aboutsummaryrefslogtreecommitdiff
path: root/test
diff options
context:
space:
mode:
Diffstat (limited to 'test')
-rw-r--r--test/requests/correlation_tests.py70
-rw-r--r--test/requests/link_checker.py5
-rw-r--r--test/requests/main_web_functionality.py10
-rwxr-xr-xtest/requests/test-website.py15
4 files changed, 94 insertions, 6 deletions
diff --git a/test/requests/correlation_tests.py b/test/requests/correlation_tests.py
new file mode 100644
index 00000000..abb5794a
--- /dev/null
+++ b/test/requests/correlation_tests.py
@@ -0,0 +1,70 @@
+import requests
+from lxml.html import parse
+from link_checker import check_page
+
+def sample_vals():
+ return '{"C57BL/6J":"10.835","DBA/2J":"11.142","B6D2F1":"11.126","D2B6F1":"11.143","BXD1":"10.811","BXD2":"11.503","BXD5":"10.766","BXD6":"10.986","BXD8":"11.050","BXD9":"10.822","BXD11":"10.670","BXD12":"10.946","BXD13":"10.890","BXD14":"x","BXD15":"10.884","BXD16":"11.222","BXD18":"x","BXD19":"10.968","BXD20":"10.962","BXD21":"10.906","BXD22":"11.080","BXD23":"11.046","BXD24":"11.146","BXD24a":"x","BXD25":"x","BXD27":"11.078","BXD28":"11.034","BXD29":"10.808","BXD30":"x","BXD31":"11.087","BXD32":"11.029","BXD33":"10.662","BXD34":"11.482","BXD35":"x","BXD36":"x","BXD37":"x","BXD38":"10.836","BXD39":"10.926","BXD40":"10.638","BXD41":"x","BXD42":"10.974","BXD43":"10.828","BXD44":"10.900","BXD45":"11.358","BXD48":"11.042","BXD48a":"10.975","BXD49":"x","BXD50":"11.228","BXD51":"11.126","BXD52":"x","BXD53":"x","BXD54":"x","BXD55":"11.580","BXD56":"x","BXD59":"x","BXD60":"10.829","BXD61":"11.152","BXD62":"11.156","BXD63":"10.942","BXD64":"10.506","BXD65":"11.126","BXD65a":"11.272","BXD65b":"11.157","BXD66":"11.071","BXD67":"11.080","BXD68":"10.997","BXD69":"11.096","BXD70":"11.152","BXD71":"x","BXD72":"x","BXD73":"11.262","BXD73a":"11.444","BXD73b":"x","BXD74":"10.974","BXD75":"11.150","BXD76":"10.920","BXD77":"10.928","BXD78":"x","BXD79":"11.371","BXD81":"x","BXD83":"10.946","BXD84":"11.181","BXD85":"10.992","BXD86":"10.770","BXD87":"11.200","BXD88":"x","BXD89":"10.930","BXD90":"11.183","BXD91":"x","BXD93":"11.056","BXD94":"10.737","BXD95":"x","BXD98":"10.986","BXD99":"10.892","BXD100":"x","BXD101":"x","BXD102":"x","BXD104":"x","BXD105":"x","BXD106":"x","BXD107":"x","BXD108":"x","BXD109":"x","BXD110":"x","BXD111":"x","BXD112":"x","BXD113":"x","BXD114":"x","BXD115":"x","BXD116":"x","BXD117":"x","BXD119":"x","BXD120":"x","BXD121":"x","BXD122":"x","BXD123":"x","BXD124":"x","BXD125":"x","BXD126":"x","BXD127":"x","BXD128":"x","BXD128a":"x","BXD130":"x","BXD131":"x","BXD132":"x","BXD133":"x","BXD134":"x","BXD135":"x","BXD136":"x","BXD137":"x","BXD138":"x","BXD139":"x","BXD141":"x","BXD142":"x","BXD144":"x","BXD145":"x","BXD146":"x","BXD147":"x","BXD148":"x","BXD149":"x","BXD150":"x","BXD151":"x","BXD152":"x","BXD153":"x","BXD154":"x","BXD155":"x","BXD156":"x","BXD157":"x","BXD160":"x","BXD161":"x","BXD162":"x","BXD165":"x","BXD168":"x","BXD169":"x","BXD170":"x","BXD171":"x","BXD172":"x","BXD173":"x","BXD174":"x","BXD175":"x","BXD176":"x","BXD177":"x","BXD178":"x","BXD180":"x","BXD181":"x","BXD183":"x","BXD184":"x","BXD186":"x","BXD187":"x","BXD188":"x","BXD189":"x","BXD190":"x","BXD191":"x","BXD192":"x","BXD193":"x","BXD194":"x","BXD195":"x","BXD196":"x","BXD197":"x","BXD198":"x","BXD199":"x","BXD200":"x","BXD201":"x","BXD202":"x","BXD203":"x","BXD204":"x","BXD205":"x","BXD206":"x","BXD207":"x","BXD208":"x","BXD209":"x","BXD210":"x","BXD211":"x","BXD212":"x","BXD213":"x","BXD214":"x","BXD215":"x","BXD216":"x","BXD217":"x","BXD218":"x","BXD219":"x","BXD220":"x"}'
+
+def do_request(url, data):
+ return requests.post(
+ url,
+ data={
+ "dataset": "HC_M2_0606_P",
+ "trait_id": "1435464_at",
+ "corr_dataset": "HC_M2_0606_P",
+ "corr_sample_method": "pearson",
+ "corr_return_results": "100",
+ "corr_samples_group": "samples_primary",
+ "sample_vals": sample_vals(),
+ **data,
+ })
+
+def check_sample_correlations(baseurl):
+ data = {
+ "corr_type": "sample",
+ "corr_sample_method": "pearson",
+ "location_type": "gene",
+ "corr_return_results": "200"
+ }
+ top_n_message = "The top 200 correlations ranked by the Genetic Correlation"
+ result = do_request(f"{baseurl}/corr_compute", data)
+ assert result.status_code == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), result.text
+ assert (result.text.find(top_n_message) >= 0), result.text
+
+def check_tissue_correlations(baseurl):
+ data = {
+ "corr_type": "tissue",
+ "location_type": "gene",
+ }
+ top_n_message = "The top 100 correlations ranked by the Tissue Correlation"
+ result = do_request(f"{baseurl}/corr_compute", data)
+ assert result.status_code == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), result.text
+ assert (result.text.find(top_n_message) >= 0), result.text
+
+def check_lit_correlations(baseurl):
+ data = {
+ "corr_type": "lit",
+ "corr_return_results": "200"
+ }
+ top_n_message = "The top 200 correlations ranked by the Literature Correlation"
+ result = do_request(f"{baseurl}/corr_compute", data)
+ assert result.status_code == 200
+ assert (result.text.find("Values of record 1435464_at") >= 0), result.text
+ assert (result.text.find(top_n_message) >= 0), result.text
+
+def check_correlations(args_obj, parser):
+ print("")
+ print("Checking the correlations...")
+ corr_type_fns = {
+ "sample": check_sample_correlations,
+ "tissue": check_tissue_correlations,
+ "lit": check_lit_correlations
+ }
+ host = args_obj.host
+ for corr_type, corr_type_fn in corr_type_fns.items():
+ print(f"\tChecking {corr_type} correlations...", end="")
+ corr_type_fn(host)
+ print(" ok")
+ print("OK")
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index feae6526..86222254 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -1,6 +1,6 @@
import re
import requests
-from lxml.html import parse
+from lxml.html import document_fromstring
from requests.exceptions import ConnectionError
DO_FAIL=False # fail on error
@@ -66,7 +66,8 @@ def verify_static_file(link):
def check_page(host, start_url):
print("")
print("Checking links host "+host+" in page `"+start_url+"`")
- doc = parse(start_url).getroot()
+ req = requests.get(start_url)
+ doc = document_fromstring(start_url)
links = get_links(doc)
in_page_links = list(filter(is_in_page_link, links))
internal_links = list(filter(is_internal_link, links))
diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
index 28033ad5..79f37bb4 100644
--- a/test/requests/main_web_functionality.py
+++ b/test/requests/main_web_functionality.py
@@ -1,10 +1,11 @@
import requests
-from lxml.html import parse
+from lxml.html import document_fromstring
from link_checker import check_page
def check_home(url):
- doc = parse(url).getroot()
+ results = requests.get(url)
+ doc = document_fromstring(results.text)
search_button = doc.cssselect("#btsearch")
assert(search_button[0].value == "Search")
print("OK")
@@ -18,7 +19,7 @@ def check_search_page(host):
search_terms_or="",
search_terms_and="MEAN=(15 16) LRS=(23 46)")
result = requests.get(host+"/search", params=data)
- found = result.text.find("records were found")
+ found = result.text.find("records found")
assert(found >= 0)
assert(result.status_code == 200)
print("OK")
@@ -27,7 +28,8 @@ def check_search_page(host):
def check_traits_page(host, traits_url):
- doc = parse(host+traits_url).getroot()
+ results = requests.get(host+traits_url)
+ doc = document_fromstring(results.text)
traits_form = doc.forms[1]
assert(traits_form.fields["corr_dataset"] == "HC_M2_0606_P")
print("OK")
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 71055fca..c0b36182 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
@@ -18,16 +19,30 @@ from unittest import TestSuite, TextTestRunner, TestLoader
print("Mechanical Rob firing up...")
+def host_is_online(host):
+ import time
+ import requests
+ for count in range(1, 5):
+ try:
+ time.sleep(count)
+ requests.get(host)
+ return True
+ except Exception as cre:
+ print(f"Retrying in {count + 1} seconds ...")
+
+ return False
def run_all(args_obj, parser):
print("")
print("Running all tests.")
print(args_obj)
+ assert host_is_online(args_obj.host), f"Could not connect to {host}"
link_checker.DO_FAIL = args_obj.fail
check_main_web_functionality(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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 12:17:23 +0000