def handle(self, *args, **options): project_id = args[0] project = Project.objects.get(project_id=project_id) vcf_file_path = os.path.abspath(args[1]) vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0] if options.get('clear'): for individual in project.individual_set.all(): individual.vcf_files.clear() if options.get('indiv_id'): individual = Individual.objects.get( project=project, indiv_id=options.get('indiv_id') ) sample_management.add_vcf_file_to_individual(individual, vcf_file) else: sample_management.add_vcf_file_to_project(project, vcf_file) if options.get('load'): print("Loading VCF into project store") xbrowse_controls.load_project(project_id, vcf_files=[vcf_file_path]) print("Loading VCF datastore") xbrowse_controls.load_project_datastore(project_id, vcf_files=[vcf_file_path])
def handle(self, *args, **options): project_id = args[0] project = Project.objects.get(project_id=project_id) vcf_file_path = os.path.abspath(args[1]) vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0] if options.get('clear'): for individual in project.individual_set.all(): individual.vcf_files.clear() if options.get('indiv_id'): individual = Individual.objects.get( project=project, indiv_id=options.get('indiv_id')) sample_management.add_vcf_file_to_individual(individual, vcf_file) else: sample_management.add_vcf_file_to_project(project, vcf_file) if options.get('load'): print("Loading VCF into project store") xbrowse_controls.load_project(project_id, vcf_files=[vcf_file_path]) print("Loading VCF datastore") xbrowse_controls.load_project_datastore(project_id, vcf_files=[vcf_file_path])
def handle(self, *args, **options): force_load_annotations = options.get('force_load_annotations') force_load_variants = options.get('force_load_variants') force_clean = options.get('force_clean') load_datastore = options.get('data_store') load_all = options.get('load_all') if load_all: project_ids = [ p.project_id for p in Project.objects.all().order_by('-last_accessed_date') ] else: project_ids = args mark_as_loaded = True if not options.get("end_with_chrom") else False for project_id in project_ids: if force_clean: xbrowse_controls.clean_project(project_id) xbrowse_controls.load_project( project_id, force_load_annotations=force_load_annotations, force_load_variants=force_load_variants, mark_as_loaded=mark_as_loaded, start_from_chrom=options.get("start_from_chrom"), end_with_chrom=options.get("end_with_chrom")) if load_datastore: xbrowse_controls.load_project_datastore(project_id)
def handle(self, *args, **options): project_id = args[0] xbrowse_controls.load_project_datastore( project_id, start_from_chrom=options['start_from_chrom'])
def handle(self, *args, **options): project_id = args[0] xbrowse_controls.load_project_datastore(project_id)
def handle(self, *args, **options): project_id = args[0] print("Loading project datastore: %s" % project_id) xbrowse_controls.load_project_datastore(project_id, start_from_chrom=options['start_from_chrom'])
def handle(self, *args, **options): project_id = args[0] xbrowse_controls.load_project_datastore(project_id, start_from_chrom=options['start_from_chrom'])
def handle(self, *args, **options): project_id = args[0] print("Loading project datastore: %s" % project_id) xbrowse_controls.load_project_datastore( project_id, start_from_chrom=options['start_from_chrom'])