mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Nicola Soranzo
c35d8f2a06
Also: - Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected by pytest only because they were `unittest.TestCase` derived, but normally pytest collects only test classes whose name starts with `Test`, see https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
216 lines
9.5 KiB
Python
216 lines
9.5 KiB
Python
"""Integration tests for realtime tools."""
|
|
import os
|
|
import tempfile
|
|
|
|
import pytest
|
|
import requests
|
|
|
|
from galaxy_test.base import api_asserts
|
|
from galaxy_test.base.populators import (
|
|
DatasetPopulator,
|
|
wait_on,
|
|
)
|
|
from galaxy_test.driver import integration_util
|
|
from .test_containerized_jobs import (
|
|
ContainerizedIntegrationTestCase,
|
|
disable_dependency_resolution,
|
|
DOCKERIZED_JOB_CONFIG_FILE,
|
|
)
|
|
from .test_kubernetes_staging import (
|
|
CONTAINERIZED_TEMPLATE,
|
|
job_config,
|
|
set_infrastucture_url,
|
|
)
|
|
|
|
SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
|
|
EMBEDDED_PULSAR_JOB_CONFIG_FILE_DOCKER = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_docker_job_conf.yml")
|
|
|
|
|
|
class BaseInteractiveToolsIntegrationTestCase(ContainerizedIntegrationTestCase):
|
|
framework_tool_and_types = True
|
|
container_type = "docker"
|
|
enable_realtime_mapping = True
|
|
|
|
def setUp(self):
|
|
super().setUp()
|
|
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
|
|
self.history_id = self.dataset_populator.new_history()
|
|
|
|
# Move helpers to populators.py
|
|
def wait_on_proxied_content(self, target):
|
|
def get_hosted_content():
|
|
try:
|
|
scheme, rest = target.split("://", 1)
|
|
prefix, host_and_port = rest.split(".interactivetool.")
|
|
faked_host = rest
|
|
if "/" in rest:
|
|
faked_host = rest.split("/", 1)[0]
|
|
url = f"{scheme}://{host_and_port}"
|
|
response = requests.get(url, timeout=1, headers={"Host": faked_host})
|
|
response.raise_for_status()
|
|
return response.text
|
|
except Exception as e:
|
|
print(e)
|
|
return None
|
|
|
|
content = wait_on(get_hosted_content, f"realtime hosted content at {target}")
|
|
return content
|
|
|
|
def entry_point_target(self, entry_point_id):
|
|
entry_point_access_response = self._get(f"entry_points/{entry_point_id}/access")
|
|
api_asserts.assert_status_code_is(entry_point_access_response, 200)
|
|
access_json = entry_point_access_response.json()
|
|
api_asserts.assert_has_key(access_json, "target")
|
|
return access_json["target"]
|
|
|
|
def wait_on_entry_points_active(self, job_id, expected_num=1):
|
|
def active_entry_points():
|
|
entry_points = self.entry_points_for_job(job_id)
|
|
if len(entry_points) != expected_num:
|
|
return None
|
|
elif any(not e["active"] for e in entry_points):
|
|
job_json = self._get(f"jobs/{job_id}?full=true").json()
|
|
if job_json["state"] == "error":
|
|
raise Exception(f"Interactive tool job {job_id} failed: {job_json}")
|
|
return None
|
|
else:
|
|
return entry_points
|
|
|
|
# It currently takes at least 90 seconds until we can be sure the container monitor failed.
|
|
# Can be decreased when galaxy_ext/container_monitor/monitor.py changes
|
|
return wait_on(active_entry_points, "entry points to become active", timeout=120)
|
|
|
|
def entry_points_for_job(self, job_id):
|
|
entry_points_response = self._get(f"entry_points?job_id={job_id}")
|
|
api_asserts.assert_status_code_is(entry_points_response, 200)
|
|
return entry_points_response.json()
|
|
|
|
|
|
class RunsInterativeToolTests:
|
|
def test_simple_execution(self):
|
|
response_dict = self.dataset_populator.run_tool("interactivetool_simple", {}, self.history_id)
|
|
assert "jobs" in response_dict, response_dict
|
|
jobs = response_dict["jobs"]
|
|
assert isinstance(jobs, list)
|
|
assert len(jobs) == 1
|
|
job0 = jobs[0]
|
|
entry_points = self.wait_on_entry_points_active(job0["id"])
|
|
assert len(entry_points) == 1
|
|
entry_point0 = entry_points[0]
|
|
target = self.entry_point_target(entry_point0["id"])
|
|
content = self.wait_on_proxied_content(target)
|
|
assert content == "moo cow\n", content
|
|
|
|
def test_multi_server_realtime_tool(self):
|
|
response_dict = self.dataset_populator.run_tool("interactivetool_two_entry_points", {}, self.history_id)
|
|
assert "jobs" in response_dict, response_dict
|
|
jobs = response_dict["jobs"]
|
|
assert isinstance(jobs, list)
|
|
assert len(jobs) == 1
|
|
job0 = jobs[0]
|
|
entry_points = self.wait_on_entry_points_active(job0["id"], expected_num=2)
|
|
entry_point0 = entry_points[0]
|
|
entry_point1 = entry_points[1]
|
|
target0 = self.entry_point_target(entry_point0["id"])
|
|
target1 = self.entry_point_target(entry_point1["id"])
|
|
assert target0 != target1
|
|
content0 = self.wait_on_proxied_content(target0)
|
|
assert content0 == "moo cow\n", content0
|
|
|
|
content1 = self.wait_on_proxied_content(target1)
|
|
assert content1 == "moo cow\n", content1
|
|
stop_response = self.dataset_populator._delete(f'entry_points/{entry_point0["id"]}')
|
|
stop_response.raise_for_status()
|
|
self.dataset_populator.wait_for_job(job0["id"], assert_ok=True)
|
|
job_details = self.dataset_populator.get_job_details(job0["id"], full=True)
|
|
job_details.raise_for_status()
|
|
job_details = job_details.json()
|
|
assert job_details["state"] == "ok"
|
|
it_output_details = self.dataset_populator.get_history_dataset_details_raw(
|
|
self.history_id, dataset_id=job_details["outputs"]["test_output"]["id"]
|
|
)
|
|
it_output_details.raise_for_status()
|
|
it_output_details = it_output_details.json()
|
|
assert it_output_details["state"] == "ok"
|
|
assert not it_output_details["deleted"]
|
|
|
|
|
|
class TestInteractiveToolsIntegration(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
|
|
pass
|
|
|
|
|
|
class TestInteractiveToolsPulsarIntegration(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
|
|
@classmethod
|
|
def handle_galaxy_config_kwds(cls, config):
|
|
config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE_DOCKER
|
|
config["galaxy_infrastructure_url"] = "http://localhost:$GALAXY_WEB_PORT"
|
|
disable_dependency_resolution(config)
|
|
|
|
|
|
class TestInteractiveToolsRemoteProxyIntegration(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
|
|
"""
|
|
$ cd gx-it-proxy
|
|
$ ./lib/createdb.js --sessions $HOME/gxitexproxy.sqlite
|
|
$ ./lib/main.js --port 9001 --ip 0.0.0.0 --verbose --sessions $HOME/gxitexproxy.sqlite
|
|
$ # Need to create new DB for each test I think, duplicate IDs are the problem I think because each test starts at 1
|
|
$ GALAXY_TEST_EXTERNAL_PROXY_HOST="localhost:9001" GALAXY_TEST_EXTERNAL_PROXY_MAP="$HOME/gxitexproxy.sqlite" pytest -s test/integration/test_interactivetools_api.py::TestInteractiveToolsRemoteProxyIntegration
|
|
"""
|
|
|
|
@classmethod
|
|
def handle_galaxy_config_kwds(cls, config):
|
|
interactivetools_map = os.environ.get("GALAXY_TEST_EXTERNAL_PROXY_MAP")
|
|
interactivetools_proxy_host = os.environ.get("GALAXY_TEST_EXTERNAL_PROXY_HOST")
|
|
if not interactivetools_map or not interactivetools_proxy_host:
|
|
pytest.skip(
|
|
f"External proxy not configured for test [map={interactivetools_map},host={interactivetools_proxy_host}]"
|
|
)
|
|
config["job_config_file"] = DOCKERIZED_JOB_CONFIG_FILE
|
|
config["interactivetools_proxy_host"] = interactivetools_proxy_host
|
|
config["interactivetools_map"] = interactivetools_map
|
|
disable_dependency_resolution(config)
|
|
|
|
|
|
@integration_util.skip_unless_kubernetes()
|
|
@integration_util.skip_unless_amqp()
|
|
@integration_util.skip_if_github_workflow()
|
|
class TestKubeInteractiveToolsRemoteProxyIntegration(BaseInteractiveToolsIntegrationTestCase, RunsInterativeToolTests):
|
|
"""
|
|
$ git clone https://github.com/galaxyproject/gx-it-proxy.git $HOME/gx-it-proxy
|
|
$ cd $HOME/gx-it-proxy/docker/k8s
|
|
$ # Setup proxy inside K8 cluster with kubectl - including forwarding port 8910
|
|
$ bash run.sh
|
|
$ cd ../.. # back session.
|
|
$ # Need new DB for every test.
|
|
$ rm -rf $HOME/gxitk8proxy.sqlite
|
|
$ ./lib/createdb.js --sessions $HOME/gxitk8proxy.sqlite
|
|
$ ./lib/main.js --port 9002 --ip 0.0.0.0 --verbose --sessions $HOME/gxitk8proxy.sqlite --forwardIP localhost --forwardPort 8910 &
|
|
$ cd back/to/galaxy
|
|
$ GALAXY_TEST_K8S_EXTERNAL_PROXY_HOST="localhost:9002" GALAXY_TEST_K8S_EXTERNAL_PROXY_MAP="$HOME/gxitk8proxy.sqlite" pytest -s test/integration/test_interactivetools_api.py::TestKubeInteractiveToolsRemoteProxyIntegration
|
|
"""
|
|
|
|
@classmethod
|
|
def setUpClass(cls):
|
|
# realpath for docker deployed in a VM on Mac, also done in driver_util.
|
|
cls.jobs_directory = os.path.realpath(tempfile.mkdtemp())
|
|
super().setUpClass()
|
|
|
|
@classmethod
|
|
def handle_galaxy_config_kwds(cls, config):
|
|
interactivetools_map = os.environ.get("GALAXY_TEST_K8S_EXTERNAL_PROXY_MAP")
|
|
interactivetools_proxy_host = os.environ.get("GALAXY_TEST_K8S_EXTERNAL_PROXY_HOST")
|
|
if not interactivetools_map or not interactivetools_proxy_host:
|
|
pytest.skip(
|
|
f"External proxy not configured for test [map={interactivetools_map},host={interactivetools_proxy_host}]"
|
|
)
|
|
|
|
config["interactivetools_proxy_host"] = interactivetools_proxy_host
|
|
config["interactivetools_map"] = interactivetools_map
|
|
|
|
config["jobs_directory"] = cls.jobs_directory
|
|
config["file_path"] = cls.jobs_directory
|
|
config["job_config_file"] = job_config(CONTAINERIZED_TEMPLATE, cls.jobs_directory)
|
|
config["default_job_shell"] = "/bin/sh"
|
|
|
|
set_infrastucture_url(config)
|
|
disable_dependency_resolution(config)
|