scout/commands/update/phenotype_groups.py
def groups(context, institute_id, phenotype_group, group_abbreviation, group_file, add):
    """
    Update the phenotype for a institute.
    If --add the groups will be added to the default groups. Else the groups will be replaced.
    """
    adapter = context.obj['adapter']
    LOG.info("Running scout update institute")
    if group_file:
        phenotype_group = []
        group_abbreviation = []
        for line in group_file:
            if line.startswith('#'):
                continue
            if len(line) < 7:
                continue
            line = line.rstrip().split('\t')
            phenotype_group.append(line[0])
            if line[1]:
                group_abbreviation.append(line[1])
    
    if not phenotype_group:
        LOG.info("Please provide some groups")
        return

    if (phenotype_group and group_abbreviation):
        if not len(phenotype_group) == len(group_abbreviation):
            LOG.warning("Specify same number of groups and abbreviations")
            return

    # try:
    adapter.update_institute(
        internal_id=institute_id, 
        phenotype_groups=phenotype_group,
        group_abbreviations=group_abbreviation,
        add_groups = add,
        )
def groups(context, institute_id, phenotype_group, group_abbreviation, group_file, add):
    """
    Update the phenotype for a institute.
    If --add the groups will be added to the default groups. Else the groups will be replaced.
    """
    adapter = context.obj['adapter']
    LOG.info("Running scout update institute")
    if group_file:
        phenotype_group = []
        group_abbreviation = []
        for line in group_file:
            if line.startswith('#'):
                continue
            if len(line) < 7:
                continue
            line = line.rstrip().split('\t')
            phenotype_group.append(line[0])
            if line[1]:
                group_abbreviation.append(line[1])
    
    if not phenotype_group:
        LOG.info("Please provide some groups")
        return

    if (phenotype_group and group_abbreviation):
        if not len(phenotype_group) == len(group_abbreviation):
            LOG.warning("Specify same number of groups and abbreviations")
            return

    # try:
    adapter.update_institute(
        internal_id=institute_id, 
        phenotype_groups=phenotype_group,
        group_abbreviations=group_abbreviation,
        add_groups = add,
        )
def groups ( context , institute_id , phenotype_group , group_abbreviation , group_file , add ) : adapter = context . obj [ 'adapter' ] LOG . info ( "Running scout update institute" ) if group_file : phenotype_group = [ ] group_abbreviation = [ ] for line in group_file : if line . startswith ( '#' ) : continue if len ( line ) < 7 : continue line = line . rstrip ( ) . split ( '\t' ) phenotype_group . append ( line [ 0 ] ) if line [ 1 ] : group_abbreviation . append ( line [ 1 ] ) if not phenotype_group : LOG . info ( "Please provide some groups" ) return if ( phenotype_group and group_abbreviation ) : if not len ( phenotype_group ) == len ( group_abbreviation ) : LOG . warning ( "Specify same number of groups and abbreviations" ) return # try: adapter . update_institute ( internal_id = institute_id , phenotype_groups = phenotype_group , group_abbreviations = group_abbreviation , add_groups = add , )
Update the phenotype for a institute.
    If --add the groups will be added to the default groups. Else the groups will be replaced.
Update the phenotype for a institute . If -- add the groups will be added to the default groups . Else the groups will be replaced .