def _get_gene_and_transcript_stats(genome_build: GenomeBuild,
annotation_consortium):
genes_and_transcripts = {}
gene_counts = GeneVersion.objects.filter(
gene__annotation_consortium=annotation_consortium,
genome_build=genome_build).count()
transcripts_qs = TranscriptVersion.objects.filter(
transcript__annotation_consortium=annotation_consortium,
genome_build=genome_build)
transcript_counts = transcripts_qs.count()
if gene_counts and transcript_counts:
genes_and_transcripts = {
"genes": gene_counts,
"transcripts": transcript_counts
}
field_counts = get_field_counts(transcripts_qs, "import_source")
import_sources = {}
for import_source in GeneAnnotationImport.objects.filter(
pk__in=field_counts).order_by("created"):
num_transcripts = field_counts[import_source.pk]
name = os.path.basename(import_source.filename)
import_sources[name] = {
"transcripts": num_transcripts,
"created": import_source.created
}
genes_and_transcripts["import_sources"] = import_sources
return genes_and_transcripts
def view_analysis_issues(request):
all_nodes = AnalysisNode.objects.all()
field_counts = get_field_counts(all_nodes, "status")
summary_data = Counter()
for status, count in field_counts.items():
summary = NodeStatus.get_summary_state(status)
summary_data[summary] += count
field_counts = {NodeStatus(k).label: v for k, v in field_counts.items()}
context = {
"nodes_status_summary": summary_data,
"field_counts": field_counts
}
return render(request, 'analysis/view_analysis_issues.html', context)
def get_classification_counts(user: User, show_unclassified=True) -> Dict[str, int]:
qs = get_visible_classifications_qs(user)
field_counts = get_field_counts(qs, "clinical_significance")
# Add all entries as empty so colors are in the right order in graph.
classification_counts = {}
for cs, label in ClinicalSignificance.LABELS.items():
if cs or show_unclassified:
classification_counts[label] = 0
for clinical_significance, clinical_significance_count in field_counts.items():
clinical_significance_label = ClinicalSignificance.LABELS[clinical_significance]
classification_counts[clinical_significance_label] = clinical_significance_count
return classification_counts
def tag_counts_filter(context,
genome_build: GenomeBuild,
click_func=None,
show_all_func=None,
gene_symbol=None,
any_tag_button=True):
tag_kwargs = {}
if gene_symbol:
gene_variant_qs = get_variant_queryset_for_gene_symbol(
gene_symbol=gene_symbol,
genome_build=genome_build,
traverse_aliases=True)
tag_kwargs["variant_qs"] = gene_variant_qs
variant_tags_qs = VariantTag.get_for_build(genome_build=genome_build,
**tag_kwargs)
tag_counts = sorted(get_field_counts(variant_tags_qs, "tag").items())
return {
"any_tag_button": any_tag_button,
"tag_counts": tag_counts,
"click_func": click_func,
"show_all_func": show_all_func,
}
def annotation(request):
# Set Variables to None for uninstalled components, the template will show installation instructions
ensembl_biomart_transcript_genes = None
diagnostic_gene_list = None
build_contigs = get_build_contigs()
genome_build_annotations = {}
builds_ok = []
for genome_build in GenomeBuild.builds_with_annotation():
annotation_details = _get_build_annotation_details(
build_contigs, genome_build)
genome_build_annotations[genome_build.name] = annotation_details
builds_ok.append(annotation_details.get("ok", False))
gene_symbol_alias_counts = get_field_counts(GeneSymbolAlias.objects.all(),
"source")
if gene_symbol_alias_counts:
gene_symbol_alias_counts = {
GeneSymbolAliasSource(k).label: v
for k, v in gene_symbol_alias_counts.items()
}
all_ontologies_accounted_for = True
ontology_counts = list()
for service in [
OntologyService.MONDO, OntologyService.OMIM, OntologyService.HPO,
OntologyService.HGNC
]:
# don't report HGNC as it's just there as a stub for other items to relate to
count = OntologyTerm.objects.filter(ontology_service=service).count()
ontology_counts.append({"service": service, "count": count})
ontology_services = [
OntologyService.MONDO, OntologyService.OMIM, OntologyService.HPO,
OntologyService.HGNC
]
ontology_relationship_counts = dict()
for first_index, first_service in enumerate(ontology_services):
for second_service in ontology_services[first_index:]:
join_count = OntologyTermRelation.objects.filter(
source_term__ontology_service=first_service,
dest_term__ontology_service=second_service).count()
if first_service != second_service:
reverse_count = OntologyTermRelation.objects.filter(
source_term__ontology_service=second_service,
dest_term__ontology_service=first_service).count()
join_count += reverse_count
ontology_relationship_counts[
f"{first_service}{second_service}"] = join_count
ontology_relationship_counts[
f"{second_service}{first_service}"] = join_count
ontology_imports = list()
for context in [
"mondo_file", "gencc_file", "hpo_file", "omim_file",
"biomart_omim_aliases", "phenotype_to_genes"
]:
last_import = OntologyImport.objects.filter(
context=context).order_by('-created').first()
if not last_import and context != "omim_file": # don't complain about omim_file not being imported as not available to environments without license
all_ontologies_accounted_for = False
ontology_imports.append({
"context": context,
"last_import": last_import
})
diagnostic = GeneListCategory.objects.get(name='Diagnostic')
diagnostic_gene_list_count = diagnostic.genelist_set.all().count()
if diagnostic_gene_list_count:
diagnostic_gene_list = f"{diagnostic_gene_list_count} diagnostic gene lists"
clinvar_citations = ClinVarCitation.objects.count()
if clinvar_citations:
num_cached_clinvar_citations = CachedCitation.objects.count()
clinvar_citations = f"{clinvar_citations} ClinVar citations ({num_cached_clinvar_citations} cached)"
hpa_version = HumanProteinAtlasAnnotationVersion.objects.order_by(
"-annotation_date").first()
hpa_counts = HumanProteinAtlasAnnotation.objects.filter(
version=hpa_version).count()
somalier = None
if somalier_enabled := settings.SOMALIER.get("enabled"):
somalier = _verify_somalier_config()
message = f"{genome_build} - set {num_errored} annotation runs to Error"
elif f"retry-annotation-runs-{genome_build.name}" in request.POST:
num_retrying = 0
for annotation_run in annotation_runs.filter(
status=AnnotationStatus.ERROR):
annotation_run_retry(annotation_run)
num_retrying += 1
message = f"{genome_build} - retrying {num_retrying} annotation runs."
if message:
messages.add_message(request, messages.INFO, message)
for genome_build in GenomeBuild.builds_with_annotation():
qs = AnnotationRun.objects.filter(
annotation_range_lock__version__genome_build=genome_build)
field_counts = get_field_counts(qs, "status")
summary_data = Counter()
for field, count in field_counts.items():
summary = AnnotationStatus.get_summary_state(field)
summary_data[summary] += count
genome_build_summary[genome_build.pk] = summary_data
genome_build_field_counts[genome_build.pk] = {
as_display[k]: v
for k, v in field_counts.items()
}
context = {
"genome_build_summary": genome_build_summary,
"genome_build_field_counts": genome_build_field_counts,
"datatable_config": AnnotationRunColumns(request)
}