mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
939e7774a8
This is (so far a subset of) the tool utilities from galaxy-lib. galaxy-lib mocked out a fake galaxy.tools to allow these to all exist below the galaxy.tools - but this was a terrible hack - in order for the new packages to be true subsets of Galaxy they need to be refactored into a new package that doesn't depend on models, SA, galaxy.jobs, etc... [x] galaxy.tools.deps -> galaxy.tool_util.deps [x] galaxy.tools.loader -> galaxy.tool_util.loader [x] galaxy.tools.cwl -> galaxy.tool_util.cwl [x] galaxy.tools.loader -> galaxy.tool_util.loader [x] galaxy.tools.fetcher -> galaxy.tool_util.fetcher [x] galaxy.tools.locations -> galaxy.tool_util.locations [x] galaxy.tools.parser -> galaxy.tool_util.parser
111 lines
4.6 KiB
Python
111 lines
4.6 KiB
Python
"""Integration tests for running tools in Docker containers."""
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import os
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import unittest
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from base import integration_util
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from base.populators import (
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DatasetPopulator,
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)
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from galaxy.tool_util.deps.commands import which
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from .test_job_environments import RunsEnvironmentJobs
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SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
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DOCKERIZED_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "dockerized_job_conf.xml")
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SINGULARITY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "singularity_job_conf.xml")
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EXTENDED_TIMEOUT = 120
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class MulledJobTestCases(object):
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def test_explicit(self):
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self.dataset_populator.run_tool("mulled_example_explicit", {}, self.history_id)
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self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
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output = self.dataset_populator.get_history_dataset_content(self.history_id, timeout=EXTENDED_TIMEOUT)
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assert "0.7.15-r1140" in output
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def test_mulled_simple(self):
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self.dataset_populator.run_tool("mulled_example_simple", {}, self.history_id)
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self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
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output = self.dataset_populator.get_history_dataset_content(self.history_id, timeout=EXTENDED_TIMEOUT)
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assert "0.7.15-r1140" in output
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class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, RunsEnvironmentJobs, MulledJobTestCases):
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framework_tool_and_types = True
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job_config_file = DOCKERIZED_JOB_CONFIG_FILE
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build_mulled_resolver = 'build_mulled'
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container_type = 'docker'
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default_container_home_dir = '/'
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@classmethod
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def handle_galaxy_config_kwds(cls, config):
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cls.jobs_directory = cls._test_driver.mkdtemp()
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config["jobs_directory"] = cls.jobs_directory
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config["job_config_file"] = cls.job_config_file
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# Disable tool dependency resolution.
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config["tool_dependency_dir"] = "none"
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config["conda_auto_init"] = False
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config["conda_auto_install"] = False
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config["enable_beta_mulled_containers"] = "true"
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@classmethod
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def setUpClass(cls):
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if not which(cls.container_type):
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raise unittest.SkipTest("Executable '%s' not found on PATH" % cls.container_type)
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super(DockerizedJobsIntegrationTestCase, cls).setUpClass()
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def setUp(self):
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super(DockerizedJobsIntegrationTestCase, self).setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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self.history_id = self.dataset_populator.new_history()
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def test_container_job_environment(self):
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job_env = self._run_and_get_environment_properties("job_environment_default")
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euid = os.geteuid()
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egid = os.getgid()
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assert job_env.user_id == str(euid), job_env.user_id
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assert job_env.group_id == str(egid), job_env.group_id
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assert job_env.pwd.startswith(self.jobs_directory)
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assert job_env.pwd.endswith("/working")
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assert job_env.home.startswith(self.jobs_directory)
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assert job_env.home.endswith("/home")
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def test_container_job_environment_legacy(self):
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job_env = self._run_and_get_environment_properties("job_environment_default_legacy")
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euid = os.geteuid()
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egid = os.getgid()
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assert job_env.user_id == str(euid), job_env.user_id
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assert job_env.group_id == str(egid), job_env.group_id
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assert job_env.pwd.startswith(self.jobs_directory)
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assert job_env.pwd.endswith("/working")
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# Should we change env_pass_through to just always include TMP and HOME for docker?
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# I'm not sure, if yes this would change.
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assert job_env.home == self.default_container_home_dir, job_env.home
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def test_build_mulled(self):
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if not which('docker'):
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raise unittest.SkipTest("Docker not found on PATH, required for building images via involucro")
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resolver_type = self.build_mulled_resolver
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tool_id = 'mulled_example_multi_1'
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endpoint = "tools/%s/dependencies" % tool_id
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data = {'id': tool_id, 'resolver_type': resolver_type}
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create_response = self._post(endpoint, data=data, admin=True)
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self._assert_status_code_is(create_response, 200)
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response = create_response.json()
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assert any([True for d in response if d['dependency_type'] == self.container_type])
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class SingularityJobsIntegrationTestCase(DockerizedJobsIntegrationTestCase):
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job_config_file = SINGULARITY_JOB_CONFIG_FILE
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build_mulled_resolver = 'build_mulled_singularity'
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container_type = 'singularity'
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# singularity passes $HOME by default
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default_container_home_dir = os.environ.get('HOME', '/')
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