Merge pull request #7 from usegalaxy-au/uplift_code

Uplift code

Dockerfile

@@ -1,8 +1,22 @@
 # https://github.com/joyzoursky/docker-python-chromedriver
 # https://github.com/TomRoush/python-selenium-firefox-docker
-FROM tomroush/python-selenium-firefox-docker:latest
+FROM ubuntu:22.04 AS selenium
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y \
+  python3 python3-pip \
+  # firefox needs the following installed on 22.04
+  libgtk-3-common libasound2 libdbus-glib-1-2 \
+  firefox \
+  xvfb \
+  && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install --no-cache-dir selenium requests
+
+FROM selenium
 
 ENV SELENIUM_HEADLESS=true
+ARG DEBIAN_FRONTEND=noninteractive
 
 ADD page_perf_timer.py /opt/page_timer/
 

page_perf_timer.py

@@ -1,10 +1,13 @@
 import argparse
 import functools
+import hashlib
 import os
 import sys
 import time
 import uuid
 
+import requests
+
 # Generated by Selenium IDE
 from selenium import webdriver
 from selenium.common.exceptions import NoSuchElementException
@@ -38,6 +41,7 @@ class EndStepReached(Exception):
     """
     Raised when a specific action step has been reached
     """
+
     pass
 
 
@@ -127,7 +131,7 @@ def wait_for_history_panel_to_load(self):
     @clock_action("login_page_load")
     def load_galaxy_login(self):
         # Open Galaxy window
-        self.driver.get(f"{self.server}/login")
+        self.driver.get(f"{self.server}login")
         # Wait for username entry to appear
         self.wait.until(self.is_able_to_login)
 
@@ -154,10 +158,51 @@ def login_to_galaxy_homepage(self):
         # Wait for tool panel to load
         self.wait.until(
             expected_conditions.presence_of_element_located(
-                (By.XPATH, "//div[@class='tool-panel-section']//a[@class='title-link' and contains(., 'Get Data')]")
+                (
+                    By.XPATH,
+                    "//div[@class='tool-panel-section']//a[contains(@class, 'title-link') and contains(., 'Get Data')]",
+                )
+            )
+        )
+
+    @clock_action("dummy_file_upload")
+    def upload_dummy_file(self):
+        upload_activity = self.driver.find_element(By.ID, "activity-upload")
+        upload_activity.click()
+        # paste/fetch data
+        paste_button = self.driver.find_element(By.ID, "btn-new")
+        paste_button.click()
+        # paste/fetch data
+        upload_row = self.driver.find_element(By.XPATH, "//div[@id='upload-row-0']//textarea")
+        upload_row.send_keys("https://zenodo.org/records/13711466/files/(Galaxy%20History)%20Selenium_test_1_Input_data.rocrate.zip?download=1")
+        # start
+        start_button = self.driver.find_element(By.ID, "btn-start")
+        start_button.click()
+        # close
+        close_button = self.driver.find_element(By.ID, "btn-close")
+        close_button.click()
+        # wait for history item to appear
+        self.wait.until(
+            expected_conditions.presence_of_element_located(
+                (
+                    By.XPATH,
+                    "//div[@data-index='0']//div[@data-state='running' and contains(., 'Selenium_test_1_Input_data')]",
+                )
             )
         )
 
+    @clock_action("dummy_file_download")
+    def download_dummy_file(self):
+        open_download_link = self.driver.find_element(By.XPATH, "//div[@data-index='0']//div[@data-state='running' and contains(., 'Selenium_test_1_Input_data')]")
+        open_download_link.click()
+        with SeleniumCustomWait(self.driver, 1200):
+            download_link = self.driver.find_element(By.XPATH, "//div[@data-index='0']//div[@data-state='ok' and contains(., 'Selenium_test_1_Input_data')]//a[@title='Download']")
+        r = requests.get(download_link.get_attribute("href"), stream=True)
+        sig = hashlib.md5()
+        for line in r.iter_lines():
+            sig.update(line)
+        assert sig.hexdigest() == "a62aaaefa04bdc7acd3b29a127bba3e6"
+
     @clock_action("tool_search_load")
     def search_for_tool(self):
         # Select tool search box
@@ -190,38 +235,52 @@ def load_tool_form(self):
             expected_conditions.presence_of_element_located((By.ID, "execute"))
         )
 
-    @clock_action("shared_histories_page_load")
-    def load_shared_histories(self):
+    @clock_action("published_histories_page_load")
+    def load_published_histories(self):
         # Request history page
-        self.driver.get(f"{self.server}/histories/list_shared")
+        self.driver.get(f"{self.server}histories/list_published")
 
         # Wait for history page to load
         self.wait.until(
             expected_conditions.presence_of_element_located(
-                (By.XPATH, "//h2[contains(., 'Histories shared with you by others')]")
+                (
+                    By.XPATH,
+                    "//li[@id='histories-published-tab' and contains(., 'Public Histories')]",
+                )
             )
         )
         self.wait_for_history_panel_to_load()
 
-    @clock_action("import_shared_history")
-    def import_shared_history(self):
+    @clock_action("import_published_history")
+    def import_published_history(self):
+        # Search for the relevant history
+        search_history_input = self.driver.find_element(
+            By.XPATH,
+            f"//div[@id='histories-published-grid']//input[@placeholder='search histories']",
+        )
+        search_history_input.click()
+        search_history_input.send_keys(f"{self.workflow_name.lower()}_input_data")
+
         # Select relevant history
         import_history_btn = self.driver.find_element(
             By.XPATH,
-            f"//tbody[@id='grid-table-body']//button[contains(translate(., 'ABCDEFGHIJKLMNOPQRSTUVWXYZ', 'abcdefghijklmnopqrstuvwxyz'), '{self.workflow_name.lower()}_input_data')]",
+            f"//table[@class='grid-table']//button[contains(translate(., 'ABCDEFGHIJKLMNOPQRSTUVWXYZ', 'abcdefghijklmnopqrstuvwxyz'), '{self.workflow_name.lower()}_input_data')]",
         )
-        import_history_btn.click()
-        self.wait_for_history_panel_to_load()
+        # Workaround for ElementClickInterceptedException
+        self.driver.execute_script("arguments[0].click();", import_history_btn)
 
         # View history details
-        view_history_menu_item = self.driver.find_element(
+        view_history_menu_item = import_history_btn.find_element(
             By.XPATH,
-            f"//div[@id='{import_history_btn.get_attribute('id')}-menu']//a[contains(., 'View')]",
+            f"./following-sibling::div//button[contains(@data-description, 'grid operation view')]",
         )
         view_history_menu_item.click()
         self.wait.until(
             expected_conditions.presence_of_element_located(
-                (By.XPATH, f"//h3[contains(., '{self.workflow_name.lower()}_input_data')]")
+                (
+                    By.XPATH,
+                    f"//h3[contains(translate(., 'ABCDEFGHIJKLMNOPQRSTUVWXYZ', 'abcdefghijklmnopqrstuvwxyz'), '{self.workflow_name.lower()}_input_data')]",
+                )
             )
         )
         # Invoke copy history dialogue
@@ -239,6 +298,20 @@ def import_shared_history(self):
             By.XPATH,
             f"//button[contains(., 'Copy History')]",
         ).click()
+
+        # activate the history
+        self.wait.until(
+            expected_conditions.presence_of_element_located(
+                (
+                    By.XPATH,
+                    f"//div[@class='alert alert-info' and contains(., 'History imported and is now your active history')]",
+                )
+            )
+        )
+
+        # Request history page
+        self.driver.get(f"{self.server}histories/list")
+
         # Wait for history panel to load with new history
         self.wait.until(
             expected_conditions.presence_of_element_located(
@@ -252,20 +325,37 @@ def import_shared_history(self):
     @clock_action("workflow_list_page_load")
     def load_workflow_list(self):
         # Request workflows list page
-        self.driver.get(f"{self.server}/workflows/list")
+        self.driver.get(f"{self.server}workflows/list_published")
         # Wait for workflow page to load and import button to appear
         self.wait.until(
-            expected_conditions.presence_of_element_located((By.ID, "workflow-import"))
+            expected_conditions.presence_of_element_located(
+                (By.XPATH, "//li[@id='published' and contains(., 'Public workflows')]")
+            )
         )
 
     @clock_action("workflow_run_page_load")
     def load_workflow_run_form(self):
-        # Select relevant workflow
-        run_workflow_btn = self.driver.find_element(
+        # Search for the relevant history
+        search_workflow_input = self.driver.find_element(
             By.XPATH,
-            f"//table[@id='workflow-table']//tr[contains(., '{self.workflow_name}')]//button[@title='Run workflow']",
+            f"//div[@id='workflow-list-filter']//input",
         )
-        run_workflow_btn.click()
+        search_workflow_input.click()
+        search_workflow_input.send_keys(f"{self.workflow_name.lower()}")
+
+        # wait for list to be filtered
+        self.wait.until(
+            lambda d: len(
+                d.find_elements(By.CSS_SELECTOR, "#workflow-cards .workflow-card")
+            )
+            == 1
+        )
+
+        # Select relevant workflow
+        run_workflow_btn = self.driver.find_element(By.ID, "workflow-run-button")
+        # Workaround for ElementClickInterceptedException
+        self.driver.execute_script("arguments[0].click();", run_workflow_btn)
+
         # Wait for workflow form to load and run button to appear
         self.wait.until(
             expected_conditions.presence_of_element_located((By.ID, "run-workflow"))
@@ -277,13 +367,13 @@ def run_workflow(self):
             # Select relevant choice
             input_1_select = self.driver.find_element(
                 By.XPATH,
-                "//a[@class='select2-choice' and contains(., 'Subsample of reads from')]",
+                "//div[@class='ui-form-composite']//input/following-sibling::span[contains(., 'Subsample of reads from Human exome R2')][1]",
             )
             input_1_select.click()
             # Select relevant choice
             input_1_select = self.driver.find_element(
                 By.XPATH,
-                "//div[@id='select2-drop']//ul/li/div[contains(., 'Subsample of reads from human exome R1')]",
+                "//div[@class='ui-form-composite']//ul[@role='listbox']//li[@role='option']//span[contains(., 'Subsample of reads from human exome R1')]",
             )
             input_1_select.click()
             workflow_wait = 14400
@@ -293,55 +383,55 @@ def run_workflow(self):
             # Select relevant choice
             input_1_select = self.driver.find_element(
                 By.XPATH,
-                "//div[@data-label='Forward Reads']//a[@class='select2-choice']",
+                "//div[@class='ui-form-composite']//input/following-sibling::span[contains(., 'ERR019289_2.fastq.gz')][1]",
             )
             input_1_select.click()
             # Select relevant choice
             input_1_select = self.driver.find_element(
                 By.XPATH,
-                "//div[@id='select2-drop']//ul/li/div[contains(., 'ERR019289_1.fastq.gz')]",
+                "//div[@class='ui-form-composite']//ul[@role='listbox']//li[@role='option']//span[contains(., 'ERR019289_1.fastq.gz')]",
             )
             input_1_select.click()
             workflow_wait = 14400
         elif self.workflow_name == "Selenium_test_4":
-            input_select = self.driver.find_element(
+            input_1_select = self.driver.find_element(
                 By.XPATH,
-                "//div[@data-label='ARTIC primers to amplicon assignments']//a[@class='select2-choice']",
+                "//div[@class='ui-form-composite']//div[@data-label='ARTIC primers to amplicon assignments']//input/following-sibling::span[contains(., 'NC_045512.2.fna.fasta')][1]",
             )
-            input_select.click()
+            input_1_select.click()
             # Select relevant choice
-            input_select = self.driver.find_element(
+            input_1_select = self.driver.find_element(
                 By.XPATH,
-                "//div[@id='select2-drop']//ul/li/div[contains(., 'ARTIC_SARS_CoV-2_amplicon_info_v3.tsv')]",
+                "//div[@class='ui-form-composite']//div[@data-label='ARTIC primers to amplicon assignments']//ul[@role='listbox']//li[@role='option']//span[contains(., 'ARTIC_SARS_CoV-2_amplicon_info_v3.tsv')]",
             )
-            input_select.click()
+            input_1_select.click()
             workflow_wait = 14400
         else:
             raise Exception(f"Workflow name not in known list: {self.workflow_name}")
 
         # Run the workflow
         self.driver.find_element(By.ID, "run-workflow").click()
-        # Wait for view reports button to appear (workflow to finish)
-        with SeleniumCustomWait(self.driver, workflow_wait):
-            self.wait.until(
-                expected_conditions.presence_of_element_located(
-                    (
-                        By.XPATH,
-                        "//div[@id='center']//a[contains(@class, 'invocation-report-link') and contains(., 'View Report')]",
-                    )
-                )
-            )
+
+        # wait for the running message to appear
+        loading_xpath = "//div[@id='center']//div[@role='tabpanel']//div[@role='alert']//span[@data-description='loading message' and contains(., 'Waiting to complete invocation')]"
+        self.wait.until(expected_conditions.presence_of_element_located((By.XPATH, loading_xpath)))
+
+        # Wait for running message to disappear
+        custom_wait = WebDriverWait(self.driver, workflow_wait)
+        custom_wait.until(expected_conditions.invisibility_of_element_located((By.XPATH, loading_xpath)))
 
     def run_test_sequence(self):
         self.load_galaxy_login()
         self.login_to_galaxy_homepage()
         self.search_for_tool()
         self.load_tool_form()
-        self.load_shared_histories()
-        self.import_shared_history()
+        self.load_published_histories()
+        self.import_published_history()
         self.load_workflow_list()
         self.load_workflow_run_form()
         self.run_workflow()
+        self.upload_dummy_file()
+        self.download_dummy_file()
 
     def measure_timings(self):
         self.timings = {}

registration_email/registration_email_perf_timer.py

@@ -146,14 +146,16 @@ def register_new_account(self):
     def delete_test_account(self):
         gi = galaxy.GalaxyInstance(url=self.server, key=self.api_key)
         user = gi.users.get_users(f_name=self.username)[0]
-        if user['email'] == self.email:
-            gi.users.delete_user(user['id'])
-            gi.users.delete_user(user['id'], purge=True)
+        if user["email"] == self.email:
+            gi.users.delete_user(user["id"])
+            gi.users.delete_user(user["id"], purge=True)
 
     @tenacity.retry(
         retry=tenacity.retry_if_result(lambda result: not result),
         wait=tenacity.wait_fixed(int(os.environ.get("IMAP_POLL_SECONDS", 10))),
-        stop=tenacity.stop_after_attempt(int(os.environ.get("IMAP_MAX_POLL_ATTEMPTS", 12))),
+        stop=tenacity.stop_after_attempt(
+            int(os.environ.get("IMAP_MAX_POLL_ATTEMPTS", 12))
+        ),
         retry_error_callback=(lambda _: False),
     )
     def verify_email_received(self):