From 31ac939f58bf7b6d353ced995ca395376203b25f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 12 Apr 2021 09:54:12 +0300
Subject: Integrate correlation API
- add new api for gn2-gn3 sample r integration
- delete map for sample list to values
- add db util file
- add python msql-client dependency
- add db for fetching lit correlation results
- add unittests for db utils
- add tests for db_utils
- modify api for fetching lit correlation results
- refactor Mock Database Connector and unittests
- add sql url parser
- add SQL URI env variable
- refactor code for db utils
- modify return data for lit correlation
- refactor tissue correlation endpoint
- replace db_instance with conn---
gn3/api/correlation.py | 39 ++++++++++++++++++++++++++++++---------
1 file changed, 30 insertions(+), 9 deletions(-)
(limited to 'gn3/api')
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 53ea6a7..2339088 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -1,6 +1,4 @@
"""Endpoints for running correlations"""
-from unittest import mock
-
from flask import jsonify
from flask import Blueprint
from flask import request
@@ -8,11 +6,31 @@ from flask import request
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
-
+from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.db_utils import database_connector
correlation = Blueprint("correlation", __name__)
+@correlation.route("/sample_x/<string:corr_method>", methods=["POST"])
+def compute_sample_integration(corr_method="pearson"):
+ """temporary api to help integrate genenetwork2 to genenetwork3 """
+
+ correlation_input = request.get_json()
+
+ target_samplelist = correlation_input.get("target_samplelist")
+ target_data_values = correlation_input.get("target_dataset")
+ this_trait_data = correlation_input.get("trait_data")
+
+ results = map_shared_keys_to_values(target_samplelist, target_data_values)
+
+ correlation_results = compute_all_sample_correlation(corr_method=corr_method,
+ this_trait=this_trait_data,
+ target_dataset=results)
+
+ return jsonify(correlation_results)
+
+
@correlation.route("/sample_r/<string:corr_method>", methods=["POST"])
def compute_sample_r(corr_method="pearson"):
"""correlation endpoint for computing sample r correlations\
@@ -22,11 +40,11 @@ def compute_sample_r(corr_method="pearson"):
# xtodo move code below to compute_all_sampl correlation
this_trait_data = correlation_input.get("this_trait")
- target_datasets = correlation_input.get("target_dataset")
+ target_dataset_data = correlation_input.get("target_dataset")
correlation_results = compute_all_sample_correlation(corr_method=corr_method,
this_trait=this_trait_data,
- target_dataset=target_datasets)
+ target_dataset=target_dataset_data)
return jsonify({
"corr_results": correlation_results
@@ -39,13 +57,16 @@ def compute_lit_corr(species=None, gene_id=None):
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()
+ conn, _cursor_object = database_connector()
target_traits_gene_ids = request.get_json()
+ target_trait_gene_list = list(target_traits_gene_ids.items())
lit_corr_results = compute_all_lit_correlation(
- database_instance=database_instance, trait_lists=target_traits_gene_ids,
+ conn=conn, trait_lists=target_trait_gene_list,
species=species, gene_id=gene_id)
+ conn.close()
+
return jsonify(lit_corr_results)
@@ -54,10 +75,10 @@ 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"]
+ target_tissues_dict = tissue_input_data["target_tissues_dict"]
results = compute_all_tissue_correlation(primary_tissue_dict=primary_tissue_dict,
- target_tissues_dict_list=target_tissues_dict_list,
+ target_tissues_data=target_tissues_dict,
corr_method=corr_method)
return jsonify(results)
--
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