from typing import Any, Union, Iterable
 
-from django.conf import settings
 from django.contrib.auth.models import User
 from django.db.models.query_utils import Q
 

snpdb/migrations/0131_download_liftover_chain_files.py

@@ -18,6 +18,7 @@ def _test_has_missing_37_to_38_chain_file(apps):
 def _test_has_missing_38_to_37_chain_file(apps):
     return not os.path.exists(LIFTOVER_38_TO_37)
 
+
 class Migration(migrations.Migration):
 
     dependencies = [

snpdb/models/models_variant.py

@@ -227,7 +227,6 @@ def can_attempt_liftover(self, genome_build) -> bool:
 
         return False
 
-
     def merge(self, allele_linking_tool, other_allele: "Allele") -> bool:
         """ Merge other_allele into this allele """
 
@@ -281,6 +280,11 @@ def merge(self, allele_linking_tool, other_allele: "Allele") -> bool:
     def build_names(self) -> str:
         return ", ".join(sorted(self.variantallele_set.values_list("genome_build__name", flat=True)))
 
+    @staticmethod
+    def missing_variants_for_build(genome_build) -> QuerySet['Allele']:
+        alleles_with_variants_qs = Allele.objects.filter(variantallele__isnull=False)
+        return alleles_with_variants_qs.filter(~Q(variantallele__genome_build=genome_build))
+
     def __str__(self):
         name = f"Allele {self.pk}"
         if self.clingen_allele:

snpdb/tasks/liftover_tasks.py

@@ -0,0 +1,28 @@
+import logging
+
+import celery
+from django.contrib.auth.models import User
+
+from snpdb.liftover import create_liftover_pipelines
+from snpdb.models import GenomeBuild, ImportSource, Allele
+
+
+@celery.shared_task
+def liftover_alleles(username, genome_build_name):
+    user = User.objects.get(username=username)
+    genome_build = GenomeBuild.get_name_or_alias(genome_build_name)
+
+    other_build = {
+        "GRCh37": GenomeBuild.grch38(),
+        "GRCh38": GenomeBuild.grch37(),
+    }
+    inserted_genome_build = other_build[genome_build_name]
+    inserted_genome_build: GenomeBuild
+    alleles = Allele.missing_variants_for_build(genome_build)
+    logging.info("creating pipelines...")
+    try:
+        create_liftover_pipelines(user, alleles, ImportSource.WEB, inserted_genome_build, [genome_build])
+        logging.info("/ finished creating pipelines")
+    except Exception as e:
+        logging.error(e)
+

snpdb/templates/snpdb/liftover/liftover_runs.html

@@ -8,6 +8,23 @@
 {% block title %}Liftover{% endblock %}
 {% block submenu %}{% menu_bar_settings %}{% endblock submenu %}
 {% block content %}
+    <div class="container">
+        <h3>Alleles</h3>
+        <form method="post">
+            {% csrf_token %}
+
+            <table>
+            {% for genome_build_name, count in alleles_missing_variants.items %}
+                <tr>
+                    <th>Alleles missing {{ genome_build_name }} variants: </th>
+                    <td>{{ count }}</td>
+                    <td>{% if count %}<button name="liftover_to_{{ genome_build_name }}" class="btn btn-secondary">Liftover variants</button>{% endif %}</td>
+                </tr>
+            {% endfor %}
+            </table>
+        </form>
+    </div>
+
     <div class="container">
         <h3>Liftover Runs</h3>
 

snpdb/views/views.py

@@ -72,10 +72,11 @@
     Trio, AbstractNodeCountSettings, CohortGenotypeCollection, UserSettingsOverride, NodeCountSettingsCollection, Lab, \
     LabUserSettingsOverride, OrganizationUserSettingsOverride, LabHead, SomalierRelatePairs, \
     VariantZygosityCountCollection, VariantZygosityCountForVCF, ClinVarKey, AvatarDetails, State, SampleStats, \
-    SampleStatsPassingFilter, TagColorsCollection, Contig, LiftoverRun
+    SampleStatsPassingFilter, TagColorsCollection, Contig, LiftoverRun, Allele
 from snpdb.models.models_enums import ProcessingStatus, ImportStatus, BuiltInFilters, SequenceRole
 from snpdb.sample_file_path import get_example_replacements
 from snpdb.tasks.soft_delete_tasks import soft_delete_vcfs
+from snpdb.tasks.liftover_tasks import liftover_alleles
 from snpdb.utils import LabNotificationBuilder, get_tag_styles_and_colors
 from upload.models import UploadedVCF
 from upload.uploaded_file_type import retry_upload_pipeline
@@ -1499,9 +1500,27 @@ def labs_graph_detail(request):
 
 @require_superuser
 def liftover_runs(request):
+    genome_builds = GenomeBuild.builds_with_annotation()
+    if request.method == 'POST':
+        dest_genome_build = None
+        for genome_build in genome_builds:
+            if f"liftover_to_{genome_build.name}" in request.POST:
+                dest_genome_build = genome_build
+                break
+        if dest_genome_build is None:
+            raise ValueError("Could not determine dest genome build from liftover_runs POST")
+        messages.add_message(request, messages.INFO, f"Lifting over alleles to {dest_genome_build}")
+        liftover_alleles.si(request.user.username, dest_genome_build.name).apply_async()
+
+    alleles_missing_variants = {}
+    for genome_build in genome_builds:
+        alleles_missing_variants[genome_build.name] = Allele.missing_variants_for_build(genome_build).count()
+
     context = {
-        "genome_builds": GenomeBuild.builds_with_annotation()
+        "genome_builds": genome_builds,
+        "alleles_missing_variants": alleles_missing_variants,
     }
+
     return render(request, "snpdb/liftover/liftover_runs.html", context)
 
 

upload/tasks/vcf/import_vcf_tasks.py

@@ -132,7 +132,6 @@ def process_items(self, upload_step: UploadStep):
             if num_rejected:
                 child_task_class = LiftoverProcessFailureVCFTask
                 self._schedule_steps(child_task_class, upload_step, [(reject_vcf, num_rejected)])
-
         else:
             raise ValueError(f"Don't know how to produce liftover VCF for {liftover.get_conversion_tool_display()}")