diff options
Diffstat (limited to 'gn3/api/correlation.py')
| -rw-r--r-- | gn3/api/correlation.py | 77 |
1 files changed, 48 insertions, 29 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 217b7ce..56b8381 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -1,44 +1,63 @@ -"""Endpoints for computing correlation""" -import time -from flask import Blueprint +"""Endpoints for running correlations""" +from unittest import mock + from flask import jsonify +from flask import Blueprint from flask import request -from flask import g -from sqlalchemy import create_engine -from default_settings import SQL_URI -from gn3.correlation.correlation_computations import compute_correlation +from gn3.computations.correlations import compute_all_sample_correlation +from gn3.computations.correlations import compute_all_lit_correlation +from gn3.computations.correlations import compute_all_tissue_correlation + correlation = Blueprint("correlation", __name__) -# xtodo implement neat db setup -@correlation.before_request -def connect_db(): - """add connection to db method""" - print("@app.before_request connect_db") - db_connection = getattr(g, '_database', None) - if db_connection is None: - print("Get new database connector") - g.db = g._database = create_engine(SQL_URI, encoding="latin1") +@correlation.route("/sample_r/<string:corr_method>", methods=["POST"]) +def compute_sample_r(corr_method="pearson"): + """correlation endpoint for computing sample r correlations\ + api expects the trait data with has the trait and also the\ + target_dataset data""" + correlation_input = request.get_json() + + # xtodo move code below to compute_all_sampl correlation + this_trait_data = correlation_input.get("this_trait") + target_datasets = correlation_input.get("target_dataset") + + correlation_results = compute_all_sample_correlation(corr_method=corr_method, + this_trait=this_trait_data, + target_dataset=target_datasets) + + return jsonify({ + "corr_results": correlation_results + }) + - g.initial_time = time.time() +@correlation.route("/lit_corr/<string:species>/<int:gene_id>", methods=["POST"]) +def compute_lit_corr(species=None, gene_id=None): + """api endpoint for doing lit correlation.results for lit correlation\ + are fetched from the database this is the only case where the db\ + might be needed for actual computing of the correlation results""" + database_instance = mock.Mock() + target_traits_gene_ids = request.get_json() -@correlation.route("/corr_compute", methods=["POST"]) -def corr_compute_page(): - """api for doing correlation""" + lit_corr_results = compute_all_lit_correlation( + database_instance=database_instance, trait_lists=target_traits_gene_ids, + species=species, gene_id=gene_id) - correlation_input = request.json + return jsonify(lit_corr_results) - if correlation_input is None: - return jsonify({"error": str("Bad request")}), 400 - try: - corr_results = compute_correlation( - correlation_input_data=correlation_input) +@correlation.route("/tissue_corr/<string:corr_method>", methods=["POST"]) +def compute_tissue_corr(corr_method="pearson"): + """api endpoint fr doing tissue correlation""" + tissue_input_data = request.get_json() + primary_tissue_dict = tissue_input_data["primary_tissue"] + target_tissues_dict_list = tissue_input_data["target_tissues"] - except Exception as error: # pylint: disable=broad-except - return jsonify({"error": str(error)}) + results = compute_all_tissue_correlation(primary_tissue_dict=primary_tissue_dict, + target_tissues_dict_list=target_tissues_dict_list, + corr_method=corr_method) - return {"correlation_results": corr_results} + return jsonify(results)
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