scout/commands/view/case.py
def cases(context, institute, display_name, case_id, nr_variants, variants_treshold):
    """Display cases from the database"""
    LOG.info("Running scout view institutes")
    adapter = context.obj['adapter']

    models = []
    if case_id:
        case_obj = adapter.case(case_id=case_id)
        if case_obj:
            models.append(case_obj)

    else:
        models = adapter.cases(collaborator=institute, name_query=display_name)
        models = [case_obj for case_obj in models]

    if not models:
        LOG.info("No cases could be found")
        return
    
    header = ['case_id', 'display_name', 'institute']
    
    if variants_treshold:
        LOG.info("Only show cases with more than %s variants", variants_treshold)
        nr_variants = True
    
    if nr_variants:
        LOG.info("Displaying number of variants for each case")
        header.append('clinical')
        header.append('research')
    
    
    click.echo("#"+'\t'.join(header))
    for model in models:
        output_str = "{:<12}\t{:<12}\t{:<12}"
        output_values = [model['_id'],model['display_name'],model['owner']]
        if nr_variants:
            output_str += "\t{:<12}\t{:<12}"
            nr_clinical = 0
            nr_research = 0
            variants = adapter.variant_collection.find({'case_id':model['_id']})
            i = 0
            for i, var in enumerate(variants, 1):
                if var['variant_type'] == 'clinical':
                    nr_clinical += 1
                else:
                    nr_research += 1
            output_values.extend([nr_clinical, nr_research])
            
            if variants_treshold and i < variants_treshold:
                LOG.debug("Case %s had to few variants, skipping", model['_id'])
                continue
            
        click.echo(output_str.format(*output_values))
def cases(context, institute, display_name, case_id, nr_variants, variants_treshold):
    """Display cases from the database"""
    LOG.info("Running scout view institutes")
    adapter = context.obj['adapter']

    models = []
    if case_id:
        case_obj = adapter.case(case_id=case_id)
        if case_obj:
            models.append(case_obj)

    else:
        models = adapter.cases(collaborator=institute, name_query=display_name)
        models = [case_obj for case_obj in models]

    if not models:
        LOG.info("No cases could be found")
        return
    
    header = ['case_id', 'display_name', 'institute']
    
    if variants_treshold:
        LOG.info("Only show cases with more than %s variants", variants_treshold)
        nr_variants = True
    
    if nr_variants:
        LOG.info("Displaying number of variants for each case")
        header.append('clinical')
        header.append('research')
    
    
    click.echo("#"+'\t'.join(header))
    for model in models:
        output_str = "{:<12}\t{:<12}\t{:<12}"
        output_values = [model['_id'],model['display_name'],model['owner']]
        if nr_variants:
            output_str += "\t{:<12}\t{:<12}"
            nr_clinical = 0
            nr_research = 0
            variants = adapter.variant_collection.find({'case_id':model['_id']})
            i = 0
            for i, var in enumerate(variants, 1):
                if var['variant_type'] == 'clinical':
                    nr_clinical += 1
                else:
                    nr_research += 1
            output_values.extend([nr_clinical, nr_research])
            
            if variants_treshold and i < variants_treshold:
                LOG.debug("Case %s had to few variants, skipping", model['_id'])
                continue
            
        click.echo(output_str.format(*output_values))
Display cases from the database