scout/update/panel.py
def update_panel(adapter, panel_name, panel_version, new_version=None, new_date=None):
    """Update a gene panel in the database
    
    We need to update the actual gene panel and then all cases that refers to the panel.
    
    Args:
        adapter(scout.adapter.MongoAdapter)
        panel_name(str): Unique name for a gene panel
        panel_version(float)
        new_version(float)
        new_date(datetime.datetime)
    
    Returns:
        updated_panel(scout.models.GenePanel): The updated gene panel object
    """
    panel_obj = adapter.gene_panel(panel_name, panel_version)

    if not panel_obj:
        raise IntegrityError("Panel %s version %s does not exist" % (panel_name, panel_version))

    updated_panel = adapter.update_panel(panel_obj, new_version, new_date)
    
    panel_id = updated_panel['_id']

    # We need to alter the embedded panels in all affected cases
    update = {'$set': {}}
    if new_version:
        update['$set']['panels.$.version'] = updated_panel['version']
    if new_date:
        update['$set']['panels.$.updated_at'] = updated_panel['date']
    
    LOG.info('Updating affected cases with {0}'.format(update))
    
    query = {'panels': { '$elemMatch': {'panel_name': panel_name}}}
    adapter.case_collection.update_many(query, update)
    
    return updated_panel
def update_panel(adapter, panel_name, panel_version, new_version=None, new_date=None):
    """Update a gene panel in the database
    
    We need to update the actual gene panel and then all cases that refers to the panel.
    
    Args:
        adapter(scout.adapter.MongoAdapter)
        panel_name(str): Unique name for a gene panel
        panel_version(float)
        new_version(float)
        new_date(datetime.datetime)
    
    Returns:
        updated_panel(scout.models.GenePanel): The updated gene panel object
    """
    panel_obj = adapter.gene_panel(panel_name, panel_version)

    if not panel_obj:
        raise IntegrityError("Panel %s version %s does not exist" % (panel_name, panel_version))

    updated_panel = adapter.update_panel(panel_obj, new_version, new_date)
    
    panel_id = updated_panel['_id']

    # We need to alter the embedded panels in all affected cases
    update = {'$set': {}}
    if new_version:
        update['$set']['panels.$.version'] = updated_panel['version']
    if new_date:
        update['$set']['panels.$.updated_at'] = updated_panel['date']
    
    LOG.info('Updating affected cases with {0}'.format(update))
    
    query = {'panels': { '$elemMatch': {'panel_name': panel_name}}}
    adapter.case_collection.update_many(query, update)
    
    return updated_panel
Update a gene panel in the database
    
    We need to update the actual gene panel and then all cases that refers to the panel.
    
    Args:
        adapter(scout.adapter.MongoAdapter)
        panel_name(str): Unique name for a gene panel
        panel_version(float)
        new_version(float)
        new_date(datetime.datetime)
    
    Returns:
        updated_panel(scout.models.GenePanel): The updated gene panel object