scout/server/blueprints/dashboard/controllers.py
def get_general_case_info(adapter, institute_id=None, slice_query=None):
    """Return general information about cases

    Args:
        adapter(adapter.MongoAdapter)
        institute_id(str)
        slice_query(str):   Query to filter cases to obtain statistics for.


    Returns:
        general(dict)
    """
    general = {}

    # Potentially sensitive slice queries are assumed allowed if we have got this far
    name_query = slice_query

    cases = adapter.cases(owner=institute_id, name_query=name_query)

    phenotype_cases = 0
    causative_cases = 0
    pinned_cases = 0
    cohort_cases = 0

    pedigree = {
        1: {
            'title': 'Single',
            'count': 0
        },
        2: {
            'title': 'Duo',
            'count': 0
        },
        3: {
            'title': 'Trio',
            'count': 0
        },
        'many': {
            'title': 'Many',
            'count': 0
        },
    }

    case_ids = set()

    total_cases = 0
    for total_cases,case in enumerate(cases,1):
        # If only looking at one institute we need to save the case ids
        if institute_id:
            case_ids.add(case['_id'])
        if case.get('phenotype_terms'):
            phenotype_cases += 1
        if case.get('causatives'):
            causative_cases += 1
        if case.get('suspects'):
            pinned_cases += 1
        if case.get('cohorts'):
            cohort_cases += 1

        nr_individuals = len(case.get('individuals',[]))
        if nr_individuals == 0:
            continue
        if nr_individuals > 3:
            pedigree['many']['count'] += 1
        else:
            pedigree[nr_individuals]['count'] += 1

    general['total_cases'] = total_cases
    general['phenotype_cases'] = phenotype_cases
    general['causative_cases'] = causative_cases
    general['pinned_cases'] = pinned_cases
    general['cohort_cases'] = cohort_cases
    general['pedigree'] = pedigree
    general['case_ids'] = case_ids

    return general
def get_general_case_info(adapter, institute_id=None, slice_query=None):
    """Return general information about cases

    Args:
        adapter(adapter.MongoAdapter)
        institute_id(str)
        slice_query(str):   Query to filter cases to obtain statistics for.


    Returns:
        general(dict)
    """
    general = {}

    # Potentially sensitive slice queries are assumed allowed if we have got this far
    name_query = slice_query

    cases = adapter.cases(owner=institute_id, name_query=name_query)

    phenotype_cases = 0
    causative_cases = 0
    pinned_cases = 0
    cohort_cases = 0

    pedigree = {
        1: {
            'title': 'Single',
            'count': 0
        },
        2: {
            'title': 'Duo',
            'count': 0
        },
        3: {
            'title': 'Trio',
            'count': 0
        },
        'many': {
            'title': 'Many',
            'count': 0
        },
    }

    case_ids = set()

    total_cases = 0
    for total_cases,case in enumerate(cases,1):
        # If only looking at one institute we need to save the case ids
        if institute_id:
            case_ids.add(case['_id'])
        if case.get('phenotype_terms'):
            phenotype_cases += 1
        if case.get('causatives'):
            causative_cases += 1
        if case.get('suspects'):
            pinned_cases += 1
        if case.get('cohorts'):
            cohort_cases += 1

        nr_individuals = len(case.get('individuals',[]))
        if nr_individuals == 0:
            continue
        if nr_individuals > 3:
            pedigree['many']['count'] += 1
        else:
            pedigree[nr_individuals]['count'] += 1

    general['total_cases'] = total_cases
    general['phenotype_cases'] = phenotype_cases
    general['causative_cases'] = causative_cases
    general['pinned_cases'] = pinned_cases
    general['cohort_cases'] = cohort_cases
    general['pedigree'] = pedigree
    general['case_ids'] = case_ids

    return general
Return general information about cases

    Args:
        adapter(adapter.MongoAdapter)
        institute_id(str)
        slice_query(str):   Query to filter cases to obtain statistics for.


    Returns:
        general(dict)