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authorFrederick Muriuki Muriithi2022-08-10 12:02:54 +0300
committerFrederick Muriuki Muriithi2022-08-10 12:48:53 +0300
commitaebd4ec7ba5763953fefa9299e1cdcba19f7a673 (patch)
tree70dd9161d87fcc9edbce4824046387d22f5a7e5f
parent3c117eebe6b0973db7f3fe6cf15f1109b883e629 (diff)
downloadgenenetwork2-aebd4ec7ba5763953fefa9299e1cdcba19f7a673.tar.gz
Fix formatting for legibility
-rw-r--r--test/requests/correlation_tests.py44
-rwxr-xr-xtest/requests/test-website.py2
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py23
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py39
4 files changed, 73 insertions, 35 deletions
diff --git a/test/requests/correlation_tests.py b/test/requests/correlation_tests.py
new file mode 100644
index 00000000..b0213ff5
--- /dev/null
+++ b/test/requests/correlation_tests.py
@@ -0,0 +1,44 @@
+import requests
+from lxml.html import parse
+from link_checker import check_page
+
+def do_request(host, data):
+ return request.get(
+ f"{host}/corr_compute",
+ params={
+ **data,
+ "corr_dataset": "HC_M2_0606_P",
+ "corr_return_results": "100",
+ "corr_samples_group": "samples_primary",})
+
+def check_sample_correlations(baseurl):
+ data = {
+ "corr_type": "sample",
+ "corr_sample_method": "pearson",
+ "location_type": "gene"
+ }
+ result = do_request(host, data)
+ assert result.status == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), ""
+
+def check_tissue_correlations(baseurl):
+ data = {
+ "corr_type": "tissue"
+ }
+ result = do_request(host, data)
+ assert False, "Not implemented yet."
+
+def check_lit_correlations(baseurl):
+ data = {
+ "corr_type": "lit"
+ }
+ result = do_request(host, data)
+ assert False, "Not implemented yet."
+
+def check_correlations(args_obj, parser):
+ print("")
+ print("Checking the correlations...")
+ host = args_obj.host
+ check_sample_correlations(host)
+ check_tissue_correlations(host)
+ check_lit_correlations(host)
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 71055fca..8062bff1 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -9,6 +9,7 @@ from link_checker import check_links
from link_checker import check_packaged_js_files
from mapping_tests import check_mapping
from navigation_tests import check_navigation
+from correlation_tests import check_correlations
from main_web_functionality import check_main_web_functionality
import link_checker
import sys
@@ -28,6 +29,7 @@ def run_all(args_obj, parser):
check_links(args_obj, parser)
check_packaged_js_files(args_obj, parser)
check_mapping(args_obj, parser)
+ check_correlations(args_obj, parser)
# TODO: Add other functions as they are created.
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index e1e2613d..6df4eafe 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -224,19 +224,16 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
correlation_results = correlation_results[0:corr_return_results]
if (compute_all):
- correlation_results = compute_corr_for_top_results(start_vars,
- correlation_results,
- this_trait,
- this_dataset,
- target_dataset,
- corr_type)
-
- correlation_data = {"correlation_results": correlation_results,
- "this_trait": this_trait.name,
- "target_dataset": start_vars['corr_dataset'],
- "return_results": corr_return_results}
-
- return correlation_data
+ correlation_results = compute_corr_for_top_results(
+ start_vars, correlation_results, this_trait, this_dataset,
+ target_dataset, corr_type)
+
+ return {
+ "correlation_results": correlation_results,
+ "this_trait": this_trait.name,
+ "target_dataset": start_vars['corr_dataset'],
+ "return_results": corr_return_results
+ }
def compute_corr_for_top_results(start_vars,
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
index 8431f179..8a5021cc 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -33,8 +33,11 @@ def compute_top_n_tissue(this_dataset, this_trait, traits, method):
# refactor lots of rpt
- trait_symbol_dict = dict({trait_name: symbol for (
- trait_name, symbol) in this_dataset.retrieve_genes("Symbol").items() if traits.get(trait_name)})
+ trait_symbol_dict = dict({
+ trait_name: symbol
+ for (trait_name, symbol)
+ in this_dataset.retrieve_genes("Symbol").items()
+ if traits.get(trait_name)})
corr_result_tissue_vals_dict = get_trait_symbol_and_tissue_values(
symbol_list=list(trait_symbol_dict.values()))
@@ -73,8 +76,9 @@ def merge_results(dict_a, dict_b, dict_c):
return correlation_results
-def compute_correlation_rust(start_vars: dict, corr_type: str,
- method: str = "pearson", n_top: int = 500):
+def compute_correlation_rust(
+ start_vars: dict, corr_type: str, method: str = "pearson",
+ n_top: int = 500):
"""function to compute correlation"""
(this_dataset, this_trait, target_dataset,
@@ -96,25 +100,15 @@ def compute_correlation_rust(start_vars: dict, corr_type: str,
target_data.append(r)
- results = run_correlation(target_data,
- list(sample_data.values()),
- method,
- ",",
- corr_type,
- n_top)
+ results = run_correlation(
+ target_data, list(sample_data.values()), method, ",", corr_type,
+ n_top)
# example compute of compute both correlation
-
-
-
top_tissue_results = compute_top_n_tissue(this_dataset,this_trait,results,method)
-
-
top_lit_results = compute_top_n_lit(results,this_dataset,this_trait)
-
# merging the results
-
results = merge_results(results,top_tissue_results,top_lit_results)
if corr_type == "tissue":
@@ -134,8 +128,9 @@ def compute_correlation_rust(start_vars: dict, corr_type: str,
results = run_correlation(
data[1], data[0], method, ",", "tissue")
- return {"correlation_results": results,
- "this_trait": this_trait.name,
- "target_dataset": start_vars['corr_dataset'],
- "return_results": n_top
- }
+ return {
+ "correlation_results": results,
+ "this_trait": this_trait.name,
+ "target_dataset": start_vars['corr_dataset'],
+ "return_results": n_top
+ }