def start_qc_analysis(rawfile, storedfile, wf_id, dbfn_id):
analysis = Analysis(user_id=settings.QC_USER_ID,
name='{}_{}_{}'.format(rawfile.producer.name,
rawfile.name, rawfile.date))
analysis.save()
jobutil.create_file_job('run_longit_qc_workflow', storedfile.id,
analysis.id, wf_id, dbfn_id)
def save(self, commit=True):
instance = super().save(commit=False)
instance.user = self.user
if self.analysis:
analysis = self.analysis.clone()
else:
# Create empty analysis for template
user_settings = UserSettings.get_for_user(self.user)
genome_build = user_settings.default_genome_build # Doesn't matter for templates
analysis = Analysis(genome_build=genome_build,
name=f"analysis for template {instance.name}")
analysis.template_type = AnalysisTemplateType.TEMPLATE
analysis.set_defaults_and_save(self.user)
assign_permission_to_user_and_groups(self.user, analysis)
instance.analysis = analysis
if commit:
instance.save()
return instance
def setUpClass(cls):
super().setUpClass()
user = User.objects.get_or_create(username='******')[0]
cls.grch37 = GenomeBuild.get_name_or_alias("GRCh37")
cls.annotation_version_grch37 = get_fake_annotation_version(cls.grch37)
gene_annotation_release = cls.annotation_version_grch37.gene_annotation_version.gene_annotation_release
cls.transcript_version = create_fake_transcript_version(cls.grch37,
release=gene_annotation_release)
cls.gene_symbol = cls.transcript_version.gene_version.gene_symbol
cls.trio = create_fake_trio(user, cls.grch37)
cls.analysis = Analysis(genome_build=cls.grch37)
cls.analysis.set_defaults_and_save(user)
cls.sample = cls.trio.get_samples()[0]
# Gene List
cls.gene_list = GeneList.objects.get_or_create(name="fake list",
user=cls.analysis.user,
import_status=ImportStatus.SUCCESS)[0]
GeneListGeneSymbol.objects.get_or_create(gene_list=cls.gene_list, gene_symbol=cls.gene_symbol)
# Need some overlapping variants so gene list will work
create_fake_variants(cls.grch37)
# Note: Variant probably doesn't overlap with gene, just want a random one
variant = Variant.objects.filter(Variant.get_no_reference_q()).first()
annotation_run = AnnotationRun.objects.create()
VariantGeneOverlap.objects.create(version=cls.annotation_version_grch37.variant_annotation_version,
annotation_run=annotation_run,
gene=cls.transcript_version.gene,
variant=variant)
# Tag that variant
cls.tag = Tag.objects.get_or_create(pk="foo")[0]
VariantTag.objects.create(genome_build=cls.grch37, analysis=cls.analysis,
variant=variant, tag=cls.tag, user=user)
