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))
def cases ( context , institute , display_name , case_id , nr_variants , variants_treshold ) : 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
Display cases from the database