diff options
Diffstat (limited to 'test')
| -rw-r--r-- | test/requests/correlation_tests.py | 70 | ||||
| -rw-r--r-- | test/requests/link_checker.py | 5 | ||||
| -rw-r--r-- | test/requests/main_web_functionality.py | 10 | ||||
| -rwxr-xr-x | test/requests/test-website.py | 15 |
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. |