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How to use tee_redirect method in autotest

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test_command_factory.py

Source:test_command_factory.py

1import os2import shutil3from os import getcwd4from tempfile import mkdtemp5from typing import (6    List,7    Tuple,8)9from unittest import TestCase10from galaxy.jobs.command_factory import (11    build_command,12    PREPARE_DIRS,13    SETUP_GALAXY_FOR_METADATA,14)15from galaxy.tool_util.deps.container_classes import TRAP_KILL_CONTAINER16from galaxy.util.bunch import Bunch17MOCK_COMMAND_LINE = "/opt/galaxy/tools/bowtie /mnt/galaxyData/files/000/input000.dat"18TEST_METADATA_LINE = "set_metadata_and_stuff.sh"19TEST_FILES_PATH = "file_path"20TEE_REDIRECT = '> "$__out" 2> "$__err"'21RETURN_CODE_CAPTURE = "; return_code=$?; echo $return_code > galaxy_1.ec"22CP_WORK_DIR_OUTPUTS = '; \nif [ -f "foo" ] ; then cp "foo" "bar" ; fi'23class TestCommandFactory(TestCase):24    stream_stdout_stderr = False25    TEE_LOG = " "26    CAPTURE_AND_REDIRECT = f"> '../outputs/tool_stdout' 2> '../outputs/tool_stderr'{RETURN_CODE_CAPTURE}"27    def setUp(self):28        self.job_dir = mkdtemp()29        self.job_wrapper = MockJobWrapper(self.job_dir)30        self.workdir_outputs: List[Tuple[str, str]] = []31        def workdir_outputs(job_wrapper, **kwds):32            assert job_wrapper == self.job_wrapper33            return self.workdir_outputs34        self.runner = Bunch(35            app=Bunch(model=Bunch(Dataset=Bunch(file_path=TEST_FILES_PATH))), get_work_dir_outputs=workdir_outputs36        )37        self.include_metadata = False38        self.include_work_dir_outputs = True39    def tearDown(self):40        shutil.rmtree(self.job_dir)41    def test_simplest_command(self):42        self.include_work_dir_outputs = False43        self._assert_command_is(self._surround_command(MOCK_COMMAND_LINE))44    def test_shell_commands(self):45        self.include_work_dir_outputs = False46        dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]47        self.job_wrapper.dependency_shell_commands = dep_commands48        self._assert_command_is(self._surround_command(f"{dep_commands[0]}; {MOCK_COMMAND_LINE}"))49    def test_shell_commands_external(self):50        self.job_wrapper.commands_in_new_shell = True51        self.include_work_dir_outputs = False52        dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]53        self.job_wrapper.dependency_shell_commands = dep_commands54        self._assert_command_is(55            self._surround_command(56                "{} {}/tool_script.sh".format(57                    self.job_wrapper.shell,58                    self.job_wrapper.working_directory,59                )60            )61        )62        self.__assert_tool_script_is(f"#!/bin/sh\n{dep_commands[0]}; {MOCK_COMMAND_LINE}")63    def test_remote_dependency_resolution(self):64        self.include_work_dir_outputs = False65        dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]66        self.job_wrapper.dependency_shell_commands = dep_commands67        self._assert_command_is(68            self._surround_command(MOCK_COMMAND_LINE), remote_command_params=dict(dependency_resolution="remote")69        )70    def test_explicit_local_dependency_resolution(self):71        self.include_work_dir_outputs = False72        dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]73        self.job_wrapper.dependency_shell_commands = dep_commands74        self._assert_command_is(75            self._surround_command(f"{dep_commands[0]}; {MOCK_COMMAND_LINE}"),76            remote_command_params=dict(dependency_resolution="local"),77        )78    def test_task_prepare_inputs(self):79        self.include_work_dir_outputs = False80        self.job_wrapper.prepare_input_files_cmds = ["/opt/split1", "/opt/split2"]81        self._assert_command_is(self._surround_command(f"/opt/split1; /opt/split2; {MOCK_COMMAND_LINE}"))82    def test_workdir_outputs(self):83        self.include_work_dir_outputs = True84        self.workdir_outputs = [("foo", "bar")]85        self._assert_command_is(self._surround_command(MOCK_COMMAND_LINE, CP_WORK_DIR_OUTPUTS))86    def test_workdir_outputs_with_glob(self):87        self.include_work_dir_outputs = True88        self.workdir_outputs = [("foo*bar", "foo_x_bar")]89        self._assert_command_is(90            self._surround_command(91                MOCK_COMMAND_LINE, '; \nif [ -f "foo"*"bar" ] ; then cp "foo"*"bar" "foo_x_bar" ; fi'92            )93        )94    def test_set_metadata_skipped_if_unneeded(self):95        self.include_metadata = True96        self.include_work_dir_outputs = False97        self._assert_command_is(self._surround_command(MOCK_COMMAND_LINE))98    def test_set_metadata(self):99        self._test_set_metadata()100    def test_strips_trailing_semicolons(self):101        self.job_wrapper.command_line = "%s;" % MOCK_COMMAND_LINE102        self._test_set_metadata()103    def _test_set_metadata(self):104        self.include_metadata = True105        self.include_work_dir_outputs = False106        self.job_wrapper.metadata_line = TEST_METADATA_LINE107        expected_command = self._surround_command(108            MOCK_COMMAND_LINE, f"; cd '{self.job_dir}'; {SETUP_GALAXY_FOR_METADATA}{TEST_METADATA_LINE}"109        )110        self._assert_command_is(expected_command)111    def test_empty_metadata(self):112        """113        Test empty metadata as produced by TaskWrapper.114        """115        self.include_metadata = True116        self.include_work_dir_outputs = False117        self.job_wrapper.metadata_line = " "118        # Empty metadata command do not touch command line.119        expected_command = self._surround_command(MOCK_COMMAND_LINE, f"; cd '{self.job_dir}'")120        self._assert_command_is(expected_command)121    def test_metadata_kwd_defaults(self):122        configured_kwds = self.__set_metadata_with_kwds()123        assert configured_kwds["exec_dir"] == getcwd()124        assert configured_kwds["tmp_dir"] == self.job_wrapper.working_directory125        assert configured_kwds["dataset_files_path"] == TEST_FILES_PATH126        assert configured_kwds["output_fnames"] == ["output1"]127    def test_metadata_kwds_overrride(self):128        configured_kwds = self.__set_metadata_with_kwds(129            exec_dir="/path/to/remote/galaxy",130            tmp_dir="/path/to/remote/staging/directory/job1",131            dataset_files_path="/path/to/remote/datasets/",132            output_fnames=["/path/to/remote_output1"],133        )134        assert configured_kwds["exec_dir"] == "/path/to/remote/galaxy"135        assert configured_kwds["tmp_dir"] == "/path/to/remote/staging/directory/job1"136        assert configured_kwds["dataset_files_path"] == "/path/to/remote/datasets/"137        assert configured_kwds["output_fnames"] == ["/path/to/remote_output1"]138    def __set_metadata_with_kwds(self, **kwds):139        self.include_metadata = True140        self.include_work_dir_outputs = False141        self.job_wrapper.metadata_line = TEST_METADATA_LINE142        if kwds:143            self.__command(remote_command_params=dict(metadata_kwds=kwds))144        else:145            self.__command()146        return self.job_wrapper.configured_external_metadata_kwds147    def _assert_command_is(self, expected_command, **command_kwds):148        command = self.__command(**command_kwds)149        self.assertEqual(command, expected_command)150    def __assert_tool_script_is(self, expected_command):151        self.assertEqual(open(self.__tool_script).read(), expected_command)152    @property153    def __tool_script(self):154        return os.path.join(self.job_dir, "tool_script.sh")155    def __command(self, **extra_kwds):156        kwds = dict(157            runner=self.runner,158            job_wrapper=self.job_wrapper,159            include_metadata=self.include_metadata,160            include_work_dir_outputs=self.include_work_dir_outputs,161            stream_stdout_stderr=self.stream_stdout_stderr,162            **extra_kwds,163        )164        return build_command(**kwds)165    def _surround_command(self, command, post_command=""):166        command = f'''{PREPARE_DIRS};{self.TEE_LOG}{command} {self.CAPTURE_AND_REDIRECT}{post_command}; sh -c "exit $return_code"'''167        return command.replace("galaxy_1.ec", os.path.join(self.job_wrapper.working_directory, "galaxy_1.ec"), 1)168class TestCommandFactoryStreamStdoutStderr(TestCommandFactory):169    stream_stdout_stderr = True170    TEE_LOG = """ __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$"171mkfifo "$__out" "$__err"172trap 'rm -f "$__out" "$__err"' EXIT173tee -a '../outputs/tool_stdout' < "$__out" &174tee -a '../outputs/tool_stderr' < "$__err" >&2 & """175    CAPTURE_AND_REDIRECT = f"{TEE_REDIRECT}{RETURN_CODE_CAPTURE}"176    def test_kill_trap_replaced(self):177        self.include_work_dir_outputs = False178        self.job_wrapper.command_line = f"{TRAP_KILL_CONTAINER}{MOCK_COMMAND_LINE}"179        expected_command_line = self._surround_command(MOCK_COMMAND_LINE).replace(180            """trap 'rm -f "$__out" "$__err"' EXIT""", """trap 'rm -f "$__out" "$__err"; _on_exit' EXIT"""181        )182        self._assert_command_is(expected_command_line)183class MockJobWrapper:184    def __init__(self, job_dir):185        self.strict_shell = False186        self.command_line = MOCK_COMMAND_LINE187        self.dependency_shell_commands = []188        self.metadata_line = None189        self.configured_external_metadata_kwds = None190        self.working_directory = job_dir191        self.prepare_input_files_cmds = None192        self.commands_in_new_shell = False193        self.app = Bunch(194            config=Bunch(195                check_job_script_integrity=False,196            )197        )198        self.shell = "/bin/sh"199        self.use_metadata_binary = False200        self.job_id = 1201    def get_command_line(self):202        return self.command_line203    def container_monitor_command(self, *args, **kwds):204        return None205    @property206    def requires_setting_metadata(self):207        return self.metadata_line is not None208    def setup_external_metadata(self, *args, **kwds):209        self.configured_external_metadata_kwds = kwds210        return self.metadata_line211    @property212    def job_io(self):...

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