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])
Exemple #2
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    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])
Exemple #3
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    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)
Exemple #4
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 def handle(self, *args, **options):
     force_annotations = options.get('force_annotations')
     force_clean = options.get('force_clean')
     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
     for project_id in project_ids:
         if force_clean:
             xbrowse_controls.clean_project(project_id)
         xbrowse_controls.load_project(project_id, force_annotations=force_annotations)
Exemple #5
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 def handle(self, *args, **options):
     force_annotations = options.get('force_annotations')
     force_clean = options.get('force_clean')
     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
     for project_id in project_ids:
         if force_clean:
             xbrowse_controls.clean_project(project_id)
         xbrowse_controls.load_project(project_id,
                                       force_annotations=force_annotations)
Exemple #6
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    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_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"))
Exemple #7
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 def handle(self, *args, **options):
     force_annotations = options.get('force_annotations')
     for project_id in args:
         xbrowse_controls.load_project(project_id, force_annotations=force_annotations)