impc-api-helper

IMPC-API-HELPER

Name is a work in progress, we can think of something nicer

README for draft impc-api python package.

The functions in this package are intended for use on a Jupyter Notebook.

Installing the package for the first time

1. Clone the repository and navigate into it. Navigate into the package name until you can see setup.py and pyproject.toml
2. Run python3 -m build, this builds the package, a couple of new files/folders will appear.
3. Install the package running pip install .
4. Try it out: Go to Jupyter Notebook and some examples below:

Avaialble functions

The available functions can be imported as:

from impc_api_helper import solr_request, batch_request, facet_request, iterator_solr_request

Solr request

The most basic request to the IMPC solr API

num_found, df = solr_request( core='genotype-phenotype', params={
        'q': '*:*'
        'rows': 10
        'fl': 'marker_symbol,allele_symbol,parameter_stable_id'
    }
)

Batch request

For larger requests, use the batch request function to query the API responsibly.

df = batch_request(
    core="genotype-phenotype",
    params={
        'q': 'top_level_mp_term_name:"cardiovascular system phenotype" AND effect_size:[* TO *] AND life_stage_name:"Late adult"',
        'fl': 'allele_accession_id,life_stage_name,marker_symbol,mp_term_name,p_value,parameter_name,parameter_stable_id,phenotyping_center,statistical_method,top_level_mp_term_name,effect_size'
    },
    batch_size=100
)

Facet request

To obtain faceted search results for the specified field

num_found, df = facet_request(
    core='genotype-phenotype',
    params={
        'q': '*:*',
        'rows': 0,
        'facet': 'on',
        'facet.field': 'zygosity',
        'facet.limit': 15,
        'facet.mincount': 1
    }
)

Iterator solr request

To pass a list of different fields and download a file with the information

# Genes example
genes = ["Zfp580","Firrm","Gpld1","Mbip"]

# Initial query parameters
params = {
    'q': "*:*",
    'fl': 'marker_symbol,allele_symbol,parameter_stable_id',
    'field_list': genes,
    'field_type': "marker_symbol"
}
iterator_solr_request(core='genotype-phenotype', params=params, filename='marker_symbol', format ='csv')