Merge branch 'testing' into feature/generalize_tables

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.