Configuration

The GA4GH reference server has two basic elements to its configuration: the Data hierarchy and the Configuration file.

Data hierarchy

Data is input to the GA4GH server as a directory hierarchy, in which the structure of data to be served is represented by the file system. For now, we support only one dataset, but this will be generalised to multiple datasets in later releases. An example data layout might be:

ga4gh-data/
    /variants/
        variantSet1/
            chr1.vcf.gz
            chr1.vcf.gz.tbi
            chr2.vcf.gz
            chr2.vcf.gz.tbi
            # More VCFs
        variantSet2/
            chr1.bcf
            chr1.bcf.csi
            chr2.bcf
            chr2.bcf.csi
            # More BCFs
    /reads/
        readGroupSet1
            sample1.bam
            sample1.bam.bai
            sample2.bam
            sample2.bam.bai
            # More BAMS

Configuration file

The GA4GH reference server is a Flask application and uses the standard Flask configuration file mechanisms. Many configuration files will be very simple, and will consist of just one directive instructing the server where to look for data; for example, we might have

DATA_SOURCE = "/path/to/data/root"

For production deployments, we shouldn’t need to add any more configuration than this, as the all other keys have sensible defaults. However, all of Flask’s builtin configuration values are supported, as well as the extra custom configuration values documented here.

When debugging deployment issues, it can be very useful to turn on extra debugging information as follows:

DEBUG = True

Warning

Debugging should only be used temporarily and not left on by default.

Configuration Values

DEFAULT_PAGE_SIZE

The default maximum number of values to fill into a page when responding to search queries. If a client does not specify a page size in a query, this value is used.

MAX_RESPONSE_LENGTH

The approximate maximum size of a response sent to a client in bytes. This is used to control the amount of memory that the server uses when creating responses. When a client makes a search request with a given page size, the server will process this query and incrementally build a response until (a) the number of values in the page list is equal to the page size; (b) the size of the serialised response in bytes is >= MAX_RESPONSE_LENGTH; or (c) there are no more results left in the query.

REQUEST_VALIDATION

Set this to True to strictly validate all incoming requests to ensure that they conform to the protocol. This may result in clients with poor standards compliance receiving errors rather than the expected results.

RESPONSE_VALIDATION

Set this to True to strictly validate all outgoing responses to ensure that they conform to the protocol. This should only be used for development purposes.