From cf42f769ec4db2efaebca64c63454935cc28b2a3 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 25 Mar 2021 03:55:16 +0300
Subject: modify gn3 integration code
---
wqflask/wqflask/correlation/correlation_gn3_api.py | 89 +++++++++-------------
.../wqflask/templates/demo_correlation_page.html | 22 +-----
2 files changed, 38 insertions(+), 73 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 7e269e41..7e865bf3 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -10,59 +10,6 @@ from wqflask.base.trait import retrieve_sample_data
GN3_CORRELATION_API = "http://127.0.0.1:8080/api/correlation"
-def compute_sample(target_dataset, trait_data, target_samplelist, method="pearson"):
- """integration for integrating sample_r api correlation"""
- data = {
- "target_dataset": target_dataset,
- "target_samplelist": target_samplelist,
- "trait_data": {
- "trait_sample_data": trait_data,
- "trait_id": "HC_Q"
- }
- }
- requests_url = f"http://127.0.0.1:8080/api/correlation/sample_x/{method}"
-
- results = requests.post(requests_url, json=data)
-
- data = results.json()
-
- return data
-
-
-def get_tissue_correlation_input(this_trait, trait_symbol_dict):
- """Gets tissue expression values for the primary trait and target tissues values"""
- primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list=[this_trait.symbol])
-
- if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
- primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower(
- )]
-
- corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list=list(trait_symbol_dict.values()))
-
- target_tissue_data = []
- for trait, symbol in list(trait_symbol_dict.items()):
- if symbol and symbol.lower() in corr_result_tissue_vals_dict:
- this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower(
- )]
-
- this_trait_data = {"trait_id": trait,
- "tissue_values": this_trait_tissue_values}
-
- target_tissue_data.append(this_trait_data)
-
- primary_tissue_data = {
- "this_id": "TT",
- "tissue_values": primary_trait_tissue_values
-
- }
-
- return (primary_tissue_data, target_tissue_data)
-
- return None
-
-
def process_samples(start_vars, sample_names, excluded_samples=None):
"""process samples method"""
sample_data = {}
@@ -81,7 +28,7 @@ def process_samples(start_vars, sample_names, excluded_samples=None):
def create_target_this_trait(start_vars):
- """this function prefetch required data for correlation"""
+ """this function creates the required trait and target dataset for correlation"""
this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset'])
target_dataset = data_set.create_dataset(
@@ -148,3 +95,37 @@ def compute_correlation(start_vars, method="pearson"):
data = corr_results.json()
return data
+
+
+def get_tissue_correlation_input(this_trait, trait_symbol_dict):
+ """Gets tissue expression values for the primary trait and target tissues values"""
+ primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=[this_trait.symbol])
+
+ if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower(
+ )]
+
+ corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=list(trait_symbol_dict.values()))
+
+ target_tissue_data = []
+ for trait, symbol in list(trait_symbol_dict.items()):
+ if symbol and symbol.lower() in corr_result_tissue_vals_dict:
+ this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower(
+ )]
+
+ this_trait_data = {"trait_id": trait,
+ "tissue_values": this_trait_tissue_values}
+
+ target_tissue_data.append(this_trait_data)
+
+ primary_tissue_data = {
+ "this_id": "TT",
+ "tissue_values": primary_trait_tissue_values
+
+ }
+
+ return (primary_tissue_data, target_tissue_data)
+
+ return None
diff --git a/wqflask/wqflask/templates/demo_correlation_page.html b/wqflask/wqflask/templates/demo_correlation_page.html
index 4d310051..ddcdf38d 100644
--- a/wqflask/wqflask/templates/demo_correlation_page.html
+++ b/wqflask/wqflask/templates/demo_correlation_page.html
@@ -10,27 +10,11 @@
{% endblock %}
{% block content %}
- {{correlation_results}}
+
-
-
-{% endblock %}
-{% block js %}
-
-
-
-
-
-
-
-
-
-
-
-
-
+
{% endblock %}
--
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