scout/server/blueprints/cases/controllers.py
def coverage_report_contents(store, institute_obj, case_obj, base_url):
    """Posts a request to chanjo-report and capture the body of the returned response to include it in case report

    Args:
        store(adapter.MongoAdapter)
        institute_obj(models.Institute)
        case_obj(models.Case)
        base_url(str): base url of server

    Returns:
        coverage_data(str): string rendering of the content between <body </body> tags of a coverage report
    """

    request_data = {}
    # extract sample ids from case_obj and add them to the post request object:
    request_data['sample_id'] = [ ind['individual_id'] for ind in case_obj['individuals'] ]

    # extract default panel names and default genes from case_obj and add them to the post request object
    distinct_genes = set()
    panel_names = []
    for panel_info in case_obj.get('panels', []):
        if not panel_info.get('is_default'):
            continue
        panel_obj = store.gene_panel(panel_info['panel_name'], version=panel_info.get('version'))
        full_name = "{} ({})".format(panel_obj['display_name'], panel_obj['version'])
        panel_names.append(full_name)
    panel_names = ' ,'.join(panel_names)
    request_data['panel_name'] = panel_names

    # add institute-specific cutoff level to the post request object
    request_data['level'] = institute_obj.get('coverage_cutoff', 15)

    #send get request to chanjo report
    resp = requests.get(base_url+'reports/report', params=request_data)

    #read response content
    soup = BeautifulSoup(resp.text)

    # remove links in the printed version of coverage report
    for tag in soup.find_all('a'):
        tag.replaceWith('')

    #extract body content using BeautifulSoup
    coverage_data = ''.join(['%s' % x for x in soup.body.contents])

    return coverage_data
def coverage_report_contents(store, institute_obj, case_obj, base_url):
    """Posts a request to chanjo-report and capture the body of the returned response to include it in case report

    Args:
        store(adapter.MongoAdapter)
        institute_obj(models.Institute)
        case_obj(models.Case)
        base_url(str): base url of server

    Returns:
        coverage_data(str): string rendering of the content between <body </body> tags of a coverage report
    """

    request_data = {}
    # extract sample ids from case_obj and add them to the post request object:
    request_data['sample_id'] = [ ind['individual_id'] for ind in case_obj['individuals'] ]

    # extract default panel names and default genes from case_obj and add them to the post request object
    distinct_genes = set()
    panel_names = []
    for panel_info in case_obj.get('panels', []):
        if not panel_info.get('is_default'):
            continue
        panel_obj = store.gene_panel(panel_info['panel_name'], version=panel_info.get('version'))
        full_name = "{} ({})".format(panel_obj['display_name'], panel_obj['version'])
        panel_names.append(full_name)
    panel_names = ' ,'.join(panel_names)
    request_data['panel_name'] = panel_names

    # add institute-specific cutoff level to the post request object
    request_data['level'] = institute_obj.get('coverage_cutoff', 15)

    #send get request to chanjo report
    resp = requests.get(base_url+'reports/report', params=request_data)

    #read response content
    soup = BeautifulSoup(resp.text)

    # remove links in the printed version of coverage report
    for tag in soup.find_all('a'):
        tag.replaceWith('')

    #extract body content using BeautifulSoup
    coverage_data = ''.join(['%s' % x for x in soup.body.contents])

    return coverage_data
def coverage_report_contents ( store , institute_obj , case_obj , base_url ) : request_data = { } # extract sample ids from case_obj and add them to the post request object: request_data [ 'sample_id' ] = [ ind [ 'individual_id' ] for ind in case_obj [ 'individuals' ] ] # extract default panel names and default genes from case_obj and add them to the post request object distinct_genes = set ( ) panel_names = [ ] for panel_info in case_obj . get ( 'panels' , [ ] ) : if not panel_info . get ( 'is_default' ) : continue panel_obj = store . gene_panel ( panel_info [ 'panel_name' ] , version = panel_info . get ( 'version' ) ) full_name = "{} ({})" . format ( panel_obj [ 'display_name' ] , panel_obj [ 'version' ] ) panel_names . append ( full_name ) panel_names = ' ,' . join ( panel_names ) request_data [ 'panel_name' ] = panel_names # add institute-specific cutoff level to the post request object request_data [ 'level' ] = institute_obj . get ( 'coverage_cutoff' , 15 ) #send get request to chanjo report resp = requests . get ( base_url + 'reports/report' , params = request_data ) #read response content soup = BeautifulSoup ( resp . text ) # remove links in the printed version of coverage report for tag in soup . find_all ( 'a' ) : tag . replaceWith ( '' ) #extract body content using BeautifulSoup coverage_data = '' . join ( [ '%s' % x for x in soup . body . contents ] ) return coverage_data
Posts a request to chanjo-report and capture the body of the returned response to include it in case report

    Args:
        store(adapter.MongoAdapter)
        institute_obj(models.Institute)
        case_obj(models.Case)
        base_url(str): base url of server

    Returns:
        coverage_data(str): string rendering of the content between <body </body> tags of a coverage report
Posts a request to chanjo - report and capture the body of the returned response to include it in case report