sqlalchemy: query by variable attribute

Question

Here is my current code:

def hypergeometric(query_genes, filename, input_format):

    if input_format == 'ENSEMBLID':
        OCRs = OpenChromatinRegion.query
                .filter(OpenChromatinRegion.filename == filename)
                .filter(OpenChromatinRegion.ENSEMBLID.in_(query_genes))
                .filter(OpenChromatinRegion.ENSEMBLID != 'NA')
                .all()

    elif input_format == 'gene_symbol':
        OCRs = OpenChromatinRegion.query
                .filter(OpenChromatinRegion.filename == filename)
                .filter(OpenChromatinRegion.gene_symbol.in_(query_genes))
                .filter(OpenChromatinRegion.gene_symbol != 'NA')
                .all()

For obvious reasons, this is very painful. Is there some way of interpolating the input_format variable into the query?

aviator · Accepted Answer · 2016-05-10 19:49:24Z

2

You can simply extract the required attribute using getattr and use it in filter.

def hypergeometric(query_genes, filename, input_format):

     input_format_attribute = getattr(OpenChromatinRegion, input_format, None)     
     if input_format_attribute is not None:
        OCRs = OpenChromatinRegion.query
                .filter(OpenChromatinRegion.filename == filename)
                .filter(input_format_attribute.in_(query_genes))
                .filter(input_format_attribute != 'NA')
                .all()

edited May 10, 2016 at 19:49

answered May 10, 2016 at 19:44

aviator

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