scout/commands/load/research.py
def research(context, case_id, institute, force):
    """Upload research variants to cases

        If a case is specified, all variants found for that case will be
        uploaded.

        If no cases are specified then all cases that have 'research_requested'
        will have there research variants uploaded
    """
    LOG.info("Running scout load research")
    adapter = context.obj['adapter']

    if case_id:
        if not institute:
            # There was an old way to create case ids so we need a special case to handle this
            # Assume institute-case combo
            splitted_case = case_id.split('-')
            # Check if first part is institute, then we know it is the old format
            if len(splitted_case) > 1:
                institute_obj = adapter.institute(splitted_case[0])
                if institute_obj:
                    institute = institute_obj['_id']
                    case_id = splitted_case[1]
        case_obj = adapter.case(institute_id=institute, case_id=case_id)
        if case_obj is None:
            LOG.warning("No matching case found")
            context.abort()
        else:
            case_objs = [case_obj]
    else:
        # Fetch all cases that have requested research
        case_objs = adapter.cases(research_requested=True)

    default_threshold = 8
    files = False
    for case_obj in case_objs:
        if force or case_obj['research_requested']:
            # Test to upload research snvs
            if case_obj['vcf_files'].get('vcf_snv_research'):
                files = True
                adapter.delete_variants(case_id=case_obj['_id'],
                                        variant_type='research',
                                        category='snv')

                LOG.info("Load research SNV for: %s", case_obj['_id'])
                adapter.load_variants(
                    case_obj=case_obj,
                    variant_type='research',
                    category='snv',
                    rank_threshold=default_threshold,
                    )

            # Test to upload research svs
            if case_obj['vcf_files'].get('vcf_sv_research'):
                files = True
                adapter.delete_variants(case_id=case_obj['_id'],
                                        variant_type='research',
                                        category='sv')
                LOG.info("Load research SV for: %s", case_obj['_id'])
                adapter.load_variants(
                    case_obj=case_obj,
                    variant_type='research',
                    category='sv',
                    rank_threshold=default_threshold,
                    )

            # Test to upload research cancer variants
            if case_obj['vcf_files'].get('vcf_cancer_research'):
                files = True
                adapter.delete_variants(case_id=case_obj['_id'],
                                        variant_type='research',
                                        category='cancer')

                LOG.info("Load research cancer for: %s", case_obj['_id'])
                adapter.load_variants(
                    case_obj=case_obj,
                    variant_type='research',
                    category='cancer',
                    rank_threshold=default_threshold,
                    )
            if not files:
                LOG.warning("No research files found for case %s", case_id)
                context.abort()
            case_obj['is_research'] = True
            case_obj['research_requested'] = False
            adapter.update_case(case_obj)
        else:
            LOG.warn("research not requested, use '--force'")
def research(context, case_id, institute, force):
    """Upload research variants to cases

        If a case is specified, all variants found for that case will be
        uploaded.

        If no cases are specified then all cases that have 'research_requested'
        will have there research variants uploaded
    """
    LOG.info("Running scout load research")
    adapter = context.obj['adapter']

    if case_id:
        if not institute:
            # There was an old way to create case ids so we need a special case to handle this
            # Assume institute-case combo
            splitted_case = case_id.split('-')
            # Check if first part is institute, then we know it is the old format
            if len(splitted_case) > 1:
                institute_obj = adapter.institute(splitted_case[0])
                if institute_obj:
                    institute = institute_obj['_id']
                    case_id = splitted_case[1]
        case_obj = adapter.case(institute_id=institute, case_id=case_id)
        if case_obj is None:
            LOG.warning("No matching case found")
            context.abort()
        else:
            case_objs = [case_obj]
    else:
        # Fetch all cases that have requested research
        case_objs = adapter.cases(research_requested=True)

    default_threshold = 8
    files = False
    for case_obj in case_objs:
        if force or case_obj['research_requested']:
            # Test to upload research snvs
            if case_obj['vcf_files'].get('vcf_snv_research'):
                files = True
                adapter.delete_variants(case_id=case_obj['_id'],
                                        variant_type='research',
                                        category='snv')

                LOG.info("Load research SNV for: %s", case_obj['_id'])
                adapter.load_variants(
                    case_obj=case_obj,
                    variant_type='research',
                    category='snv',
                    rank_threshold=default_threshold,
                    )

            # Test to upload research svs
            if case_obj['vcf_files'].get('vcf_sv_research'):
                files = True
                adapter.delete_variants(case_id=case_obj['_id'],
                                        variant_type='research',
                                        category='sv')
                LOG.info("Load research SV for: %s", case_obj['_id'])
                adapter.load_variants(
                    case_obj=case_obj,
                    variant_type='research',
                    category='sv',
                    rank_threshold=default_threshold,
                    )

            # Test to upload research cancer variants
            if case_obj['vcf_files'].get('vcf_cancer_research'):
                files = True
                adapter.delete_variants(case_id=case_obj['_id'],
                                        variant_type='research',
                                        category='cancer')

                LOG.info("Load research cancer for: %s", case_obj['_id'])
                adapter.load_variants(
                    case_obj=case_obj,
                    variant_type='research',
                    category='cancer',
                    rank_threshold=default_threshold,
                    )
            if not files:
                LOG.warning("No research files found for case %s", case_id)
                context.abort()
            case_obj['is_research'] = True
            case_obj['research_requested'] = False
            adapter.update_case(case_obj)
        else:
            LOG.warn("research not requested, use '--force'")
Upload research variants to cases

        If a case is specified, all variants found for that case will be
        uploaded.

        If no cases are specified then all cases that have 'research_requested'
        will have there research variants uploaded