Revert "TN-3324 robust handling of unsortable patient list attributes"

portal/models/patient_list.py

@@ -53,53 +53,49 @@ def patient_list_update_patient(patient_id, research_study_id=None):
     if not user.has_role(ROLE.PATIENT.value):
         return
 
-    from ..timeout_lock import TimeoutLock
-    # async possibility, only allow one thread at a time
-    key = f"patient_list_update_patient:{patient_id}"
-    with TimeoutLock(key, expires=60, timeout=60):
-        patient = PatientList.query.get(patient_id)
-        new_record = False
-        if not patient:
-            new_record = True
-            patient = PatientList(userid=patient_id)
-            db.session.add(patient)
+    patient = PatientList.query.get(patient_id)
+    new_record = False
+    if not patient:
+        new_record = True
+        patient = PatientList(userid=patient_id)
+        db.session.add(patient)
 
-        if research_study_id is None or new_record:
-            patient.study_id = user.external_study_id
-            patient.firstname = user.first_name
-            patient.lastname = user.last_name
-            patient.email = user.email
-            patient.birthdate = user.birthdate
-            patient.deleted = user.deleted_id is not None
-            patient.test_role = True if user.has_role(ROLE.TEST.value) else False
-            patient.org_id = user.organizations[0].id if user.organizations else None
-            patient.org_name = user.organizations[0].name if user.organizations else None
+    if research_study_id is None or new_record:
+        patient.study_id = user.external_study_id
+        patient.firstname = user.first_name
+        patient.lastname = user.last_name
+        patient.email = user.email
+        patient.birthdate = user.birthdate
+        patient.deleted = user.deleted_id is not None
+        patient.test_role = True if user.has_role(ROLE.TEST.value) else False
+        patient.org_id = user.organizations[0].id if user.organizations else None
+        patient.org_name = user.organizations[0].name if user.organizations else None
 
-        # necessary to avoid recursive loop via some update paths
-        now = datetime.utcnow()
-        if patient.last_updated and patient.last_updated + timedelta(seconds=10) > now:
-            db.session.commit()
-            return
+    # necessary to avoid recursive loop via some update paths
+    now = datetime.utcnow()
+    if patient.last_updated and patient.last_updated + timedelta(seconds=10) > now:
+        db.session.commit()
+        return
 
-        patient.last_updated = now
-        if research_study_id == BASE_RS_ID or research_study_id is None:
-            rs_id = BASE_RS_ID
-            qb_status = qb_status_visit_name(
-                 patient.userid, research_study_id=rs_id, as_of_date=now)
-            patient.questionnaire_status = str(qb_status['status'])
-            patient.visit = qb_status['visit_name']
-            patient.consentdate, _ = consent_withdrawal_dates(user=user, research_study_id=rs_id)
+    patient.last_updated = now
+    if research_study_id == BASE_RS_ID or research_study_id is None:
+        rs_id = BASE_RS_ID
+        qb_status = qb_status_visit_name(
+             patient.userid, research_study_id=rs_id, as_of_date=now)
+        patient.questionnaire_status = str(qb_status['status'])
+        patient.visit = qb_status['visit_name']
+        patient.consentdate, _ = consent_withdrawal_dates(user=user, research_study_id=rs_id)
 
-        if (research_study_id == EMPRO_RS_ID or research_study_id is None) and user.clinicians:
-            rs_id = EMPRO_RS_ID
-            patient.clinician = '; '.join(
-                (clinician_name_map().get(c.id, "not in map") for c in user.clinicians)) or ""
-            qb_status = qb_status_visit_name(
-                patient.userid, research_study_id=rs_id, as_of_date=now)
-            patient.empro_status = str(qb_status['status'])
-            patient.empro_visit = qb_status['visit_name']
-            patient.action_state = qb_status['action_state'].title() \
-                if qb_status['action_state'] else ""
-            patient.empro_consentdate, _ = consent_withdrawal_dates(
-                user=user, research_study_id=rs_id)
-        db.session.commit()
+    if (research_study_id == EMPRO_RS_ID or research_study_id is None) and user.clinicians:
+        rs_id = EMPRO_RS_ID
+        patient.clinician = '; '.join(
+            (clinician_name_map().get(c.id, "not in map") for c in user.clinicians)) or ""
+        qb_status = qb_status_visit_name(
+            patient.userid, research_study_id=rs_id, as_of_date=now)
+        patient.empro_status = str(qb_status['status'])
+        patient.empro_visit = qb_status['visit_name']
+        patient.action_state = qb_status['action_state'].title() \
+            if qb_status['action_state'] else ""
+        patient.empro_consentdate, _ = consent_withdrawal_dates(
+            user=user, research_study_id=rs_id)
+    db.session.commit()

portal/models/qb_status.py

@@ -49,8 +49,8 @@ def _sync_timeline(self):
 
         completed = QBT.query.filter(QBT.user_id == self.user.id).filter(
             QBT.research_study_id == self.research_study_id).filter(
-            QBT.status == OverallStatus.completed).with_entities(QBT.id).first()
-        self.at_least_one_completed = completed is not None
+            QBT.status == OverallStatus.completed).count()
+        self.at_least_one_completed = completed > 0
 
         # Obtain withdrawal date if applicable
         withdrawn = QBT.query.filter(QBT.user_id == self.user.id).filter(

portal/static/js/src/admin.js

@@ -1323,8 +1323,7 @@ let requestTimerId = 0;
       ) {
         var tnthAjax = this.getDependency("tnthAjax");
         tableName = tableName || this.tableIdentifier;
-        if (!tableName || !document.querySelector("#adminTable")) {
-          if (callback) callback();
+        if (!tableName) {
           return false;
         }
         userId = userId || this.userId;

portal/static/js/src/modules/TnthAjax.js

@@ -93,16 +93,6 @@ export default { /*global $ */
             $.ajax("/api/me").done(
                 function() {
                     console.log("user authorized");
-                    if ((typeof CsrfTokenChecker !== "undefined") && 
-                        !CsrfTokenChecker.checkTokenValidity()) {
-                        //if CSRF Token not valid, return error
-                        if (callback) {
-                            callback({"error": DEFAULT_SERVER_DATA_ERROR});
-                            fieldHelper.showError(targetField);
-                        }
-                        return;
-                    }
-
                     ajaxCall();
                 }
             ).fail(function() {

portal/templates/admin/admin_base.html

@@ -93,8 +93,6 @@
     // custom ajax request here
     function patientDataAjaxRequest(params) {
 		loadIntervalId = setInterval(() => {
-			//document DOM not ready, don't make ajax call yet
-			if (!document.querySelector("#adminTable")) return;
 			if (typeof window.AdminObj === "undefined") return;
 			window.AdminObj.getRemotePatientListData(params);
 			clearInterval(loadIntervalId);

portal/views/patients.py

@@ -109,10 +109,6 @@ def filter_query(query, filter_field, filter_value):
         # ignore requests to filter by unknown column
         return query
 
-    if filter_field in ('birthdate', 'consentdate', 'empro_consentdate'):
-        # these are not filterable (partial strings on date complexity) - ignore such a request
-        return query
-
     if filter_field == 'userid':
         query = query.filter(PatientList.userid == int(filter_value))
         return query

requirements.dev.txt

@@ -20,6 +20,7 @@ pyparsing==2.4.7          # via packaging
 pytest >= 6.1.0
 pytest-flask==0.15.1
 pytest-timeout==1.4.2
+selenium==3.141.0
 snowballstemmer==2.0.0    # via sphinx
 sphinx-rtd-theme==0.5.1
 sphinx==3.3.1
@@ -35,4 +36,5 @@ virtualenv==20.4.2        # via tox
 waitress==1.4.3           # via webtest
 webob==1.8.5              # via webtest
 webtest==2.0.33           # via flask-webtest
+xvfbwrapper==0.2.9
 --editable .

tests/integration_tests/__init__.py

@@ -0,0 +1,141 @@
+"""Unit test module for Selenium testing"""
+
+import os
+import sys
+import unittest
+
+from flask_testing import LiveServerTestCase
+import pytest
+from selenium import webdriver
+from selenium.webdriver.support.ui import WebDriverWait
+import xvfbwrapper
+
+from tests import TestCase
+
+
+@unittest.skipUnless(
+    (
+        "SAUCE_USERNAME" in os.environ or
+        xvfbwrapper.Xvfb().xvfb_exists()
+    ),
+    "Xvfb not installed"
+)
+class IntegrationTestCase(TestCase, LiveServerTestCase):
+    """Test class for UI integration/workflow testing"""
+
+    def setUp(self):
+        """Reset all tables before testing."""
+
+        if "SAUCE_USERNAME" in os.environ:
+            # Configure driver for Sauce Labs
+            # Presumes tunnel setup by Sauce Connect
+            # On TravisCI, Sauce Connect tunnel setup by Sauce Labs addon
+            # https://docs.travis-ci.com/user/sauce-connect
+            platform = {
+                "browserName": "firefox",
+                "platform": "Windows 10",
+                "version": "60.0",
+            }
+            capabilities = {
+                "tunnel-identifier": os.environ["TRAVIS_JOB_NUMBER"],
+                "extendedDebugging": "true",
+            }
+            metadata = {
+                "name": self.id(),
+                "build": "#%s %s" % (
+                    os.environ["TRAVIS_BUILD_NUMBER"],
+                    os.environ["TRAVIS_BRANCH"],
+                ),
+                "tags": [
+                    "py" + os.environ["TRAVIS_PYTHON_VERSION"],
+                    "CI",
+                ],
+                "passed": False,
+            }
+            capabilities.update(platform)
+            capabilities.update(metadata)
+
+            url = "http://{user}:{access_key}@localhost:4445/wd/hub".format(
+                user=os.environ["SAUCE_USERNAME"],
+                access_key=os.environ["SAUCE_ACCESS_KEY"],
+            )
+
+            self.driver = webdriver.Remote(
+                desired_capabilities=capabilities,
+                command_executor=url
+            )
+
+        else:
+            if "DISPLAY" not in os.environ:
+                # Non-graphical environment; use xvfb
+                self.xvfb = xvfbwrapper.Xvfb()
+                self.addCleanup(self.xvfb.stop)
+                self.xvfb.start()
+            self.driver = webdriver.Firefox(timeout=60)
+
+        self.addCleanup(self.driver.quit)
+
+        self.driver.root_uri = self.get_server_url()
+        self.driver.implicitly_wait(30)
+        self.verificationErrors = []
+        # default explicit wait time; use with Expected Conditions as needed
+        self.wait = WebDriverWait(self.driver, 60)
+        self.accept_next_alert = True
+
+        super(IntegrationTestCase, self).setUp()
+
+    def is_element_present(self, how, what):
+        """Detects whether or not an element can be found in DOM
+
+        This function was exported from Selenium IDE
+        """
+        try:
+            self.driver.find_element(by=how, value=what)
+        except NoSuchElementException as e:
+            return False
+        return True
+
+    def is_alert_present(self):
+        """Detects whether an alert message is present
+
+        This function was exported from Selenium IDE
+        """
+        try:
+            self.driver.switch_to_alert()
+        except NoAlertPresentException as e:
+            return False
+        return True
+
+    def close_alert_and_get_its_text(self):
+        """Closes an alert, if present, and returns its text
+
+        If an alert is not present a NoAlertPresentException
+        will be thrown.
+        This function was exported from Selenium IDE
+        """
+        try:
+            alert = self.driver.switch_to_alert()
+            alert_text = alert.text
+            if self.accept_next_alert:
+                alert.accept()
+            else:
+                alert.dismiss()
+            return alert_text
+        finally:
+            self.accept_next_alert = True
+
+    def tearDown(self):
+        """Clean db session, drop all tables."""
+
+        # Update job result metadata on Sauce Labs, if available
+        if (
+            "SAUCE_USERNAME" in os.environ and
+
+            # No exception being handled - test completed successfully
+            sys.exc_info() == (None, None, None)
+        ):
+            self.driver.execute_script("sauce:job-result=passed")
+
+        self.assertEqual([], self.verificationErrors)
+
+        super(IntegrationTestCase, self).tearDown()

tests/integration_tests/pages.py

@@ -0,0 +1,8 @@
+from page_objects import PageElement, PageObject
+
+
+class LoginPage(PageObject):
+    username = PageElement(name='email')
+    password = PageElement(name='password')
+    login_button = PageElement(css='input[type="submit"]')
+    facebook_button = PageElement(css='.btn-facebook')

tests/integration_tests/test_login.py

@@ -0,0 +1,64 @@
+from flask import url_for
+import pytest
+from selenium.webdriver.support.ui import Select
+
+from tests import DEFAULT_PASSWORD, TEST_USERNAME
+from tests.integration_tests import IntegrationTestCase
+
+
+class TestLogin(IntegrationTestCase):
+    """Test class for Login integration tests"""
+
+    def test_login_page(self):
+        """Ensure login works properly"""
+        driver = self.driver
+        driver.get(url_for("user.login", _external=True))
+
+        driver.find_element_by_name("email").click()
+        driver.find_element_by_name("email").clear()
+        driver.find_element_by_name("email").send_keys(TEST_USERNAME)
+        driver.find_element_by_name("password").click()
+        driver.find_element_by_name("password").clear()
+        driver.find_element_by_name("password").send_keys(DEFAULT_PASSWORD)
+        driver.find_element_by_xpath(
+            "//input[@class='btn btn-tnth-primary btn-lg' and @value='LOG IN']"
+        ).click()
+        driver.find_element_by_id("tnthUserBtn").click()
+        driver.find_element_by_link_text("Log Out of TrueNTH").click()
+
+    @pytest.mark.skip(reason="not able to complete consent page")
+    def test_consent_after_login(self):
+        driver = self.driver
+        driver.get(url_for("eproms.home", _external=True))
+        driver.find_element_by_id("email").click()
+        driver.find_element_by_id("email").clear()
+        driver.find_element_by_id("email").send_keys(TEST_USERNAME)
+        driver.find_element_by_id("password").click()
+        driver.find_element_by_id("password").clear()
+        driver.find_element_by_id("password").send_keys(DEFAULT_PASSWORD)
+        driver.find_element_by_id("btnLogin").click()
+        driver.find_element_by_xpath("(.//*[normalize-space(text()) and normalize-space(.)='General Terms of Use'])[1]/following::i[1]").click()
+        driver.find_element_by_xpath("(.//*[normalize-space(text()) and normalize-space(.)='General Terms of Use'])[1]/following::i[2]").click()
+        driver.find_element_by_id("next").click()
+        driver.find_element_by_id("firstname").clear()
+        driver.find_element_by_id("firstname").send_keys("Test")
+        driver.find_element_by_id("lastname").click()
+        driver.find_element_by_id("lastname").clear()
+        driver.find_element_by_id("lastname").send_keys("User")
+        driver.find_element_by_id("date").click()
+        driver.find_element_by_id("month").click()
+        driver.find_element_by_xpath("(.//*[normalize-space(text()) and normalize-space(.)='(optional)'])[1]/following::option[11]").click()
+        driver.find_element_by_id("year").click()
+        driver.find_element_by_id("year").clear()
+        driver.find_element_by_id("year").send_keys("1988")
+        driver.find_element_by_id("role_patient").click()
+        driver.find_element_by_id("next").click()
+        driver.find_element_by_id("biopsy_no").click()
+        driver.find_element_by_id("next").click()
+        driver.find_element_by_id("stateSelector").click()
+        Select(driver.find_element_by_id("stateSelector")).select_by_visible_text("Washington")
+        driver.find_element_by_xpath("(.//*[normalize-space(text()) and normalize-space(.)='Your clinic of care.'])[1]/following::option[12]").click()
+        driver.find_element_by_xpath("(.//*[normalize-space(text()) and normalize-space(.)='UW Medicine (University of Washington)'])[1]/following::label[1]").click()
+        driver.find_element_by_id("updateProfile").click()
+        driver.find_element_by_id("tnthUserBtn").click()
+        driver.find_element_by_link_text("Log Out of TrueNTH").click()