added more tests and refactorings

GC-HBOC · May 3, 2024 · 99b1e95 · 99b1e95
1 parent dd533fa
commit 99b1e95
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Showing 8 changed files with 375 additions and 144 deletions.
diff --git a/resources/update_database/update_database_9.sql b/resources/update_database/update_database_9.sql
@@ -1,2 +1,4 @@
 ALTER TABLE `HerediVar_ahdoebm1`.`annotation_queue` 
 CHANGE COLUMN `status` `status` ENUM('pending', 'success', 'error', 'retry', 'aborted', 'progress') NOT NULL DEFAULT 'pending' ;
+
+UPDATE HerediVar_ahdoebm1.annotation_type SET is_deleted = 1 WHERE title = "maxentscan_ref" OR title = "maxentscan_alt";
diff --git a/src/frontend_celery/playwright/conftest.py b/src/frontend_celery/playwright/conftest.py
@@ -53,7 +53,7 @@ def page(browser):
     utils.screenshot(page)
 
 
-@pytest.fixture(autouse=True)
+@pytest.fixture(autouse=False)
 def _rollback():
     yield
     utils.execute_sql_script("/mnt/storage2/users/ahdoebm1/HerediVar/src/frontend_celery/playwright/data/truncate.sql")

diff --git a/src/frontend_celery/playwright/start_tests.sh b/src/frontend_celery/playwright/start_tests.sh
@@ -54,7 +54,7 @@ fi
 cd $TESTDIR
 export TESTUSER=$TEST_READONLY
 export TESTUSERPW=$TEST_READONLY_PW
-pytest --screenshot=only-on-failure --browser firefox tests/read_only/ -k 'test_varaint_details_access' #-k 'test_dev' --browser webkit --browser chromium --numprocesses 2
+pytest --screenshot=only-on-failure --browser firefox tests/read_only/ -k 'test_variant_details_consequences' #-k 'test_dev' --browser webkit --browser chromium --numprocesses 2
 
 # stop services
 #pkill -s 0 -e java

diff --git a/src/frontend_celery/playwright/tests/read_only/test_variant_details.py b/src/frontend_celery/playwright/tests/read_only/test_variant_details.py
diff --git a/src/frontend_celery/playwright/update_static_data.sh b/src/frontend_celery/playwright/update_static_data.sh
@@ -79,7 +79,7 @@ echo $path_to_structure
 echo $path_to_data
 
 
-static_data_tables="annotation_type classification_scheme classification_criterium classification_criterium_strength classification_scheme_alias mutually_exclusive_criteria mutually_inclusive_criteria user"
+static_data_tables="annotation_type classification_scheme classification_criterium classification_criterium_strength classification_scheme_alias mutually_exclusive_criteria mutually_inclusive_criteria user heredicare_ZID"
 
 
 # dump structure

diff --git a/src/frontend_celery/playwright/utils/functions.py b/src/frontend_celery/playwright/utils/functions.py
@@ -9,7 +9,7 @@
 sys.path.append(path.dirname(path.dirname(path.dirname(path.dirname(path.abspath(__file__))))))
 import common.functions as functions
 from subprocess import Popen, PIPE, STDOUT
-
+import requests
 
 GOOD_STATI=[200, 302, 304]
 ERROR_STATI=[500, 302, 304]
@@ -86,6 +86,29 @@ def nav(meth, expected_stati, *args, **kwargs):
     assert response.status in expected_stati, f"{response.request.method} {response.url} returned {response.status}"
 
 
+
+
+def check_all_links(page):
+    # check external links
+    locator = page.locator(".external_link")
+    nlinks = locator.count()
+    for i in range(1, nlinks+1): # idk why it is not possible to iterate over the locator which matches multiple elements. Thus, we do this shiz
+        url = page.locator(":nth-match(.external_link, " + str(i) + ")").get_attribute("uri")
+        resp = requests.get(url)
+        assert resp.status_code in GOOD_STATI, "The external link " + url + " returned status code " + resp.status_code
+
+    # check standard href links
+    base_url = get_base_url(page)
+    link_handles = page.locator("[href]")
+    for handle in link_handles.element_handles():
+        link = handle.get_attribute('href')
+        if link == '#':
+            continue
+        if not link.startswith("http"):
+            link = base_url.strip('/') + link
+        resp = requests.get(link)
+        assert resp.status_code in GOOD_STATI, "The href powered link " + link + " returned status code " + resp.status_code
+
 #import json
 #def test(route, post_data):
 #    post_data = json.dumps(post_data)

diff --git a/src/frontend_celery/webapp/templates/macros.html b/src/frontend_celery/webapp/templates/macros.html
diff --git a/src/frontend_celery/webapp/templates/variant/variant_base.html b/src/frontend_celery/webapp/templates/variant/variant_base.html
@@ -326,7 +326,7 @@ <h4 class="card-subcaption">ClinVar classifications</h4>
                     {% if variant.annotations.brca_exchange_clinical_significance is not none %}
                     <div class="ssb">
                         <h4 class="card-subcaption">BRCA exchange classification</h4>
-                        <div class="ssl">
+                        <div class="ssl" data-testid="annotation-{{variant.annotations.brca_exchange_clinical_significance.title}}">
                             {{variant.annotations.brca_exchange_clinical_significance.value}}
                         </div>
                     </div>