backup

app-testing/Pipfile

@@ -5,21 +5,17 @@ verify_ssl = true
 
 [packages]
 pytest = "==7.4.3"
-black = "==23.11.0"
-selenium = "==4.15.2"
-importlib-metadata = "==6.8.0"
+black = "==24.1.1"
+selenium = "==4.17.2"
+importlib-metadata = "==7.0.1"
 requests = "==2.31.0"
-python-dotenv = "==1.0.0"
-pytest-xdist = "==3.5.0"
-mypy = "==1.7.1"
-types-requests = "==2.31.0.10"
+python-dotenv = "==1.0.1"
+mypy = "==1.8.0"
+types-requests = "==2.31.0.20240125"
 rich = "==13.7.0"
-atomicwrites = "==1.4.1"
-pyreadline3 = "==3.4.1"
-pydantic = "==2.5.2"
-pygithub = "==2.1.1"
-ruff = "==0.1.6"
-docker = "==6.1.3"
+pydantic = "==2.6.0"
+ruff = "==0.1.15"
+docker = "==7.0.0"
 syrupy = "==4.6.0"
 pytest-html = "==4.1.1"
 

app-testing/automation/data/protocol.py

@@ -1,4 +1,5 @@
 """Model of a protocol for testing."""
+
 import hashlib
 import os
 from pathlib import Path

app-testing/automation/data/protocol_files.py

@@ -1,4 +1,5 @@
 """Define the possible names of protocol files to use in testing."""
+
 from typing import Literal
 
 names = Literal[

app-testing/automation/data/protocols.py

@@ -1,4 +1,5 @@
 """Map for protocol files available for testing."""
+
 from automation.data.protocol import Protocol
 
 

app-testing/automation/driver/base.py

@@ -2,6 +2,7 @@
 
 Expose clear information upon failure.
 """
+
 from __future__ import annotations
 
 import os

app-testing/automation/driver/drag_drop.py

@@ -1,4 +1,5 @@
 """Inject javascript to utilize drag and drop functionality."""
+
 from pathlib import Path
 
 from selenium.webdriver.chrome.webdriver import WebDriver

app-testing/automation/driver/wait.py

@@ -2,6 +2,7 @@
 
 https://stackoverflow.com/questions/2785821/is-there-an-easy-way-in-python-to-wait-until-certain-condition-is-true
 """
+
 import time
 from typing import Any, Callable, Optional
 

app-testing/automation/menus/left_menu.py

@@ -1,4 +1,5 @@
 """Left Menu Locators."""
+
 from typing import Literal
 
 from rich.console import Console

app-testing/automation/pages/app_settings.py

@@ -1,4 +1,5 @@
 """Model for the App Settings page that displays info and settings for the app."""
+
 from typing import Optional
 
 from rich.console import Console

app-testing/automation/pages/deck_calibrate.py

@@ -1,4 +1,5 @@
 """Model for the screens of deck calibration."""
+
 from enum import Enum
 from typing import Optional
 

app-testing/automation/pages/device_landing.py

@@ -1,4 +1,5 @@
 """Model for the App page that displays info and settings for the app."""
+
 import time
 from typing import List, Optional
 

app-testing/automation/pages/labware_landing.py

@@ -1,4 +1,5 @@
 """Model for the Labware Landing page that displays labware info for the app."""
+
 from typing import Optional
 
 from rich.console import Console

app-testing/automation/pages/labware_setup.py

@@ -1,4 +1,5 @@
 """Model for the screen of Labware Setup."""
+
 from rich.console import Console
 from selenium.webdriver.chrome.webdriver import WebDriver
 from selenium.webdriver.common.action_chains import ActionChains

app-testing/automation/pages/modal.py

@@ -1,4 +1,5 @@
 """Model for the App page that displays info and settings for the app."""
+
 from typing import Optional
 
 from rich.console import Console

app-testing/automation/pages/module_setup.py

@@ -1,6 +1,5 @@
 """Model for the screen of module setup."""
 
-
 from rich.console import Console
 from selenium.webdriver.chrome.webdriver import WebDriver
 from selenium.webdriver.common.action_chains import ActionChains

app-testing/automation/resources/ot_robot.py

@@ -1,4 +1,5 @@
 """Model the the Opentrons Robot."""
+
 from typing import List
 
 import requests

app-testing/automation/resources/robot_data.py

@@ -1,4 +1,5 @@
 """Robot data."""
+
 from dataclasses import dataclass
 from typing import Literal
 

app-testing/citools/generate_analyses.py

@@ -7,11 +7,13 @@
 
 import json
 import os
+import signal
 import time
+from contextlib import contextmanager
 from dataclasses import dataclass
 from enum import Enum, auto
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any, Dict, List, Optional
 
 import docker  # type: ignore
 from automation.data.protocol import Protocol
@@ -33,6 +35,21 @@
 console = Console()
 
 
+@contextmanager
+def timeout(time):
+    # Signal handler function
+    def raise_timeout(signum, frame):
+        raise TimeoutError
+
+    # Set the signal handler for the alarm signal
+    signal.signal(signal.SIGALRM, raise_timeout)
+    signal.alarm(time)  # Set the alarm
+    try:
+        yield
+    finally:
+        signal.alarm(0)  # Disable the alarm
+
+
 class ProtocolType(Enum):
     PROTOCOL_DESIGNER = auto()
     PYTHON = auto()
@@ -45,10 +62,10 @@ class AnalyzeProtocol:
     host_analysis_file: Path
     container_analysis_file: Path
     tag: str
-    analysis_execution_time: float | None = None
-    exit_code: int | None = None
-    output: str | None = None
-    analysis: Dict[str, Any] | None = None
+    analysis_execution_time: Optional[float] = None
+    exit_code: Optional[int] = None
+    output: Optional[str] = None
+    analysis: Optional[Dict[str, Any]] = None
 
     @property
     def analysis_file_exists(self) -> bool:
@@ -71,25 +88,25 @@ def set_analysis_execution_time(self, analysis_execution_time: float) -> None:
         self.analysis_execution_time = analysis_execution_time
 
 
-def run_container(image_name: str, timeout: int = 60) -> docker.models.containers.Container:
+def stop_and_restart_container(image_name: str, timeout: int = 60) -> docker.models.containers.Container:
     client = docker.from_env()
     volumes = {
         str(HOST_LABWARE): {"bind": CONTAINER_LABWARE, "mode": "rw"},
         str(HOST_RESULTS): {"bind": CONTAINER_RESULTS, "mode": "rw"},
         str(HOST_PROTOCOLS_ROOT): {"bind": CONTAINER_PROTOCOLS_ROOT, "mode": "rw"},
     }
 
-    # Check for running containers using the specified image
+    # Find the running container using the specified image
     containers = client.containers.list(filters={"ancestor": image_name, "status": "running"})
 
     if containers:
-        print("Container already running.")
-        print("Exiting, stop this container so that you may be sure to have the right volumes attached.")
-        exit(1)
-    else:
-        # If no running container is found, start a new one with the specified volume
-        print("Starting a new container.")
-        container = client.containers.run(image_name, detach=True, volumes=volumes)
+        console.print("Stopping the running container(s)...")
+        for container in containers:
+            container.stop(timeout=10)
+
+    # Start a new container with the specified volume
+    console.print("Starting a new container.")
+    container = client.containers.run(image_name, detach=True, volumes=volumes)
 
     # Wait for the container to be ready if a readiness command is provided
     start_time = time.time()
@@ -117,7 +134,7 @@ def stop_and_remove_containers(image_name: str) -> None:
             # Stop the container if it's running
             if container.status == "running":
                 print(f"Stopping container {container.short_id}...")
-                container.stop()
+                container.stop(timeout=10)
 
             # Remove the container
             print(f"Removing container {container.short_id}...")
@@ -207,7 +224,6 @@ def report(protocol: AnalyzeProtocol) -> None:
             console.print(protocol.output)
     else:
         console.print(f"[bold red]Analysis not created for {protocol.protocol_file_name}[/bold red]")
-        console.print(protocol.output)
 
 
 def container_custom_labware_paths() -> List[str]:
@@ -216,15 +232,38 @@ def container_custom_labware_paths() -> List[str]:
     return []
 
 
-def analyze(protocol: AnalyzeProtocol, container: docker.models.containers.Container) -> None:
+def analyze(protocol: AnalyzeProtocol, container: docker.models.containers.Container) -> bool:
     # Run the analyze command
     command = f"python -I -m opentrons.cli analyze --json-output {protocol.container_analysis_file} {protocol.container_protocol_file} {' '.join(map(str, container_custom_labware_paths()))}"  # noqa: E501
     start_time = time.time()
-    exit_code, result = container.exec_run(command)  # Assuming container is a defined object
-    protocol.output = result.decode("utf-8")
-    protocol.exit_code = exit_code
-    protocol.set_analysis()
+    timeout_duration = 15  # seconds
+    try:
+        with timeout(timeout_duration):
+            command_result = container.exec_run(cmd=command)
+            exit_code = command_result.exit_code
+            result = command_result.output
+            protocol.output = result.decode("utf-8")
+            protocol.exit_code = exit_code
+            protocol.set_analysis()
+            protocol.set_analysis_execution_time(time.time() - start_time)
+            return True
+    except TimeoutError:
+        console.print(f"Command execution exceeded {timeout_duration} seconds and was aborted.")
+        logs = container.logs()
+        # Decode and print the logs
+        console.print(f"container logs{logs.decode('utf-8')}")
+    except KeyboardInterrupt:
+        console.print("Execution was interrupted by the user.")
+        raise
+    except Exception as e:
+        console.error(f"An unexpected error occurred: {e}")
+    console.print("Out of the try block...")
+    protocol.output = None
+    protocol.exit_code = None
+    protocol.analysis = None
     protocol.set_analysis_execution_time(time.time() - start_time)
+    report(protocol)
+    return False
 
 
 def analyze_many(protocol_files: List[AnalyzeProtocol], container: docker.models.containers.Container) -> None:
@@ -241,7 +280,7 @@ def analyze_against_image(tag: str) -> List[AnalyzeProtocol]:
     # protocols_to_process = protocols[:1]  # For testing
     try:
         console.print(f"Analyzing {len(protocols_to_process)} protocol(s) against {image_name}...")
-        container = run_container(image_name)
+        container = stop_and_restart_container(image_name)
         analyze_many(protocols_to_process, container)
     finally:
         stop_and_remove_containers(image_name)
@@ -262,7 +301,16 @@ def generate_analyses_from_test(tag: str, protocols: List[Protocol]) -> None:
         )
     try:
         console.print(f"Analyzing {len(protocols_to_process)} protocol(s) against {tag}...")
-        container = run_container(image_name)
-        analyze_many(protocols_to_process, container)
+        container = stop_and_restart_container(image_name)
+        for protocol in protocols_to_process:
+            console.print(f"Analyzing {protocol.protocol_file_name}...")
+            analyzed = analyze(protocol, container)
+        if not analyzed:
+            console.print("Analysis failed. Exiting.")
+            stop_and_remove_containers(image_name)
+        accumulated_time = sum(
+            protocol.analysis_execution_time for protocol in protocols_to_process if protocol.analysis_execution_time is not None
+        )
+        console.print(f"{len(protocols_to_process)} protocols with total analysis time of {accumulated_time:.2f} seconds.\n")
     finally:
         stop_and_remove_containers(image_name)

app-testing/conftest.py

@@ -1,4 +1,5 @@
 """Pytest setup."""
+
 import os
 from typing import Generator, List, Optional
 

app-testing/files/protocols/py/OT2_P300M_P20S_2_16_aspirateDispenseMix0Volume.py

@@ -1,4 +1,5 @@
 """Smoke Test v3.0 """
+
 from opentrons import protocol_api
 
 metadata = {

app-testing/files/protocols/py/OT2_P300M_P20S_TC_HS_TM_2_13_SmokeTestV3.py

@@ -1,4 +1,5 @@
 """Smoke Test v3.0 """
+
 # https://opentrons.atlassian.net/projects/RQA?selectedItem=com.atlassian.plugins.atlassian-connect-plugin:com.kanoah.test-manager__main-project-page#!/testCase/QB-T497
 from opentrons import protocol_api
 

app-testing/files/protocols/py/OT2_P300M_P20S_TC_HS_TM_2_14_SmokeTestV3.py

@@ -1,4 +1,5 @@
 """Smoke Test v3.0 """
+
 # https://opentrons.atlassian.net/projects/RQA?selectedItem=com.atlassian.plugins.atlassian-connect-plugin:com.kanoah.test-manager__main-project-page#!/testCase/QB-T497
 from opentrons import protocol_api
 

app-testing/files/protocols/py/OT2_P300M_P20S_TC_HS_TM_2_15_SmokeTestV3.py

@@ -1,4 +1,5 @@
 """Smoke Test v3.0 """
+
 # https://opentrons.atlassian.net/projects/RQA?selectedItem=com.atlassian.plugins.atlassian-connect-plugin:com.kanoah.test-manager__main-project-page#!/testCase/QB-T497
 from opentrons import protocol_api
 

app-testing/files/protocols/py/OT2_P300M_P20S_TC_HS_TM_2_16_SmokeTestV3.py

@@ -1,4 +1,5 @@
 """Smoke Test v3.0 """
+
 # https://opentrons.atlassian.net/projects/RQA?selectedItem=com.atlassian.plugins.atlassian-connect-plugin:com.kanoah.test-manager__main-project-page#!/testCase/QB-T497
 from opentrons import protocol_api
 

app-testing/files/protocols/py/OT2_P300M_P20S_TC_HS_TM_2_16_aspirateDispenseMix0Volume.py

@@ -1,4 +1,5 @@
 """Smoke Test v3.0 """
+
 from opentrons import protocol_api
 
 metadata = {

app-testing/locators.py

@@ -3,6 +3,7 @@
 pipenv run python -i locators.py
 This launches the installed app.
 """
+
 import importlib
 import os
 

app-testing/pytest.ini

@@ -1,4 +1,4 @@
 [pytest]
 generate_report_on_test = True
 junit_family = legacy
-addopts = --junitxml=results/results.xml --log-cli-level info --html=results/report.html --self-contained-html
+addopts = -s -vv --junitxml=results/results.xml --log-cli-level info --html=results/report.html --self-contained-html

app-testing/tests/calibrate_test.py

@@ -1,4 +1,5 @@
 """Test the initial state the application with various setups."""
+
 import time
 from typing import List
 

app-testing/tests/labware_landing_test.py

@@ -1,4 +1,5 @@
 """Test the Labware Landing of the page."""
+
 from pathlib import Path
 from typing import Dict, List
 

app-testing/tests/lpc_test.py

@@ -1,4 +1,5 @@
 """todo these tests for refactoring"""
+
 # flake8: noqa
 import time
 from pathlib import Path

app-testing/tests/protocol_analyze_test.py

@@ -1,4 +1,5 @@
 """Test the Protocol Landing of the page."""
+
 import os
 
 import pytest

app-testing/tests/protocol_landing_test.py

@@ -1,4 +1,5 @@
 """Test the Protocol Landing of the page."""
+
 import time
 from pathlib import Path
 from typing import Dict