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test_cmd_serve.py
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import os
import tempfile
import time
import uuid
import requests
from planemo import network_util
from planemo.galaxy import api
from planemo.io import kill_pid_file
from .test_utils import (
cli_daemon_galaxy,
CliTestCase,
launch_and_wait_for_galaxy,
mark,
PROJECT_TEMPLATES_DIR,
run_verbosely,
safe_rmtree,
skip_if_environ,
skip_unless_environ,
skip_unless_executable,
target_galaxy_branch,
TEST_DATA_DIR,
TEST_REPOS_DIR,
)
TEST_HISTORY_NAME = "Cool History 42"
SERVE_TEST_VERBOSE = True
class UsesServeCommand:
def _run(self, serve_args=[], serve_cmd="serve"):
serve_cmd = self._serve_command_list(serve_args, serve_cmd)
if run_verbosely():
print("Running command for test [%s]" % serve_cmd)
self._check_exit_code(serve_cmd)
def _serve_command_list(self, serve_args=[], serve_cmd="serve"):
test_cmd = ["--verbose"] if run_verbosely() else []
test_cmd.extend([
serve_cmd,
"--galaxy_root", self.galaxy_root,
"--galaxy_branch", target_galaxy_branch(),
"--no_dependency_resolution",
"--port", str(self._port),
self._serve_artifact,
])
test_cmd.extend(serve_args)
return test_cmd
def _launch_thread_and_wait(self, func, args=[], **kwd):
future = launch_and_wait_for_galaxy(self._port, func, [args], **kwd)
if future is not None:
self._futures.append(future)
@property
def _user_gi(self):
admin_gi = api.gi(self._port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(self._port, key=user_api_key)
return user_gi
class ServeTestCase(CliTestCase, UsesServeCommand):
@classmethod
def setUpClass(cls):
cls.galaxy_root = tempfile.mkdtemp()
@classmethod
def tearDownClass(cls):
safe_rmtree(cls.galaxy_root)
def setUp(self):
super(ServeTestCase, self).setUp()
self._port = network_util.get_free_port()
self._pid_file = os.path.join(self._home, "test.pid")
self._serve_artifact = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_serve(self):
extra_args = [
"--skip_client_build",
]
self._launch_thread_and_wait(self._run, extra_args)
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@skip_if_environ("PLANEMO_SKIP_GALAXY_CLIENT_TESTS")
@skip_unless_executable("python3")
def test_serve_client_python3(self):
extra_args = [
"--galaxy_python_version", "3"
]
# Given the client build - give this more time.
timeout_multiplier = 3
self._launch_thread_and_wait(self._run, extra_args, timeout_multiplier=timeout_multiplier)
# Check that the client was correctly built
url = "http://localhost:%d/static/dist/analysis.bundled.js" % int(self._port)
r = requests.get(url)
assert r.status_code == 200
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_serve_daemon(self):
extra_args = [
"--daemon",
"--skip_client_build",
"--pid_file", self._pid_file]
self._launch_thread_and_wait(self._run, extra_args)
user_gi = self._user_gi
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(self._pid_file)
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_serve_workflow(self):
random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "randomlines.xml")
cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
self._serve_artifact = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
extra_args = [
"--daemon",
"--skip_client_build",
"--pid_file", self._pid_file,
"--extra_tools", random_lines,
"--extra_tools", cat,
]
self._launch_thread_and_wait(self._run, extra_args)
time.sleep(30)
user_gi = self._user_gi
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
assert user_gi.tools.get_tools(tool_id="random_lines1")
workflows = user_gi.workflows.get_workflows()
assert len(workflows) == 1
workflow = workflows[0]
workflow_id = workflow["id"]
assert workflow_id
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@skip_if_environ("PLANEMO_SKIP_SHED_TESTS")
@mark.tests_galaxy_branch
def test_shed_serve(self):
extra_args = [
"--daemon",
"--skip_client_build",
"--pid_file", self._pid_file,
"--shed_target", "toolshed"]
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
self._serve_artifact = fastqc_path
self._launch_thread_and_wait(self._run_shed, extra_args)
user_gi = self._user_gi
found = False
tool_ids = None
for i in range(30):
tool_ids = [t["id"] for t in user_gi.tools.get_tools()]
if any(_.startswith("toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/") for _ in tool_ids):
found = True
break
time.sleep(5)
assert found, "Failed to find fastqc id in %s" % tool_ids
kill_pid_file(self._pid_file)
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
def test_serve_profile(self):
self._test_serve_profile()
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@skip_unless_environ("PLANEMO_ENABLE_POSTGRES_TESTS")
@skip_unless_executable("psql")
def test_serve_postgres_profile(self):
self._test_serve_profile("--database_type", "postgres")
def _test_serve_profile(self, *db_options):
new_profile = "planemo_test_profile_%s" % uuid.uuid4()
extra_args = [
"--daemon",
"--skip_client_build",
"--pid_file", self._pid_file,
"--profile", new_profile,
]
serve_cmd = self._serve_command_list(extra_args)
with cli_daemon_galaxy(self._runner, self._pid_file, self._port, serve_cmd):
user_gi = self._user_gi
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
# TODO: Pretty sure this is getting killed, but we should verify.
with cli_daemon_galaxy(self._runner, self._pid_file, self._port, serve_cmd):
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 1
def _run_shed(self, serve_args=[]):
return self._run(serve_args=serve_args, serve_cmd="shed_serve")